doc fixes + package updates

pypeit · Aug 9, 2023 · 35f1222 · 35f1222
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diff --git a/README.rst b/README.rst
@@ -171,4 +171,5 @@ development of PypeIt.
 * Timothy Pickering
 * Timothy Ellsworth-Bowers
 * Gregory Simonian
-* Heather Martin
+* Heather Martin
+
diff --git a/doc/conf.py b/doc/conf.py
@@ -349,5 +349,5 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
 
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.dev537+g0261baa1b.d20230728[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.13.1.dev562+g146ed41eb.d20230809[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

diff --git a/doc/include/class_datamodel_datacube.rst b/doc/include/class_datamodel_datacube.rst
@@ -1,15 +1,15 @@
 
 **Version**: 1.1.0
 
-==============  ================  =================  ================================================================================
-Attribute       Type              Array Type         Description                                                                     
-==============  ================  =================  ================================================================================
-``PYP_SPEC``    str                                  PypeIt: Spectrograph name                                                       
-``blaze_spec``  `numpy.ndarray`_  `numpy.floating`_  The spectral blaze function                                                     
-``blaze_wave``  `numpy.ndarray`_  `numpy.floating`_  Wavelength array of the spectral blaze function                                 
-``bpm``         `numpy.ndarray`_  `numpy.uint8`_     Bad pixel mask of the datacube (0=good, 1=bad)                                  
-``flux``        `numpy.ndarray`_  `numpy.floating`_  Flux datacube in units of counts/s/Ang/arcsec^2or 10^-17 erg/s/cm^2/Ang/arcsec^2
-``fluxed``      bool                                 Boolean indicating if the datacube is fluxed.                                   
-``sensfunc``    `numpy.ndarray`_  `numpy.floating`_  Sensitivity function 10^-17 erg/(counts/cm^2)                                   
-``sig``         `numpy.ndarray`_  `numpy.floating`_  Error datacube (matches units of flux)                                          
-==============  ================  =================  ================================================================================
+==============  ================  =================  =================================================================================
+Attribute       Type              Array Type         Description                                                                      
+==============  ================  =================  =================================================================================
+``PYP_SPEC``    str                                  PypeIt: Spectrograph name                                                        
+``blaze_spec``  `numpy.ndarray`_  `numpy.floating`_  The spectral blaze function                                                      
+``blaze_wave``  `numpy.ndarray`_  `numpy.floating`_  Wavelength array of the spectral blaze function                                  
+``bpm``         `numpy.ndarray`_  `numpy.uint8`_     Bad pixel mask of the datacube (0=good, 1=bad)                                   
+``flux``        `numpy.ndarray`_  `numpy.floating`_  Flux datacube in units of counts/s/Ang/arcsec^2 or 10^-17 erg/s/cm^2/Ang/arcsec^2
+``fluxed``      bool                                 Boolean indicating if the datacube is fluxed.                                    
+``sensfunc``    `numpy.ndarray`_  `numpy.floating`_  Sensitivity function 10^-17 erg/(counts/cm^2)                                    
+``sig``         `numpy.ndarray`_  `numpy.floating`_  Error datacube (matches units of flux)                                           
+==============  ================  =================  =================================================================================
diff --git a/doc/include/dependencies_table.rst b/doc/include/dependencies_table.rst
@@ -1,5 +1,5 @@
 =======================  =================================================================================================================================================================================================================================================================================================
 Python Version           ``>=3.9,<3.12``                                                                                                                                                                                                                                                                                  
 Required for users       ``IPython>=7.10.0``, ``PyYAML>=5.1``, ``astropy>=4.3``, ``bottleneck``, ``configobj>=5.0.6``, ``extension-helpers>=0.1``, ``ginga>=3.2``, ``linetools``, ``matplotlib>=3.7``, ``numpy>=1.22``, ``packaging>=0.19``, ``pygithub``, ``pyqt6``, ``qtpy>=1.9``, ``scikit-learn>=1.0``, ``scipy>=1.7``
-Required for developers  ``coverage``, ``docutils<0.18``, ``pytest-astropy``, ``pytest-cov``, ``pytest>=6.0.0``, ``sphinx-automodapi``, ``sphinx<6,>=1.6``, ``sphinx_rtd_theme==1.1.1``, ``tox``                                                                                                                          
+Required for developers  ``coverage``, ``docutils<0.19``, ``pytest-astropy``, ``pytest-cov``, ``pytest>=6.0.0``, ``scikit-image``, ``specutils``, ``sphinx-automodapi``, ``sphinx<7,>=1.6``, ``sphinx_rtd_theme==1.2.2``, ``tox``                                                                                         
 =======================  =================================================================================================================================================================================================================================================================================================
diff --git a/doc/include/links.rst b/doc/include/links.rst
@@ -154,3 +154,5 @@
 .. _L.A.Cosmic: http://www.astro.yale.edu/dokkum/lacosmic/
 .. _van Dokkum (2001, PASP, 113, 1420): https://ui.adsabs.harvard.edu/abs/2001PASP..113.1420V/abstract
 .. _LowRedux: http://www.ucolick.org/~xavier/LowRedux/
+
+
diff --git a/doc/spectrographs/gemini_gmos.rst b/doc/spectrographs/gemini_gmos.rst
@@ -163,4 +163,5 @@ The modifications to the :ref:`pypeit_file` will look like:
 The two files provided must be located either:
  (1) in the path(s) of the raw files provided in the :ref:`data_block`,
  (2) the current working data, and/or
- (3) be named with the full path.
+ (3) be named with the full path.
+
diff --git a/doc/spectrographs/mmt_bluechannel.rst b/doc/spectrographs/mmt_bluechannel.rst
@@ -43,4 +43,5 @@ A few notes on setting up observations to work optimally with ``pypeit`` and wha
   this is not the case or otherwise define which observations are standard stars.
 
 * Images taken as part of spectrograph focus runs are automatically identified and configured as ``tilt`` images, but not ``arc``. This
-  is because their line widths can vary by quite a bit and thus shouldn't be coadded to/averaged with in-focus ``arc`` images.
+  is because their line widths can vary by quite a bit and thus shouldn't be coadded to/averaged with in-focus ``arc`` images.
+
diff --git a/doc/spectrographs/soar_goodman.rst b/doc/spectrographs/soar_goodman.rst
@@ -15,3 +15,4 @@ archive:
 
 PypeIt will only work with the .fz format, so please
 ensure that you are only using data in this format.
+
diff --git a/doc/spectrographs/spectrographs.rst b/doc/spectrographs/spectrographs.rst
@@ -53,3 +53,5 @@ instrument-specific details for running PypeIt.
    shane_kast
    soar_goodman
    xshooter
+
+
diff --git a/pypeit/bitmask.py b/pypeit/bitmask.py
@@ -8,8 +8,6 @@
 
 .. include:: ../include/bitmask_usage.rst
 
-----
-
 .. include common links, assuming primary doc root is up one directory
 .. include:: ../include/links.rst