Merge branch 'develop' into patch-1

.gitignore

@@ -34,7 +34,6 @@ QA/
 # git has its own built in compression methods
 *.7z
 *.dmg
-*.gz
 *.iso
 *.jar
 *.rar

doc/Makefile

@@ -70,6 +70,7 @@ apirst:
 	python ./scripts/build_bitmask_rst.py
 	python ./scripts/build_spectbl_rst.py
 	python ./scripts/make_example_files.py
+	python ./scripts/build_standardstbl_rst.py
 
 html:
 	make apirst

doc/api/pypeit.scripts.compile_wvarxiv.rst

@@ -0,0 +1,8 @@
+pypeit.scripts.compile\_wvarxiv module
+======================================
+
+.. automodule:: pypeit.scripts.compile_wvarxiv
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:

doc/api/pypeit.scripts.rst

@@ -23,6 +23,7 @@ Submodules
    pypeit.scripts.coadd_datacube
    pypeit.scripts.collate_1d
    pypeit.scripts.compare_sky
+   pypeit.scripts.compile_wvarxiv
    pypeit.scripts.edge_inspector
    pypeit.scripts.flux_calib
    pypeit.scripts.flux_setup

doc/help/pypeit_compile_wvarxiv.rst

@@ -0,0 +1,19 @@
+.. code-block:: console
+
+    $ pypeit_compile_wvarxiv -h
+    usage: pypeit_compile_wvarxiv [-h] [--append] wvarxiv_folder instrument grating
+    
+    Read in a set of wxarxiv solutions from Identify and compile them into a single
+    fits file to be used with the reidentify method.
+    
+    positional arguments:
+      wvarxiv_folder  Location of the WVarxiv files
+      instrument      Name of instrument. e.g. keck_lris_blue, keck_deimos,
+                      gemini_gmos_south_ham
+      grating         Instrument grating name. E.g. b600, r400, 600_10000.
+    
+    options:
+      -h, --help      show this help message and exit
+      --append        Append to an existing file for this instrument. (default:
+                      False)
+    

doc/help/run_pypeit.rst

@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev126+ga20cda141.d20240305[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev192+gf7d381a4b.d20240516[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

doc/include/class_datamodel_spec2dobj.rst

@@ -1,27 +1,28 @@
 
-**Version**: 1.1.0
+**Version**: 1.1.1
 
-=====================  ===================================================================================================  =================  ================================================================================================================================================================================
-Attribute              Type                                                                                                 Array Type         Description                                                                                                                                                                     
-=====================  ===================================================================================================  =================  ================================================================================================================================================================================
-``bpmmask``            :class:`~pypeit.images.imagebitmask.ImageBitMaskArray`                                                                  2D bad-pixel mask for the image                                                                                                                                                 
-``det``                int                                                                                                                     Detector index                                                                                                                                                                  
-``detector``           :class:`~pypeit.images.detector_container.DetectorContainer`, :class:`~pypeit.images.mosaic.Mosaic`                     Detector or Mosaic metadata                                                                                                                                                     
-``ivarmodel``          `numpy.ndarray`_                                                                                     `numpy.floating`_  2D ivar model image (float32)                                                                                                                                                   
-``ivarraw``            `numpy.ndarray`_                                                                                     `numpy.floating`_  2D processed inverse variance image (float32)                                                                                                                                   
-``maskdef_designtab``  `astropy.table.table.Table`_                                                                                            Table with slitmask design and object info                                                                                                                                      
-``med_chis``           `numpy.ndarray`_                                                                                     `numpy.floating`_  Median of the chi image for each slit/order                                                                                                                                     
-``objmodel``           `numpy.ndarray`_                                                                                     `numpy.floating`_  2D object model image (float32)                                                                                                                                                 
-``scaleimg``           `numpy.ndarray`_                                                                                     `numpy.floating`_  2D multiplicative scale image [or a single scalar as an array] that has been applied to the science image (float32)                                                             
-``sci_spat_flexure``   float                                                                                                                   Shift, in spatial pixels, between this image and SlitTrace                                                                                                                      
-``sci_spec_flexure``   `astropy.table.table.Table`_                                                                                            Global shift of the spectrum to correct for spectralflexure (pixels). This is based on the sky spectrum atthe center of each slit                                               
-``sciimg``             `numpy.ndarray`_                                                                                     `numpy.floating`_  2D processed science image (float32)                                                                                                                                            
-``skymodel``           `numpy.ndarray`_                                                                                     `numpy.floating`_  2D sky model image (float32)                                                                                                                                                    
-``slits``              :class:`~pypeit.slittrace.SlitTraceSet`                                                                                 SlitTraceSet defining the slits                                                                                                                                                 
-``std_chis``           `numpy.ndarray`_                                                                                     `numpy.floating`_  std of the chi image for each slit/order                                                                                                                                        
-``tilts``              `numpy.ndarray`_                                                                                     `numpy.floating`_  2D tilts image (float64)                                                                                                                                                        
-``vel_corr``           float                                                                                                                   Relativistic velocity correction for wavelengths                                                                                                                                
-``vel_type``           str                                                                                                                     Type of reference frame correction (if any). Options are listed in the routine: WavelengthSolutionPar.valid_reference_frames() Current list: observed, heliocentric, barycentric
-``waveimg``            `numpy.ndarray`_                                                                                     `numpy.floating`_  2D wavelength image in vacuum (float64)                                                                                                                                         
-``wavesol``            `astropy.table.table.Table`_                                                                                            Table with WaveCalib diagnostic info                                                                                                                                            
-=====================  ===================================================================================================  =================  ================================================================================================================================================================================
+======================  ===================================================================================================  =================  ================================================================================================================================================================================
+Attribute               Type                                                                                                 Array Type         Description                                                                                                                                                                     
+======================  ===================================================================================================  =================  ================================================================================================================================================================================
+``bkg_redux_skymodel``  `numpy.ndarray`_                                                                                     `numpy.floating`_  2D sky model image without the background subtraction (float32)                                                                                                                 
+``bpmmask``             :class:`~pypeit.images.imagebitmask.ImageBitMaskArray`                                                                  2D bad-pixel mask for the image                                                                                                                                                 
+``det``                 int                                                                                                                     Detector index                                                                                                                                                                  
+``detector``            :class:`~pypeit.images.detector_container.DetectorContainer`, :class:`~pypeit.images.mosaic.Mosaic`                     Detector or Mosaic metadata                                                                                                                                                     
+``ivarmodel``           `numpy.ndarray`_                                                                                     `numpy.floating`_  2D ivar model image (float32)                                                                                                                                                   
+``ivarraw``             `numpy.ndarray`_                                                                                     `numpy.floating`_  2D processed inverse variance image (float32)                                                                                                                                   
+``maskdef_designtab``   `astropy.table.table.Table`_                                                                                            Table with slitmask design and object info                                                                                                                                      
+``med_chis``            `numpy.ndarray`_                                                                                     `numpy.floating`_  Median of the chi image for each slit/order                                                                                                                                     
+``objmodel``            `numpy.ndarray`_                                                                                     `numpy.floating`_  2D object model image (float32)                                                                                                                                                 
+``scaleimg``            `numpy.ndarray`_                                                                                     `numpy.floating`_  2D multiplicative scale image [or a single scalar as an array] that has been applied to the science image (float32)                                                             
+``sci_spat_flexure``    float                                                                                                                   Shift, in spatial pixels, between this image and SlitTrace                                                                                                                      
+``sci_spec_flexure``    `astropy.table.table.Table`_                                                                                            Global shift of the spectrum to correct for spectralflexure (pixels). This is based on the sky spectrum atthe center of each slit                                               
+``sciimg``              `numpy.ndarray`_                                                                                     `numpy.floating`_  2D processed science image (float32)                                                                                                                                            
+``skymodel``            `numpy.ndarray`_                                                                                     `numpy.floating`_  2D sky model image (float32)                                                                                                                                                    
+``slits``               :class:`~pypeit.slittrace.SlitTraceSet`                                                                                 SlitTraceSet defining the slits                                                                                                                                                 
+``std_chis``            `numpy.ndarray`_                                                                                     `numpy.floating`_  std of the chi image for each slit/order                                                                                                                                        
+``tilts``               `numpy.ndarray`_                                                                                     `numpy.floating`_  2D tilts image (float64)                                                                                                                                                        
+``vel_corr``            float                                                                                                                   Relativistic velocity correction for wavelengths                                                                                                                                
+``vel_type``            str                                                                                                                     Type of reference frame correction (if any). Options are listed in the routine: WavelengthSolutionPar.valid_reference_frames() Current list: observed, heliocentric, barycentric
+``waveimg``             `numpy.ndarray`_                                                                                     `numpy.floating`_  2D wavelength image in vacuum (float64)                                                                                                                                         
+``wavesol``             `astropy.table.table.Table`_                                                                                            Table with WaveCalib diagnostic info                                                                                                                                            
+======================  ===================================================================================================  =================  ================================================================================================================================================================================