diff --git a/README.rst b/README.rst index c12df29cb..da8fe0701 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ ShapePipe ========= -|CI| |CD| |python38| +|CI| |CD| |python39| |release| .. |CI| image:: https://github.com/CosmoStat/shapepipe/workflows/CI/badge.svg :target: https://github.com/CosmoStat/shapepipe/actions?query=workflow%3ACI @@ -9,10 +9,11 @@ ShapePipe .. |CD| image:: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment/badge.svg :target: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment -.. |python38| image:: https://img.shields.io/badge/python-3.8-green.svg - :target: https://www.python.org/ +.. |python39| image:: https://img.shields.io/badge/python-3.9-green.svg + :target: https://www.python.org/‰ -:Version: 0.0.4 +.. |release| image:: https://img.shields.io/github/v/release/CosmoStat/shapepipe + :target: https://github.com/CosmoStat/shapepipe/releases/latest ShapePipe is a galaxy shape measurement pipeline developed within the CosmoStat lab at CEA Paris-Saclay. diff --git a/docs/requirements.txt b/docs/requirements.txt index 69071c7b6..8aa90168c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,5 @@ -myst-parser>=0.16.1 -numpydoc>=1.1.0 -sphinx>=4.3.1 -sphinxcontrib-bibtex>=2.4.1 -sphinx-book-theme>=0.1.10 +myst-parser==0.17.0 +numpydoc==1.2 +sphinx==4.4.0 +sphinxcontrib-bibtex==2.4.1 +sphinx-book-theme==0.2.0 diff --git a/docs/source/conf.py b/docs/source/conf.py index 3ca876fdc..622686974 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,9 +23,9 @@ author = 'CosmoStat' # The short X.Y version -version = '0.0' +version = '1.0' # The full version, including alpha/beta/rc tags -release = '0.0.4' +release = '1.0.0' # -- General configuration --------------------------------------------------- diff --git a/environment.yml b/environment.yml index 0f36c0959..24f6dfd5f 100644 --- a/environment.yml +++ b/environment.yml @@ -2,30 +2,30 @@ name: shapepipe channels: - conda-forge dependencies: - - python=3.8 - - pip>=21 - - astropy==4.1 + - python=3.9 + - pip>=21.2.4 + - astropy==5.0 - automake==1.16.2 - autoconf==2.69 - cmake==3.19.6 - galsim==2.2.5 - - joblib==1.0.1 + - joblib==1.1.0 - libtool==2.4.6 - - matplotlib==3.3.4 + - matplotlib==3.5.1 + - numba==0.54.1 + - pandas==1.4.1 - pip: - - mccd==1.2.1 - - modopt==1.5.1 - - numba==0.53.1 - - pandas==1.2.4 - - PyQt5==5.15.4 - - pyqtgraph==0.11.1 - - python-pysap==0.0.5 - - reproject==0.7.1 + - mccd==1.2.3 + - modopt==1.6.0 + - PyQt5==5.15.6 + - pyqtgraph==0.12.4 + - python-pysap==0.0.6 + - reproject==0.8 - sip_tpv==1.1 - sf_tools==2.0.4 - - sqlitedict==1.7.0 + - sqlitedict==2.0.0 - termcolor==1.1.0 - - tqdm==4.60.0 - - treecorr==4.1.7 + - tqdm==4.63.0 + - treecorr==4.2.6 - git+https://github.com/aguinot/ngmix@stable_version - git+https://github.com/tobias-liaudat/Stile@v0.1 diff --git a/install_shapepipe b/install_shapepipe index c2af77393..c370d91d0 100755 --- a/install_shapepipe +++ b/install_shapepipe @@ -10,7 +10,8 @@ export LC_CTYPE=en_US.utf8 # ############################################################################## -version="1.5" +version="1.6" +last_update="08/03/22" ############################################################################## # EXTERNAL PACKAGES AND SCRIPTS @@ -18,6 +19,12 @@ version="1.5" # External packages +# Conda package versions +fftw_ver="3.3.10" +libpng_ver="1.6.37" +mpi4py_ver="3.1.3" +openblas_ver="0.3.18" + # SExtractor Package sex_url="https://github.com/astromatic/sextractor/archive/2.25.0.tar.gz" sex_tar="2.25.0.tar.gz" @@ -47,9 +54,9 @@ cdsclient_bin="findgsc2.2" cdsclient_version=FALSE # mpi4py Package -mpi_url="https://github.com/mpi4py/mpi4py/archive/3.0.3.tar.gz" -mpi_tar="3.0.3.tar.gz" -mpi_dir="mpi4py-3.0.3" +mpi_url="https://github.com/mpi4py/mpi4py/archive/${mpi4py_ver}.tar.gz" +mpi_tar="${mpi4py_ver}.tar.gz" +mpi_dir="mpi4py-${mpi4py_ver}" mpi_bin="mpiexec" mpi_version=TRUE @@ -251,7 +258,7 @@ check_binary2() { # Check if a python site-package is installed correctly in the conda environment check_site_pkg() { - if compgen -G "$CONDA_PREFIX/lib/python3.8/site-packages/$1*" > /dev/null + if compgen -G "$CONDA_PREFIX/lib/python3.*/site-packages/$1*" > /dev/null then echo -ne " - $1:\t \xe2\x9c\x85\n" else @@ -276,7 +283,7 @@ start() { echo '' echo 'Author: Samuel Farrens' echo 'Version:' $version - echo 'Last Update: 26/01/2022' + echo 'Last Update:' $last_update echo $line echo '' } @@ -698,7 +705,7 @@ then report_progress 'MPI' if [ -z "$MPI_ROOT" ] then - conda install -n $ENV_NAME -c conda-forge "mpi4py>=3.0.1" -y + conda install -n $ENV_NAME -c conda-forge "mpi4py==${mpi4py_ver}" -y else download_package $mpi_url $mpi_tar build_mpi $mpi_dir @@ -713,13 +720,13 @@ fi if [ "$INSTALL_SEX" == TRUE ] && check_binary $sex_bin then report_progress 'SExtractor' - conda install -n $ENV_NAME -c conda-forge fftw -y + conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y download_package $sex_url $sex_tar if [ "$use_atlas" == TRUE ] then build_sex_atlas $sex_dir else - conda install -n $ENV_NAME -c conda-forge openblas -y + conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y build_sex_blas $sex_dir fi fi @@ -728,14 +735,14 @@ fi if [ "$INSTALL_PSFEX" == TRUE ] && check_binary $psfex_bin then report_progress 'PSFEx' - conda install libpng -y - conda install -n $ENV_NAME -c conda-forge fftw -y + conda install "libpng==${libpng_ver}" -y + conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y download_package $psfex_url $psfex_tar if [ "$use_atlas" == TRUE ] then build_psfex_atlas $psfex_dir else - conda install -n $ENV_NAME -c conda-forge openblas -y + conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y build_psfex_blas $psfex_dir fi fi diff --git a/shapepipe/info.py b/shapepipe/info.py index f35454ddc..9be0577d6 100644 --- a/shapepipe/info.py +++ b/shapepipe/info.py @@ -15,7 +15,7 @@ # Package Info -version_info = (0, 0, 4) +version_info = (1, 0, 0) __version__ = '.'.join(str(c) for c in version_info) __name__ = 'shapepipe' __author__ = 'Samuel Farrens' diff --git a/shapepipe/utilities/galaxy.py b/shapepipe/utilities/galaxy.py index 7a037b5f3..eb05c4bc2 100644 --- a/shapepipe/utilities/galaxy.py +++ b/shapepipe/utilities/galaxy.py @@ -47,14 +47,14 @@ def sigma_to_fwhm(sigma, pixel_scale=1.0): ----- To compute the FWHMh for a 1D Gaussian N(x), solve the equation - ..math:: + .. math:: N(x) = (\sigma \sqrt{2\pi})^{-1} \exp[x^2/2\sigma^2] = \frac 1 2 N(x) for :math:`x`. The FWHM is :math:`x + (-x) = 2x`. The solution is - ..math:: + .. math:: \textrm{FWHM} = 2 \sqrt(2 \ln 2) \sigma \approx 2.355 \sigma