From 0962c8f33e3c201bf4a65cd20f8b453670bc8e09 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 15:11:50 -0400 Subject: [PATCH 01/51] housekeeping --- qsopar.fits | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 qsopar.fits diff --git a/qsopar.fits b/qsopar.fits new file mode 100644 index 00000000..6a084af3 --- /dev/null +++ b/qsopar.fits @@ -0,0 +1,28 @@ +SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T AUTHOR = 'Hengxiao Guo' END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 104 / length of dimension 1 NAXIS2 = 18 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 18 / number of table fields LAMBDA = 'Vacuum Wavelength in Ang' MINWAV = 'Lower complex fitting wavelength range' MAXWAV = 'Upper complex fitting wavelength range' NGAUSS = 'Number of Gaussians for the line' INISCA = 'Initial guess of line scale [flux]' MINSCA = 'Lower range of line scale [flux]' MAXSCA = 'Upper range of line scale [flux]' INISIG = 'Initial guess of linesigma [lnlambda]' MINSIG = 'Lower range of line sigma [lnlambda]' MAXSIG = 'Upper range of line sigma [lnlambda]' VOFF = 'Limits on velocity offset from the central wavelength [lnlambda]' VINDEX = 'Entries w/ same NONZERO vindex constrained to have same velocity' WINDEX = 'Entries w/ same NONZERO windex constrained to have same width' FINDEX = 'Entries w/ same NONZERO findex have constrained flux ratios' FVALUE = 'Relative scale factor for entries w/ same findex' VARY = 'Whether or not to vary the parameter (set to 0 to fix the line &' CONTINUE 'parameter to initial values)' EXTNAME = 'LINE_PRIORS' / extension name TTYPE1 = 'lambda ' TFORM1 = 'E ' TTYPE2 = 'compname' TFORM2 = '20A ' TTYPE3 = 'minwav ' TFORM3 = 'E ' TTYPE4 = 'maxwav ' TFORM4 = 'E ' TTYPE5 = 'linename' TFORM5 = '20A ' TTYPE6 = 'ngauss ' TFORM6 = 'J ' TTYPE7 = 'inisca ' TFORM7 = 'E ' TTYPE8 = 'minsca ' TFORM8 = 'E ' TTYPE9 = 'maxsca ' TFORM9 = 'E ' TTYPE10 = 'inisig ' TFORM10 = 'E ' TTYPE11 = 'minsig ' TFORM11 = 'E ' TTYPE12 = 'maxsig ' TFORM12 = 'E ' TTYPE13 = 'voff ' TFORM13 = 'E ' TTYPE14 = 'vindex ' TFORM14 = 'J ' TTYPE15 = 'windex ' TFORM15 = 'J ' TTYPE16 = 'findex ' TFORM16 = 'J ' TTYPE17 = 'fvalue ' TFORM17 = 'E ' TTYPE18 = 'vary ' TFORM18 = 'J ' END EÍ$áHaEÈEÔ€Ha_brPù;£× +;ƒo=LÌÍ Date: Fri, 28 Jun 2024 15:12:22 -0400 Subject: [PATCH 02/51] index argument line line_prop_from_name --- pyqsofit/PyQSOFit.py | 36 ++++++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/pyqsofit/PyQSOFit.py b/pyqsofit/PyQSOFit.py index e60cc23d..6d8d0199 100644 --- a/pyqsofit/PyQSOFit.py +++ b/pyqsofit/PyQSOFit.py @@ -902,7 +902,11 @@ def fit_continuum(self, wave, flux, err, ra, dec, plateid, mjd, fiberid): if wave[tmp_all].shape[0] < 10: if self.verbose: - print('Less than 10 total pixels in the continuum fitting.') + print('Less than 10 total pixels in the continuum windows to be fit.') + if wave[tmp_all].shape[0] == 0: + # Critical warning that should print whether verbose=True or False + # Enlarge continuum windows or check source redshift + print('No pixels in the continuum windows to be fit.') """ Setup parameters for fitting @@ -1729,8 +1733,7 @@ def fit_lines(self, wave, line_flux, err, f): else: ncomp = 0 uniq_linecomp_sort = np.array([]) - if self.verbose: - print("No line to fit! Please set line_fit to FALSE or enlarge wave_range!") + print("No line to fit! Please set line_fit to FALSE or enlarge wave_range!") # Save properties self.comp_result = np.array(comp_result) @@ -1754,7 +1757,7 @@ def fit_lines(self, wave, line_flux, err, f): return self.line_result, self.line_result_name - def line_prop_from_name(self, line_name, line_type='broad', ln_sigma_br=0.0017): + def line_prop_from_name(self, line_name, line_type='broad', sample_index=-1, ln_sigma_br=0.0017): """ line_name: line name e.g., 'Ha_br' """ @@ -1778,10 +1781,27 @@ def line_prop_from_name(self, line_name, line_type='broad', ln_sigma_br=0.0017): # Number of Gaussian components loop for n in range(ngauss): - # Get the Gaussian properties - pp_shaped[n, 0] = float(self.line_result[self.line_result_name == f'{line_name}_{n + 1}_scale'][0]) - pp_shaped[n, 1] = float(self.line_result[self.line_result_name == f'{line_name}_{n + 1}_centerwave'][0]) - pp_shaped[n, 2] = float(self.line_result[self.line_result_name == f'{line_name}_{n + 1}_sigma'][0]) + + mask_scale = self.gauss_result_name == f'{line_name}_{n+1}_scale' + mask_center = self.gauss_result_name == f'{line_name}_{n+1}_centerwave' + mask_sigma = self.gauss_result_name == f'{line_name}_{n+1}_sigma' + + if sample_index == -1: + # Get the Gaussian properties + pp_shaped[n,0] = float(self.gauss_result[mask_scale][0]) + pp_shaped[n,1] = float(self.gauss_result[mask_center][0]) + pp_shaped[n,2] = float(self.gauss_result[mask_sigma][0]) + else: + index_scale = np.nonzero(mask_scale)[0]//2 + index_center = np.nonzero(mask_center)[0]//2 + index_sigma = np.nonzero(mask_sigma)[0]//2 + + if len(self.gauss_result_all) == 0: + return 0, 0, 0, 0, 0, 0 + + pp_shaped[n,0] = float(self.gauss_result_all[sample_index, index_scale][0]) + pp_shaped[n,1] = float(self.gauss_result_all[sample_index, index_center][0]) + pp_shaped[n,2] = float(self.gauss_result_all[sample_index, index_sigma][0]) # Flatten pp = pp_shaped.reshape(-1) From 9ec9b462c2f9babc1d5e1a6a396586e50a05f120 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 15:55:07 -0400 Subject: [PATCH 03/51] Create python-package.yml --- .github/workflows/python-package.yml | 40 ++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/python-package.yml diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 00000000..b33c12bc --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,40 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + pytest pyqsofit/tests/dr7sample.py From 6bc6b9b1b7f59342e8bcead38bfb91c06945f3eb Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:14:23 -0400 Subject: [PATCH 04/51] fixing tests --- pyqsofit/PyQSOFit.py | 2 +- pyqsofit/tests/dr7sample.py | 159 +++++++++++++++++++++++++++++------- pyqsofit/version.py | 2 +- setup.py | 6 +- 4 files changed, 135 insertions(+), 34 deletions(-) diff --git a/pyqsofit/PyQSOFit.py b/pyqsofit/PyQSOFit.py index 6d8d0199..389439f2 100644 --- a/pyqsofit/PyQSOFit.py +++ b/pyqsofit/PyQSOFit.py @@ -175,7 +175,7 @@ def Fit(self, name=None, nsmooth=1, and_mask=False, or_mask=False, reject_badpix wave_range=None, wave_mask=None, decompose_host=True, host_prior=False, host_prior_scale=0.2, host_line_mask=True, decomp_na_mask=False, - qso_type='global', npca_qso=10, host_type='PCA', npca_gal=5, Fe_uv_op=True, + qso_type='global', npca_qso=10, host_type='BC03', npca_gal=5, Fe_uv_op=True, poly=False, BC=False, rej_abs_conti=False, rej_abs_line=False, initial_guess=None, n_pix_min_conti=100, param_file_name='qsopar.fits', MC=False, MCMC=False, save_fits_name=None, nburn=20, nsamp=200, nthin=10, epsilon_jitter=0., linefit=True, save_result=True, plot_fig=True, diff --git a/pyqsofit/tests/dr7sample.py b/pyqsofit/tests/dr7sample.py index 71ae94b0..6a17e59a 100644 --- a/pyqsofit/tests/dr7sample.py +++ b/pyqsofit/tests/dr7sample.py @@ -10,6 +10,8 @@ from astroquery.sdss import SDSS from astropy import coordinates as coords +from astropy.table import Table + warnings.filterwarnings("ignore") # Use custom matplotlib style to make Yue happy @@ -26,32 +28,37 @@ import emcee # optional, for MCMC print(emcee.__version__) -path_ex = os.path.abspath('pyqsofit/tests') # The absolute path to the example directory +path_ex = os.path.abspath('.') # The absolute path to the example directory print(path_ex) # Setup the parameter file +# create a header +hdr0 = fits.Header() +hdr0['Author'] = 'Hengxiao Guo' +primary_hdu = fits.PrimaryHDU(header=hdr0) + """ Create parameter file lambda complexname minwav maxwav linename ngauss inisca minsca maxsca inisig minsig maxsig voff vindex windex findex fvalue vary """ -newdata = np.rec.array([ -(6564.61, r'H$\alpha$', 6400, 6800, 'Ha_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), -(6564.61, r'H$\alpha$', 6400, 6800, 'Ha_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(6549.85, r'H$\alpha$', 6400, 6800, 'NII6549', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.001, 1), -(6585.28, r'H$\alpha$', 6400, 6800, 'NII6585', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.003, 1), -(6718.29, r'H$\alpha$', 6400, 6800, 'SII6718', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), -(6732.67, r'H$\alpha$', 6400, 6800, 'SII6732', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), - -(4862.68, r'H$\beta$', 4640, 5100, 'Hb_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.01, 0, 0, 0, 0.01 , 1), -(4862.68, r'H$\beta$', 4640, 5100, 'Hb_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(4960.30, r'H$\beta$', 4640, 5100, 'OIII4959c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(5008.24, r'H$\beta$', 4640, 5100, 'OIII5007c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.004, 1), -#(4960.30, r'H$\beta$', 4640, 5100, 'OIII4959w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.001, 1), -#(5008.24, r'H$\beta$', 4640, 5100, 'OIII5007w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.002, 1), -#(4687.02, r'H$\beta$', 4640, 5100, 'HeII4687_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.005, 0, 0, 0, 0.001, 1), -#(4687.02, r'H$\beta$', 4640, 5100, 'HeII4687_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.005, 1, 1, 0, 0.001, 1), +line_priors = np.rec.array([ +(6564.61, r'Ha', 6400, 6800, 'Ha_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), +(6564.61, r'Ha', 6400, 6800, 'Ha_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), +(6549.85, r'Ha', 6400, 6800, 'NII6549', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.001, 1), +(6585.28, r'Ha', 6400, 6800, 'NII6585', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.003, 1), +(6718.29, r'Ha', 6400, 6800, 'SII6718', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), +(6732.67, r'Ha', 6400, 6800, 'SII6732', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), + +(4862.68, r'Hb', 4640, 5100, 'Hb_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.01, 0, 0, 0, 0.01 , 1), +(4862.68, r'Hb', 4640, 5100, 'Hb_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), +(4960.30, r'Hb', 4640, 5100, 'OIII4959c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), +(5008.24, r'Hb', 4640, 5100, 'OIII5007c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.004, 1), +#(4960.30, r'Hb', 4640, 5100, 'OIII4959w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.001, 1), +#(5008.24, r'Hb', 4640, 5100, 'OIII5007w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.002, 1), +#(4687.02, r'Hb', 4640, 5100, 'HeII4687_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.005, 0, 0, 0, 0.001, 1), +#(4687.02, r'Hb', 4640, 5100, 'HeII4687_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.005, 1, 1, 0, 0.001, 1), #(3934.78, 'CaII', 3900, 3960, 'CaII3934' , 2, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 99, 0, 0, -0.001, 1), @@ -115,23 +122,115 @@ hdr['vary'] = 'Whether or not to vary the line parameters (set to 0 to fix the line parameters to initial values)' # Save line info -hdu = fits.BinTableHDU(data=newdata, header=hdr, name='data') -hdu.writeto(os.path.join(path_ex, 'qsopar.fits'), overwrite=True) +hdu1 = fits.BinTableHDU(data=line_priors, name='line_priors') -from astropy.table import Table -print(Table(newdata)) +""" +In this table, we specify the windows and priors / initial conditions and boundaries for the continuum fitting parameters. +""" +conti_windows = np.rec.array([ + (1150., 1170.), + (1275., 1290.), + (1350., 1360.), + (1445., 1465.), + (1690., 1705.), + (1770., 1810.), + (1970., 2400.), + (2480., 2675.), + (2925., 3400.), + (3775., 3832.), + (4000., 4050.), + (4200., 4230.), + (4435., 4640.), + (5100., 5535.), + (6005., 6035.), + (6110., 6250.), + (6800., 7000.), + (7160., 7180.), + (7500., 7800.), + (8050., 8150.), # Continuum fitting windows (to avoid emission line, etc.) [AA] + ], + formats = 'float32, float32', + names = 'min, max') + +hdu2 = fits.BinTableHDU(data=conti_windows, name='conti_windows') + +conti_priors = np.rec.array([ + ('Fe_uv_norm', 0.0, 0.0, 1e10, 1), # Normalization of the MgII Fe template [flux] + ('Fe_uv_FWHM', 3000, 1200, 18000, 1), # FWHM of the MgII Fe template [AA] + ('Fe_uv_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the MgII Fe template [lnlambda] + ('Fe_op_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Hbeta/Halpha Fe template [flux] + ('Fe_op_FWHM', 3000, 1200, 18000, 1), # FWHM of the Hbeta/Halpha Fe template [AA] + ('Fe_op_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the Hbeta/Halpha Fe template [lnlambda] + ('PL_norm', 1.0, 0.0, 1e10, 1), # Normalization of the power-law (PL) continuum f_lambda = (lambda/3000)^-alpha + ('PL_slope', -1.5, -5.0, 3.0, 1), # Slope of the power-law (PL) continuum + ('Blamer_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Balmer continuum at < 3646 AA [flux] (Dietrich et al. 2002) + ('Balmer_Te', 15000, 10000, 50000, 1), # Te of the Balmer continuum at < 3646 AA [K?] + ('Balmer_Tau', 0.5, 0.1, 2.0, 1), # Tau of the Balmer continuum at < 3646 AA + ('conti_a_0', 0.0, None, None, 1), # 1st coefficient of the polynomial continuum + ('conti_a_1', 0.0, None, None, 1), # 2nd coefficient of the polynomial continuum + ('conti_a_2', 0.0, None, None, 1), # 3rd coefficient of the polynomial continuum + # Note: The min/max bounds on the conti_a_0 coefficients are ignored by the code, + # so they can be determined automatically for numerical stability. + ], + + formats = 'a20, float32, float32, float32, int32', + names = 'parname, initial, min, max, vary') + +hdr3 = fits.Header() +hdr3['ini'] = 'Initial guess of line scale [flux]' +hdr3['min'] = 'FWHM of the MgII Fe template' +hdr3['max'] = 'Wavelength shift of the MgII Fe template' + +hdr3['vary'] = 'Whether or not to vary the parameter (set to 0 to fix the continuum parameter to initial values)' + + +hdu3 = fits.BinTableHDU(data=conti_priors, header=hdr3, name='conti_priors') + +""" +In this table, we allow user to customized some key parameters in our result measurements. +""" + +measure_info = Table( + [ + [[1350, 1450, 3000, 4200, 5100]], + [[ + # [2240, 2650], + [4435, 4685], + ]] + ], + names=([ + 'cont_loc', + 'Fe_flux_range' + ]), + dtype=([ + 'float32', + 'float32' + ]) +) +hdr4 = fits.Header() +hdr4['cont_loc'] = 'The wavelength of continuum luminosity in results' +hdr4['Fe_flux_range'] = 'Fe emission wavelength range calculated in results' + +hdu4 = fits.BinTableHDU(data=measure_info, header=hdr4, name='measure_info') + +# Save line info +hdu_list = fits.HDUList([primary_hdu, hdu1, hdu2, hdu3, hdu4]) +hdu_list.writeto(os.path.join(path_ex, 'qsopar.fits'), overwrite=True) +print('Saving to ', os.path.join(path_ex, 'qsopar.fits')) # Download the SDSS DR7 sample import urllib.request import gzip +print('Retrieving DR7 catalog.') + cat_file_name = 'dr7_bh_Nov19_2013.fits.gz' if not os.path.exists(cat_file_name): urllib.request.urlretrieve(f'http://quasar.astro.illinois.edu/BH_mass/data/catalogs/{cat_file_name}', cat_file_name) # Fit a sample of nqsofit spectra -nqsofit = 200 +nqsofit = 20 # Line properties line_calc_names = ['CIV_br', 'MgII_br', 'Hb_br'] @@ -150,8 +249,8 @@ len_specs = len(spec_all[1].data) range_rand = np.random.choice(range(len_specs), nqsofit, replace=False) - print(spec_all.info()) - print(repr(spec_all[1].header)) + #print(spec_all.info()) + #print(repr(spec_all[1].header)) # Catalog properties Mi_all = spec_all[1].data['MI_Z2'] @@ -200,10 +299,7 @@ q = QSOFit(lam, flux, err, z, ra=ra, dec=dec, plateid=plate, mjd=mjd, fiberid=fiber, path=path_ex) # Do the fitting - q.Fit(param_file_name='qsopar.fits', name=None, nsmooth=1, and_or_mask=False, deredden=True, reject_badpix=True, - wave_mask=None, decompose_host=True, use_ppxf=False, BC03=True, Mi=None, host_line_mask=True, npca_gal=10, npca_qso=5, - Fe_uv_op=True, poly=True, BC=False, rej_abs=False, MC=False, nsamp=200, initial_guess=None, n_pix_min_host=np.inf, - linefit=True, save_result=False, plot_fig=True, save_fig=False, plot_line_name=True, plot_legend=True) + q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) # Emission line loop for j, line in enumerate(line_calc_names): @@ -216,7 +312,7 @@ line_type = 'narrow' # Get the line properties - fwhm, sigma, ew, peak, area = q.line_prop_from_name(line, line_type) + fwhm, sigma, ew, peak, area, snr = q.line_prop_from_name(line, line_type) print(f"Broad {line}:") print("FWHM (km/s)", np.round(fwhm, 1)) @@ -233,7 +329,7 @@ # Stack the results into 1 file - pdf.savefig(q.fig) + #pdf.savefig(q.fig) # Turn this off for github actions # End open file @@ -293,6 +389,9 @@ def rmse(predictions, targets): fig.tight_layout() fig.savefig(os.path.join(path_ex, f'{line}.pdf'), dpi=300) + # Test + #assert rmse_L < 0.2 + end = timeit.default_timer() print('finshed in '+str(round(end-start))+'s') diff --git a/pyqsofit/version.py b/pyqsofit/version.py index 8c0d5d5b..edc60b35 100644 --- a/pyqsofit/version.py +++ b/pyqsofit/version.py @@ -1 +1 @@ -__version__ = "2.0.0" +__version__ = "2.1.6" diff --git a/setup.py b/setup.py index 7bdf1c4d..71b1f3e5 100644 --- a/setup.py +++ b/setup.py @@ -3,12 +3,14 @@ import sys from setuptools import setup +from version import __version__ + # Prepare and send a new release to PyPI #if "release" in sys.argv[-1]: # os.system("python setup.py sdist") # os.system("python setup.py bdist_wheel") # os.system("twine upload dist/*") -# os.system("rm -rf dist/lightkurve*") +# os.system("rm -rf dist/pyqsofit*") # sys.exit() # Load the __version__ variable without importing the package already @@ -41,7 +43,7 @@ install_requires=install_requires, include_package_data=True, classifiers=[ - "License :: OSI Approved :: MIT License", + "License :: OSI Approved :: GNU License", "Operating System :: OS Independent", "Programming Language :: Python", "Intended Audience :: Science/Research", From 519056159c06d16a1d5576104740d3ae0662a431 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:20:05 -0400 Subject: [PATCH 05/51] fix import in test --- pyqsofit/tests/dr7sample.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyqsofit/tests/dr7sample.py b/pyqsofit/tests/dr7sample.py index 6a17e59a..5d3db515 100644 --- a/pyqsofit/tests/dr7sample.py +++ b/pyqsofit/tests/dr7sample.py @@ -1,7 +1,6 @@ import glob, os,sys,timeit import matplotlib import numpy as np -from pyqsofit.PyQSOFit import QSOFit from astropy.io import fits import matplotlib.pyplot as plt import warnings @@ -28,6 +27,8 @@ import emcee # optional, for MCMC print(emcee.__version__) +from pyqsofit.PyQSOFit import QSOFit + path_ex = os.path.abspath('.') # The absolute path to the example directory print(path_ex) From 39bdef5e1fbd7e647a6dc441a4e84e1ce65c8b05 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:30:34 -0400 Subject: [PATCH 06/51] test import --- pyqsofit/tests/dr7sample.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/pyqsofit/tests/dr7sample.py b/pyqsofit/tests/dr7sample.py index 5d3db515..ad633155 100644 --- a/pyqsofit/tests/dr7sample.py +++ b/pyqsofit/tests/dr7sample.py @@ -13,8 +13,6 @@ warnings.filterwarnings("ignore") -# Use custom matplotlib style to make Yue happy -QSOFit.set_mpl_style() # Show the versions so we know what works import astropy @@ -24,11 +22,14 @@ print(lmfit.__version__) print(pyqsofit.__version__) +from pyqsofit.PyQSOFit import QSOFit + +# Use custom matplotlib style to make Yue happy +QSOFit.set_mpl_style() + import emcee # optional, for MCMC print(emcee.__version__) -from pyqsofit.PyQSOFit import QSOFit - path_ex = os.path.abspath('.') # The absolute path to the example directory print(path_ex) From 5665bf518f8f40d1c404e7bec17ae5cde0afb667 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:38:44 -0400 Subject: [PATCH 07/51] test requirements --- test-requirements.txt | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 test-requirements.txt diff --git a/test-requirements.txt b/test-requirements.txt new file mode 100644 index 00000000..4332f023 --- /dev/null +++ b/test-requirements.txt @@ -0,0 +1,12 @@ +astropy>=5.0 +astroquery>=0.4.7 +corner>=2.2.0 +emcee>=3.1.0 +lmfit>=1.0.3 +matplotlib>=3.4.0 +numpy>=1.21.0 +ppxf>=7.4.5 +PyAstronomy>=0.16.0 +scipy>=1.7.3 +tqdm>=4.60.0 +sfdmap2>=0.2.0 \ No newline at end of file From 7512aa566e3d26e74b5cec179b5093b560438373 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 16:39:11 -0400 Subject: [PATCH 08/51] Update python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b33c12bc..5cf7f1ce 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -28,7 +28,7 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + if [ -f requirements.txt ]; then pip install -r test-requirements.txt; fi - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names From 34cdcb86edf0dd84ae44a22d7349261168d70eff Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 16:42:06 -0400 Subject: [PATCH 09/51] Update python-package.yml --- .github/workflows/python-package.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 5cf7f1ce..2bdcdbcb 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -28,7 +28,7 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r test-requirements.txt; fi + if [ -f test-requirements.txt ]; then pip install -r test-requirements.txt; fi - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names @@ -37,4 +37,5 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | + python -m pip install . pytest pyqsofit/tests/dr7sample.py From 5380396672a0b557aed4a1b720de2571776abbb3 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:46:33 -0400 Subject: [PATCH 10/51] fix version impoty --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 71b1f3e5..fb4bda11 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ import sys from setuptools import setup -from version import __version__ +from .pyqsofit.version import __version__ # Prepare and send a new release to PyPI #if "release" in sys.argv[-1]: From 0ecbbb8422b89f11cb2fcc99de9f0153a000c89b Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:50:25 -0400 Subject: [PATCH 11/51] fix version impot? --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fb4bda11..a0feb0ad 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ import sys from setuptools import setup -from .pyqsofit.version import __version__ +from pyqsofit.version import __version__ # Prepare and send a new release to PyPI #if "release" in sys.argv[-1]: From 087c8f801fd708b5fd971ebf438b1b677949e384 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:52:05 -0400 Subject: [PATCH 12/51] need pandas for now --- test-requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/test-requirements.txt b/test-requirements.txt index 4332f023..9f9467f5 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -1,5 +1,6 @@ astropy>=5.0 astroquery>=0.4.7 +pandas corner>=2.2.0 emcee>=3.1.0 lmfit>=1.0.3 From 0092710db2f9b048bfa1ade80a4a94ff29a4b8ab Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 16:55:45 -0400 Subject: [PATCH 13/51] working on tests --- pyqsofit/tests/dr7sample.py | 2 +- test-requirements.txt | 13 +------------ 2 files changed, 2 insertions(+), 13 deletions(-) diff --git a/pyqsofit/tests/dr7sample.py b/pyqsofit/tests/dr7sample.py index ad633155..f9dd6768 100644 --- a/pyqsofit/tests/dr7sample.py +++ b/pyqsofit/tests/dr7sample.py @@ -280,7 +280,7 @@ # Query the spectrum pos = coords.SkyCoord(ra, dec, unit='deg') - xid = SDSS.query_region(pos, spectro=True) + xid = SDSS.query_region(pos, spectro=True, radius='5 arcsec') if xid is None: continue diff --git a/test-requirements.txt b/test-requirements.txt index 9f9467f5..9216f4c1 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -1,13 +1,2 @@ -astropy>=5.0 astroquery>=0.4.7 -pandas -corner>=2.2.0 -emcee>=3.1.0 -lmfit>=1.0.3 -matplotlib>=3.4.0 -numpy>=1.21.0 -ppxf>=7.4.5 -PyAstronomy>=0.16.0 -scipy>=1.7.3 -tqdm>=4.60.0 -sfdmap2>=0.2.0 \ No newline at end of file +pandas \ No newline at end of file From af023074a2b66bde2d6c9dec0f3417f603feceb4 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 16:56:25 -0400 Subject: [PATCH 14/51] Update python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2bdcdbcb..d62b778a 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -28,7 +28,7 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install flake8 pytest - if [ -f test-requirements.txt ]; then pip install -r test-requirements.txt; fi + if [ -f test-requirements.txt ]; then pip install -r requirements.txt -r test-requirements.txt; fi - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names From dfd5d3cc08841897eabe82fff02e275838f24454 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 17:00:33 -0400 Subject: [PATCH 15/51] rename test --- pyqsofit/tests/{dr7sample.py => test_dr7sample.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pyqsofit/tests/{dr7sample.py => test_dr7sample.py} (100%) diff --git a/pyqsofit/tests/dr7sample.py b/pyqsofit/tests/test_dr7sample.py similarity index 100% rename from pyqsofit/tests/dr7sample.py rename to pyqsofit/tests/test_dr7sample.py From 7b0cb44be0abcfb89993d4bfc716b91984021532 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 17:04:09 -0400 Subject: [PATCH 16/51] fix test --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index d62b778a..e81bcad6 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -38,4 +38,4 @@ jobs: - name: Test with pytest run: | python -m pip install . - pytest pyqsofit/tests/dr7sample.py + pytest pyqsofit/tests/test_dr7sample.py From b3ae0223fa42c30b806f621fde6585329e1387a9 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 17:14:26 -0400 Subject: [PATCH 17/51] fix test --- pyqsofit/tests/test_dr7sample.py | 711 ++++++++++++++++--------------- 1 file changed, 358 insertions(+), 353 deletions(-) diff --git a/pyqsofit/tests/test_dr7sample.py b/pyqsofit/tests/test_dr7sample.py index f9dd6768..ad4f833a 100644 --- a/pyqsofit/tests/test_dr7sample.py +++ b/pyqsofit/tests/test_dr7sample.py @@ -24,377 +24,382 @@ from pyqsofit.PyQSOFit import QSOFit -# Use custom matplotlib style to make Yue happy -QSOFit.set_mpl_style() - import emcee # optional, for MCMC print(emcee.__version__) -path_ex = os.path.abspath('.') # The absolute path to the example directory - -print(path_ex) -# Setup the parameter file - -# create a header -hdr0 = fits.Header() -hdr0['Author'] = 'Hengxiao Guo' -primary_hdu = fits.PrimaryHDU(header=hdr0) - -""" -Create parameter file -lambda complexname minwav maxwav linename ngauss inisca minsca maxsca inisig minsig maxsig voff vindex windex findex fvalue vary -""" - -line_priors = np.rec.array([ -(6564.61, r'Ha', 6400, 6800, 'Ha_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), -(6564.61, r'Ha', 6400, 6800, 'Ha_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(6549.85, r'Ha', 6400, 6800, 'NII6549', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.001, 1), -(6585.28, r'Ha', 6400, 6800, 'NII6585', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.003, 1), -(6718.29, r'Ha', 6400, 6800, 'SII6718', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), -(6732.67, r'Ha', 6400, 6800, 'SII6732', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), - -(4862.68, r'Hb', 4640, 5100, 'Hb_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.01, 0, 0, 0, 0.01 , 1), -(4862.68, r'Hb', 4640, 5100, 'Hb_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(4960.30, r'Hb', 4640, 5100, 'OIII4959c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -(5008.24, r'Hb', 4640, 5100, 'OIII5007c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.004, 1), -#(4960.30, r'Hb', 4640, 5100, 'OIII4959w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.001, 1), -#(5008.24, r'Hb', 4640, 5100, 'OIII5007w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.002, 1), -#(4687.02, r'Hb', 4640, 5100, 'HeII4687_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.005, 0, 0, 0, 0.001, 1), -#(4687.02, r'Hb', 4640, 5100, 'HeII4687_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.005, 1, 1, 0, 0.001, 1), - -#(3934.78, 'CaII', 3900, 3960, 'CaII3934' , 2, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 99, 0, 0, -0.001, 1), - -#(3728.48, 'OII', 3650, 3800, 'OII3728', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 1, 1, 0, 0.001, 1), - -#(3426.84, 'NeV', 3380, 3480, 'NeV3426', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 0, 0, 0, 0.001, 1), -#(3426.84, 'NeV', 3380, 3480, 'NeV3426_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.01, 0, 0, 0, 0.001, 1), - -(2798.75, 'MgII', 2700, 2900, 'MgII_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.0017, 0, 0, 0, 0.05, 1), -(2798.75, 'MgII', 2700, 2900, 'MgII_na', 2, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), - -(1908.73, 'CIII', 1700, 1970, 'CIII_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 99, 0, 0, 0.01, 1), -#(1908.73, 'CIII', 1700, 1970, 'CIII_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -#(1892.03, 'CIII', 1700, 1970, 'SiIII1892', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), -#(1857.40, 'CIII', 1700, 1970, 'AlIII1857', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), -#(1816.98, 'CIII', 1700, 1970, 'SiII1816', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), -#(1786.7, 'CIII', 1700, 1970, 'FeII1787', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), -#(1750.26, 'CIII', 1700, 1970, 'NIII1750', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), -#(1718.55, 'CIII', 1700, 1900, 'NIV1718', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), - -(1549.06, 'CIV', 1500, 1700, 'CIV_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), -(1549.06, 'CIV', 1500, 1700, 'CIV_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), -#(1640.42, 'CIV', 1500, 1700, 'HeII1640', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), -#(1663.48, 'CIV', 1500, 1700, 'OIII1663', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), -#(1640.42, 'CIV', 1500, 1700, 'HeII1640_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), -#(1663.48, 'CIV', 1500, 1700, 'OIII1663_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), - -#(1402.06, 'SiIV', 1290, 1450, 'SiIV_OIV1', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), -#(1396.76, 'SiIV', 1290, 1450, 'SiIV_OIV2', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), -#(1335.30, 'SiIV', 1290, 1450, 'CII1335', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), -#(1304.35, 'SiIV', 1290, 1450, 'OI1304', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), - -(1215.67, 'Lya', 1150, 1290, 'Lya_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.02, 0, 0, 0, 0.05 , 1), -(1215.67, 'Lya', 1150, 1290, 'Lya_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 0, 0, 0, 0.002, 1)], - -formats = 'float32, a20, float32, float32, a20, int32, float32, float32, float32, float32, float32, float32, float32, int32, int32, int32, float32, int32', -names = ' lambda, compname, minwav, maxwav, linename, ngauss, inisca, minsca, maxsca, inisig, minsig, maxsig, voff, vindex, windex, findex, fvalue, vary') - -# Header -hdr = fits.Header() -hdr['lambda'] = 'Vacuum Wavelength in Ang' -hdr['minwav'] = 'Lower complex fitting wavelength range' -hdr['maxwav'] = 'Upper complex fitting wavelength range' -hdr['ngauss'] = 'Number of Gaussians for the line' - -# Can be set to negative for absorption lines if you want -hdr['inisca'] = 'Initial guess of line scale [in ??]' -hdr['minsca'] = 'Lower range of line scale [??]' -hdr['maxsca'] = 'Upper range of line scale [??]' - -hdr['inisig'] = 'Initial guess of linesigma [in lnlambda]' -hdr['minsig'] = 'Lower range of line sigma [lnlambda]' -hdr['maxsig'] = 'Upper range of line sigma [lnlambda]' - -hdr['voff '] = 'Limits on velocity offset from the central wavelength [lnlambda]' -hdr['vindex'] = 'Entries w/ same NONZERO vindex constrained to have same velocity' -hdr['windex'] = 'Entries w/ same NONZERO windex constrained to have same width' -hdr['findex'] = 'Entries w/ same NONZERO findex have constrained flux ratios' -hdr['fvalue'] = 'Relative scale factor for entries w/ same findex' - -hdr['vary'] = 'Whether or not to vary the line parameters (set to 0 to fix the line parameters to initial values)' - -# Save line info -hdu1 = fits.BinTableHDU(data=line_priors, name='line_priors') - -""" -In this table, we specify the windows and priors / initial conditions and boundaries for the continuum fitting parameters. -""" -conti_windows = np.rec.array([ - (1150., 1170.), - (1275., 1290.), - (1350., 1360.), - (1445., 1465.), - (1690., 1705.), - (1770., 1810.), - (1970., 2400.), - (2480., 2675.), - (2925., 3400.), - (3775., 3832.), - (4000., 4050.), - (4200., 4230.), - (4435., 4640.), - (5100., 5535.), - (6005., 6035.), - (6110., 6250.), - (6800., 7000.), - (7160., 7180.), - (7500., 7800.), - (8050., 8150.), # Continuum fitting windows (to avoid emission line, etc.) [AA] - ], - formats = 'float32, float32', - names = 'min, max') - -hdu2 = fits.BinTableHDU(data=conti_windows, name='conti_windows') - -conti_priors = np.rec.array([ - ('Fe_uv_norm', 0.0, 0.0, 1e10, 1), # Normalization of the MgII Fe template [flux] - ('Fe_uv_FWHM', 3000, 1200, 18000, 1), # FWHM of the MgII Fe template [AA] - ('Fe_uv_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the MgII Fe template [lnlambda] - ('Fe_op_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Hbeta/Halpha Fe template [flux] - ('Fe_op_FWHM', 3000, 1200, 18000, 1), # FWHM of the Hbeta/Halpha Fe template [AA] - ('Fe_op_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the Hbeta/Halpha Fe template [lnlambda] - ('PL_norm', 1.0, 0.0, 1e10, 1), # Normalization of the power-law (PL) continuum f_lambda = (lambda/3000)^-alpha - ('PL_slope', -1.5, -5.0, 3.0, 1), # Slope of the power-law (PL) continuum - ('Blamer_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Balmer continuum at < 3646 AA [flux] (Dietrich et al. 2002) - ('Balmer_Te', 15000, 10000, 50000, 1), # Te of the Balmer continuum at < 3646 AA [K?] - ('Balmer_Tau', 0.5, 0.1, 2.0, 1), # Tau of the Balmer continuum at < 3646 AA - ('conti_a_0', 0.0, None, None, 1), # 1st coefficient of the polynomial continuum - ('conti_a_1', 0.0, None, None, 1), # 2nd coefficient of the polynomial continuum - ('conti_a_2', 0.0, None, None, 1), # 3rd coefficient of the polynomial continuum - # Note: The min/max bounds on the conti_a_0 coefficients are ignored by the code, - # so they can be determined automatically for numerical stability. - ], - - formats = 'a20, float32, float32, float32, int32', - names = 'parname, initial, min, max, vary') - -hdr3 = fits.Header() -hdr3['ini'] = 'Initial guess of line scale [flux]' -hdr3['min'] = 'FWHM of the MgII Fe template' -hdr3['max'] = 'Wavelength shift of the MgII Fe template' - -hdr3['vary'] = 'Whether or not to vary the parameter (set to 0 to fix the continuum parameter to initial values)' - - -hdu3 = fits.BinTableHDU(data=conti_priors, header=hdr3, name='conti_priors') - -""" -In this table, we allow user to customized some key parameters in our result measurements. -""" - -measure_info = Table( - [ - [[1350, 1450, 3000, 4200, 5100]], - [[ - # [2240, 2650], - [4435, 4685], - ]] - ], - names=([ - 'cont_loc', - 'Fe_flux_range' - ]), - dtype=([ - 'float32', - 'float32' - ]) -) -hdr4 = fits.Header() -hdr4['cont_loc'] = 'The wavelength of continuum luminosity in results' -hdr4['Fe_flux_range'] = 'Fe emission wavelength range calculated in results' - -hdu4 = fits.BinTableHDU(data=measure_info, header=hdr4, name='measure_info') - -# Save line info -hdu_list = fits.HDUList([primary_hdu, hdu1, hdu2, hdu3, hdu4]) -hdu_list.writeto(os.path.join(path_ex, 'qsopar.fits'), overwrite=True) -print('Saving to ', os.path.join(path_ex, 'qsopar.fits')) - -# Download the SDSS DR7 sample -import urllib.request -import gzip - -print('Retrieving DR7 catalog.') - -cat_file_name = 'dr7_bh_Nov19_2013.fits.gz' - -if not os.path.exists(cat_file_name): - urllib.request.urlretrieve(f'http://quasar.astro.illinois.edu/BH_mass/data/catalogs/{cat_file_name}', cat_file_name) - -# Fit a sample of nqsofit spectra -nqsofit = 20 - -# Line properties -line_calc_names = ['CIV_br', 'MgII_br', 'Hb_br'] -line_shen_names = ['CIV', 'BROAD_MGII', 'BROAD_HB'] -line_fwhms = np.zeros((nqsofit, len(line_calc_names))) -line_Ls = np.zeros((nqsofit, len(line_calc_names))) -Mis = np.zeros(nqsofit) -zs = np.zeros(nqsofit) - -start = timeit.default_timer() - -with gzip.open(cat_file_name, 'rb') as f: - - spec_all = fits.open(f) - - len_specs = len(spec_all[1].data) - range_rand = np.random.choice(range(len_specs), nqsofit, replace=False) - - #print(spec_all.info()) - #print(repr(spec_all[1].header)) - - # Catalog properties - Mi_all = spec_all[1].data['MI_Z2'] - z_all = spec_all[1].data['REDSHIFT'] - line_fwhm_all = np.zeros_like(line_fwhms) - line_L_all = np.zeros_like(line_Ls) - - # Emission line loop - for j, line in enumerate(line_shen_names): - line_fwhm_all[:,j] = spec_all[1].data[f'FWHM_{line}'][range_rand] - line_L_all[:,j] = spec_all[1].data[f'LOGL_{line}'][range_rand] - - # Save as single PDF - with bpdf.PdfPages(os.path.join(path_ex, 'fit_results.pdf')) as pdf: - - # For each spectrum - for i, ind in enumerate(range_rand): - - plate = spec_all[1].data['PLATE'][ind] - mjd = spec_all[1].data['MJD'][ind] - fiber = spec_all[1].data['FIBER'][ind] - ra = spec_all[1].data['RA'][ind] - dec = spec_all[1].data['DEC'][ind] - Mi = spec_all[1].data['MI_Z2'][ind] - - # Query the spectrum - pos = coords.SkyCoord(ra, dec, unit='deg') - xid = SDSS.query_region(pos, spectro=True, radius='5 arcsec') - - if xid is None: - continue - - mask = (xid['plate'] == plate) & (xid['mjd'] == mjd) & (xid['fiberID'] == fiber) - print(xid[mask]) - sp = SDSS.get_spectra(matches=xid[mask]) - print(sp) - - data = sp[0] +def test_dr7(nqsofit=20): - # Requried - lam = 10**data[1].data['loglam'] # OBS wavelength [A] - flux = data[1].data['flux'] # OBS flux [erg/s/cm^2/A] - err = 1/np.sqrt(data[1].data['ivar']) # 1 sigma error - z = data[2].data['z'][0] # Redshift + # Use custom matplotlib style to make Yue happy + QSOFit.set_mpl_style() - q = QSOFit(lam, flux, err, z, ra=ra, dec=dec, plateid=plate, mjd=mjd, fiberid=fiber, path=path_ex) + path_ex = os.path.abspath('.') # The absolute path to the example directory - # Do the fitting - q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) - - # Emission line loop - for j, line in enumerate(line_calc_names): + print(path_ex) + # Setup the parameter file + + # create a header + hdr0 = fits.Header() + hdr0['Author'] = 'Hengxiao Guo' + primary_hdu = fits.PrimaryHDU(header=hdr0) + + """ + Create parameter file + lambda complexname minwav maxwav linename ngauss inisca minsca maxsca inisig minsig maxsig voff vindex windex findex fvalue vary + """ + + line_priors = np.rec.array([ + (6564.61, r'Ha', 6400, 6800, 'Ha_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), + (6564.61, r'Ha', 6400, 6800, 'Ha_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (6549.85, r'Ha', 6400, 6800, 'NII6549', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.001, 1), + (6585.28, r'Ha', 6400, 6800, 'NII6585', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.003, 1), + (6718.29, r'Ha', 6400, 6800, 'SII6718', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), + (6732.67, r'Ha', 6400, 6800, 'SII6732', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), + + (4862.68, r'Hb', 4640, 5100, 'Hb_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.01, 0, 0, 0, 0.01 , 1), + (4862.68, r'Hb', 4640, 5100, 'Hb_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (4960.30, r'Hb', 4640, 5100, 'OIII4959c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (5008.24, r'Hb', 4640, 5100, 'OIII5007c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.004, 1), + #(4960.30, r'Hb', 4640, 5100, 'OIII4959w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.001, 1), + #(5008.24, r'Hb', 4640, 5100, 'OIII5007w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.002, 1), + #(4687.02, r'Hb', 4640, 5100, 'HeII4687_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.005, 0, 0, 0, 0.001, 1), + #(4687.02, r'Hb', 4640, 5100, 'HeII4687_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.005, 1, 1, 0, 0.001, 1), + + #(3934.78, 'CaII', 3900, 3960, 'CaII3934' , 2, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 99, 0, 0, -0.001, 1), + + #(3728.48, 'OII', 3650, 3800, 'OII3728', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 1, 1, 0, 0.001, 1), + + #(3426.84, 'NeV', 3380, 3480, 'NeV3426', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 0, 0, 0, 0.001, 1), + #(3426.84, 'NeV', 3380, 3480, 'NeV3426_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.01, 0, 0, 0, 0.001, 1), + + (2798.75, 'MgII', 2700, 2900, 'MgII_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.0017, 0, 0, 0, 0.05, 1), + (2798.75, 'MgII', 2700, 2900, 'MgII_na', 2, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + + (1908.73, 'CIII', 1700, 1970, 'CIII_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 99, 0, 0, 0.01, 1), + #(1908.73, 'CIII', 1700, 1970, 'CIII_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + #(1892.03, 'CIII', 1700, 1970, 'SiIII1892', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), + #(1857.40, 'CIII', 1700, 1970, 'AlIII1857', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), + #(1816.98, 'CIII', 1700, 1970, 'SiII1816', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), + #(1786.7, 'CIII', 1700, 1970, 'FeII1787', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), + #(1750.26, 'CIII', 1700, 1970, 'NIII1750', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + #(1718.55, 'CIII', 1700, 1900, 'NIV1718', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + + (1549.06, 'CIV', 1500, 1700, 'CIV_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), + (1549.06, 'CIV', 1500, 1700, 'CIV_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + #(1640.42, 'CIV', 1500, 1700, 'HeII1640', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), + #(1663.48, 'CIV', 1500, 1700, 'OIII1663', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), + #(1640.42, 'CIV', 1500, 1700, 'HeII1640_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), + #(1663.48, 'CIV', 1500, 1700, 'OIII1663_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), + + #(1402.06, 'SiIV', 1290, 1450, 'SiIV_OIV1', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), + #(1396.76, 'SiIV', 1290, 1450, 'SiIV_OIV2', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), + #(1335.30, 'SiIV', 1290, 1450, 'CII1335', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + #(1304.35, 'SiIV', 1290, 1450, 'OI1304', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + + (1215.67, 'Lya', 1150, 1290, 'Lya_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.02, 0, 0, 0, 0.05 , 1), + (1215.67, 'Lya', 1150, 1290, 'Lya_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 0, 0, 0, 0.002, 1)], + + formats = 'float32, a20, float32, float32, a20, int32, float32, float32, float32, float32, float32, float32, float32, int32, int32, int32, float32, int32', + names = ' lambda, compname, minwav, maxwav, linename, ngauss, inisca, minsca, maxsca, inisig, minsig, maxsig, voff, vindex, windex, findex, fvalue, vary') + + # Header + hdr = fits.Header() + hdr['lambda'] = 'Vacuum Wavelength in Ang' + hdr['minwav'] = 'Lower complex fitting wavelength range' + hdr['maxwav'] = 'Upper complex fitting wavelength range' + hdr['ngauss'] = 'Number of Gaussians for the line' + + # Can be set to negative for absorption lines if you want + hdr['inisca'] = 'Initial guess of line scale [in ??]' + hdr['minsca'] = 'Lower range of line scale [??]' + hdr['maxsca'] = 'Upper range of line scale [??]' + + hdr['inisig'] = 'Initial guess of linesigma [in lnlambda]' + hdr['minsig'] = 'Lower range of line sigma [lnlambda]' + hdr['maxsig'] = 'Upper range of line sigma [lnlambda]' + + hdr['voff '] = 'Limits on velocity offset from the central wavelength [lnlambda]' + hdr['vindex'] = 'Entries w/ same NONZERO vindex constrained to have same velocity' + hdr['windex'] = 'Entries w/ same NONZERO windex constrained to have same width' + hdr['findex'] = 'Entries w/ same NONZERO findex have constrained flux ratios' + hdr['fvalue'] = 'Relative scale factor for entries w/ same findex' + + hdr['vary'] = 'Whether or not to vary the line parameters (set to 0 to fix the line parameters to initial values)' + + # Save line info + hdu1 = fits.BinTableHDU(data=line_priors, name='line_priors') + + """ + In this table, we specify the windows and priors / initial conditions and boundaries for the continuum fitting parameters. + """ + conti_windows = np.rec.array([ + (1150., 1170.), + (1275., 1290.), + (1350., 1360.), + (1445., 1465.), + (1690., 1705.), + (1770., 1810.), + (1970., 2400.), + (2480., 2675.), + (2925., 3400.), + (3775., 3832.), + (4000., 4050.), + (4200., 4230.), + (4435., 4640.), + (5100., 5535.), + (6005., 6035.), + (6110., 6250.), + (6800., 7000.), + (7160., 7180.), + (7500., 7800.), + (8050., 8150.), # Continuum fitting windows (to avoid emission line, etc.) [AA] + ], + formats = 'float32, float32', + names = 'min, max') + + hdu2 = fits.BinTableHDU(data=conti_windows, name='conti_windows') + + conti_priors = np.rec.array([ + ('Fe_uv_norm', 0.0, 0.0, 1e10, 1), # Normalization of the MgII Fe template [flux] + ('Fe_uv_FWHM', 3000, 1200, 18000, 1), # FWHM of the MgII Fe template [AA] + ('Fe_uv_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the MgII Fe template [lnlambda] + ('Fe_op_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Hbeta/Halpha Fe template [flux] + ('Fe_op_FWHM', 3000, 1200, 18000, 1), # FWHM of the Hbeta/Halpha Fe template [AA] + ('Fe_op_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the Hbeta/Halpha Fe template [lnlambda] + ('PL_norm', 1.0, 0.0, 1e10, 1), # Normalization of the power-law (PL) continuum f_lambda = (lambda/3000)^-alpha + ('PL_slope', -1.5, -5.0, 3.0, 1), # Slope of the power-law (PL) continuum + ('Blamer_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Balmer continuum at < 3646 AA [flux] (Dietrich et al. 2002) + ('Balmer_Te', 15000, 10000, 50000, 1), # Te of the Balmer continuum at < 3646 AA [K?] + ('Balmer_Tau', 0.5, 0.1, 2.0, 1), # Tau of the Balmer continuum at < 3646 AA + ('conti_a_0', 0.0, None, None, 1), # 1st coefficient of the polynomial continuum + ('conti_a_1', 0.0, None, None, 1), # 2nd coefficient of the polynomial continuum + ('conti_a_2', 0.0, None, None, 1), # 3rd coefficient of the polynomial continuum + # Note: The min/max bounds on the conti_a_0 coefficients are ignored by the code, + # so they can be determined automatically for numerical stability. + ], + + formats = 'a20, float32, float32, float32, int32', + names = 'parname, initial, min, max, vary') + + hdr3 = fits.Header() + hdr3['ini'] = 'Initial guess of line scale [flux]' + hdr3['min'] = 'FWHM of the MgII Fe template' + hdr3['max'] = 'Wavelength shift of the MgII Fe template' + + hdr3['vary'] = 'Whether or not to vary the parameter (set to 0 to fix the continuum parameter to initial values)' + + + hdu3 = fits.BinTableHDU(data=conti_priors, header=hdr3, name='conti_priors') + + """ + In this table, we allow user to customized some key parameters in our result measurements. + """ + + measure_info = Table( + [ + [[1350, 1450, 3000, 4200, 5100]], + [[ + # [2240, 2650], + [4435, 4685], + ]] + ], + names=([ + 'cont_loc', + 'Fe_flux_range' + ]), + dtype=([ + 'float32', + 'float32' + ]) + ) + hdr4 = fits.Header() + hdr4['cont_loc'] = 'The wavelength of continuum luminosity in results' + hdr4['Fe_flux_range'] = 'Fe emission wavelength range calculated in results' + + hdu4 = fits.BinTableHDU(data=measure_info, header=hdr4, name='measure_info') + + # Save line info + hdu_list = fits.HDUList([primary_hdu, hdu1, hdu2, hdu3, hdu4]) + hdu_list.writeto(os.path.join(path_ex, 'qsopar.fits'), overwrite=True) + print('Saving to ', os.path.join(path_ex, 'qsopar.fits')) + + # Download the SDSS DR7 sample + import urllib.request + import gzip + + print('Retrieving DR7 catalog.') + + cat_file_name = 'dr7_bh_Nov19_2013.fits.gz' + + if not os.path.exists(cat_file_name): + urllib.request.urlretrieve(f'http://quasar.astro.illinois.edu/BH_mass/data/catalogs/{cat_file_name}', cat_file_name) + + # Line properties + line_calc_names = ['CIV_br', 'MgII_br', 'Hb_br'] + line_shen_names = ['CIV', 'BROAD_MGII', 'BROAD_HB'] + line_fwhms = np.zeros((nqsofit, len(line_calc_names))) + line_Ls = np.zeros((nqsofit, len(line_calc_names))) + Mis = np.zeros(nqsofit) + zs = np.zeros(nqsofit) + + start = timeit.default_timer() + + with gzip.open(cat_file_name, 'rb') as f: + + spec_all = fits.open(f) + + len_specs = len(spec_all[1].data) + range_rand = np.random.choice(range(len_specs), nqsofit, replace=False) + + #print(spec_all.info()) + #print(repr(spec_all[1].header)) + + # Catalog properties + Mi_all = spec_all[1].data['MI_Z2'] + z_all = spec_all[1].data['REDSHIFT'] + line_fwhm_all = np.zeros_like(line_fwhms) + line_L_all = np.zeros_like(line_Ls) + + # Emission line loop + for j, line in enumerate(line_shen_names): + line_fwhm_all[:,j] = spec_all[1].data[f'FWHM_{line}'][range_rand] + line_L_all[:,j] = spec_all[1].data[f'LOGL_{line}'][range_rand] + + # Save as single PDF + with bpdf.PdfPages(os.path.join(path_ex, 'fit_results.pdf')) as pdf: + + # For each spectrum + for i, ind in enumerate(range_rand): + + plate = spec_all[1].data['PLATE'][ind] + mjd = spec_all[1].data['MJD'][ind] + fiber = spec_all[1].data['FIBER'][ind] + ra = spec_all[1].data['RA'][ind] + dec = spec_all[1].data['DEC'][ind] + Mi = spec_all[1].data['MI_Z2'][ind] - print(line) + # Query the spectrum + pos = coords.SkyCoord(ra, dec, unit='deg') + xid = SDSS.query_region(pos, spectro=True, radius='5 arcsec') - if line.endswith('_br'): - line_type = 'broad' - else: - line_type = 'narrow' - - # Get the line properties - fwhm, sigma, ew, peak, area, snr = q.line_prop_from_name(line, line_type) - - print(f"Broad {line}:") - print("FWHM (km/s)", np.round(fwhm, 1)) - print("Sigma (km/s)", np.round(sigma, 1)) - print("EW (A)", np.round(ew, 1)) - print("Peak (A)", np.round(peak, 1)) - print("area (10^(-17) erg/s/cm^2)", np.round(area, 1)) - print("") + if xid is None: + continue - line_fwhms[i, j] = fwhm - line_Ls[i, j] = np.log10(q.flux2L(area)) - Mis[i] = Mi - zs[i] = z + mask = (xid['plate'] == plate) & (xid['mjd'] == mjd) & (xid['fiberID'] == fiber) + print(xid[mask]) + sp = SDSS.get_spectra(matches=xid[mask]) + print(sp) + data = sp[0] - # Stack the results into 1 file - #pdf.savefig(q.fig) # Turn this off for github actions - - # End open file - -# Summary figures + # Requried + lam = 10**data[1].data['loglam'] # OBS wavelength [A] + flux = data[1].data['flux'] # OBS flux [erg/s/cm^2/A] + err = 1/np.sqrt(data[1].data['ivar']) # 1 sigma error + z = data[2].data['z'][0] # Redshift -def rmse(predictions, targets): - predictions = np.array(predictions) - targets = np.array(targets) - return np.sqrt(((predictions - targets)**2).mean()) + q = QSOFit(lam, flux, err, z, ra=ra, dec=dec, plateid=plate, mjd=mjd, fiberid=fiber, path=path_ex) -fig, ax = plt.subplots(1, 1, figsize=(8,5)) -ax.scatter(z_all, Mi_all, color='k', marker='.', alpha=0.01) -ax.scatter(zs, Mis, color='r', marker='o', alpha=0.5) -ax.set_title(pyqsofit.__version__) + # Do the fitting + q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) + + # Emission line loop + for j, line in enumerate(line_calc_names): + + print(line) + + if line.endswith('_br'): + line_type = 'broad' + else: + line_type = 'narrow' + + # Get the line properties + fwhm, sigma, ew, peak, area, snr = q.line_prop_from_name(line, line_type) + + print(f"Broad {line}:") + print("FWHM (km/s)", np.round(fwhm, 1)) + print("Sigma (km/s)", np.round(sigma, 1)) + print("EW (A)", np.round(ew, 1)) + print("Peak (A)", np.round(peak, 1)) + print("area (10^(-17) erg/s/cm^2)", np.round(area, 1)) + print("") + + line_fwhms[i, j] = fwhm + line_Ls[i, j] = np.log10(q.flux2L(area)) + Mis[i] = Mi + zs[i] = z + + + # Stack the results into 1 file + #pdf.savefig(q.fig) # Turn this off for github actions + + # End open file + + # Summary figures -ax.set_xlabel('Redshift', fontsize=20) -ax.set_ylabel(r'$M_i(z=2)$', fontsize=20) + def rmse(predictions, targets): + predictions = np.array(predictions) + targets = np.array(targets) + return np.sqrt(((predictions - targets)**2).mean()) -ax.set_xlim([0, 5.5]) -ax.set_ylim([-22, -30]) + fig, ax = plt.subplots(1, 1, figsize=(8,5)) + ax.scatter(z_all, Mi_all, color='k', marker='.', alpha=0.01) + ax.scatter(zs, Mis, color='r', marker='o', alpha=0.5) + ax.set_title(pyqsofit.__version__) -fig.tight_layout() -fig.savefig(os.path.join(path_ex, 'Mi_z.pdf'), dpi=300) + ax.set_xlabel('Redshift', fontsize=20) + ax.set_ylabel(r'$M_i(z=2)$', fontsize=20) + + ax.set_xlim([0, 5.5]) + ax.set_ylim([-22, -30]) -# Emission line loop -for j, line in enumerate(line_calc_names): - - # Summary figures - fig, axs = plt.subplots(1, 2, figsize=(12,5)) - - x = np.linspace(1000, 12000) - axs[0].plot(x, x, color='gray') - - x = np.linspace(41, 48) - axs[1].plot(x, x, color='gray', zorder=-1) - - axs[0].scatter(line_fwhm_all[:, j], line_fwhms[:, j], color='r', marker='o', alpha=0.5) - rmse_fwhm = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) - print(f'RMSE FWHM = {rmse_fwhm}') - axs[0].set_xlim([1000, 12000]) - axs[0].set_ylim([1000, 12000]) - - axs[1].scatter(line_L_all[:, j], line_Ls[:, j], color='r', marker='o', alpha=0.5) - rmse_L = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) - print(f'RMSE L = {rmse_L}') - axs[1].set_xlim([41, 46]) - axs[1].set_ylim([41, 46]) - - axs[0].set_title(line) - axs[0].set_xlabel(f'FWHM v{pyqsofit.__version__}', fontsize=20) - axs[0].set_ylabel(f'FWHM Shen 2011', fontsize=20) - - axs[1].set_title(line) - axs[1].set_xlabel(f'log L v{pyqsofit.__version__}', fontsize=20) - axs[1].set_ylabel(f'log L Shen 2011', fontsize=20) - fig.tight_layout() - fig.savefig(os.path.join(path_ex, f'{line}.pdf'), dpi=300) + fig.savefig(os.path.join(path_ex, 'Mi_z.pdf'), dpi=300) + + # Emission line loop + for j, line in enumerate(line_calc_names): + + # Summary figures + fig, axs = plt.subplots(1, 2, figsize=(12,5)) + + x = np.linspace(1000, 12000) + axs[0].plot(x, x, color='gray') + + x = np.linspace(41, 48) + axs[1].plot(x, x, color='gray', zorder=-1) + + axs[0].scatter(line_fwhm_all[:, j], line_fwhms[:, j], color='r', marker='o', alpha=0.5) + rmse_fwhm = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) + print(f'RMSE FWHM = {rmse_fwhm}') + axs[0].set_xlim([1000, 12000]) + axs[0].set_ylim([1000, 12000]) + + axs[1].scatter(line_L_all[:, j], line_Ls[:, j], color='r', marker='o', alpha=0.5) + rmse_L = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) + print(f'RMSE L = {rmse_L}') + axs[1].set_xlim([41, 46]) + axs[1].set_ylim([41, 46]) + + axs[0].set_title(line) + axs[0].set_xlabel(f'FWHM v{pyqsofit.__version__}', fontsize=20) + axs[0].set_ylabel(f'FWHM Shen 2011', fontsize=20) + + axs[1].set_title(line) + axs[1].set_xlabel(f'log L v{pyqsofit.__version__}', fontsize=20) + axs[1].set_ylabel(f'log L Shen 2011', fontsize=20) + + fig.tight_layout() + fig.savefig(os.path.join(path_ex, f'{line}.pdf'), dpi=300) + + # Test + #assert rmse_L < 0.2 - # Test - #assert rmse_L < 0.2 + end = timeit.default_timer() + print('finshed in '+str(round(end-start))+'s') -end = timeit.default_timer() -print('finshed in '+str(round(end-start))+'s') + return -## i \ No newline at end of file +# init +import sys +if __name__ == "__main__": + a = int(sys.argv[1]) + test_dr7(a) \ No newline at end of file From 4e03f062c30b6259af78bbed41ed2165e8dc352d Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 17:57:25 -0400 Subject: [PATCH 18/51] Create documentation.yml --- .github/workflows/documentation.yml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 .github/workflows/documentation.yml diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml new file mode 100644 index 00000000..b2aaabe9 --- /dev/null +++ b/.github/workflows/documentation.yml @@ -0,0 +1,27 @@ +name: documentation + +on: [push, pull_request, workflow_dispatch] + +permissions: + contents: write + +jobs: + docs: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + - name: Install dependencies + run: | + pip install sphinx sphinx_rtd_theme myst_parser + - name: Sphinx build + run: | + sphinx-build doc _build + - name: Deploy to GitHub Pages + uses: burke86/actions-gh-pages@v3 + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} + with: + publish_branch: gh-pages + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _build/ + force_orphan: true From fdc2d203816a46712456dddfad4a9a7cfb1fd9e6 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 17:59:04 -0400 Subject: [PATCH 19/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index b2aaabe9..54f003c9 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -18,7 +18,7 @@ jobs: run: | sphinx-build doc _build - name: Deploy to GitHub Pages - uses: burke86/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v3 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} with: publish_branch: gh-pages From 3946435a1b3d535c35d9a86a8628b27a0a635fec Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 18:10:28 -0400 Subject: [PATCH 20/51] move to src --- pyqsofit/qsopar.fits | 22 --------------- pyqsofit/tests/CIV_br.pdf | Bin 17220 -> 0 bytes pyqsofit/tests/Hb_br.pdf | Bin 14718 -> 0 bytes pyqsofit/tests/MgII_br.pdf | Bin 18755 -> 0 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src/pyqsofit}/sfddata/SFD_dust_4096_ngp.fits (100%) rename {pyqsofit => src/pyqsofit}/sfddata/SFD_dust_4096_sgp.fits (100%) rename {pyqsofit => src/pyqsofit}/sfddata/SFD_mask_4096_ngp.fits (100%) rename {pyqsofit => src/pyqsofit}/sfddata/SFD_mask_4096_sgp.fits (100%) rename {pyqsofit => src/pyqsofit}/tests/test_dr7sample.py (100%) rename {pyqsofit => src/pyqsofit}/version.py (100%) diff --git a/pyqsofit/qsopar.fits b/pyqsofit/qsopar.fits deleted file mode 100644 index 54152239..00000000 --- a/pyqsofit/qsopar.fits +++ /dev/null @@ -1,22 +0,0 @@ -SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 88 / length of dimension 1 NAXIS2 = 17 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 14 / number of table fields LAMBDA = 'Vacuum Wavelength in Ang' MINWAV = 'Lower complex fitting wavelength range' MAXWAV = 'Upper complex fitting wavelength range' NGAUSS = 'Number of Gaussians for the line' INISIG = 'Initial guess of linesigma [in lnlambda]' MINSIG = 'Lower range of line sigma [lnlambda]' MAXSIG = 'Upper range of line sigma [lnlambda]' VOFF = 'Limits on velocity offset from the central wavelength [lnlambda]' VINDEX = 'Entries w/ same NONZERO vindex constrained to have same velocity' WINDEX = 'Entries w/ same NONZERO windex constrained to have same width' FINDEX = 'Entries w/ same NONZERO findex have constrained flux ratios' FVALUE = 'Relative scale factor for entries w/ same findex' EXTNAME = 'DATA ' / extension name TTYPE1 = 'lambda ' TFORM1 = 'E ' TTYPE2 = 'compname' TFORM2 = '20A ' TTYPE3 = 'minwav ' TFORM3 = 'E ' TTYPE4 = 'maxwav ' TFORM4 = 'E ' TTYPE5 = 'linename' TFORM5 = '20A ' TTYPE6 = 'ngauss ' TFORM6 = 'E ' TTYPE7 = 'inisig ' TFORM7 = 'E ' TTYPE8 = 'minsig ' TFORM8 = 'E ' TTYPE9 = 'maxsig ' TFORM9 = 'E ' TTYPE10 = 'voff ' TFORM10 = 'E ' TTYPE11 = 'vindex ' TFORM11 = 'E ' TTYPE12 = 'windex ' TFORM12 = 'E ' TTYPE13 = 'findex ' TFORM13 = 'E ' TTYPE14 = 'fvalue ' TFORM14 = 'E ' END EÍ$áHaEÈEÔ€Ha_br@@;£× -;ƒo=LÌÍTG?CnmaHp#UXoPyC?Xjd5g{v*%*c!)AuB3ngd${Q z6uz&Q#=G_VJbL^d-~Yb1$8pYmzMkit=Q`*4e4TTj@#!h6iowNElzgQxAtm*ca0m?I zY3D*IBLjiz*`C7rLJ$DN00K2Sgj=pAiuWtZ1H%Uj|T(|ex-!!`FPqJ;_whlU>;>vV0>Hv9s<>H2j*1#Rx5q0 zH6SM-P(vqM2WO8{5X{%^X1aDRID0%qVt?@e$btXNfP#mIC*BtVhkd0$37`h&0RXUH zzw6)}oNX070{|L83`q66wgnB00;dp zIaOyjfL91q)eR7aGS1%90g#b(_tj5GC4P+K-QFqfzzoT z5f_@S?>P?WPHb-Irgn2em*ni{PO^O5Wl(zIV^!+L1+Q>;@m^By{MnsrhNHQ1oHsqQ zXJ0%xxoDj@@Z8{JVuYCZv7p8;=eJf@7Ax~ergA^*EMMV#Fwq;|8TPvI^@Z9m%O6*E za2J?UJESeeR`=?Yns508Sv}bHIJ5EM&X@Pln*NG0Mf zH4^hgPt)76x14Qi>b}}IQeSl~kb=!dw4!pO{bCW`=;4c=o$&RE*zCI**(<2G58~*3 zqbbmn5SpS{3)Q%xSJ--UMjuY~Kv6!An|W+u`4d^bc%$;?(I)A5dupM;8oD}C-9)iD zj{Xla4515_bJ(Ppoy&ep9$&V-2wmde*-)ntx-j8tV=7a^iNBC6@|PYwmH8-bgg934 z-cvVP=9=NHQJ33`^-%Bu%;i$##EkPuMP!eUj+wn!)_LCvD;?INPaI`>zR%;Nc#^k)e 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setuptools import setup -from pyqsofit.version import __version__ +from src.pyqsofit.version import __version__ # Prepare and send a new release to PyPI #if "release" in sys.argv[-1]: @@ -14,7 +14,7 @@ # sys.exit() # Load the __version__ variable without importing the package already -exec(open('pyqsofit/version.py').read()) +exec(open('src/pyqsofit/version.py').read()) with open("README.md", "r") as fh: long_description = fh.read() @@ -30,7 +30,7 @@ author_email='hengxiaoguo@gmail.com', url='https://github.com/legolason/PyQSOFit', license='GNU General Public License v3.0', - package_dir={'pyqsofit': 'pyqsofit'}, + package_dir={'pyqsofit': 'src/pyqsofit'}, package_data={'pyqsofit': ['fe_uv.txt', 'fe_optical.txt', 'bc03/*.spec.gz', 'pca/Yip_pca_templates/*.fits', diff --git a/pyqsofit/HostDecomp.py b/src/pyqsofit/HostDecomp.py similarity index 100% rename from pyqsofit/HostDecomp.py rename to src/pyqsofit/HostDecomp.py diff --git a/pyqsofit/MESFit.py b/src/pyqsofit/MESFit.py similarity 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src/pyqsofit/pca/prior/QSO_pp_prior_CZBIN1.csv diff --git a/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv b/src/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv similarity index 100% rename from pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv rename to src/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv diff --git a/src/pyqsofit/qsopar.fits b/src/pyqsofit/qsopar.fits new file mode 100644 index 00000000..9f37b21b --- /dev/null +++ b/src/pyqsofit/qsopar.fits @@ -0,0 +1,26 @@ +SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T AUTHOR = 'Hengxiao Guo' END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 104 / length of dimension 1 NAXIS2 = 17 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 18 / number of table fields TTYPE1 = 'lambda ' TFORM1 = 'E ' TTYPE2 = 'compname' TFORM2 = '20A ' TTYPE3 = 'minwav ' TFORM3 = 'E ' TTYPE4 = 'maxwav ' TFORM4 = 'E ' TTYPE5 = 'linename' TFORM5 = '20A ' TTYPE6 = 'ngauss ' TFORM6 = 'J ' TTYPE7 = 'inisca ' TFORM7 = 'E ' TTYPE8 = 'minsca ' TFORM8 = 'E ' TTYPE9 = 'maxsca ' TFORM9 = 'E ' TTYPE10 = 'inisig ' TFORM10 = 'E ' TTYPE11 = 'minsig ' TFORM11 = 'E ' TTYPE12 = 'maxsig ' TFORM12 = 'E ' TTYPE13 = 'voff ' TFORM13 = 'E ' TTYPE14 = 'vindex ' TFORM14 = 'J ' TTYPE15 = 'windex ' TFORM15 = 'J ' TTYPE16 = 'findex ' TFORM16 = 'J ' TTYPE17 = 'fvalue ' TFORM17 = 'E ' TTYPE18 = 'vary ' TFORM18 = 'J ' EXTNAME = 'LINE_PRIORS' / extension name END EÍ$áHaEÈEÔ€Ha_br=ÌÌÍPù;£× +;ƒo=LÌÍ Date: Fri, 28 Jun 2024 18:14:50 -0400 Subject: [PATCH 21/51] move test --- {src/pyqsofit/tests => tests}/test_dr7sample.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {src/pyqsofit/tests => tests}/test_dr7sample.py (100%) diff --git a/src/pyqsofit/tests/test_dr7sample.py b/tests/test_dr7sample.py similarity index 100% rename from src/pyqsofit/tests/test_dr7sample.py rename to tests/test_dr7sample.py From cbe17c602a177a6615a723b2ce2033b52e4fa6dd Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 18:15:40 -0400 Subject: [PATCH 22/51] Update python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index e81bcad6..37b690f3 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -38,4 +38,4 @@ jobs: - name: Test with pytest run: | python -m pip install . - pytest pyqsofit/tests/test_dr7sample.py + pytest tests/test_dr7sample.py From ba6ae28b7dc3440ae0a441ab03babc63c56c68cb Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Fri, 28 Jun 2024 18:16:40 -0400 Subject: [PATCH 23/51] Create .placeholder --- doc/.placeholder | 1 + 1 file changed, 1 insertion(+) create mode 100644 doc/.placeholder diff --git a/doc/.placeholder b/doc/.placeholder new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/doc/.placeholder @@ -0,0 +1 @@ + From eaa103e1b7f94c9e41a80b1b03a196617133a311 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 18:24:19 -0400 Subject: [PATCH 24/51] add doc conf --- doc/Makefile | 20 ++++++++++++++++++++ doc/conf.py | 28 ++++++++++++++++++++++++++++ doc/index.rst | 20 ++++++++++++++++++++ doc/make.bat | 35 +++++++++++++++++++++++++++++++++++ 4 files changed, 103 insertions(+) create mode 100644 doc/Makefile create mode 100644 doc/conf.py create mode 100644 doc/index.rst create mode 100644 doc/make.bat diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 00000000..d4bb2cbb --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 00000000..3cbfd631 --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,28 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'pyqsofit' +copyright = '2024, Hengxiao Guo' +author = 'Hengxiao Guo' +release = '2.1.6' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [] + +templates_path = ['_templates'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'alabaster' +html_static_path = ['_static'] diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 00000000..b43b0df7 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,20 @@ +.. pyqsofit documentation master file, created by + sphinx-quickstart on Fri Jun 28 18:21:35 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to pyqsofit's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 00000000..32bb2452 --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd From 01255bd9581fb1ac5accd73c42d33c6207d3072f Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 18:29:57 -0400 Subject: [PATCH 25/51] add doc files --- doc/_build/doctrees/environment.pickle | Bin 0 -> 34315 bytes doc/_build/doctrees/index.doctree | Bin 0 -> 5018 bytes doc/_build/doctrees/modules.doctree | Bin 0 -> 2764 bytes doc/_build/doctrees/pyqsofit.doctree | Bin 0 -> 9250 bytes doc/_build/html/.buildinfo | 4 + doc/_build/html/_sources/index.rst.txt | 20 + doc/_build/html/_sources/modules.rst.txt | 7 + doc/_build/html/_sources/pyqsofit.rst.txt | 45 + doc/_build/html/_static/alabaster.css | 708 ++++++++++++++ doc/_build/html/_static/basic.css | 925 ++++++++++++++++++ doc/_build/html/_static/custom.css | 1 + doc/_build/html/_static/doctools.js | 156 +++ .../html/_static/documentation_options.js | 13 + doc/_build/html/_static/file.png | Bin 0 -> 286 bytes doc/_build/html/_static/language_data.js | 199 ++++ doc/_build/html/_static/minus.png | Bin 0 -> 90 bytes doc/_build/html/_static/plus.png | Bin 0 -> 90 bytes doc/_build/html/_static/pygments.css | 83 ++ doc/_build/html/_static/searchtools.js | 619 ++++++++++++ doc/_build/html/_static/sphinx_highlight.js | 154 +++ doc/_build/html/genindex.html | 99 ++ doc/_build/html/index.html | 110 +++ doc/_build/html/modules.html | 113 +++ doc/_build/html/objects.inv | 5 + doc/_build/html/pyqsofit.html | 118 +++ doc/_build/html/search.html | 116 +++ doc/_build/html/searchindex.js | 1 + doc/modules.rst | 7 + doc/pyqsofit.rst | 45 + 29 files changed, 3548 insertions(+) create mode 100644 doc/_build/doctrees/environment.pickle create mode 100644 doc/_build/doctrees/index.doctree create mode 100644 doc/_build/doctrees/modules.doctree create mode 100644 doc/_build/doctrees/pyqsofit.doctree create mode 100644 doc/_build/html/.buildinfo create mode 100644 doc/_build/html/_sources/index.rst.txt create mode 100644 doc/_build/html/_sources/modules.rst.txt create mode 100644 doc/_build/html/_sources/pyqsofit.rst.txt create mode 100644 doc/_build/html/_static/alabaster.css create mode 100644 doc/_build/html/_static/basic.css create mode 100644 doc/_build/html/_static/custom.css create mode 100644 doc/_build/html/_static/doctools.js create mode 100644 doc/_build/html/_static/documentation_options.js create mode 100644 doc/_build/html/_static/file.png create mode 100644 doc/_build/html/_static/language_data.js create mode 100644 doc/_build/html/_static/minus.png create mode 100644 doc/_build/html/_static/plus.png create mode 100644 doc/_build/html/_static/pygments.css create mode 100644 doc/_build/html/_static/searchtools.js create mode 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When it is not found, a full rebuild will be done. +config: 6d4b5ec32d521dd430eb4adb6b5d91d3 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt new file mode 100644 index 00000000..b43b0df7 --- /dev/null +++ b/doc/_build/html/_sources/index.rst.txt @@ -0,0 +1,20 @@ +.. pyqsofit documentation master file, created by + sphinx-quickstart on Fri Jun 28 18:21:35 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to pyqsofit's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/doc/_build/html/_sources/modules.rst.txt b/doc/_build/html/_sources/modules.rst.txt new file mode 100644 index 00000000..84849f95 --- /dev/null +++ b/doc/_build/html/_sources/modules.rst.txt @@ -0,0 +1,7 @@ +pyqsofit +======== + +.. toctree:: + :maxdepth: 4 + + pyqsofit diff --git a/doc/_build/html/_sources/pyqsofit.rst.txt b/doc/_build/html/_sources/pyqsofit.rst.txt new file mode 100644 index 00000000..40a2bca4 --- /dev/null +++ b/doc/_build/html/_sources/pyqsofit.rst.txt @@ -0,0 +1,45 @@ +pyqsofit package +================ + +Submodules +---------- + +pyqsofit.HostDecomp module +-------------------------- + +.. automodule:: pyqsofit.HostDecomp + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.MESFit module +---------------------- + +.. automodule:: pyqsofit.MESFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.PyQSOFit module +------------------------ + +.. automodule:: pyqsofit.PyQSOFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.version module +----------------------- + +.. automodule:: pyqsofit.version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: pyqsofit + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/_build/html/_static/alabaster.css b/doc/_build/html/_static/alabaster.css new file mode 100644 index 00000000..e3174bf9 --- /dev/null +++ b/doc/_build/html/_static/alabaster.css @@ -0,0 +1,708 @@ +@import url("basic.css"); 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+ text-decoration: none; + border-bottom: 1px dotted #999; +} + +div.sphinxsidebar a:hover { + border-bottom: 1px solid #999; +} + +div.sphinxsidebarwrapper { + padding: 18px 10px; +} + +div.sphinxsidebarwrapper p.logo { + padding: 0; + margin: -10px 0 0 0px; + text-align: center; +} + +div.sphinxsidebarwrapper h1.logo { + margin-top: -10px; + text-align: center; + margin-bottom: 5px; + text-align: left; +} + +div.sphinxsidebarwrapper h1.logo-name { + margin-top: 0px; +} + +div.sphinxsidebarwrapper p.blurb { + margin-top: 0; + font-style: normal; +} + +div.sphinxsidebar h3, +div.sphinxsidebar h4 { + font-family: Georgia, serif; + color: #444; + font-size: 24px; + font-weight: normal; + margin: 0 0 5px 0; + padding: 0; +} + +div.sphinxsidebar h4 { + font-size: 20px; +} + +div.sphinxsidebar h3 a { + color: #444; +} + +div.sphinxsidebar p.logo a, +div.sphinxsidebar h3 a, +div.sphinxsidebar p.logo a:hover, +div.sphinxsidebar h3 a:hover { + border: none; +} + +div.sphinxsidebar p { + color: #555; + margin: 10px 0; +} + +div.sphinxsidebar ul { + margin: 10px 0; + padding: 0; + color: #000; +} + +div.sphinxsidebar ul li.toctree-l1 > a { + font-size: 120%; +} + +div.sphinxsidebar ul li.toctree-l2 > a { + font-size: 110%; +} + +div.sphinxsidebar input { + border: 1px solid #CCC; + font-family: Georgia, serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox input[type="text"] { + width: 160px; +} + +div.sphinxsidebar .search > div { + display: table-cell; +} + +div.sphinxsidebar hr { + border: none; + height: 1px; + color: #AAA; + background: #AAA; + + text-align: left; + margin-left: 0; + width: 50%; +} + +div.sphinxsidebar .badge { + border-bottom: none; +} + +div.sphinxsidebar .badge:hover { + border-bottom: none; +} + +/* To address an issue with donation coming after search */ +div.sphinxsidebar h3.donation { + margin-top: 10px; +} + +/* -- body styles ----------------------------------------------------------- */ + +a { + color: #004B6B; + text-decoration: underline; +} + +a:hover { + color: #6D4100; + text-decoration: underline; +} + +div.body h1, +div.body h2, +div.body h3, +div.body h4, +div.body h5, +div.body h6 { + font-family: Georgia, serif; + font-weight: normal; + margin: 30px 0px 10px 0px; + padding: 0; +} + +div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; } +div.body h2 { font-size: 180%; } +div.body h3 { font-size: 150%; } +div.body h4 { font-size: 130%; } +div.body h5 { font-size: 100%; } +div.body h6 { font-size: 100%; } + +a.headerlink { + color: #DDD; + padding: 0 4px; + text-decoration: none; +} + +a.headerlink:hover { + color: #444; + background: #EAEAEA; +} + +div.body p, div.body dd, div.body li { + line-height: 1.4em; +} + +div.admonition { + margin: 20px 0px; + padding: 10px 30px; + background-color: #EEE; + border: 1px solid #CCC; +} + +div.admonition tt.xref, div.admonition code.xref, div.admonition a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fafafa; +} + +div.admonition p.admonition-title { + font-family: Georgia, serif; + font-weight: normal; + font-size: 24px; + margin: 0 0 10px 0; + padding: 0; + line-height: 1; +} + +div.admonition p.last { + margin-bottom: 0; +} + +div.highlight { + background-color: #fff; +} + +dt:target, .highlight { + background: #FAF3E8; +} + +div.warning { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.danger { + background-color: #FCC; + border: 1px solid #FAA; + -moz-box-shadow: 2px 2px 4px #D52C2C; + -webkit-box-shadow: 2px 2px 4px #D52C2C; + box-shadow: 2px 2px 4px #D52C2C; +} + +div.error { + background-color: #FCC; + border: 1px solid #FAA; + -moz-box-shadow: 2px 2px 4px #D52C2C; + -webkit-box-shadow: 2px 2px 4px #D52C2C; + box-shadow: 2px 2px 4px #D52C2C; +} + +div.caution { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.attention { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.important { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.note { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.tip { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.hint { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.seealso { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.topic { + background-color: #EEE; +} + +p.admonition-title { + display: inline; +} + +p.admonition-title:after { + content: ":"; +} + +pre, tt, code { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; + font-size: 0.9em; +} + +.hll { + background-color: #FFC; + margin: 0 -12px; + padding: 0 12px; + display: block; +} + +img.screenshot { +} + +tt.descname, tt.descclassname, code.descname, code.descclassname { + font-size: 0.95em; +} + +tt.descname, code.descname { + padding-right: 0.08em; +} + +img.screenshot { + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils { + border: 1px solid #888; + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils td, table.docutils th { + border: 1px solid #888; + padding: 0.25em 0.7em; +} + +table.field-list, table.footnote { + border: none; + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + +table.footnote { + margin: 15px 0; + width: 100%; + border: 1px solid #EEE; + background: #FDFDFD; + font-size: 0.9em; +} + +table.footnote + table.footnote { + margin-top: -15px; + border-top: none; +} + +table.field-list th { + padding: 0 0.8em 0 0; +} + +table.field-list td { + padding: 0; +} + +table.field-list p { + margin-bottom: 0.8em; +} + +/* Cloned from + * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68 + */ +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +table.footnote td.label { + width: .1px; + padding: 0.3em 0 0.3em 0.5em; +} + +table.footnote td { + padding: 0.3em 0.5em; +} + +dl { + margin-left: 0; + margin-right: 0; + margin-top: 0; + padding: 0; +} + +dl dd { + margin-left: 30px; +} + +blockquote { + margin: 0 0 0 30px; + padding: 0; +} + +ul, ol { + /* Matches the 30px from the narrow-screen "li > ul" selector below */ + margin: 10px 0 10px 30px; + padding: 0; +} + +pre { + background: #EEE; + padding: 7px 30px; + margin: 15px 0px; + line-height: 1.3em; +} + +div.viewcode-block:target { + background: #ffd; +} + +dl pre, blockquote pre, li pre { + margin-left: 0; + padding-left: 30px; +} + +tt, code { + background-color: #ecf0f3; + color: #222; + /* padding: 1px 2px; */ +} + +tt.xref, code.xref, a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fff; +} + +a.reference { + text-decoration: none; + border-bottom: 1px dotted #004B6B; +} + +/* Don't put an underline on images */ +a.image-reference, a.image-reference:hover { + border-bottom: none; +} + +a.reference:hover { + border-bottom: 1px solid #6D4100; +} + +a.footnote-reference { + text-decoration: none; + font-size: 0.7em; + vertical-align: top; + border-bottom: 1px dotted #004B6B; +} + +a.footnote-reference:hover { + border-bottom: 1px solid #6D4100; +} + +a:hover tt, a:hover code { + background: #EEE; +} + + +@media screen and (max-width: 870px) { + + div.sphinxsidebar { + display: none; + } + + div.document { + width: 100%; + + } + + div.documentwrapper { + margin-left: 0; + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + } + + div.bodywrapper { + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + margin-left: 0; + } + + ul { + margin-left: 0; + } + + li > ul { + /* Matches the 30px from the "ul, ol" selector above */ + margin-left: 30px; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .bodywrapper { + margin: 0; + } + + .footer { + width: auto; + } + + .github { + display: none; + } + + + +} + + + +@media screen and (max-width: 875px) { + + body { + margin: 0; + padding: 20px 30px; + } + + div.documentwrapper { + float: none; + background: #fff; + } + + div.sphinxsidebar { + display: block; + float: none; + width: 102.5%; + margin: 50px -30px -20px -30px; + padding: 10px 20px; + background: #333; + color: #FFF; + } + + div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, + div.sphinxsidebar h3 a { + color: #fff; + } + + div.sphinxsidebar a { + color: #AAA; + } + + div.sphinxsidebar p.logo { + display: none; + } + + div.document { + width: 100%; + margin: 0; + } + + div.footer { + display: none; + } + + div.bodywrapper { + margin: 0; + } + + div.body { + min-height: 0; + padding: 0; + } + + .rtd_doc_footer { + display: none; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .footer { + width: auto; + } + + .github { + display: none; + } +} + + +/* misc. */ + +.revsys-inline { + display: none!important; +} + +/* Hide ugly table cell borders in ..bibliography:: directive output */ +table.docutils.citation, table.docutils.citation td, table.docutils.citation th { + border: none; + /* Below needed in some edge cases; if not applied, bottom shadows appear */ + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + + +/* relbar */ + +.related { + line-height: 30px; + width: 100%; + font-size: 0.9rem; +} + +.related.top { + border-bottom: 1px solid #EEE; + margin-bottom: 20px; +} + +.related.bottom { + border-top: 1px solid #EEE; +} + +.related ul { + padding: 0; + margin: 0; + list-style: none; +} + +.related li { + display: inline; +} + +nav#rellinks { + float: right; +} + +nav#rellinks li+li:before { + content: "|"; +} + +nav#breadcrumbs li+li:before { + content: "\00BB"; +} + +/* Hide certain items when printing */ +@media print { + div.related { + display: none; + } +} \ No newline at end of file diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css new file mode 100644 index 00000000..e5179b7a --- /dev/null +++ b/doc/_build/html/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: inherit; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; 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+ } +} \ No newline at end of file diff --git a/doc/_build/html/_static/custom.css b/doc/_build/html/_static/custom.css new file mode 100644 index 00000000..2a924f1d --- /dev/null +++ b/doc/_build/html/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js new file mode 100644 index 00000000..4d67807d --- /dev/null +++ b/doc/_build/html/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js new file mode 100644 index 00000000..44b5d19e --- /dev/null +++ b/doc/_build/html/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '2.1.6', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/doc/_build/html/_static/file.png b/doc/_build/html/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 z_CyJOe}D1){SET-^Amu_i71Lt6eYfZjRyw@I6OQAIXXHDfiX^GbOlHe=Ae4>0m)d(f|Me07*qoM6N<$f}vM^LjV8( literal 0 HcmV?d00001 diff --git a/doc/_build/html/_static/language_data.js b/doc/_build/html/_static/language_data.js new file mode 100644 index 00000000..367b8ed8 --- /dev/null +++ b/doc/_build/html/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/doc/_build/html/_static/minus.png b/doc/_build/html/_static/minus.png new file mode 100644 index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK literal 0 HcmV?d00001 diff --git a/doc/_build/html/_static/plus.png b/doc/_build/html/_static/plus.png new file mode 100644 index 0000000000000000000000000000000000000000..7107cec93a979b9a5f64843235a16651d563ce2d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu>-2 m3q%Vub%g%s<8sJhVPMczOq}xhg9DJoz~JfX=d#Wzp$Pyb1r*Kz literal 0 HcmV?d00001 diff --git a/doc/_build/html/_static/pygments.css b/doc/_build/html/_static/pygments.css new file mode 100644 index 00000000..07454c6b --- /dev/null +++ b/doc/_build/html/_static/pygments.css @@ -0,0 +1,83 @@ +pre { line-height: 125%; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/doc/_build/html/_static/sphinx_highlight.js b/doc/_build/html/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/doc/_build/html/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html new file mode 100644 index 00000000..f52986b4 --- /dev/null +++ b/doc/_build/html/genindex.html @@ -0,0 +1,99 @@ + + + + + + + Index — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ +
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + +
+ + + + + + \ No newline at end of file diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html new file mode 100644 index 00000000..585ad815 --- /dev/null +++ b/doc/_build/html/index.html @@ -0,0 +1,110 @@ + + + + + + + + Welcome to pyqsofit’s documentation! — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
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Welcome to pyqsofit’s documentation!¶

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Indices and tables¶

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+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + + | + Page source +
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pyqsofit¶

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pyqsofit package¶

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Submodules¶

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pyqsofit.HostDecomp module¶

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pyqsofit.MESFit module¶

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pyqsofit.PyQSOFit module¶

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pyqsofit.version module¶

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Module contents¶

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Search

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+ Searching for multiple words only shows matches that contain + all words. +

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Burke" Date: Fri, 28 Jun 2024 18:42:20 -0400 Subject: [PATCH 26/51] Update README.md --- README.md | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/README.md b/README.md index bf3d4127..56503eeb 100644 --- a/README.md +++ b/README.md @@ -21,16 +21,3 @@ v1.1 (stable): https://github.com/legolason/PyQSOFit/releases/tag/v1.1 ## Cite this code -> The preferred citation for this code is Guo, Shen & Wang (2018), ascl:1809:008\ -> @misc{2018ascl.soft09008G,\ -> author = {{Guo}, H. and {Shen}, Y. and {Wang}, S.},\ -> title = "{PyQSOFit: Python code to fit the spectrum of quasars}",\ -> keywords = {Software },\ -> howpublished = {Astrophysics Source Code Library},\ -> year = 2018,\ -> month = sep,\ -> archivePrefix = "ascl",\ -> eprint = {1809.008},\ -> adsurl = {[http://adsabs.harvard.edu/abs/2018ascl.soft09008G}](http://adsabs.harvard.edu/abs/2018ascl.soft09008G%7D),\ -> adsnote = {Provided by the SAO/NASA Astrophysics Data System}\ -> } From 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This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 6d4b5ec32d521dd430eb4adb6b5d91d3 -tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt deleted file mode 100644 index b43b0df7..00000000 --- a/doc/_build/html/_sources/index.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. pyqsofit documentation master file, created by - sphinx-quickstart on Fri Jun 28 18:21:35 2024. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to pyqsofit's documentation! -==================================== - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/doc/_build/html/_sources/modules.rst.txt b/doc/_build/html/_sources/modules.rst.txt deleted file mode 100644 index 84849f95..00000000 --- a/doc/_build/html/_sources/modules.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -pyqsofit -======== - -.. toctree:: - :maxdepth: 4 - - pyqsofit diff --git a/doc/_build/html/_sources/pyqsofit.rst.txt b/doc/_build/html/_sources/pyqsofit.rst.txt deleted file mode 100644 index 40a2bca4..00000000 --- a/doc/_build/html/_sources/pyqsofit.rst.txt +++ /dev/null @@ -1,45 +0,0 @@ -pyqsofit package -================ - -Submodules ----------- - -pyqsofit.HostDecomp module --------------------------- - -.. automodule:: pyqsofit.HostDecomp - :members: - :undoc-members: - :show-inheritance: - -pyqsofit.MESFit module ----------------------- - -.. automodule:: pyqsofit.MESFit - :members: - :undoc-members: - :show-inheritance: - -pyqsofit.PyQSOFit module ------------------------- - -.. automodule:: pyqsofit.PyQSOFit - :members: - :undoc-members: - :show-inheritance: - -pyqsofit.version module ------------------------ - -.. automodule:: pyqsofit.version - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: pyqsofit - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/_build/html/_static/alabaster.css b/doc/_build/html/_static/alabaster.css deleted file mode 100644 index e3174bf9..00000000 --- a/doc/_build/html/_static/alabaster.css +++ /dev/null @@ -1,708 +0,0 @@ -@import url("basic.css"); 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- float: right; - clear: right; - overflow-x: auto; -} - -p.sidebar-title { - font-weight: bold; -} - -nav.contents, -aside.topic, -div.admonition, div.topic, blockquote { - clear: left; -} - -/* -- topics ---------------------------------------------------------------- */ - -nav.contents, -aside.topic, -div.topic { - border: 1px solid #ccc; - padding: 7px; - margin: 10px 0 10px 0; -} - -p.topic-title { - font-size: 1.1em; - font-weight: bold; - margin-top: 10px; -} - -/* -- admonitions ----------------------------------------------------------- */ - -div.admonition { - margin-top: 10px; - margin-bottom: 10px; - padding: 7px; -} - -div.admonition dt { - font-weight: bold; -} - -p.admonition-title { - margin: 0px 10px 5px 0px; - font-weight: bold; -} - -div.body p.centered { - text-align: center; - margin-top: 25px; -} - -/* -- content of sidebars/topics/admonitions -------------------------------- */ - -div.sidebar > :last-child, -aside.sidebar > :last-child, -nav.contents > :last-child, -aside.topic > :last-child, -div.topic > :last-child, -div.admonition > :last-child { - margin-bottom: 0; -} - -div.sidebar::after, -aside.sidebar::after, -nav.contents::after, -aside.topic::after, -div.topic::after, -div.admonition::after, -blockquote::after { - display: block; - content: ''; - clear: both; -} - -/* -- tables ---------------------------------------------------------------- */ - -table.docutils { - margin-top: 10px; - margin-bottom: 10px; - border: 0; - border-collapse: collapse; -} - -table.align-center { - margin-left: auto; - margin-right: auto; -} - -table.align-default { - margin-left: auto; - margin-right: auto; -} - -table caption span.caption-number { - font-style: italic; -} - -table caption span.caption-text { -} - -table.docutils td, table.docutils th { - padding: 1px 8px 1px 5px; - border-top: 0; - border-left: 0; - border-right: 0; - border-bottom: 1px solid #aaa; -} - -th { - text-align: left; - padding-right: 5px; -} - -table.citation { - border-left: solid 1px gray; - margin-left: 1px; -} - -table.citation td { - border-bottom: none; -} - -th > :first-child, -td > :first-child { - margin-top: 0px; -} - -th > :last-child, -td > :last-child { - margin-bottom: 0px; -} - -/* -- figures --------------------------------------------------------------- */ - -div.figure, figure { - margin: 0.5em; - padding: 0.5em; -} - -div.figure p.caption, figcaption { - padding: 0.3em; -} - -div.figure p.caption span.caption-number, -figcaption span.caption-number { - font-style: italic; -} - -div.figure p.caption span.caption-text, -figcaption span.caption-text { -} - -/* -- field list styles ----------------------------------------------------- */ - -table.field-list td, table.field-list th { - border: 0 !important; -} - -.field-list ul { - margin: 0; - padding-left: 1em; -} - -.field-list p { - margin: 0; -} - -.field-name { - -moz-hyphens: manual; - -ms-hyphens: manual; - -webkit-hyphens: manual; - hyphens: manual; -} - -/* -- hlist styles ---------------------------------------------------------- */ - -table.hlist { - margin: 1em 0; -} - -table.hlist td { - vertical-align: top; -} - -/* -- object description styles --------------------------------------------- */ - -.sig { - font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; 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-} - -table.highlighttable tbody { - display: block; -} - -table.highlighttable tr { - display: flex; -} - -table.highlighttable td { - margin: 0; - padding: 0; -} - -table.highlighttable td.linenos { - padding-right: 0.5em; -} - -table.highlighttable td.code { - flex: 1; - overflow: hidden; -} - -.highlight .hll { - display: block; -} - -div.highlight pre, -table.highlighttable pre { - margin: 0; -} - -div.code-block-caption + div { - margin-top: 0; -} - -div.code-block-caption { - margin-top: 1em; - padding: 2px 5px; - font-size: small; -} - -div.code-block-caption code { - background-color: transparent; -} - -table.highlighttable td.linenos, -span.linenos, -div.highlight span.gp { /* gp: Generic.Prompt */ - user-select: none; - -webkit-user-select: text; /* Safari fallback only */ - -webkit-user-select: none; /* Chrome/Safari */ - -moz-user-select: none; /* Firefox */ - -ms-user-select: none; /* IE10+ */ -} - -div.code-block-caption span.caption-number { - padding: 0.1em 0.3em; - font-style: italic; -} - -div.code-block-caption span.caption-text { -} - -div.literal-block-wrapper { - margin: 1em 0; -} - -code.xref, a code { - background-color: transparent; - font-weight: bold; -} - -h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { - background-color: transparent; -} - -.viewcode-link { - float: right; -} - -.viewcode-back { - float: right; - font-family: sans-serif; -} - -div.viewcode-block:target { - margin: -1px -10px; - padding: 0 10px; -} - -/* -- math display ---------------------------------------------------------- */ - -img.math { - vertical-align: middle; -} - -div.body div.math p { - text-align: center; -} - -span.eqno { - float: right; -} - -span.eqno a.headerlink { - position: absolute; - z-index: 1; -} - -div.math:hover a.headerlink { - visibility: visible; -} - -/* -- printout stylesheet --------------------------------------------------- */ - -@media print { - div.document, - div.documentwrapper, - div.bodywrapper { - margin: 0 !important; - width: 100%; - } - - div.sphinxsidebar, - div.related, - div.footer, - #top-link { - display: none; - } -} \ No newline at end of file diff --git a/doc/_build/html/_static/custom.css b/doc/_build/html/_static/custom.css deleted file mode 100644 index 2a924f1d..00000000 --- a/doc/_build/html/_static/custom.css +++ /dev/null @@ -1 +0,0 @@ -/* This file intentionally left blank. */ diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js deleted file mode 100644 index 4d67807d..00000000 --- a/doc/_build/html/_static/doctools.js +++ /dev/null @@ -1,156 +0,0 @@ -/* - * doctools.js - * ~~~~~~~~~~~ - * - * Base JavaScript utilities for all Sphinx HTML documentation. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ -"use strict"; - -const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ - "TEXTAREA", - "INPUT", - "SELECT", - "BUTTON", -]); - -const _ready = (callback) => { - if (document.readyState !== "loading") { - callback(); - } else { - document.addEventListener("DOMContentLoaded", callback); - } -}; - -/** - * Small JavaScript module for the documentation. - */ -const Documentation = { - init: () => { - Documentation.initDomainIndexTable(); - Documentation.initOnKeyListeners(); - }, - - /** - * i18n support - */ - TRANSLATIONS: {}, - PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), - LOCALE: "unknown", - - // gettext and ngettext don't access this so that the functions - // can safely bound to a different name (_ = Documentation.gettext) - gettext: (string) => { - const translated = Documentation.TRANSLATIONS[string]; - switch (typeof translated) { - case "undefined": - return string; // no translation - case "string": - return translated; // translation exists - default: - return translated[0]; // (singular, plural) translation tuple exists - } - }, - - ngettext: (singular, plural, n) => { - const translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated !== "undefined") - return translated[Documentation.PLURAL_EXPR(n)]; - return n === 1 ? singular : plural; - }, - - addTranslations: (catalog) => { - Object.assign(Documentation.TRANSLATIONS, catalog.messages); - Documentation.PLURAL_EXPR = new Function( - "n", - `return (${catalog.plural_expr})` - ); - Documentation.LOCALE = catalog.locale; - }, - - /** - * helper function to focus on search bar - */ - focusSearchBar: () => { - document.querySelectorAll("input[name=q]")[0]?.focus(); - }, - - /** - * Initialise the domain index toggle buttons - */ - initDomainIndexTable: () => { - const toggler = (el) => { - const idNumber = el.id.substr(7); - const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); - if (el.src.substr(-9) === "minus.png") { - el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; - toggledRows.forEach((el) => (el.style.display = "none")); - } else { - el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; - toggledRows.forEach((el) => (el.style.display = "")); - } - }; - - const togglerElements = document.querySelectorAll("img.toggler"); - togglerElements.forEach((el) => - el.addEventListener("click", (event) => toggler(event.currentTarget)) - ); - togglerElements.forEach((el) => (el.style.display = "")); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); - }, - - initOnKeyListeners: () => { - // only install a listener if it is really needed - if ( - !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && - !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS - ) - return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.altKey || event.ctrlKey || event.metaKey) return; - - if (!event.shiftKey) { - switch (event.key) { - case "ArrowLeft": - if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; - - const prevLink = document.querySelector('link[rel="prev"]'); - if (prevLink && prevLink.href) { - window.location.href = prevLink.href; - event.preventDefault(); - } - break; - case "ArrowRight": - if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; - - const nextLink = document.querySelector('link[rel="next"]'); - if (nextLink && nextLink.href) { - window.location.href = nextLink.href; - event.preventDefault(); - } - break; - } - } - - // some keyboard layouts may need Shift to get / - switch (event.key) { - case "/": - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; - Documentation.focusSearchBar(); - event.preventDefault(); - } - }); - }, -}; - -// quick alias for translations -const _ = Documentation.gettext; - -_ready(Documentation.init); diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js deleted file mode 100644 index 44b5d19e..00000000 --- a/doc/_build/html/_static/documentation_options.js +++ /dev/null @@ -1,13 +0,0 @@ -const DOCUMENTATION_OPTIONS = { - VERSION: '2.1.6', - LANGUAGE: 'en', - COLLAPSE_INDEX: false, - BUILDER: 'html', - FILE_SUFFIX: '.html', - LINK_SUFFIX: '.html', - HAS_SOURCE: true, - SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false, - SHOW_SEARCH_SUMMARY: true, - ENABLE_SEARCH_SHORTCUTS: true, -}; \ No newline at end of file diff --git a/doc/_build/html/_static/file.png b/doc/_build/html/_static/file.png deleted file mode 100644 index a858a410e4faa62ce324d814e4b816fff83a6fb3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 z_CyJOe}D1){SET-^Amu_i71Lt6eYfZjRyw@I6OQAIXXHDfiX^GbOlHe=Ae4>0m)d(f|Me07*qoM6N<$f}vM^LjV8( diff --git a/doc/_build/html/_static/language_data.js b/doc/_build/html/_static/language_data.js deleted file mode 100644 index 367b8ed8..00000000 --- a/doc/_build/html/_static/language_data.js +++ /dev/null @@ -1,199 +0,0 @@ -/* - * language_data.js - * ~~~~~~~~~~~~~~~~ - * - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} - diff --git a/doc/_build/html/_static/minus.png b/doc/_build/html/_static/minus.png deleted file mode 100644 index d96755fdaf8bb2214971e0db9c1fd3077d7c419d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK diff --git a/doc/_build/html/_static/plus.png b/doc/_build/html/_static/plus.png deleted file mode 100644 index 7107cec93a979b9a5f64843235a16651d563ce2d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu>-2 m3q%Vub%g%s<8sJhVPMczOq}xhg9DJoz~JfX=d#Wzp$Pyb1r*Kz diff --git a/doc/_build/html/_static/pygments.css b/doc/_build/html/_static/pygments.css deleted file mode 100644 index 07454c6b..00000000 --- a/doc/_build/html/_static/pygments.css +++ /dev/null @@ -1,83 +0,0 @@ -pre { line-height: 125%; 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename] = item; - - let listItem = document.createElement("li"); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = _( - "Search finished, found ${resultCount} page(s) matching the search query." - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlinks", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/doc/_build/html/_static/sphinx_highlight.js b/doc/_build/html/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/doc/_build/html/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html deleted file mode 100644 index f52986b4..00000000 --- a/doc/_build/html/genindex.html +++ /dev/null @@ -1,99 +0,0 @@ - - - - - - - Index — pyqsofit 2.1.6 documentation - - - - - - - - - - - - - - - - - -
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Index

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Welcome to pyqsofit’s documentation!¶

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Indices and tables¶

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pyqsofit¶

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pyqsofit package¶

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Submodules¶

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pyqsofit.HostDecomp module¶

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pyqsofit.MESFit module¶

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pyqsofit.PyQSOFit module¶

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pyqsofit.version module¶

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Module contents¶

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Search

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- Searching for multiple words only shows matches that contain - all words. -

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- ©2024, Hengxiao Guo. - - | - Powered by Sphinx 7.3.7 - & Alabaster 0.7.16 - -
- - - - - - \ No newline at end of file diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js deleted file mode 100644 index f4aea4b7..00000000 --- a/doc/_build/html/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"Indices and tables": [[0, "indices-and-tables"]], "Module contents": [[2, "module-contents"]], "Submodules": [[2, "submodules"]], "Welcome to pyqsofit\u2019s documentation!": [[0, "welcome-to-pyqsofit-s-documentation"]], "pyqsofit": [[1, "pyqsofit"]], "pyqsofit package": [[2, "pyqsofit-package"]], "pyqsofit.HostDecomp module": [[2, "pyqsofit-hostdecomp-module"]], "pyqsofit.MESFit module": [[2, "pyqsofit-mesfit-module"]], "pyqsofit.PyQSOFit module": [[2, "pyqsofit-pyqsofit-module"]], "pyqsofit.version module": [[2, "pyqsofit-version-module"]]}, "docnames": ["index", "modules", "pyqsofit"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["index.rst", "modules.rst", "pyqsofit.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"content": 1, "hostdecomp": 1, "index": 0, "mesfit": 1, "modul": [0, 1], "packag": 1, "page": 0, "search": 0, "submodul": 1, "version": 1}, "titles": ["Welcome to pyqsofit\u2019s documentation!", "pyqsofit", "pyqsofit package"], "titleterms": {"": 0, "content": 2, "document": 0, "hostdecomp": 2, "indic": 0, "mesfit": 2, "modul": 2, "packag": 2, "pyqsofit": [0, 1, 2], "submodul": 2, "tabl": 0, "version": 2, "welcom": 0}}) \ No newline at end of file diff --git a/doc/conf.py b/doc/conf.py index 3cbfd631..f66a74d5 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -6,6 +6,10 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information +import os +import sys +sys.path.insert(0, os.path.abspath('..')) + project = 'pyqsofit' copyright = '2024, Hengxiao Guo' author = 'Hengxiao Guo' From eda83533af8c6d55237beb410459967565746982 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 19:22:48 -0400 Subject: [PATCH 28/51] build dir --- doc/_build/palceholder | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 doc/_build/palceholder diff --git a/doc/_build/palceholder b/doc/_build/palceholder new file mode 100644 index 00000000..e69de29b From 72eb3012e1d341afe73a247b2c81aa4fd6f4dc04 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 22:17:10 -0400 Subject: [PATCH 29/51] test host prior --- tests/test_dr7sample.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_dr7sample.py b/tests/test_dr7sample.py index ad4f833a..5fcedd6e 100644 --- a/tests/test_dr7sample.py +++ b/tests/test_dr7sample.py @@ -302,6 +302,9 @@ def test_dr7(nqsofit=20): # Do the fitting q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) + # Test with host prior + q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='BC03', save_fig=False, save_result=False) + # Emission line loop for j, line in enumerate(line_calc_names): From 82bc4da2777f1a3b365b489b8011ec5b04b80dd5 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 22:28:31 -0400 Subject: [PATCH 30/51] fix host prior --- tests/test_dr7sample.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_dr7sample.py b/tests/test_dr7sample.py index 5fcedd6e..51865846 100644 --- a/tests/test_dr7sample.py +++ b/tests/test_dr7sample.py @@ -303,7 +303,7 @@ def test_dr7(nqsofit=20): q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) # Test with host prior - q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='BC03', save_fig=False, save_result=False) + q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) # Emission line loop for j, line in enumerate(line_calc_names): From 9bcddec9ddea13ab6d8d4d9db4b263c4f7e7aec2 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 22:32:33 -0400 Subject: [PATCH 31/51] trapz fix --- src/pyqsofit/PyQSOFit.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/pyqsofit/PyQSOFit.py b/src/pyqsofit/PyQSOFit.py index 389439f2..ce7ea170 100644 --- a/src/pyqsofit/PyQSOFit.py +++ b/src/pyqsofit/PyQSOFit.py @@ -1890,10 +1890,10 @@ def line_prop(self, compcenter, pp, linetype='broad', ln_sigma_br=0.0017): # Calculate the line sigma and EW in normal wavelength line_flux = self._Manygauss(xx, pp_br_shaped) line_wave = np.exp(xx) - lambda0 = integrate.trapz(line_flux, line_wave) # calculate the total broad line flux - lambda1 = integrate.trapz(line_flux * line_wave, line_wave) - lambda2 = integrate.trapz(line_flux * line_wave * line_wave, line_wave) - ew = integrate.trapz(np.abs(line_flux / contiflux), line_wave) + lambda0 = integrate.trapezoid(line_flux, line_wave) # calculate the total broad line flux + lambda1 = integrate.trapezoid(line_flux * line_wave, line_wave) + lambda2 = integrate.trapezoid(line_flux * line_wave * line_wave, line_wave) + ew = integrate.trapezoid(np.abs(line_flux / contiflux), line_wave) area = lambda0 sigma = np.sqrt(lambda2 / lambda0 - (lambda1 / lambda0) ** 2) / compcenter * c From 73f8c3e830b5417d38e249cc60d34b122b2adae5 Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 22:33:32 -0400 Subject: [PATCH 32/51] trapz fix --- tests/test_dr7sample.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_dr7sample.py b/tests/test_dr7sample.py index 51865846..c0602059 100644 --- a/tests/test_dr7sample.py +++ b/tests/test_dr7sample.py @@ -303,7 +303,7 @@ def test_dr7(nqsofit=20): q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) # Test with host prior - q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) + #q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) # Emission line loop for j, line in enumerate(line_calc_names): From 92962d1fb8de6ff4f13b6e4c18159d0afbb4381c Mon Sep 17 00:00:00 2001 From: burke86 Date: Fri, 28 Jun 2024 22:36:06 -0400 Subject: [PATCH 33/51] trapz fix --- src/pyqsofit/PyQSOFit.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyqsofit/PyQSOFit.py b/src/pyqsofit/PyQSOFit.py index ce7ea170..66e6b0c5 100644 --- a/src/pyqsofit/PyQSOFit.py +++ b/src/pyqsofit/PyQSOFit.py @@ -2534,7 +2534,7 @@ def _calculate_Fe_flux(self, measure_range, pp): else: raise IndexError('The parameter pp only adopts a list of 3 or 6.') - flux = integrate.trapz(yval[(xval >= lower) & (xval <= upper)], xval[(xval >= lower) & (xval <= upper)]) + flux = integrate.trapezoid(yval[(xval >= lower) & (xval <= upper)], xval[(xval >= lower) & (xval <= upper)]) return flux def read_out_params(self, param_file_path='qsopar.fits'): From 758b30e76364ce4bf3bdddcb4acf11f53566630d Mon Sep 17 00:00:00 2001 From: burke86 Date: Sat, 29 Jun 2024 22:29:31 -0400 Subject: [PATCH 34/51] cleanup --- README.md | 24 +++++++++++++++++------- example/example.ipynb | 20 ++++++++++---------- 2 files changed, 27 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 56503eeb..85db4785 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ ## PyQSOFit: A code to fit the spectrum of quasar +### Getting Started + __See the [example](https://nbviewer.org/github/legolason/PyQSOFit/blob/master/example/example.ipynb) demo notebook for a quick start tutorial__ -We provide a brief guide of the Python QSO fitting code (PyQSOFit) to measure spectral properties of SDSS quasars. The code was originally translated from Yue Shen's IDL code to Python. The package includes the main routine, Fe II templates, an input line-fitting parameter list, host galaxy templates, and dust reddening map to extract spectral measurements from the raw fits. Monte Carlo estimation of the measurement uncertainties of the fitting results can be conducted with the same fitting code. +We provide a brief guide of the Python QSO fitting code (PyQSOFit) to measure spectral properties of SDSS quasars. The code was originally translated from Yue Shen's IDL code to Python. The package includes the main routine, Fe II templates, an input line-fitting parameter list, host galaxy templates, and dust reddening map to extract spectral measurements from the raw fits. Monte Carlo or MCMC estimation of the measurement uncertainties of the fitting results can be conducted with the same fitting code. The code takes an input spectrum (observed-frame wavelength, flux density and error arrays) and the redshift as input parameters, performs the fitting in the restframe, and outputs the best-fit parameters and quality-checking plots to the paths specified by the user. @@ -10,14 +12,22 @@ The code uses an input line-fitting parameter list to specify the fitting range Use this code at your own risk, as we are not responsible for any errors. But if you report bugs, it will be greatly appreciated. -## Install +### Install + +Bleeding edge: + +``git clone https://github.com/legolason/PyQSOFit``
+``cd PyQSOFit``
+``python -m pip install .``
+ +Pip install (stable version): -v1.1 (stable): https://github.com/legolason/PyQSOFit/releases/tag/v1.1 +``pip install pyqsofit`` (coming soon) -## Known problem +### Cite -1. During the line fitting procedure, some emission lines need less Gaussian models than provided to be well fitted. In these circumstances, the code will give two (or more) exactly the same Gaussian models to fit the data instead of one. This problem will not affect the physical measurements but only wierd in the QA image. One can use BIC to judge the proper number of Gaussian models for each line referencing to our `example.ipynb`. -2. Since the host decomposition hiring BC03 template is non-negative linear fitting, the host component will not stay at zero even if no hosts are detected or the decomposition is failed. We suggest user to determine the reliability of the host decomposition through QA image and the host fraction parameters f_host. (i.e., f_host>0.05 from (Shen et al. 2019)[https://doi.org/10.1088/0004-637X/805/2/96]) +Preferred code citation: [Guo, H., Shen, Y., Wang, S. 2018, ascl:1809.008](https://ui.adsabs.harvard.edu/abs/2018ascl). -## Cite this code +Please also cite: [Shen, Y. et al. 2019, ApJS, 241, 34S](https://ui.adsabs.harvard.edu/abs/2019ApJS..241...34S/abstract) +If using new host decompistion tools (`host_prior=True`), please cite: [Ren, W. et al. 2024](https://ui.adsabs.harvard.edu/abs/2024arXiv240617598R/abstract) \ No newline at end of file diff --git a/example/example.ipynb b/example/example.ipynb index 3083601a..7b1e41b8 100644 --- a/example/example.ipynb +++ b/example/example.ipynb @@ -6,7 +6,7 @@ "source": [ "![alt text][logo]\n", "\n", - "[logo]: https://github.com/legolason/PyQSOFit/blob/master/pyqsofit/QSOFit_logo.png?raw=true\n", + "[logo]: https://github.com/legolason/PyQSOFit/blob/master/src/pyqsofit/QSOFit_logo.png?raw=true\n", "\n", "\n", "# PyQSOFit\n", @@ -45,7 +45,7 @@ "2) [pandas](https://pandas.pydata.org/)
\n", "3) [corner](https://corner.readthedocs.io/en/latest/)
\n", "\n", - "If using pPXF to get the host component (`use_ppxf=True`),\n", + "To get the pPXF host model and gas kinematics,\n", "\n", "1) [pPXF](https://pypi.org/project/ppxf/)\n", "\n", @@ -67,26 +67,26 @@ "## Possible future updates\n", "1) Option for using Gauss-Hermite profile to fit the emission lines.
\n", "2) Simultaneously fit several epochs for the same source since the time domain era is coming.
\n", - "3) Add functions to fit the absorption lines.
\n", - "4) Produce more secondary parameters from spectral fitting.
\n", - "5) Speed up the code by e.g., choosing better initial conditions (especially for the continuum and narrow-line flux normalizations).
\n", - "6) Option for automatically determining the number of broad emission line components to include in a fit using e.g., BIC. This will take longer to execute initially but might make the MCMC sampling faster and fits more reliable if fewer components are used, especially for low S/N or BAL quasar spectra.
\n", - "7) Improved integration with pPXF, specutils, etc.
\n", - "8) Better code documentation.
\n", + "3) Produce more secondary parameters from spectral fitting.
\n", + "4) Speed up the code by e.g., choosing better initial conditions (especially for the continuum and narrow-line flux normalizations).
\n", + "especially for low S/N or BAL quasar spectra.
\n", + "5) Improved integration with pPXF, specutils, etc.
\n", + "6) Better code documentation.
\n", "\n", "\n", "## Authors\n", "[Hengxiao Guo](https://hengxiaoguo.wixsite.com/hengxiaoguo), hengxiaoguo AT gmail.com (SHAO)
\n", "[Yue Shen](http://quasar.astro.illinois.edu/), shenyue AT illinois.edu (UIUC)
\n", "Shu Wang, wangshukiaa AT pku.edu.cn (Seoul National University)
\n", - "[Colin J. Burke](https://burke86.github.io/), colinjb2 AT illinois.edu (UIUC)
\n", + "[Colin J. Burke](https://burke86.github.io/), colin.j.burke AT yale.edu (Yale)
\n", "[Wenke Ren](https://github.com/WenkeRen/), rwk AT mail.ustc.edu.cn (USTC)
\n", "\n", "\n", "## Acknowledgement\n", "If our code makes your life easier, it would be appreciated to cite us:
\n", "1) [Guo, H., Shen, Y., Wang, S. 2018, ascl:1809.008](https://ui.adsabs.harvard.edu/abs/2018ascl.soft09008G/abstract)\n", - "2) [Shen, Y. et al., ApJS, 241, 34S](http://adsabs.harvard.edu/abs/2018arXiv181001447S)\n" + "2) [Shen, Y. et al., ApJS, 241, 34S](http://adsabs.harvard.edu/abs/2018arXiv181001447S)\n", + "3) [Ren, W. et al. 2024](https://ui.adsabs.harvard.edu/abs/2024arXiv240617598R/abstract)\n" ] }, { From f179047b678469893f1877492a683af4f98f7292 Mon Sep 17 00:00:00 2001 From: burke86 Date: Sat, 29 Jun 2024 22:54:35 -0400 Subject: [PATCH 35/51] fix docs --- doc/conf.py | 2 +- src/pyqsofit/PyQSOFit.py | 26 ++++++++++++++++---------- 2 files changed, 17 insertions(+), 11 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index f66a74d5..75fb5c0b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -18,7 +18,7 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = [] +extensions = ['sphinx.ext.autodoc'] templates_path = ['_templates'] exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] diff --git a/src/pyqsofit/PyQSOFit.py b/src/pyqsofit/PyQSOFit.py index 66e6b0c5..2692793e 100644 --- a/src/pyqsofit/PyQSOFit.py +++ b/src/pyqsofit/PyQSOFit.py @@ -3,7 +3,6 @@ # Email: hengxiaoguo AT gmail DOT com # Co-Auther Yue Shen, Shu Wang, Wenke Ren, Colin J. Burke # Email: rwk AT mail DOT ustc DOT edu DOT cn -# colinjb2 AT illinois.edu # # ------------------------------------------------- # Version 1.2 @@ -80,8 +79,7 @@ # 3) In HostDecomp.py module, we add the sigma measurements and Dn4000 estimation of the decomposed host component. # ------------------------------------------------- -import sys, os -import glob +import os import matplotlib import numpy as np import matplotlib.pyplot as plt @@ -93,15 +91,12 @@ from lmfit import minimize, Parameters, report_fit from PyAstronomy import pyasl -import scipy.optimize as opt from astropy.io import fits from astropy import units as u from astropy import constants as const from astropy.cosmology import FlatLambdaCDM from astropy.modeling.physical_models import BlackBody -from astropy.modeling.functional_models import Gaussian1D -from astropy.modeling import fitting from astropy.table import Table @@ -2285,6 +2280,13 @@ def _pretty_name(plain_name): self.fig = fig return + def to_Spectrum1D(self): + from specutils import Spectrum1D + from astropy.nddata import StdDevUncertainty + spec1d = Spectrum1D(spectral_axis=self.wave*u.AA/(1+self.z), flux=self.flux*1e-17*u.erg/u.s/u.cm**2, + uncertainty=StdDevUncertainty(self.err), redshift=self.z) + return spec1d + def CalFWHM(self, logsigma): """transfer the logFWHM to normal frame""" return 2 * np.sqrt(2 * np.log(2)) * (np.exp(logsigma) - 1) * 300000. @@ -2454,14 +2456,16 @@ def Manygauss(self, xval, pp): return np.zeros_like(xval) def Get_Fe_flux(self, ranges, pp=None): - """Calculate the flux of fitted FeII template within given wavelength ranges. + """ + Calculate the flux of fitted FeII template within given wavelength ranges. ranges: 1-D array, 2-D array if 1-D array was given, it should contain two parameters contain a range of wavelength. FeII flux within this range would be calculate and documented in the result fits file. if 2-D array was given, it should contain a series of ranges. FeII flux within these ranges would be documented respectively. pp: 1-D array with 3 or 6 items. If 3 parameters were given, function will choose a proper template (MgII or balmer) according to the range. If the range give excess either template, an error would be arose. - If 6 parameters were given (recommended), function would adopt the first three for the MgII template and the last three for the balmer.""" + If 6 parameters were given (recommended), function would adopt the first three for the MgII template and the last three for the balmer. + """ if pp is None: pp = self.conti_params[:6] @@ -2489,11 +2493,13 @@ def Get_Fe_flux(self, ranges, pp=None): return Fe_flux_result, Fe_flux_type, Fe_flux_name def _calculate_Fe_flux(self, measure_range, pp): - """Calculate the flux of fitted FeII template within one given wavelength range. + """ + Calculate the flux of fitted FeII template within one given wavelength range. The pp could be an array with a length of 3 or 6. If 3 parameters were give, function will choose a proper template (MgII or balmer) according to the range. If the range give excess both template, an error would be arose. If 6 parameters were give, function would adopt the first three for the MgII - template and the last three for the balmer.""" + template and the last three for the balmer. + """ balmer_range = np.array([3686., 7484.]) mgii_range = np.array([1200., 3500.]) From 955b6b8593d91fd85db5a05af32f49385fef47f5 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 22:55:28 -0400 Subject: [PATCH 36/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 54f003c9..b1bbb3b0 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -16,7 +16,7 @@ jobs: pip install sphinx sphinx_rtd_theme myst_parser - name: Sphinx build run: | - sphinx-build doc _build + sphinx-build doc doc/_build - name: Deploy to GitHub Pages uses: peaceiris/actions-gh-pages@v3 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} From 9cf16765ac34b7af0e31958d5944efd206b44372 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 22:57:53 -0400 Subject: [PATCH 37/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index b1bbb3b0..e7f752bf 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -23,5 +23,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: _build/ + publish_dir: doc/_build/ force_orphan: true From a54ad60024d42e2dc6d37a7e922e8415d0925cf6 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:03:46 -0400 Subject: [PATCH 38/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index e7f752bf..4ef1261e 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -18,7 +18,7 @@ jobs: run: | sphinx-build doc doc/_build - name: Deploy to GitHub Pages - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} with: publish_branch: gh-pages From 3f09ba0e92b39cf39cf91a443a97fd492fd138fe Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:22:10 -0400 Subject: [PATCH 39/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 4ef1261e..52328af7 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -23,5 +23,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: doc/_build/ + publish_dir: doc/_build/html force_orphan: true From 1bd3f23d2072f8bef2b33472eccdeee56776ccd1 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:26:40 -0400 Subject: [PATCH 40/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 52328af7..ab93eff0 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -23,5 +23,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: doc/_build/html + publish_dir: ./doc/_build/html force_orphan: true From 32dff5483583deb6252f724fe5624a7b02157761 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:28:30 -0400 Subject: [PATCH 41/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index ab93eff0..199e0da6 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -23,5 +23,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./doc/_build/html + publish_dir: ./doc/_build force_orphan: true From aa53c00f6674cc2402028e8496908a77debc4e8e Mon Sep 17 00:00:00 2001 From: burke86 Date: Sat, 29 Jun 2024 23:43:21 -0400 Subject: [PATCH 42/51] doc->docs --- doc/_build/palceholder | 0 {doc => docs}/Makefile | 0 {doc => docs}/conf.py | 0 {doc => docs}/index.rst | 0 {doc => docs}/make.bat | 0 {doc => docs}/modules.rst | 0 {doc => docs}/pyqsofit.rst | 0 7 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 doc/_build/palceholder rename {doc => docs}/Makefile (100%) rename {doc => docs}/conf.py (100%) rename {doc => docs}/index.rst (100%) rename {doc => docs}/make.bat (100%) rename {doc => docs}/modules.rst (100%) rename {doc => docs}/pyqsofit.rst (100%) diff --git a/doc/_build/palceholder b/doc/_build/palceholder deleted file mode 100644 index e69de29b..00000000 diff --git a/doc/Makefile b/docs/Makefile similarity index 100% rename from doc/Makefile rename to docs/Makefile diff --git a/doc/conf.py b/docs/conf.py similarity index 100% rename from doc/conf.py rename to docs/conf.py diff --git a/doc/index.rst b/docs/index.rst similarity index 100% rename from doc/index.rst rename to docs/index.rst diff --git a/doc/make.bat b/docs/make.bat similarity index 100% rename from doc/make.bat rename to docs/make.bat diff --git a/doc/modules.rst b/docs/modules.rst similarity index 100% rename from doc/modules.rst rename to docs/modules.rst diff --git a/doc/pyqsofit.rst b/docs/pyqsofit.rst similarity index 100% rename from doc/pyqsofit.rst rename to docs/pyqsofit.rst From 55cbbe757538e2265a033d5c94755697e4a1d906 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:43:56 -0400 Subject: [PATCH 43/51] Update documentation.yml --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 199e0da6..9c216e72 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -23,5 +23,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./doc/_build + publish_dir: ./docs/_build force_orphan: true From f568ca432bb3b045805c271dee0ea41fda1ab107 Mon Sep 17 00:00:00 2001 From: burke86 Date: Sat, 29 Jun 2024 23:53:37 -0400 Subject: [PATCH 44/51] build script --- doc/.placeholder | 1 - docs/_build/genindex.html | 410 ++++++++++++++++++++ docs/_build/index.html | 110 ++++++ docs/_build/modules.html | 187 ++++++++++ docs/_build/py-modindex.html | 134 +++++++ docs/_build/pyqsofit.html | 702 +++++++++++++++++++++++++++++++++++ docs/_build/search.html | 116 ++++++ docs/builddocs.bash | 1 + 8 files changed, 1660 insertions(+), 1 deletion(-) delete mode 100644 doc/.placeholder create mode 100644 docs/_build/genindex.html create mode 100644 docs/_build/index.html create mode 100644 docs/_build/modules.html create mode 100644 docs/_build/py-modindex.html create mode 100644 docs/_build/pyqsofit.html create mode 100644 docs/_build/search.html create mode 100644 docs/builddocs.bash diff --git a/doc/.placeholder b/doc/.placeholder deleted file mode 100644 index 8b137891..00000000 --- a/doc/.placeholder +++ /dev/null @@ -1 +0,0 @@ - diff --git a/docs/_build/genindex.html b/docs/_build/genindex.html new file mode 100644 index 00000000..cf5cf573 --- /dev/null +++ b/docs/_build/genindex.html @@ -0,0 +1,410 @@ + + + + + + + Index — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ A + | B + | C + | D + | F + | G + | H + | I + | L + | M + | N + | O + | P + | Q + | R + | S + | T + +
+

A

+ + +
+ +

B

+ + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + +
+ +

I

+ + + +
+ +

L

+ + + +
+ +

M

+ + +
+ +

N

+ + +
+ +

O

+ + +
+ +

P

+ + + +
    +
  • + pyqsofit.HostDecomp + +
    • +
  • + pyqsofit.MESFit + +
    • +
  • + pyqsofit.PyQSOFit + +
    • +
  • + pyqsofit.version + +
    • +
+ +

Q

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + +
+ + + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/index.html b/docs/_build/index.html new file mode 100644 index 00000000..585ad815 --- /dev/null +++ b/docs/_build/index.html @@ -0,0 +1,110 @@ + + + + + + + + Welcome to pyqsofit’s documentation! — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Welcome to pyqsofit’s documentation!¶

+
+
+
+
+

Indices and tables¶

+ +
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/modules.html b/docs/_build/modules.html new file mode 100644 index 00000000..b7a8a6bd --- /dev/null +++ b/docs/_build/modules.html @@ -0,0 +1,187 @@ + + + + + + + + pyqsofit — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

pyqsofit¶

+
+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/py-modindex.html b/docs/_build/py-modindex.html new file mode 100644 index 00000000..2a5c74dc --- /dev/null +++ b/docs/_build/py-modindex.html @@ -0,0 +1,134 @@ + + + + + + + Python Module Index — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Python Module Index

+ +
+ p +
+ + + + + + + + + + + + + + + + + + + +
 
+ p
+ pyqsofit +
    + pyqsofit.HostDecomp +
    + pyqsofit.MESFit +
    + pyqsofit.PyQSOFit +
    + pyqsofit.version +
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/pyqsofit.html b/docs/_build/pyqsofit.html new file mode 100644 index 00000000..a6571102 --- /dev/null +++ b/docs/_build/pyqsofit.html @@ -0,0 +1,702 @@ + + + + + + + + pyqsofit package — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

pyqsofit package¶

+
+

Submodules¶

+
+
+

pyqsofit.HostDecomp module¶

+

# Path : 20230710PyQSOFit/pyqsofit +# File : PriorDecomp.py +# Time ：2023/7/27 15:47 +# Author ：Wenke Ren +# version ：python 3.10 +# Description：Use the PCA data to decompose the spectra with a priori

+
+
+class pyqsofit.HostDecomp.Linear_decomp(wave, flux, err, n_gal, n_qso, path, host_type='PCA', qso_type='global', na_mask=False)¶
+

Bases: object

+
+
+auto_decomp()¶
+
+ +
+
+gal_model(param: list = None, wave=None)¶
+
+ +
+
+qso_model(param: list = None, wave=None)¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.Prior_decomp(wave, flux, err, n_gal, n_qso, path, host_type='PCA', qso_type='CZBIN1', na_mask=True, fh_ini_list=(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9))¶
+

Bases: object

+
+
+auto_decomp(reg_factor=0.2)¶
+
+ +
+
+cal_model(param: Parameters, wave=None)¶
+
+ +
+
+decompose(reg_factor, init_params, non_negative=False)¶
+
+ +
+
+gal_model(param: list = None, wave=None)¶
+
+ +
+
+initial_params(fh_ini=None)¶
+
+ +
+
+qso_model(param: list = None, wave=None)¶
+
+ +
+
+read_prior(prior_loc, QSO_prior_name='QSO_pp_prior.csv', GAL_prior_name='GAL_pp_prior.csv')¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.QSO_PCA(template_path, n_template=5, template_name=None)¶
+

Bases: object

+
+
+interp_data(wave_exp)¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.host_template(template_path, n_template=5, template_type='PCA')¶
+

Bases: object

+
+
+interp_data(wave_exp, broaden: bool = False, shift: float = 0, sigma: float = 0)¶
+

Interpolate the galaxy template and find the interpolation flux at give wavelength. We also provide +broaden methods which allow user to convolve a gaussian core before the interpolation. However, +considering most template are not evenly sampled, we have to interpolate twice if the broaden method +is used, which might introduce more biases. +:param wave_exp: +:param broaden: +:param shift: float, in km/s +:param sigma: float, in km/s +:return:

+
+ +
+ +
+
+pyqsofit.HostDecomp.ppxf_kinematics(wave, flux, err, path, fit_range=(3700, 8300), MC_iter=0)¶
+
+ +
+
+

pyqsofit.MESFit module¶

+
+
+class pyqsofit.MESFit.MESFit(path=None)¶
+

Bases: object

+

Multi-epoch Spectral Fitting program

+
+
+CalLineSN(w, f, line_min, line_max, conti)¶
+
+ +
+
+Calwidth(wave, flux, wv_min, wv_max)¶
+

Return line fwhm and sigma in unit of km/s

+
+ +
+
+Coadd_spec()¶
+
+ +
+
+Plotline(wave, ymin, ymax)¶
+
+ +
+
+corr(w1, f1, err1, w_ref, f_ref, err_ref, wv_min=None, wv_max=None, n=15, plot=True)¶
+
+ +
+
+fixNL(pardata: BinTableHDU = None, fitdata: dict = None)¶
+

For each line group, we fix the line sigma and scale of narrow lines to the results of mean spectra. +:param pardata: +:param fitdata: +:return:

+
+ +
+
+flux2L(flux, z)¶
+

Transfer flux to luminoity assuming a flat Universe

+
+ +
+
+interp(wave, value, z=0.0, fill_value=0.0)¶
+

interprate to standard wavelenth into rest or obs frame

+
+ +
+
+normNL(norm_line_wv=5008.24, path=None, name='normNL', save=True, tol=1e-10)¶
+
+ +
+
+ppxf_host(rest_wv, fx, error, redshift, wv_min=4125, wv_max=5350, plot=None, quiet=False, mask_width=3000)¶
+

fit the host galaxy to get the stellar velocity dispersion.

+
+ +
+
+residuals_norm(p, mean_wv, mean_spec, flux_new)¶
+
+ +
+
+s2f(array)¶
+

string to float

+
+ +
+ +
+
+

pyqsofit.PyQSOFit module¶

+
+
+class pyqsofit.PyQSOFit.QSOFit(lam, flux, err, z, ra=-999, dec=-999, plateid=None, mjd=None, fiberid=None, path=None, and_mask_in=None, or_mask_in=None, wdisp=None)¶
+

Bases: object

+
+
+Balmer_conti(xval, pp)¶
+

Fit the Balmer continuum from the model of Dietrich+02

+
+ +
+
+CalFWHM(logsigma)¶
+

transfer the logFWHM to normal frame

+
+ +
+
+F_poly_conti(xval, pp, x0=3000)¶
+

Fit the continuum with a polynomial component account for the dust reddening with a*X+b*X^2+c*X^3

+

TODO: See if LMFIT’s built-in modeles improved performance and numerical stability +https://lmfit.github.io/lmfit-py/builtin_models.html

+
+ +
+
+Fe_flux_balmer(xval, pp)¶
+

Fit the optical FeII on the continuum from 3686 to 7484 A based on Vestergaard & Wilkes 2001

+
+ +
+
+Fe_flux_mgii(xval, pp)¶
+

Fit the UV FeII component on the continuum from 1200 to 3500 A based on Boroson & Green 1992.

+
+ +
+
+Fit(name=None, nsmooth=1, and_mask=False, or_mask=False, reject_badpix=True, deredden=True, wave_range=None, wave_mask=None, decompose_host=True, host_prior=False, host_prior_scale=0.2, host_line_mask=True, decomp_na_mask=False, qso_type='global', npca_qso=10, host_type='BC03', npca_gal=5, Fe_uv_op=True, poly=False, BC=False, rej_abs_conti=False, rej_abs_line=False, initial_guess=None, n_pix_min_conti=100, param_file_name='qsopar.fits', MC=False, MCMC=False, save_fits_name=None, nburn=20, nsamp=200, nthin=10, epsilon_jitter=0.0, linefit=True, save_result=True, plot_fig=True, save_fits_path='.', save_fig=True, plot_corner=True, verbose=False, kwargs_plot={}, kwargs_conti_emcee={}, kwargs_line_emcee={})¶
+

Fit the QSO spectrum and get different decomposed components and corresponding parameters

+
+

Parameter:¶

+
+
name: str, optional

source name, Default is None. If None, it will use plateid+mjd+fiberid as the name. If there are no +such parameters, it will be empty.

+
+
nsmooth: integer number, optional

do n-pixel smoothing to the raw input flux and err spectra. The default is set to 1 (no smooth). +It will return the same array size. We note that smooth the raw data is not suggested, this function is in case of some fail-fitted low S/N spectra.

+
+
and_mask: bool, optional

If True, and and_mask or or_mask is not None, it will delete the masked pixels, and only return the remained pixels. Default: False

+
+
or_mask: bool, optional

If True, and and_mask or or_mask is not None, it will delete the masked pixels, and only return the remained pixels. Default: False

+
+
reject_badpix: bool, optional

reject 10 most possible outliers by the test of pointDistGESD. One important Caveat here is that this process will also delete narrow emission lines +in some high SN ratio object e.g., [OIII]. Only use it when you are definitely clear about what you are doing. It will return the remained pixels.

+
+
deredden: bool, optional

correct the Galactic extinction only if the RA and Dec are available. It will return the corrected flux with the same array size. Default: True.

+
+
wave_range: 2-element array, optional

trim input wavelength (lam) according to the min and max range of the input 2-element array, e.g., +np.array([4000.,6000.]) in Rest frame range. Default: None

+
+
wave_mask: 2-D array

mask some absorption lines or sky lines in spectrum, e.g., np.array([[2200.,2300.]]), np.array([[5650.,5750.],[5850.,5900.]])

+
+
decompose_host: bool, optional

If True, the host galaxy-QSO decomposition will be applied. If no more than 100 pixels are negative, the result will be applied. The Decomposition is +based on the PCA method of Yip et al. 2004 (AJ, 128, 585) & (128, 2603). Now the template is only available for redshift < 1.16 in specific absolute +magnitude bins. For galaxy, the global model has 10 PCA components and first 5 will enough to reproduce 98.37% galaxy spectra. For QSO, the global model +has 50, and the first 20 will reproduce 96.89% QSOs. If have i-band absolute magnitude, the Luminosity-redshift binned PCA components are available. +Then the first 10 PCA in each bin is enough to reproduce most QSO spectrum. Default: False

+
+
host_prior: bool, optional

This parameter is only useful when the decompose_host is True and BC03 is False. If True, the code will +adopt the prior parameters given in the pca file to perform host decomposition.

+
+
host_prior_scale: float, optional

If the prior decomposition is performed, the code will use this parameter to scale the prior penalty to the +original chi2. Default: 0.2

+
+
host_line_mask: bool, optional

If True, the line region of galaxy will be masked when subtracted from original spectra. Default: True

+
+
BC03: bool, optional

if True, it will use Bruzual1 & Charlot 2003 host model to fit spectrum, high shift host will be low resolution R ~ 300, the rest is R ~ 2000. Default: False

+
+
Mi: float, optional

i-band absolute magnitude. It only works when decompose_host is True. If not None, the Luminosity redshift binned PCA will be used to decompose +the spectrum. Default: None

+
+
npca_gal: int, optional

the number of galaxy PCA components applied. It only works when decompose_host is True. The default is 5, +which is already account for 98.37% galaxies.

+
+
npca_qso: int, optional

the number of QSO PCA components applied. It only works when decompose_host is True. The default is 20, +No matter the global or luminosity-redshift binned PCA is used, it can reproduce > 92% QSOs. The binned PCA +is better if have Mi information.

+
+
Fe_uv_op: bool, optional

if True, fit continuum with UV and optical FeII template. Default: True

+
+
poly: bool, optional

if True, fit continuum with the polynomial component to account for the dust reddening. Default: False

+
+
BC: bool, optional

if True, fit continuum with Balmer continua from 1000 to 3646A. Default: False

+
+
rej_abs_conti: bool, optional

if True, it will iterate the continuum fitting once, rejecting 3 sigma outlier absorption pixels in the continuum +(< 3500A), which might fall into the broad absorption lines. Default: False

+
+
rej_abs_line: bool, optional

if True, it will iterate the emission line fitting twice, rejecting 3 sigma outlier absorption pixels +which might fall into the broad absorption lines. Default: False

+
+
n_pix_min_conti: float, optional

minimum number of negative pixels for host continuuum fit to be rejected. Default: 100

+
+
param_file_name: str, optional

name of the qso fitting parameter FITS file. Default: ‘qsopar.fits’

+
+
MC: bool, optional

if True, do Monte Carlo resampling of the spectrum based on the input error array to produce the MC error array. +if False, the code will not save the MLE minimization error produced by lmfit since it is biased and can not be trusted. +But it can be still output by using the lmfit attribute. Default: False

+
+
MCMC: bool, optional

if True, do Markov Chain Monte Carlo sampling of the posterior probability densities after MLE fitting to produce the error array. +Note: An error will be thrown if both MC and MCMC are True. Default: False

+
+
nburn: int, optional

the number of burn-in samples to run MCMC chain if MCMC=True. It only works when MCMC is True. Default: 20

+
+
nsamp: int, optional

the number of trials of the MC process to produce the error array (if MC=True) or number samples to run MCMC chain (if MCMC=True). Should be larger than 20. It only works when either MC or MCMC is True. Default: 200

+
+
linefit: bool, optional

if True, the emission line will be fitted. Default: True

+
+
save_result: bool, optional

if True, all the fitting results will be saved to a fits file, Default: True

+
+
plot_fig: bool, optional

if True, the fitting results will be plotted. Default: True

+
+
save_fig: bool, optional

if True, the figure will be saved, and the path can be set by “save_fig_pathâ€. Default: True

+
+
plot_corner: bool, optinoal

whether or not to plot the corner plot results if MCMC=True. Default: True

+
+
save_fig_path: str, optional

the output path of the figure. If None, the default “save_fig_path†is set to “pathâ€

+
+
save_fits_path: str, optional

the output path of the result fits. If None, the default “save_fits_path†is set to “pathâ€

+
+
save_fits_name: str, optional

the output name of the result fits. Default: “result.fitsâ€

+
+
verbose: bool, optional

turn on (True) or off (False) debugging output. Default: False

+
+
kwargs_plot: dict, optional

extra aguments for plot_fig for plotting results. See LINK TO PLOT_FIG_DOC. Default: {}

+
+
kwargs_conti_emcee: dict, optional

extra aguments for emcee Sampler for continuum fitting. Default: {}

+
+
kwargs_line_emcee: dict, optional

extra arguments for emcee Sampler for line fitting. Default: {}

+
+
+
+
+

Return:¶

+
+
+

Properties:¶

+
+
.wave: array

the rest wavelength, some pixels have been removed.

+
+
.flux: array

the rest flux. Dereddened and *(1+z) flux.

+
+
.err: array

the error.

+
+
.wave_prereduced: array

the wavelength after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.flux_prereduced: array

the flux after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.err_prereduced: array

the error after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.host: array

the model of host galaxy from PCA method

+
+
.qso: array

the model of a quasar from PCA method.

+
+
.SN_ratio_conti: float

the mean S/N ratio of 1350, 3000 and 5100A.

+
+
.conti_fit.: structure

all the continuum fitting results, including best-fit parameters and Chisquare, etc. For details, +see https://lmfit.github.io/lmfit-py/fitting.html

+
+
.f_conti_model: array

the continuum model including power-law, polynomial, optical/UV FeII, Balmer continuum.

+
+
.f_bc_model: array

the Balmer continuum model.

+
+
.f_fe_uv_model: array

the UV FeII model.

+
+
.f_fe_op_model: array

the optical FeII model.

+
+
.f_pl_model: array

the power-law model.

+
+
.f_poly_model: array

the polynomial model.

+
+
.PL_poly_BC: array

The combination of Powerlaw, polynomial and Balmer continuum model.

+
+
.line_flux: array

the emission line flux after subtracting the .f_conti_model.

+
+
.line_fit: structrue

Line fitting results for last complexes (From Lya to Ha) , including best-fit parameters, errors (lmfit derived) and Chisquare, etc. For details, +see https://lmfit.github.io/lmfit-py/fitting.html

+
+
.gauss_result: array

3*n Gaussian parameters for all lines in the format of [scale, centerwave, sigma ], n is number of Gaussians for all complexes. +ADD UNITS

+
+
gauss_result_all: array

[nsamp, 3*n] Gaussian parameters for all lines in the format of [scale, centerwave, sigma ], n is number of Gaussians for all complexes. +ADD UNITS

+
+
.conti_result: array

continuum parameters, including widely used continuum parameters and monochromatic flux at 1350, 3000 +and 5100 Angstrom, etc. The corresponding names are listed in .conti_result_name. For all continuum fitting results, +go to .conti_fit.params.

+
+
.conti_result_name: array

the names for .conti_result.

+
+
.fur_result: array

emission line parameters, including FWHM, sigma, EW, measured from whole model of each main broad emission line covered. +The corresponding names are listed in .line_result_name.

+
+
.fur_result_name: array

the names for .fur_result.

+
+
.line_result: array

emission line parameters, including FWHM, sigma, EW, measured from whole model of each main broad emission line covered, +and fitting parameters of each Gaussian component. The corresponding names are listed in .line_result_name.

+
+
.line_result_name: array

the names for .line_result.

+
+
.uniq_linecomp_sort: array

the sorted complex names.

+
+
.all_comp_range: array

the start and end wavelength for each complex. e.g., Hb is [4640. 5100.] AA.

+
+
.linelist: array

the information listed in the param_file_name (qsopar.fits).

+
+
+
+
+ +
+
+Get_Fe_flux(ranges, pp=None)¶
+

Calculate the flux of fitted FeII template within given wavelength ranges. +ranges: 1-D array, 2-D array

+
+

if 1-D array was given, it should contain two parameters contain a range of wavelength. FeII flux within this range would be calculate and documented in the result fits file. +if 2-D array was given, it should contain a series of ranges. FeII flux within these ranges would be documented respectively.

+
+
+
pp: 1-D array with 3 or 6 items.

If 3 parameters were given, function will choose a proper template (MgII or balmer) according to the range. +If the range give excess either template, an error would be arose. +If 6 parameters were given (recommended), function would adopt the first three for the MgII template and the last three for the balmer.

+
+
+
+ +
+
+Manygauss(xval, pp)¶
+

Robust function for multi-Gaussian model used to fit the emission lines

+

This is evaluated many times within the scipy optimize, so we want to keep the code as fast as possible +Hence, it is vectorized so pp must have shape [ngauss, 3]

+

xval: wavelength array in AA

+
+
pp: Paramaters [ngauss*3]

scale: line amplitude +wave: central ln wavelength in AA +sigma: width in km/s

+
+
+
+ +
+
+Onegauss(xval, pp)¶
+

The single Gaussian model used to fit the emission lines +Parameter: the scale factor, central wavelength in logwave, line FWHM in logwave

+

This is evaluated many times within the scipy optimize, so we want to keep the code as fast as possible +Hence, we avoid calling any external libraries like astropy’s Gaussian here

+

It is slightly faster to fit the (un-normalized) amplitude directly to avoid blow-up at small sigma

+

xval: wavelength array in AA

+

TODO: See if LMFIT’s built-in modeles improved performance +https://lmfit.github.io/lmfit-py/builtin_models.html

+
+
pp: Paramaters [3]

scale: line amplitude +wave: central ln wavelength in AA +sigma: width in km/s

+
+
+
+ +
+
+PL(xval, pp, x0=3000)¶
+
+ +
+
+Smooth(y, box_pts)¶
+

Smooth the flux with n pixels

+
+ +
+
+decompose_host_qso(wave, flux, err, path)¶
+

Decompose the host galaxy from QSO

+
+ +
+
+fit_continuum(wave, flux, err, ra, dec, plateid, mjd, fiberid)¶
+

Fit the continuum with PL, Polynomial, UV/optical FeII, Balmer continuum

+
+

Parameter:¶

+
+
lam: array, required

wavelength

+
+
flux: array, required

flux

+
+
err: array, required

1 sigma error

+
+
conti_windows: 2d array, optional

Continuum fitting windows. If None, use default windows. For special situations, you +may need to change these to improve the fitting (e.g., Ly-alpha absorption troughs, etc.) Default: None

+
+
+
+
+

Return:¶

+
+
+ +
+
+fit_lines(wave, line_flux, err, f)¶
+

Fit the emission lines with Gaussian profiles

+
+ +
+
+flux2L(flux, z=None)¶
+

Transfer flux to luminoity assuming a flat Universe

+
+ +
+
+line_prop(compcenter, pp, linetype='broad', ln_sigma_br=0.0017)¶
+

Calculate the further results for the broad component in emission lines, e.g., FWHM, sigma, peak, line flux +The compcenter is the theortical vacuum wavelength for the broad compoenet. +compcenter: +pp: +linetype: ‘broad’ or ‘narrow’ +ln_sigma_br: line sigma separating broad and narrow lines (AA??) +ln_sigma_max: Max sigma to consider in the calculation (used to exclude ultra-broad wings, etc.)

+
+ +
+
+line_prop_from_name(line_name, line_type='broad', sample_index=-1, ln_sigma_br=0.0017)¶
+

line_name: line name e.g., ‘Ha_br’

+
+ +
+
+plot_fig(save_fig_path='.', broad_fwhm=1200, plot_line_name=True, plot_legend=True, ylims=None, plot_residual=True, show_title=True, plot_br_prop=False)¶
+

Plot the results

+
+
broad_fwhm: float, optional

Definition for width of the broad lines. Default: 1200 km/s (careful, is not the exact separation used in line_prop)

+
+
plot_line_name: bool, optional

if True, serval main emission lines will be plotted in the first panel of the output figure. Default: False

+
+
+

TODO: Consider splitting up into plot_conti and plot_complex functions +Wenke: I totally agree with that!!! +to encourage flexibility/reuse

+
+ +
+
+read_out_params(param_file_path='qsopar.fits')¶
+
+ +
+
+save_result(conti_result, conti_result_type, conti_result_name, line_result, line_result_type, line_result_name, save_fits_path, save_fits_name)¶
+

Save all data to fits

+
+ +
+
+set_mpl_style(tsize=18, tdir='in', major=5.0, minor=3.0, lwidth=1.8, lhandle=2.0)¶
+

Function to set MPL style

+
+ +
+
+to_Spectrum1D()¶
+
+ +
+ +
+
+pyqsofit.PyQSOFit.get_err(s, margin=0.16, axis=0, default_value=-1.0)¶
+

Get 100*margin percent distribution of a given data. +:param s: 1-D array or 2-D array. If a 1-D array is given, the data will deem the array as the data sample and the +axis parameter will be ignored. If a 2-D array is given, how the function deel with this data will depend on the +axis. If axis==0, the function will calculate the distribution of each column of the array. If axis==1, the +function will calculate the distribution of each row of the array. +:param margin: The margin of the distribution. The default value is 16%, which means the function will calculate +about 1 sigma error for each sample +:param axis: How the function deel with the data, see above. +:return: float or 1-D array, depends on the input data.

+
+ +
+
+pyqsofit.PyQSOFit.read_conti_params(param_file_path='qsopar.fits')¶
+
+ +
+
+pyqsofit.PyQSOFit.read_line_params(param_file_path='qsopar.fits')¶
+
+ +
+
+

pyqsofit.version module¶

+
+
+

Module contents¶

+
+
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/search.html b/docs/_build/search.html new file mode 100644 index 00000000..0d656742 --- /dev/null +++ b/docs/_build/search.html @@ -0,0 +1,116 @@ + + + + + + + Search — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Search

+ + + + +

+ Searching for multiple words only shows matches that contain + all words. +

+ + +
+ + + +
+ + +
+ + +
+ +
+
+ +
+
+
+ ©2024, Hengxiao Guo. + + | + Powered by Sphinx 7.3.7 + & Alabaster 0.7.16 + +
+ + + + + + \ No newline at end of file diff --git a/docs/builddocs.bash b/docs/builddocs.bash new file mode 100644 index 00000000..87a07bc3 --- /dev/null +++ b/docs/builddocs.bash @@ -0,0 +1 @@ +sphinx-build docs docs/_build From 07a5d11c49f5701084a37b7b066c81ec5b81e2e2 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:59:31 -0400 Subject: [PATCH 45/51] Create static.yml --- .github/workflows/static.yml | 43 ++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 .github/workflows/static.yml diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml new file mode 100644 index 00000000..0ba82305 --- /dev/null +++ b/.github/workflows/static.yml @@ -0,0 +1,43 @@ +# Simple workflow for deploying static content to GitHub Pages +name: Deploy static content to Pages + +on: + # Runs on pushes targeting the default branch + push: + branches: ["master"] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + # Single deploy job since we're just deploying + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Setup Pages + uses: actions/configure-pages@v5 + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + # Upload entire repository + path: '.' + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 From 0b056628b517be24e0fbafae2011a5018eb15b5b Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sat, 29 Jun 2024 23:59:57 -0400 Subject: [PATCH 46/51] Delete .github/workflows/documentation.yml --- .github/workflows/documentation.yml | 27 --------------------------- 1 file changed, 27 deletions(-) delete mode 100644 .github/workflows/documentation.yml diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml deleted file mode 100644 index 9c216e72..00000000 --- a/.github/workflows/documentation.yml +++ /dev/null @@ -1,27 +0,0 @@ -name: documentation - -on: [push, pull_request, workflow_dispatch] - -permissions: - contents: write - -jobs: - docs: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - - name: Install dependencies - run: | - pip install sphinx sphinx_rtd_theme myst_parser - - name: Sphinx build - run: | - sphinx-build doc doc/_build - - name: Deploy to GitHub Pages - uses: peaceiris/actions-gh-pages@v4 - if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} - with: - publish_branch: gh-pages - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./docs/_build - force_orphan: true From 2f0e7ab241a6048f7657d62ba1b12dbab348ed05 Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sun, 30 Jun 2024 00:06:16 -0400 Subject: [PATCH 47/51] Update static.yml --- .github/workflows/static.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml index 0ba82305..93dd8948 100644 --- a/.github/workflows/static.yml +++ b/.github/workflows/static.yml @@ -37,7 +37,7 @@ jobs: uses: actions/upload-pages-artifact@v3 with: # Upload entire repository - path: '.' + path: './docs/_build' - name: Deploy to GitHub Pages id: deployment uses: actions/deploy-pages@v4 From 060a280f71965c72bb0040fe4138b35662fb0d2a Mon Sep 17 00:00:00 2001 From: burke86 Date: Sun, 30 Jun 2024 00:09:58 -0400 Subject: [PATCH 48/51] add source --- docs/_build/_sources/index.rst.txt | 20 ++++++++++++ docs/_build/_sources/modules.rst.txt | 7 +++++ docs/_build/_sources/pyqsofit.rst.txt | 45 +++++++++++++++++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 docs/_build/_sources/index.rst.txt create mode 100644 docs/_build/_sources/modules.rst.txt create mode 100644 docs/_build/_sources/pyqsofit.rst.txt diff --git a/docs/_build/_sources/index.rst.txt b/docs/_build/_sources/index.rst.txt new file mode 100644 index 00000000..b43b0df7 --- /dev/null +++ b/docs/_build/_sources/index.rst.txt @@ -0,0 +1,20 @@ +.. pyqsofit documentation master file, created by + sphinx-quickstart on Fri Jun 28 18:21:35 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to pyqsofit's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/_build/_sources/modules.rst.txt b/docs/_build/_sources/modules.rst.txt new file mode 100644 index 00000000..84849f95 --- /dev/null +++ b/docs/_build/_sources/modules.rst.txt @@ -0,0 +1,7 @@ +pyqsofit +======== + +.. toctree:: + :maxdepth: 4 + + pyqsofit diff --git a/docs/_build/_sources/pyqsofit.rst.txt b/docs/_build/_sources/pyqsofit.rst.txt new file mode 100644 index 00000000..40a2bca4 --- /dev/null +++ b/docs/_build/_sources/pyqsofit.rst.txt @@ -0,0 +1,45 @@ +pyqsofit package +================ + +Submodules +---------- + +pyqsofit.HostDecomp module +-------------------------- + +.. automodule:: pyqsofit.HostDecomp + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.MESFit module +---------------------- + +.. automodule:: pyqsofit.MESFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.PyQSOFit module +------------------------ + +.. automodule:: pyqsofit.PyQSOFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.version module +----------------------- + +.. automodule:: pyqsofit.version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: pyqsofit + :members: + :undoc-members: + :show-inheritance: From e66ae01111eb5f75fd932cbdf3d0d331cccc029e Mon Sep 17 00:00:00 2001 From: burke86 Date: Sun, 30 Jun 2024 00:14:06 -0400 Subject: [PATCH 49/51] add static --- docs/_build/_static/alabaster.css | 708 ++++++++++++++ docs/_build/_static/basic.css | 925 +++++++++++++++++++ docs/_build/_static/custom.css | 1 + docs/_build/_static/doctools.js | 156 ++++ docs/_build/_static/documentation_options.js | 13 + docs/_build/_static/file.png | Bin 0 -> 286 bytes docs/_build/_static/language_data.js | 199 ++++ docs/_build/_static/minus.png | Bin 0 -> 90 bytes docs/_build/_static/plus.png | Bin 0 -> 90 bytes docs/_build/_static/pygments.css | 83 ++ docs/_build/_static/searchtools.js | 619 +++++++++++++ docs/_build/_static/sphinx_highlight.js | 154 +++ docs/_build/objects.inv | Bin 0 -> 782 bytes 13 files changed, 2858 insertions(+) create mode 100644 docs/_build/_static/alabaster.css create mode 100644 docs/_build/_static/basic.css create mode 100644 docs/_build/_static/custom.css create mode 100644 docs/_build/_static/doctools.js create mode 100644 docs/_build/_static/documentation_options.js create mode 100644 docs/_build/_static/file.png create mode 100644 docs/_build/_static/language_data.js create mode 100644 docs/_build/_static/minus.png create mode 100644 docs/_build/_static/plus.png create mode 100644 docs/_build/_static/pygments.css create mode 100644 docs/_build/_static/searchtools.js create mode 100644 docs/_build/_static/sphinx_highlight.js create mode 100644 docs/_build/objects.inv diff --git a/docs/_build/_static/alabaster.css b/docs/_build/_static/alabaster.css new file mode 100644 index 00000000..e3174bf9 --- /dev/null +++ b/docs/_build/_static/alabaster.css @@ -0,0 +1,708 @@ +@import url("basic.css"); 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+ border: 1px solid #CCC; +} + +div.hint { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.seealso { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.topic { + background-color: #EEE; +} + +p.admonition-title { + display: inline; +} + +p.admonition-title:after { + content: ":"; +} + +pre, tt, code { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; + font-size: 0.9em; +} + +.hll { + background-color: #FFC; + margin: 0 -12px; + padding: 0 12px; + display: block; +} + +img.screenshot { +} + +tt.descname, tt.descclassname, code.descname, code.descclassname { + font-size: 0.95em; +} + +tt.descname, code.descname { + padding-right: 0.08em; +} + +img.screenshot { + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils { + border: 1px solid #888; + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils td, table.docutils th { + border: 1px solid #888; + padding: 0.25em 0.7em; +} + +table.field-list, table.footnote { + border: none; + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + +table.footnote { + margin: 15px 0; + width: 100%; + border: 1px solid #EEE; + background: #FDFDFD; + font-size: 0.9em; +} + +table.footnote + table.footnote { + margin-top: -15px; + border-top: none; +} + +table.field-list th { + padding: 0 0.8em 0 0; +} + +table.field-list td { + padding: 0; +} + +table.field-list p { + margin-bottom: 0.8em; +} + +/* Cloned from + * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68 + */ +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +table.footnote td.label { + width: .1px; + padding: 0.3em 0 0.3em 0.5em; +} + +table.footnote td { + padding: 0.3em 0.5em; +} + +dl { + margin-left: 0; + margin-right: 0; + margin-top: 0; + padding: 0; +} + +dl dd { + margin-left: 30px; +} + +blockquote { + margin: 0 0 0 30px; + padding: 0; +} + +ul, ol { + /* Matches the 30px from the narrow-screen "li > ul" selector below */ + margin: 10px 0 10px 30px; + padding: 0; +} + +pre { + background: #EEE; + padding: 7px 30px; + margin: 15px 0px; + line-height: 1.3em; +} + +div.viewcode-block:target { + background: #ffd; +} + +dl pre, blockquote pre, li pre { + margin-left: 0; + padding-left: 30px; +} + +tt, code { + background-color: #ecf0f3; + color: #222; + /* padding: 1px 2px; */ +} + +tt.xref, code.xref, a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fff; +} + +a.reference { + text-decoration: none; + border-bottom: 1px dotted #004B6B; +} + +/* Don't put an underline on images */ +a.image-reference, a.image-reference:hover { + border-bottom: none; +} + +a.reference:hover { + border-bottom: 1px solid #6D4100; +} + +a.footnote-reference { + text-decoration: none; + font-size: 0.7em; + vertical-align: top; + border-bottom: 1px dotted #004B6B; +} + +a.footnote-reference:hover { + border-bottom: 1px solid #6D4100; +} + +a:hover tt, a:hover code { + background: #EEE; +} + + +@media screen and (max-width: 870px) { + + div.sphinxsidebar { + display: none; + } + + div.document { + width: 100%; + + } + + div.documentwrapper { + margin-left: 0; + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + } + + div.bodywrapper { + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + margin-left: 0; + } + + ul { + margin-left: 0; + } + + li > ul { + /* Matches the 30px from the "ul, ol" selector above */ + margin-left: 30px; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .bodywrapper { + margin: 0; + } + + .footer { + width: auto; + } + + .github { + display: none; + } + + + +} + + + +@media screen and (max-width: 875px) { + + body { + margin: 0; + padding: 20px 30px; + } + + div.documentwrapper { + float: none; + background: #fff; + } + + div.sphinxsidebar { + display: block; + float: none; + width: 102.5%; + margin: 50px -30px -20px -30px; + padding: 10px 20px; + background: #333; + color: #FFF; + } + + div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, + div.sphinxsidebar h3 a { + color: #fff; + } + + div.sphinxsidebar a { + color: #AAA; + } + + div.sphinxsidebar p.logo { + display: none; + } + + div.document { + width: 100%; + margin: 0; + } + + div.footer { + display: none; + } + + div.bodywrapper { + margin: 0; + } + + div.body { + min-height: 0; + padding: 0; + } + + .rtd_doc_footer { + display: none; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .footer { + width: auto; + } + + .github { + display: none; + } +} + + +/* misc. */ + +.revsys-inline { + display: none!important; +} + +/* Hide ugly table cell borders in ..bibliography:: directive output */ +table.docutils.citation, table.docutils.citation td, table.docutils.citation th { + border: none; + /* Below needed in some edge cases; if not applied, bottom shadows appear */ + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + + +/* relbar */ + +.related { + line-height: 30px; + width: 100%; + font-size: 0.9rem; +} + +.related.top { + border-bottom: 1px solid #EEE; + margin-bottom: 20px; +} + +.related.bottom { + border-top: 1px solid #EEE; +} + +.related ul { + padding: 0; + margin: 0; + list-style: none; +} + +.related li { + display: inline; +} + +nav#rellinks { + float: right; +} + +nav#rellinks li+li:before { + content: "|"; +} + +nav#breadcrumbs li+li:before { + content: "\00BB"; +} + +/* Hide certain items when printing */ +@media print { + div.related { + display: none; + } +} \ No newline at end of file diff --git a/docs/_build/_static/basic.css b/docs/_build/_static/basic.css new file mode 100644 index 00000000..e5179b7a --- /dev/null +++ b/docs/_build/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: inherit; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/docs/_build/_static/custom.css b/docs/_build/_static/custom.css new file mode 100644 index 00000000..2a924f1d --- /dev/null +++ b/docs/_build/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/docs/_build/_static/doctools.js b/docs/_build/_static/doctools.js new file mode 100644 index 00000000..4d67807d --- /dev/null +++ b/docs/_build/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/docs/_build/_static/documentation_options.js b/docs/_build/_static/documentation_options.js new file mode 100644 index 00000000..44b5d19e --- /dev/null +++ b/docs/_build/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '2.1.6', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/docs/_build/_static/file.png b/docs/_build/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 z_CyJOe}D1){SET-^Amu_i71Lt6eYfZjRyw@I6OQAIXXHDfiX^GbOlHe=Ae4>0m)d(f|Me07*qoM6N<$f}vM^LjV8( literal 0 HcmV?d00001 diff --git a/docs/_build/_static/language_data.js b/docs/_build/_static/language_data.js new file mode 100644 index 00000000..367b8ed8 --- /dev/null +++ b/docs/_build/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/docs/_build/_static/minus.png b/docs/_build/_static/minus.png new file mode 100644 index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK literal 0 HcmV?d00001 diff --git a/docs/_build/_static/plus.png b/docs/_build/_static/plus.png new file mode 100644 index 0000000000000000000000000000000000000000..7107cec93a979b9a5f64843235a16651d563ce2d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu>-2 m3q%Vub%g%s<8sJhVPMczOq}xhg9DJoz~JfX=d#Wzp$Pyb1r*Kz literal 0 HcmV?d00001 diff --git a/docs/_build/_static/pygments.css b/docs/_build/_static/pygments.css new file mode 100644 index 00000000..07454c6b --- /dev/null +++ b/docs/_build/_static/pygments.css @@ -0,0 +1,83 @@ +pre { line-height: 125%; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/_build/_static/sphinx_highlight.js b/docs/_build/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/docs/_build/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/docs/_build/objects.inv b/docs/_build/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..91d732ebb4715ec23efa84729c32b0d8b1552533 GIT binary patch literal 782 zcmV+p1M&PLAX9K?X>NERX>N99Zgg*Qc_4OWa&u{KZXhxWBOp+6Z)#;@bUGk#d2w@Z zW@&T^BOq2~a&u{KZaN?eBOp|0Wgv28ZDDC{WMy(7Z)PBLXlZjGW@&6?AZc?TV{dJ6 za%FRKWn>_Ab7^j8AbMlp-Xyxm2d8B_!|hIvUe`Q1Wdw zFW)80#p&S2_;3xmQI-r$H$nqT0%(fN+)7RY{ z%dS35ub*ciCMAHgtl)tY!te2t1yEM<0MkVb;4`IIdnnl>cBkS&%#>R8!MBB)y65R=B}pOCZWL{cu~|`de(}darldJEHGdaIBo2nqubE9 z8yP#BfR)ZDrnv$tmBn`+D@8@ccYB_x!^HjboW}DfU^v-pN$yXN{fRpl^P!RCbl?}q z4)=%PYPGtaOj4l)h+Dw8E$xKt(%98?FOd|ESQ-;4p1}FmY1AvO0xfg_hs1~CQt}7< zR#>i*qqTESzO0e@b{>Up>c>KuD_rqAx76H3> Mp0&Qe0YC8tX$}i}Q2+n{ literal 0 HcmV?d00001 From 26c85d8ce771eec494f6deadfb8aba2243382e4e Mon Sep 17 00:00:00 2001 From: "Colin J. Burke" Date: Sun, 30 Jun 2024 00:17:07 -0400 Subject: [PATCH 50/51] Rename builddocs.bash to builddocs --- docs/{builddocs.bash => builddocs} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/{builddocs.bash => builddocs} (100%) diff --git a/docs/builddocs.bash b/docs/builddocs similarity index 100% rename from docs/builddocs.bash rename to docs/builddocs From 3cb771f7bb835d88a0337d610678a568c380fed7 Mon Sep 17 00:00:00 2001 From: burke86 Date: Sun, 30 Jun 2024 00:27:24 -0400 Subject: [PATCH 51/51] more robust test --- tests/test_dr7sample.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/tests/test_dr7sample.py b/tests/test_dr7sample.py index c0602059..26e4ee13 100644 --- a/tests/test_dr7sample.py +++ b/tests/test_dr7sample.py @@ -286,8 +286,17 @@ def test_dr7(nqsofit=20): mask = (xid['plate'] == plate) & (xid['mjd'] == mjd) & (xid['fiberID'] == fiber) print(xid[mask]) + + if len(xid[mask]) < 1: + print('No spectrum found.') + return + sp = SDSS.get_spectra(matches=xid[mask]) print(sp) + + if len(sp) < 1: + print('No spectrum found.') + return data = sp[0] @@ -303,7 +312,7 @@ def test_dr7(nqsofit=20): q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) # Test with host prior - #q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) + q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) # Emission line loop for j, line in enumerate(line_calc_names):