Updates develop to the release branch

MANIFEST.in

@@ -17,6 +17,7 @@ global-exclude *.pyc *.o *.so *.DS_Store *.ipynb
 # update the defined_paths dictionary in pypeit.pypeitdata.PypeItDataPaths!
 recursive-exclude pypeit/data/arc_lines/reid_arxiv *.fits *.json *.pdf *.tar.gz
 recursive-exclude pypeit/data/arc_lines/NIST *.ascii
+recursive-exclude pypeit/data/pixelflats *.fits.gz
 recursive-exclude pypeit/data/sensfuncs *.fits
 recursive-exclude pypeit/data/skisim *.dat
 recursive-exclude pypeit/data/standards *.gz *.fits *.dat

doc/help/run_pypeit.rst

@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
 
-    ##  PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev95+g35e103c10
+    ##  PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev635+g9540496b9
     ##  
     ##  Available spectrographs include:
     ##   aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,

doc/pypeit_par.rst

@@ -482,8 +482,8 @@ Key                       Type                       Options
 ``echelle_pad``           int                        ..                                                                            3                 Number of orders by which to pad the echellogram reference in the echelle method. Values > 0 allow for some error in the reddest order guess, but require sufficient reference orders.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
 ``frac_rms_thresh``       float                      ..                                                                            1.5               For echelle spectrographs (i.e., ``echelle=True``), this is the fractional change in the RMS threshold used when a 1D fit is re-attempted for failed orders.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
 ``func``                  str                        ..                                                                            ``legendre``      Function used for wavelength solution fits                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
-``fwhm``                  int, float                 ..                                                                            4.0               Spectral sampling of the arc lines. This is the FWHM of an arcline in binned pixels of the input arc image                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
-``fwhm_fromlines``        bool                       ..                                                                            True              Estimate spectral resolution in each slit using the arc lines. If True, the estimated FWHM will override ``fwhm`` only in the determination of the wavelength solution (including the calculation of the threshold for the solution RMS, see ``rms_thresh_frac_fwhm``), but not for the wave tilts calibration.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
+``fwhm``                  int, float                 ..                                                                            4.0               Spectral sampling of the arc lines. This is the FWHM of an arcline in binned pixels of the input arc image. Note that this is used also in the wave tilts calibration.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
+``fwhm_fromlines``        bool                       ..                                                                            True              Estimate spectral resolution in each slit using the arc lines. If True, the estimated FWHM will override ``fwhm`` in the determination of the wavelength solution (including the calculation of the threshold for the solution RMS, see ``rms_thresh_frac_fwhm``), and ALSO for the wave tilts calibration.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
 ``fwhm_spat_order``       int                        ..                                                                            0                 This parameter determines the spatial polynomial order to use in the 2D polynomial fit to the FWHM of the arc lines. See also, fwhm_spec_order.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
 ``fwhm_spec_order``       int                        ..                                                                            1                 This parameter determines the spectral polynomial order to use in the 2D polynomial fit to the FWHM of the arc lines. See also, fwhm_spat_order.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
 ``lamps``                 list                       ..                                                                            ..                Name of one or more ions used for the wavelength calibration.  Use ``None`` for no calibration. Choose ``use_header`` to use the list of lamps recorded in the header of the arc frames (this is currently available only for Keck DEIMOS, Keck LRIS, MMT Blue Channel, and LDT DeVeny).