Merge branch 'develop' into coadd1d_badspec1d

pypeit · Aug 3, 2023 · 23da51c · 23da51c
2 parents 0d7519d + 6fd1ba0
commit 23da51c
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diff --git a/doc/api/pypeit.scripts.ql_multislit.rst b/doc/api/pypeit.scripts.ql_multislit.rst
diff --git a/doc/api/pypeit.scripts.rst b/doc/api/pypeit.scripts.rst
@@ -35,7 +35,6 @@ Submodules
    pypeit.scripts.parse_slits
    pypeit.scripts.qa_html
    pypeit.scripts.ql
-   pypeit.scripts.ql_multislit
    pypeit.scripts.run_pypeit
    pypeit.scripts.scriptbase
    pypeit.scripts.sensfunc

diff --git a/doc/calibrations/image_proc.rst b/doc/calibrations/image_proc.rst
@@ -198,7 +198,7 @@ in our documentation as ``(nspec,nspat)``.  The operations required to
 flip/transpose the image arrays to match the PypeIt convention are dictated by
 instrument-specific :class:`~pypeit.images.detector_container.DetectorContainer`
 parameters and performed by
-:func:`~pypeit.spectrograph.spectrographs.Spectrograph.orient_image`.  Image
+:func:`~pypeit.spectrographs.spectrograph.Spectrograph.orient_image`.  Image
 orientation will be performed if the ``orient`` parameter is true.
 
 .. warning::

diff --git a/doc/calibrations/tilt.rst b/doc/calibrations/tilt.rst
@@ -58,7 +58,7 @@ Current TiltImage Data Model
 ============================
 
 Internally, the image is held in
-:class:`pypeit.tiltimage.TiltImage`
+:class:`pypeit.images.buildimage.tiltimage.TiltImage`
 which subclasses from :class:`pypeit.images.pypeitimage.PypeItImage` and
 :class:`pypeit.datamodel.DataContainer`.
 

diff --git a/doc/conf.py b/doc/conf.py
@@ -120,9 +120,16 @@
 
 # When nit-picking, ignore these warnings:
 nitpick_ignore = [ ('py:class', 'optional'),
+                   ('py:class', 'iterable'),
+                   ('py:class', 'ndarray'),
+                   ('py:class', 'dict-like'),
                    ('py:class', 'array-like'),
+                   ('py:class', 'table-like'),
+                   ('py:class', 'float-like'),
                    ('py:class', 'scalar-like'),
-                   ('py:class', 'default') ]
+                   ('py:class', 'default'),
+                   ('py:class', 'callable'),
+                    ]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.

diff --git a/doc/fluxing.rst b/doc/fluxing.rst
@@ -589,6 +589,5 @@ FluxSpec Class
 ==============
 
 The guts of the flux algorithms are guided by the
-:class:`~pypeit.fluxcalibrate.FluxCalibrate`
-class.
+:func:`~pypeit.fluxcalibrate.apply_flux_calib` class.
 
diff --git a/doc/help/pypeit_coadd_1dspec.rst b/doc/help/pypeit_coadd_1dspec.rst
@@ -10,7 +10,8 @@
     positional arguments:
       coadd1d_file          File to guide coadding process.
                              
-                            ------------------------  MultiSlit
+                            ------------------------
+                                   MultiSlit
                             ------------------------
                              
                             For coadding Multislit spectra the file must have the
@@ -50,7 +51,8 @@
                             inspect the spec1d_*.txt files or run pypeit_show_1dspec
                             spec1dfile --list
                              
-                            ------------------------  Echelle
+                            ------------------------
+                                     Echelle
                             ------------------------
                              
                             For coadding Echelle spectra the file must have the
@@ -93,7 +95,7 @@
                             file for the echelle setup in question
                              
                             setup_id: string identifier for the echelle setup in
-                            question, i.e. 'VIS', 'NIR', or '
+                            question, i.e. 'VIS', 'NIR', or 'UVB'
                              
                             If the coaddfile is not given the output file will be
                             placed in the same directory as the first spec1d file.

diff --git a/doc/help/pypeit_ql_multislit.rst b/doc/help/pypeit_ql_multislit.rst
diff --git a/doc/help/run_pypeit.rst b/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 v1.13.1.dev504+ge3211bd33.d20230721[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.13.1.dev537+g0261baa1b.d20230728[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

diff --git a/doc/include/bitmaskarray_usage.rst b/doc/include/bitmaskarray_usage.rst
@@ -38,7 +38,7 @@ You can access the bit flag names using:
 Bit access
 ++++++++++
 
-You can flag bits using :func:`~pypeit.bitmaskarray.BitMaskArray.turn_on`.  For
+You can flag bits using :func:`~pypeit.images.bitmaskarray.BitMaskArray.turn_on`.  For
 example, the following code flags the center column of the image as being
 part of the detector bad-pixel mask:
 

diff --git a/doc/include/class_datamodel_wavetilts.rst b/doc/include/class_datamodel_wavetilts.rst
@@ -1,19 +1,19 @@
 
 **Version**: 1.2.0
 
-====================  ============================  =================  ==============================================================================================================================
-Attribute             Type                          Array Type         Description                                                                                                                   
-====================  ============================  =================  ==============================================================================================================================
-``PYP_SPEC``          str                                              PypeIt spectrograph name                                                                                                      
-``bpmtilts``          `numpy.ndarray`_              `numpy.integer`_   Bad pixel mask for tilt solutions. Keys are taken from SlitTraceSetBitmask                                                    
-``coeffs``            `numpy.ndarray`_              `numpy.floating`_  2D coefficents for the fit on the initial slits.  One set per slit/order (3D array).                                          
-``func2d``            str                                              Function used for the 2D fit                                                                                                  
-``nslit``             int                                              Total number of slits.  This can include masked slits                                                                         
-``slits_filename``    str                                              Path to SlitTraceSet file. This helps to find the Slits calibration file when running pypeit_chk_tilts()                      
-``spat_flexure``      float                                            Flexure shift from the input TiltImage                                                                                        
-``spat_id``           `numpy.ndarray`_              `numpy.integer`_   Slit spat_id                                                                                                                  
-``spat_order``        `numpy.ndarray`_              `numpy.integer`_   Order for spatial fit (nslit)                                                                                                 
-``spec_order``        `numpy.ndarray`_              `numpy.integer`_   Order for spectral fit (nslit)                                                                                                
-``tilt_traces``       `astropy.table.table.Table`_                     Table with the positions of the traced and fitted tilts for all the slits. see :func:`make_tbl_tilt_traces` for more details. 
-``tiltimg_filename``  str                                              Path to Tiltimg file. This helps to find Tiltimg file when running pypeit_chk_tilts()                                         
-====================  ============================  =================  ==============================================================================================================================
+====================  ============================  =================  ===============================================================================================================================================================
+Attribute             Type                          Array Type         Description                                                                                                                                                    
+====================  ============================  =================  ===============================================================================================================================================================
+``PYP_SPEC``          str                                              PypeIt spectrograph name                                                                                                                                       
+``bpmtilts``          `numpy.ndarray`_              `numpy.integer`_   Bad pixel mask for tilt solutions. Keys are taken from SlitTraceSetBitmask                                                                                     
+``coeffs``            `numpy.ndarray`_              `numpy.floating`_  2D coefficents for the fit on the initial slits.  One set per slit/order (3D array).                                                                           
+``func2d``            str                                              Function used for the 2D fit                                                                                                                                   
+``nslit``             int                                              Total number of slits.  This can include masked slits                                                                                                          
+``slits_filename``    str                                              Path to SlitTraceSet file. This helps to find the Slits calibration file when running pypeit_chk_tilts()                                                       
+``spat_flexure``      float                                            Flexure shift from the input TiltImage                                                                                                                         
+``spat_id``           `numpy.ndarray`_              `numpy.integer`_   Slit spat_id                                                                                                                                                   
+``spat_order``        `numpy.ndarray`_              `numpy.integer`_   Order for spatial fit (nslit)                                                                                                                                  
+``spec_order``        `numpy.ndarray`_              `numpy.integer`_   Order for spectral fit (nslit)                                                                                                                                 
+``tilt_traces``       `astropy.table.table.Table`_                     Table with the positions of the traced and fitted tilts for all the slits. see :func:`~pypeit.wavetilts.BuildWaveTilts.make_tbl_tilt_traces` for more details. 
+``tiltimg_filename``  str                                              Path to Tiltimg file. This helps to find Tiltimg file when running pypeit_chk_tilts()                                                                          
+====================  ============================  =================  ===============================================================================================================================================================