Merge branch 'develop' into s3_url_hotfix

.github/workflows/ci_cron.yml

@@ -15,15 +15,15 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: [3.8, 3.9]
+        python: ['3.9', '3.10']
         toxenv: [test-alldeps, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev, conda]
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: develop
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - name: Install base dependencies

.github/workflows/ci_tests.yml

@@ -6,9 +6,6 @@ on:
     - release
     - develop
   pull_request:
-  schedule:
-    # run every Monday at 6am UTC
-    - cron: '0 6 * * 1'
 
 env:
   SETUP_XVFB: True  # avoid issues if something tries to open a GUI window
@@ -20,13 +17,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: [3.8, 3.9]
+        python: ['3.9', '3.10']
         toxenv: [test, test-alldeps-cov, test-linetoolsdev, test-gingadev, test-astropydev, conda]
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - name: Install base dependencies
@@ -37,7 +34,7 @@ jobs:
         tox -e ${{ matrix.toxenv }}
     - name: Upload coverage to codecov
       if: "contains(matrix.toxenv, '-cov')"
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV }}
         file: ./coverage.xml
@@ -51,13 +48,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macos-latest]
-        python: [3.8, 3.9]
+        python: ['3.9', '3.10']
         toxenv: [test-alldeps]
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - name: Install base dependencies
@@ -87,9 +84,10 @@ jobs:
     steps:
     - name: Install base CentOS dependencies
       run: |
-        yum update -y && yum install -y wget git gcc
+        yum install -y https://packages.endpointdev.com/rhel/7/os/x86_64/endpoint-repo.x86_64.rpm
+        yum update -y && yum install -y wget git gcc libgomp
     - name: Check out repository
-      uses: actions/checkout@v1
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Install and configure miniconda
@@ -101,19 +99,19 @@ jobs:
         /conda/bin/conda init
     - name: Install base dependencies
       run: |
-        source ~/.bashrc && python -m pip install --upgrade pip tox && python --version
+        source ~/.bashrc && python -m pip install --upgrade pip tox setuptools_scm && python --version
     - name: Test with tox
       run: |
         source ~/.bashrc && tox -e ${{ matrix.toxenv }}
 
   codestyle:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Python codestyle check
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip

CHANGES.rst

@@ -6,6 +6,11 @@
   sphinx_rtd_theme
 - (Hotfix) Fixed bug that caused crash of sensfunc routines using
   telluric grids in offline processing
+- (Hotfix) Fixed error when showing flats in Ginga when the fine correction is not performed
+- Implemented the upgraded GTC/OSIRIS+
+- (Hotfix) keymap error when displaying GUIs
+- Added support for more NOT/ALFOSC grisms as well as NOT recommended standards
+- Implemented the SOAR/Goodman (blue) M1 only
 
 1.12.0 (31 Jan 2023)
 --------------------
@@ -28,6 +33,9 @@
 - Parse Keck/NIRES dither patterns, similar to MOSFIRE
 - Introduce BitMaskArray class to ease use of bitmasks
 - Fixed memory hogging by matplotlib when using version >= 3.6.1
+- New docs on OneSpec 
+- Modify install notes to allow 3.10
+- Allow for bad orders during extraction  (without crashing)
 
 1.11.0 (21 Oct 2022)
 --------------------

MANIFEST.in

@@ -6,6 +6,7 @@ include setup.cfg
 
 recursive-include pypeit *.pyx *.c *.pxd *.h
 recursive-include pypeit/data *
+recursive-include pypeit/tests *
 recursive-include docs *
 recursive-include licenses *
 recursive-include cextern *

doc/coadd1d.rst

@@ -284,16 +284,19 @@ be provided directly using the ``coadd1dfile`` parameter in the
 is ``coadd1d_<target>_<instrument name>_<YYYYMMDD>.fits`` or
 ``coadd1d_<target>_<instrument name>_<YYYYMMDD>-<YYYYMMDD>.fits``, if the coadd
 included more than one day's worth of data. The default location of the file
-will be along side the first spec1d file.  Currently ``instrument_name`` is
+will be along side the first spec1d file.  
+Currently ``instrument_name`` is
 taken from the ``camera`` attribute of the relevant
 :class:`~pypeit.spectrographs.spectrograph.Spectrograph` class.
 
-The format of the 1D coadd file follows follows the general
-class :class:`~pypeit.onespec.OneSpec`, such that its file extensions are:
+The format of the 1D coadd file follows the general
+class :class:`~pypeit.onespec.OneSpec`, such 
+that its file extensions are:
 
 .. include:: include/datamodel_onespec.rst
 
-You view the spectrum using the ``lt_xspec`` script, which loads the data
+You view the spectrum using the ``lt_xspec`` script 
+(``pypeit_show_1dspec`` will not work), which loads the data
 and launches a GUI from the `linetools`_ package. e.g.:
 
 .. code-block:: console

doc/include/spectrographs_table.rst

@@ -10,7 +10,8 @@ gemini_gmos_north_ham_ns  :class:`~pypeit.spectrographs.gemini_gmos.GeminiGMOSNH
 gemini_gmos_south_ham     :class:`~pypeit.spectrographs.gemini_gmos.GeminiGMOSSHamSpectrograph`         GEMINI-S   GMOS-S        `Link <http://www.gemini.edu/instrumentation/gmos>`__                                                                            MultiSlit  True       False      Hamamatsu detector (R400, B600, R831); see :doc:`gemini_gmos`                          
 gemini_gnirs              :class:`~pypeit.spectrographs.gemini_gnirs.GeminiGNIRSSpectrograph`           GEMINI-N   GNIRS         `Link <https://www.gemini.edu/instrumentation/gnirs>`__                                                                          Echelle    True       False                                                                                             
 gtc_osiris                :class:`~pypeit.spectrographs.gtc_osiris.GTCOSIRISSpectrograph`               GTC        OSIRIS        `Link <http://www.gtc.iac.es/instruments/osiris/>`__                                                                             MultiSlit  True       False      See :doc:`gtc_osiris`                                                                  
-jwst_nircam               :class:`~pypeit.spectrographs.jwst_nircam.JWSTNIRCamSpectrograph`             JWST       NIRCAM        `Link <https://jwst-docs.stsci.edu/jwst-near-infrared-camera/nircam-observing-modes/nircam-wide-field-slitless-spectroscopy>`__  MultiSlit  False      False                                                                                             
+gtc_osiris_plus           :class:`~pypeit.spectrographs.gtc_osiris.GTCOSIRISPlusSpectrograph`           GTC        OSIRIS+       `Link <http://www.gtc.iac.es/instruments/osiris/>`__                                                                             MultiSlit  True       False      See :doc:`gtc_osiris`
+jwst_nircam               :class:`~pypeit.spectrographs.jwst_nircam.JWSTNIRCamSpectrograph`             JWST       NIRCAM        `Link <https://jwst-docs.stsci.edu/jwst-near-infrared-camera/nircam-observing-modes/nircam-wide-field-slitless-spectroscopy>`__  MultiSlit  False      False
 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_hires                :class:`~pypeit.spectrographs.keck_hires.KECKHIRESSpectrograph`               KECK       HIRES         `Link <https://www2.keck.hawaii.edu/inst/hires/>`__                                                                              Echelle    True       False                                                                                             
@@ -47,7 +48,8 @@ shane_kast_blue           :class:`~pypeit.spectrographs.shane_kast.ShaneKastBlue
 shane_kast_red            :class:`~pypeit.spectrographs.shane_kast.ShaneKastRedSpectrograph`            SHANE      KASTr         `Link <http://mthamilton.ucolick.org/techdocs/instruments/kast/>`__                                                              MultiSlit  True       True                                                                                              
 shane_kast_red_ret        :class:`~pypeit.spectrographs.shane_kast.ShaneKastRedRetSpectrograph`         SHANE      KASTr         `Link <http://mthamilton.ucolick.org/techdocs/instruments/kast/>`__                                                              MultiSlit  True       True       Red reticon                                                                            
 soar_goodman_red          :class:`~pypeit.spectrographs.soar_goodman.SOARGoodmanRedSpectrograph`        SOAR       red           `Link <https://noirlab.edu/science/programs/ctio/instruments/goodman-high-throughput-spectrograph>`__                            MultiSlit  True       False      Supported gratings: 400_SYZY at M1 and M2 tilts                                        
-tng_dolores               :class:`~pypeit.spectrographs.tng_dolores.TNGDoloresSpectrograph`             TNG        DOLORES       `Link <https://oapd.inaf.it/mos/>`__                                                                                             MultiSlit  False      False      DOLORES (LRS) spectrograph; LR-R                                                       
+soar_goodman_blue         :class:`~pypeit.spectrographs.soar_goodman.SOARGoodmanBlueSpectrograph`       SOAR       blue          `Link <https://noirlab.edu/science/programs/ctio/instruments/goodman-high-throughput-spectrograph>`__                            MultiSlit  True       False      Supported gratings: 400_SYZY at M1 tilts
+tng_dolores               :class:`~pypeit.spectrographs.tng_dolores.TNGDoloresSpectrograph`             TNG        DOLORES       `Link <https://oapd.inaf.it/mos/>`__                                                                                             MultiSlit  False      False      DOLORES (LRS) spectrograph; LR-R
 vlt_fors2                 :class:`~pypeit.spectrographs.vlt_fors.VLTFORS2Spectrograph`                  VLT        FORS2         `Link <https://www.eso.org/sci/facilities/paranal/instruments/fors.html>`__                                                      MultiSlit  True       False      300I, 300V gratings                                                                    
 vlt_sinfoni               :class:`~pypeit.spectrographs.vlt_sinfoni.VLTSINFONISpectrograph`             VLT        SINFONI       `Link <https://www.eso.org/sci/facilities/paranal/decommissioned/sinfoni.html>`__                                                MultiSlit  True       False      Gratings tested: K                                                                     
 vlt_xshooter_nir          :class:`~pypeit.spectrographs.vlt_xshooter.VLTXShooterNIRSpectrograph`        VLT        XShooter_NIR  `Link <https://www.eso.org/sci/facilities/paranal/instruments/xshooter.html>`__                                                  Echelle    True       False      See :doc:`xshooter`                                                                    

doc/installing.rst

@@ -18,7 +18,7 @@ Installation
 
 .. warning::
 
-    Python 3.10 is not yet supported.
+    Python 3.11 is not yet supported.
 
 Below, we provide detailed instructions for installing PypeIt.  For
 troubleshooting, please consult the PypeIt :ref:`community` and/or `submit

doc/out_onespec.rst

@@ -0,0 +1,52 @@
+
+.. include:: include/links.rst
+
+.. _onespec:
+
+=======
+OneSpec 
+=======
+
+Overview
+========
+
+Generally, the ultimate PypeIt spectrum output is a single
+spectrum per source, fully calibrated and (as desired)
+with a :doc:`telluric` performed.
+
+The standard way to generate this file is 
+with the :ref:`_pypeit_coadd_1dspec` script.
+
+The naming of this file is user-generated,
+i.e. it can be anything you wish.
+
+The header of the primary extension includes the
+`core_meta` of PypeIt, e.g. RA, DEC, MJD, and 
+configuration parameters of the instrument.
+
+Inspection
+==========
+
+You view the spectrum using the ``lt_xspec`` script 
+(``pypeit_show_1dspec`` will not work), which loads the data
+and launches a GUI from the `linetools`_ package. e.g.:
+
+.. code-block:: console
+
+    lt_xspec J1217p3905_coadd.fits
+
+
+Current Data Model
+==================
+
+Internally, the spectrum for a single object is held by the
+:class:`~pypeit.onespec.OneSpec` class.
+
+Here is its datamodel, which
+is written as an `astropy.io.fits.BinTableHDU`_ in the 
+first HDU of the file.
+
+.. include:: include/datamodel_onespec.rst
+
+All wavelengths are in vacuum and flux units
+depend on whether :doc:`Fluxing` was performed.

doc/spectrographs/not_alfosc.rst

@@ -15,7 +15,14 @@ Common Items
 Grisms
 ++++++
 
-Currently only grisms 4, 7, 8, 17, 18 and 19 have full template solutions.
+Currently only grisms 3, 4, 5, 7, 8, 10, 11 17, 18, 19 and 20 have full template solutions.
+
+Grisms 10 and 11 are very low-resolution and only occupy part of the detector. Depending on the window used, it may be useful to set the find_min_max parameter to some suitable range, e.g.,
+[reduce]
+  [[findobj]]
+    find_min_max = [0,680]
+Furthermore, grisms 10 and 11 are so low resolution that the rms of the wavelength solution is often quite poor (roughly 0.2 pixels).
+
 
 Vertical slits
 ++++++++++++++

pypeit/core/gui/identify.py

@@ -139,19 +139,11 @@ def __init__(self, canvas, axes, spec, specres, detns, line_lists, par, lflag_co
         self.anntexts = []
 
         # Unset some of the matplotlib keymaps
-        matplotlib.pyplot.rcParams['keymap.fullscreen'] = ''        # toggling fullscreen (Default: f, ctrl+f)
-        matplotlib.pyplot.rcParams['keymap.home'] = ''              # home or reset mnemonic (Default: h, r, home)
-        matplotlib.pyplot.rcParams['keymap.back'] = ''              # forward / backward keys to enable (Default: left, c, backspace)
-        matplotlib.pyplot.rcParams['keymap.forward'] = ''           # left handed quick navigation (Default: right, v)
-        #matplotlib.pyplot.rcParams['keymap.pan'] = ''              # pan mnemonic (Default: p)
-        matplotlib.pyplot.rcParams['keymap.zoom'] = ''              # zoom mnemonic (Default: o)
-        matplotlib.pyplot.rcParams['keymap.save'] = ''              # saving current figure (Default: s)
-        matplotlib.pyplot.rcParams['keymap.quit'] = ''              # close the current figure (Default: ctrl+w, cmd+w)
-        matplotlib.pyplot.rcParams['keymap.grid'] = ''              # switching on/off a grid in current axes (Default: g)
-        matplotlib.pyplot.rcParams['keymap.grid_minor'] = ''        # switching on/off a (minor) grid in current axes (Default: G)
-        matplotlib.pyplot.rcParams['keymap.yscale'] = ''            # toggle scaling of y-axes ('log'/'linear') (Default: l)
-        matplotlib.pyplot.rcParams['keymap.xscale'] = ''            # toggle scaling of x-axes ('log'/'linear') (Default: L, k)
-        #matplotlib.pyplot.rcParams['keymap.all_axes'] = ''          # enable all axes (Default: a)
+        for key in plt.rcParams.keys():
+            if 'keymap' in key:
+                plt.rcParams[key] = []
+        # Enable some useful ones, though
+        matplotlib.pyplot.rcParams['keymap.pan'] = ['p']
 
         # Initialise the main canvas tools
         canvas.mpl_connect('draw_event', self.draw_callback)

pypeit/core/gui/object_find.py

@@ -216,18 +216,12 @@ def __init__(self, canvas, image, frame, det, sobjs, left, right, obj_trace, tra
             self._object_traces.from_specobj(sobjs, det)
 
         # Unset some of the matplotlib keymaps
-        matplotlib.pyplot.rcParams['keymap.fullscreen'] = ''        # toggling fullscreen (Default: f, ctrl+f)
-        #matplotlib.pyplot.rcParams['keymap.home'] = ''              # home or reset mnemonic (Default: h, r, home)
-        matplotlib.pyplot.rcParams['keymap.back'] = ''              # forward / backward keys to enable (Default: left, c, backspace)
-        matplotlib.pyplot.rcParams['keymap.forward'] = ''           # left handed quick navigation (Default: right, v)
-        #matplotlib.pyplot.rcParams['keymap.pan'] = ''              # pan mnemonic (Default: p)
-        matplotlib.pyplot.rcParams['keymap.zoom'] = ''              # zoom mnemonic (Default: o)
-        matplotlib.pyplot.rcParams['keymap.save'] = ''              # saving current figure (Default: s)
-        matplotlib.pyplot.rcParams['keymap.quit'] = ''              # close the current figure (Default: ctrl+w, cmd+w)
-        matplotlib.pyplot.rcParams['keymap.grid'] = ''              # switching on/off a grid in current axes (Default: g)
-        matplotlib.pyplot.rcParams['keymap.yscale'] = ''            # toggle scaling of y-axes ('log'/'linear') (Default: l)
-        matplotlib.pyplot.rcParams['keymap.xscale'] = ''            # toggle scaling of x-axes ('log'/'linear') (Default: L, k)
-        matplotlib.pyplot.rcParams['keymap.all_axes'] = ''          # enable all axes (Default: a)
+        for key in plt.rcParams.keys():
+            if 'keymap' in key:
+                plt.rcParams[key] = []
+        # Enable some useful ones, though
+        matplotlib.pyplot.rcParams['keymap.home'] = ['h', 'r', 'home']
+        matplotlib.pyplot.rcParams['keymap.pan'] = ['p']
 
         # Initialise the main canvas tools
         canvas.mpl_connect('draw_event', self.draw_callback)