Merge branch 'develop' into spatflex_options

# Conflicts: # doc/releases/1.16.1dev.rst # pypeit/core/flexure.py
pypeit · Sep 11, 2024 · f399958 · f399958
2 parents 0fe9901 + 3d26a0b
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diff --git a/.github/workflows/ci_cron.yml b/.github/workflows/ci_cron.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: ['3.10', '3.11', '3.12']
+        python: ['3.11', '3.12']
         toxenv: [test-alldeps, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev]
     steps:
     - name: Check out repository

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -17,8 +17,8 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: ['3.10', '3.11', '3.12']
-        toxenv: [test, test-alldeps-cov, test-linetoolsdev, test-gingadev, test-astropydev]
+        python: ['3.11', '3.12']
+        toxenv: [test, test-alldeps-cov, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev]
     steps:
     - name: Check out repository
       uses: actions/checkout@v3
@@ -48,7 +48,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macos-latest]
-        python: ['3.10', '3.11', '3.12']
+        python: ['3.11', '3.12']
         toxenv: [test-alldeps]
     steps:
     - name: Check out repository
@@ -71,7 +71,7 @@ jobs:
     - name: Conda environment check
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip tox
@@ -86,7 +86,7 @@ jobs:
     - name: Python codestyle check
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/doc/api/pypeit.scripts.chk_flexure.rst b/doc/api/pypeit.scripts.chk_flexure.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.chk\_flexure module
+==================================
+
+.. automodule:: pypeit.scripts.chk_flexure
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.scripts.rst b/doc/api/pypeit.scripts.rst
@@ -12,6 +12,7 @@ Submodules
    pypeit.scripts.chk_alignments
    pypeit.scripts.chk_edges
    pypeit.scripts.chk_flats
+   pypeit.scripts.chk_flexure
    pypeit.scripts.chk_for_calibs
    pypeit.scripts.chk_noise_1dspec
    pypeit.scripts.chk_noise_2dspec
@@ -51,6 +52,7 @@ Submodules
    pypeit.scripts.show_1dspec
    pypeit.scripts.show_2dspec
    pypeit.scripts.show_arxiv
+   pypeit.scripts.show_pixflat
    pypeit.scripts.show_wvcalib
    pypeit.scripts.skysub_regions
    pypeit.scripts.tellfit

diff --git a/doc/api/pypeit.scripts.show_pixflat.rst b/doc/api/pypeit.scripts.show_pixflat.rst
@@ -0,0 +1,8 @@
+pypeit.scripts.show\_pixflat module
+===================================
+
+.. automodule:: pypeit.scripts.show_pixflat
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/dev/hiresconfig.rst b/doc/dev/hiresconfig.rst
@@ -28,7 +28,7 @@ by the :ref:`pypeit_setup` script, which sorts the frames and writes a
 
 
 HIRES configuration identification
----------------------------------
+----------------------------------
 
 The HIRES instrument configurations are determined by the function
 :func:`pypeit.metadata.PypeItMetaData.unique_configurations`,
@@ -62,7 +62,7 @@ to the relevant unique configuration ("setup"), by assigning a setup identifier
 values of the specific unique configuration.
 
 HIRES calibration groups
------------------------
+------------------------
 
 PypeIt uses the concept of a "calibration group" to define a complete set of
 calibration frames (e.g., arcs, flats) and the science frames to which these calibration

diff --git a/doc/dev/hiresframes.rst b/doc/dev/hiresframes.rst
@@ -24,7 +24,7 @@ The general procedure used to assign frames a given type is described
 here: :ref:`frame_types`.
 
 HIRES frame typing
------------------
+------------------
 
 The primary typing of HIRES frames is performed by
 :func:`pypeit.spectrographs.keck_hires.KECKHIRESSpectrograph.check_frame_type`.

diff --git a/doc/help/pypeit_cache_github_data.rst b/doc/help/pypeit_cache_github_data.rst
@@ -36,14 +36,15 @@
       --exclude EXCLUDE [EXCLUDE ...]
                             A subset of the directories to *exclude* from the list
                             of files to download. Options are: tests, reid_arxiv,
-                            nist, standards, skisim, sensfunc. This option is
-                            mutually exclusive with --include. (default: ['tests'])
+                            nist, standards, skisim, sensfunc, pixelflat. This
+                            option is mutually exclusive with --include. (default:
+                            ['tests'])
       --include INCLUDE [INCLUDE ...]
                             The directories to *include* in the list of files to
                             download. Use "--include all" to include all
                             directories. Options are: all, tests, reid_arxiv, nist,
-                            standards, skisim, sensfunc. This option is mutually
-                            exclusive with --exclude. (default: None)
+                            standards, skisim, sensfunc, pixelflat. This option is
+                            mutually exclusive with --exclude. (default: None)
       --spec_dependent_only
                             Only include files that are specific to the provided
                             list of spectrographs. By default, the script also

diff --git a/doc/help/pypeit_chk_flexure.rst b/doc/help/pypeit_chk_flexure.rst
@@ -0,0 +1,18 @@
+.. code-block:: console
+
+    $ pypeit_chk_flexure -h
+    usage: pypeit_chk_flexure [-h] (--spec | --spat) [--try_old]
+                              input_file [input_file ...]
+    
+    Print QA on flexure to the screen
+    
+    positional arguments:
+      input_file  One or more PypeIt spec2d or spec1d file
+    
+    options:
+      -h, --help  show this help message and exit
+      --spec      Check the spectral flexure (default: False)
+      --spat      Check the spatial flexure (default: False)
+      --try_old   Attempt to load old datamodel versions. A crash may ensue..
+                  (default: False)
+    
diff --git a/doc/help/pypeit_show_pixflat.rst b/doc/help/pypeit_show_pixflat.rst
@@ -0,0 +1,17 @@
+.. code-block:: console
+
+    $ pypeit_show_pixflat -h
+    usage: pypeit_show_pixflat [-h] [--det DET [DET ...]] file
+    
+    Show an archived Pixel Flat image in a ginga window.
+    
+    positional arguments:
+      file                 Pixel Flat filename, e.g.
+                           pixelflat_keck_lris_blue.fits.gz
+    
+    options:
+      -h, --help           show this help message and exit
+      --det DET [DET ...]  Detector(s) to show. If more than one, list the detectors
+                           as, e.g. --det 1 2 to show detectors 1 and 2. If not
+                           provided, all detectors will be shown. (default: 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 v1.16.1.dev109+g885cb1823[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev468+g832ee84e4[0m
     ##  
     ##  Available spectrographs include:
     ##   aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,

diff --git a/doc/include/class_datamodel_mosaic.rst b/doc/include/class_datamodel_mosaic.rst
@@ -1,13 +1,13 @@
 
-**Version**: 1.0.0
+**Version**: 1.0.1
 
 ==============  ================  ============================================================  ===================================================================================
 Attribute       Type              Array Type                                                    Description                                                                        
 ==============  ================  ============================================================  ===================================================================================
 ``binning``     str                                                                             On-chip binning                                                                    
 ``detectors``   `numpy.ndarray`_  :class:`~pypeit.images.detector_container.DetectorContainer`  List of objects with detector parameters.                                          
 ``id``          int                                                                             Mosaic ID number                                                                   
-``msc_order``   int                                                                             Order of the interpolation used to construct the mosaic.                           
+``msc_ord``     int                                                                             Order of the interpolation used to construct the mosaic.                           
 ``platescale``  float                                                                           Detector platescale in arcsec/pixel                                                
 ``rot``         `numpy.ndarray`_  float                                                         Raw, hard-coded rotations (counter-clockwise in degrees) for each unbinned detector
 ``shape``       tuple                                                                           Shape of each processed detector image                                             

diff --git a/doc/include/data_dir.rst b/doc/include/data_dir.rst
@@ -7,6 +7,7 @@ extinction     extinction            ...
 filters        filters               ...     
 linelist       arc_lines/lists       ...     
 nist           arc_lines/NIST        github  
+pixelflat      pixelflats            github  
 reid_arxiv     arc_lines/reid_arxiv  github  
 sensfunc       sensfuncs             github  
 skisim         skisim                github  

diff --git a/doc/include/dependencies_table.rst b/doc/include/dependencies_table.rst
@@ -1,5 +1,5 @@
-=======================  =======================================================================================================================================================================================================================================================================================================================================================================
-Python Version           ``>=3.10,<3.13``                                                                                                                                                                                                                                                                                                                                                       
-Required for users       ``IPython>=7.10.0``, ``PyERFA>=2.0.0``, ``PyYAML>=5.1``, ``astropy>=6.0``, ``bottleneck``, ``configobj>=5.0.6``, ``extension-helpers>=0.1``, ``fast-histogram>=0.11``, ``ginga>=5.1.0``, ``linetools>=0.3.1``, ``matplotlib>=3.7``, ``numpy>=1.23,<2.0.0``, ``packaging>=0.19``, ``pygithub``, ``pyqt6<=6.7.0``, ``qtpy>=2.0.1``, ``scikit-learn>=1.0``, ``scipy>=1.7``
-Required for developers  ``coverage``, ``docutils<0.21``, ``psutil``, ``pygit2``, ``pytest-astropy``, ``pytest-cov``, ``pytest-qt``, ``pytest>=6.0.0``, ``scikit-image``, ``specutils>=1.13``, ``sphinx-automodapi``, ``sphinx>=1.6,<8``, ``sphinx_rtd_theme==2.0.0``, ``tox``                                                                                                                  
-=======================  =======================================================================================================================================================================================================================================================================================================================================================================
+=======================  ========================================================================================================================================================================================================================================================================================================================================================
+Python Version           ``>=3.11,<3.13``                                                                                                                                                                                                                                                                                                                                        
+Required for users       ``IPython>=8.0.0``, ``PyERFA>=2.0.0``, ``PyYAML>=6.0``, ``astropy>=6.0``, ``bottleneck``, ``configobj>=5.0.6``, ``extension-helpers>=1.0``, ``fast-histogram>=0.11``, ``ginga>=5.1.0``, ``linetools>=0.3.2``, ``matplotlib>=3.7``, ``numpy>=1.24``, ``packaging>=22.0``, ``pygithub``, ``pyqt6``, ``qtpy>=2.2.0``, ``scikit-learn>=1.2``, ``scipy>=1.9``
+Required for developers  ``coverage``, ``docutils<0.21``, ``psutil``, ``pygit2``, ``pytest-astropy``, ``pytest-cov``, ``pytest-qt``, ``pytest>=7.0.0``, ``scikit-image>=0.23``, ``specutils>=1.13``, ``sphinx-automodapi``, ``sphinx>=1.6,<8``, ``sphinx_rtd_theme==2.0.0``, ``tox``                                                                                             
+=======================  ========================================================================================================================================================================================================================================================================================================================================================
diff --git a/doc/include/inst_detector_table.rst b/doc/include/inst_detector_table.rst
@@ -86,9 +86,9 @@ Instrument                    Det  specaxis  specflip  spatflip  namp      gain
 ``vlt_fors2``                 1    1         False     False     1         0.7                         2.9                     2.1       -1.0e+10  200000.0      0.8000     0.1260    
 ...                           2    1         False     False     1         0.7                         3.15                    1.4       -1.0e+10  200000.0      0.8000     0.1260    
 ``vlt_sinfoni``               1    0         True      False     1         2.42                        7.0                     540.0     -1.0e+10  1000000000.0  1.0000     0.0125    
-``vlt_xshooter_nir``          1    1         False     False     1         2.12                        8.0                     0.0       -1.0e+10  200000.0      0.8600     0.1970    
-``vlt_xshooter_uvb``          1    0         True      True      1         1.61                        2.6                     0.0       -1.0e+10  65000.0       0.8600     0.1610    
-``vlt_xshooter_vis``          1    0         False     False     1         0.595                       3.1                     0.0       -1.0e+10  65535.0       0.8600     0.1600    
+``vlt_xshooter_nir``          1    1         False     False     1         2.29                        8.0                     72.0      -1.0e+10  200000.0      0.8600     0.2450    
+``vlt_xshooter_uvb``          1    0         True      True      1         ``None``                    ``None``                0.0       -1.0e+10  65000.0       0.8600     0.1640    
+``vlt_xshooter_vis``          1    0         False     False     1         ``None``                    ``None``                0.0       -1.0e+10  65535.0       0.8600     0.1540    
 ``wht_isis_blue``             1    0         False     False     1         1.2                         5.0                     0.0       -1.0e+10  65535.0       0.7600     0.2000    
 ``wht_isis_red``              1    0         False     False     1         0.98                        4.0                     0.0       -1.0e+10  65535.0       0.7600     0.2200    
 ============================  ===  ========  ========  ========  ========  ==========================  ======================  ========  ========  ============  =========  ==========
diff --git a/doc/include/links.rst b/doc/include/links.rst
@@ -128,7 +128,7 @@
 .. _pip: https://pip.pypa.io/en/stable/
 .. _anaconda: https://www.anaconda.com/products/individual
 .. _conda: https://docs.conda.io/projects/conda/en/latest/index.html
-.. _virtualenv: https://virtualenv.pypa.io/en/latest/
+.. _venv: https://docs.python.org/3/library/venv.html
 .. _pdb: https://docs.python.org/3/library/pdb.html
 .. _IPython.embed: https://ipython.readthedocs.io/en/stable/api/generated/IPython.terminal.embed.html#function
 .. _pytest: https://docs.pytest.org/en/latest/

diff --git a/doc/include/spectrographs_table.rst b/doc/include/spectrographs_table.rst
@@ -18,7 +18,7 @@ jwst_nircam               :class:`~pypeit.spectrographs.jwst_nircam.JWSTNIRCamSp
 jwst_nirspec              :class:`~pypeit.spectrographs.jwst_nirspec.JWSTNIRSpecSpectrograph`           JWST       NIRSPEC       `Link <https://jwst-docs.stsci.edu/jwst-near-infrared-spectrograph>`__                                                           MultiSlit  True       False                                                                                                     
 keck_deimos               :class:`~pypeit.spectrographs.keck_deimos.KeckDEIMOSSpectrograph`             KECK       DEIMOS        `Link <https://www2.keck.hawaii.edu/inst/deimos/>`__                                                                             MultiSlit  True       True       Supported gratings: 600ZD, 830G, 900ZD, 1200B, 1200G; see :doc:`deimos`                        
 keck_esi                  :class:`~pypeit.spectrographs.keck_esi.KeckESISpectrograph`                   KECK       ESI                                                                                                                                            Echelle    True       False                                                                                                     
-keck_hires                :class:`~pypeit.spectrographs.keck_hires.KECKHIRESSpectrograph`               KECK       HIRES         `Link <https://www2.keck.hawaii.edu/inst/hires/>`__                                                                              Echelle    False      False                                                                                                     
+keck_hires                :class:`~pypeit.spectrographs.keck_hires.KECKHIRESSpectrograph`               KECK       HIRES         `Link <https://www2.keck.hawaii.edu/inst/hires/>`__                                                                              Echelle    False      False      Post detector upgrade (~ August 2004). See :doc:`keck_hires`                                   
 keck_kcrm                 :class:`~pypeit.spectrographs.keck_kcwi.KeckKCRMSpectrograph`                 KECK       KCRM          `Link <https://www2.keck.hawaii.edu/inst/kcwi/>`__                                                                               SlicerIFU  True       False      Supported setups: RL, RM1, RM2, RH3; see :doc:`keck_kcwi`                                      
 keck_kcwi                 :class:`~pypeit.spectrographs.keck_kcwi.KeckKCWISpectrograph`                 KECK       KCWI          `Link <https://www2.keck.hawaii.edu/inst/kcwi/>`__                                                                               SlicerIFU  True       False      Supported setups: BL, BM, BH2, BH3; see :doc:`keck_kcwi`
 keck_lris_blue            :class:`~pypeit.spectrographs.keck_lris.KeckLRISBSpectrograph`                KECK       LRISb         `Link <https://www2.keck.hawaii.edu/inst/lris/>`__                                                                               MultiSlit  True       False      Blue camera; Current FITS file format; used from May 2009, see :doc:`lris`