Merge branch 'develop' into coron_pupil_mask_alignment_defaults

.github/workflows/build.yml

@@ -0,0 +1,15 @@
+name: build
+
+on:
+  release:
+    types: [ released ]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
+    with:
+      upload_to_pypi: ${{ (github.event_name == 'release') && (github.event.action == 'released') }}
+    secrets:
+      pypi_token: ${{ secrets.PYPI_PASSWORD_STSCI_MAINTAINER }}

.github/workflows/ci_workflows.yml

@@ -44,12 +44,12 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python }}
 
@@ -58,7 +58,7 @@ jobs:
 
     - name: Get WebbPSF Data
       run: | # Get WebbPSF data files (just a subset of the full dataset!) and set up environment variable
-           wget https://stsci.box.com/shared/static/n1fealx9q0m6sdnass6wnyfikvxtc0zz.gz  -O /tmp/minimal-webbpsf-data.tar.gz
+           wget https://stsci.box.com/shared/static/0ojjfg3cieqdpd18vl1bjnpe63r82dx8.gz -O /tmp/minimal-webbpsf-data.tar.gz
            tar -xzvf /tmp/minimal-webbpsf-data.tar.gz
            echo "WEBBPSF_PATH=${{github.workspace}}/webbpsf-data" >> $GITHUB_ENV
 

README.rst

@@ -1,7 +1,7 @@
 WebbPSF: Simulated Point Spread Functions for the James Webb and Nancy Grace Roman Space Telescopes
 ===================================================================================================
 
-.. image:: docs/readme_fig.png
+.. image:: https://github.com/spacetelescope/webbpsf/blob/stable/docs/readme_fig.png?raw=true
 
 .. image:: https://img.shields.io/pypi/v/webbpsf.svg
    :target: https://pypi.python.org/pypi/webbpsf
@@ -21,7 +21,7 @@ WebbPSF: Simulated Point Spread Functions for the James Webb and Nancy Grace Rom
 .. image:: https://img.shields.io/badge/ascl-1504.007-blue.svg?colorB=262255
    :target: http://ascl.net/1504.007
 
-WebbPSF produces simulated PSFs for the James Webb Space Telescope, NASA's next
+WebbPSF produces simulated PSFs for the James Webb Space Telescope, NASA's
 flagship infrared space telescope. WebbPSF can simulate images for any of the
 four science instruments plus the fine guidance sensor, including both direct
 imaging and coronagraphic modes.
@@ -37,4 +37,4 @@ Documentation can be found online at https://webbpsf.readthedocs.io
 WebbPSF requires input data for its simulations, including optical path
 difference (OPD) maps, filter transmission curves, and coronagraph Lyot mask
 shapes. These data files are not included in this source distribution.
-Please see the documentation to download the required data files.
+Please see the documentation to download the required data files.

dev_utils/make-data-sdist.sh

@@ -9,7 +9,7 @@ if ! [[ $1 ]]; then
 fi
 
 if ! [[ $DATAROOT ]]; then
-  DATAROOT="/itar/jwst/tel/share/webbpsf/webbpsf-data-source/"
+  DATAROOT="/grp/jwst/ote/webbpsf-data-source/"
 fi
 echo "Using data from $DATAROOT"
 

dev_utils/master_data_release.sh

@@ -14,11 +14,23 @@ TMPDIR="/tmp/webbpsf-data"
 
 ./make-data-sdist.sh $VER
 
-./make-minimal-datafiles.py  ${PWD}/webbpsf-data-${VER}.tar.gz $VER
+echo
+echo "Copying latest data to /grp/jwst/ote for internal stsci use..."
+main_directory="/grp/jwst/ote"
+new_directory="$main_directory/webbpsf-data-$VER"
+symlink_directory="/grp/jwst/ote/webbpsf-data"
 
+cp "$PWD/webbpsf-data-$VER.tar.gz" "$main_directory"
+tar -xzf "$PWD/webbpsf-data-$VER.tar.gz" -C "$main_directory"
+mv "$main_directory/webbpsf-data" "$new_directory"
+ln -s "$new_directory" "$symlink_directory"
+
+./make-minimal-datafiles.py  ${PWD}/webbpsf-data-${VER}.tar.gz $VER
 
 echo
 echo "================================================="
+echo "Data extracted for internal use with updated symlink  $symlink_directory -> $new_directory"
+echo
 echo "OUTPUT FILES:"
 echo
 echo ${PWD}/webbpsf-data-${VER}.tar.gz

docs/conf.py

@@ -75,10 +75,12 @@
     "sphinx.ext.inheritance_diagram",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosummary",
+    "sphinxcontrib.jquery",
     "sphinx_automodapi.automodapi",
     "sphinx_issues",
     "nbsphinx",
     "numpydoc",
+    "astroquery",
 ]
 
 numpydoc_show_class_members = False

docs/index.rst

@@ -1,7 +1,7 @@
 Documentation for WebbPSF
 ===============================
 
-WebbPSF is a Python package that computes simulated point spread functions (PSFs) for NASA's James Webb Space Telescope (JWST) and Nancy Grace Roman Space Telescope (formerly WFIRST). WebbPSF transforms models of telescope and instrument optical state into PSFs, taking into account detector pixel scales, rotations, filter profiles, and point source spectra. It is *not* a full optical model of JWST, but rather a tool for transforming optical path difference (OPD) maps, created with some other tool, into the resulting PSFs as observed with JWST's or Roman's instruments.
+WebbPSF is a Python package that computes simulated point spread functions (PSFs) for NASA's James Webb Space Telescope (JWST) and Nancy Grace Roman Space Telescope. WebbPSF transforms models of telescope and instrument optical state into PSFs, taking into account detector pixel scales, rotations, filter profiles, and point source spectra. It is rather a tool for transforming optical path difference (OPD) maps, created with observatory systems engineering models, into the resulting PSFs as observed with JWST's or Roman's instruments.
 
 .. figure:: ./fig_instrument_comparison.png
    :scale: 45 %
@@ -19,7 +19,7 @@ WebbPSF is a Python package that computes simulated point spread functions (PSFs
 
 
 **Contributors:**
-WebbPSF has been developed by Marshall Perrin, Shannon Osborne, Robel Geda, Joseph Long, Justin Otor, Jarron Leisenring, Neil Zimmerman, Keira Brooks, and Anand Sivaramakrishnan, with contributions from Marcio Meléndez Hernandez, Alden Jurling, Lauren Chambers, Ewan Douglas, Charles Lajoie, Megan Sosey, and Kathryn St.Laurent. We also are grateful to the contributors of the astropy-helpers and stsci package templates.
+WebbPSF has been developed by Marshall Perrin, Marcio Meléndez, Shannon Osborne, Robel Geda, Brad Sappington, Charles-Philippe Lajoie, Joseph Long, Justin Otor, Jarron Leisenring, Neil Zimmerman, Keira Brooks, and Anand Sivaramakrishnan, with contributions from Alden Jurling, Lauren Chambers, Ewan Douglas, and `others <https://github.com/spacetelescope/webbpsf/graphs/contributors>`_. 
 
 Getting Started with WebbPSF
 ----------------------------
@@ -30,8 +30,10 @@ See :ref:`using_api`.
 
    This documentation is complemented by an `Jupyter Notebook format quickstart tutorial <http://nbviewer.jupyter.org/github/spacetelescope/webbpsf/blob/stable/notebooks/WebbPSF_tutorial.ipynb>`_. Downloading and running that notebook is a great way to get started using WebbPSF.
 
-.. note:: 
-   *Getting help:* For help using or installing webbpsf, you can contact the STScI JWST Help Desk at jwsthelp.stsci.edu. Note that WebbPSF is included in the Astroconda python distribution, as well as being installable via :ref:`standard Python packaging tools <installation>`.
+
+.. admonition:: Getting Help
+
+   For help using or installing webbpsf, you can contact the STScI JWST Help Desk at jwsthelp.stsci.edu, category WebbPSF/JWST Telescope.
 
 
 :ref:`What's new in the latest release? <whatsnew>`
@@ -47,8 +49,10 @@ Contents
    relnotes.rst
    usage.rst
    jwst.rst
-   jwst_optical_budgets.ipynb
    jwst_measured_opds.ipynb
+   jwst_detector_effects.ipynb
+   jwst_matching_psfs_to_data.ipynb
+   jwst_optical_budgets.ipynb
    jwst_wavefront_deltas.ipynb
    roman.rst
    psf_grids.rst

docs/installation.rst

@@ -69,8 +69,8 @@ Installing the Required Data Files
 
 Files containing such information as the JWST pupil shape, instrument throughputs, and aperture positions are distributed separately from WebbPSF. To run WebbPSF, you must download these files and tell WebbPSF where to find them using the ``WEBBPSF_PATH`` environment variable.
 
-1. Download the following file:  `webbpsf-data-1.1.1.tar.gz <https://stsci.box.com/shared/static/t90gqazqs82d8nh25249oq1obbjfstq8.gz>`_  [approx. 80 MB]
-2. Untar ``webbpsf-data-1.1.1.tar.gz`` into a directory of your choosing.
+1. Download the following file:  `webbpsf-data-LATEST.tar.gz <https://stsci.box.com/shared/static/qxpiaxsjwo15ml6m4pkhtk36c9jgj70k.gz>`_  [approx. 70 MB]
+2. Untar ``webbpsf-data-LATEST.tar.gz`` into a directory of your choosing.
 3. Set the environment variable ``WEBBPSF_PATH`` to point to that directory. e.g. ::
 
    export WEBBPSF_PATH=$HOME/data/webbpsf-data
@@ -87,7 +87,6 @@ You should now be able to successfully ``import webbpsf`` in a Python session.
 .. Note::
 
    **For STScI Users Only:** Users at STScI may access the required data files from the Central Storage network. Set the following environment variables in your ``bash`` shell. (You will probably want to add this to your ``.bashrc``.) ::
-
       export WEBBPSF_PATH="/grp/jwst/ote/webbpsf-data"
       export PYSYN_CDBS="/grp/hst/cdbs"
 

docs/more_examples.rst

@@ -75,7 +75,7 @@ Perhaps you want to calculate PSFs for all filters of a given instrument, using
                 niriss.filter=filtname
                 fov=18
                 outname = "PSF_NIRISS_%scen_wfe%d.fits" % (filtname, i)
-                psf = niriss.calc_psf(outname, nlambda=1, oversample=4, fov_arcsec=fov, rebin=True, display=True)
+                psf = niriss.calc_psf(outname, nlambda=1, oversample=4, fov_arcsec=fov, display=True)
 
 
 
@@ -97,7 +97,7 @@ Monochromatic PSFs with steps of 0.1 micron from 5-28.3 micron.
 
     for iw, wavelength in enumerate(waves):
         psffile = 'psf_MIRI_mono_%.1fum_opd1.fits' % (wavelength*1e6)
-        psf = m.calc_psf(fov_arcsec=30, oversample=4, rebin=True, monochromatic=wavelength, display=False,
+        psf = m.calc_psf(fov_arcsec=30, oversample=4, monochromatic=wavelength, display=False,
                    outfile=psffile)
         ax = plt.subplot(16,16,iw+1)
         webbpsf.display_psf(psffile, ext='DET_SAMP', colorbar=False, imagecrop=8)
@@ -135,7 +135,7 @@ NIRSpec fixed slits
 
     psfs = {}
     for wave in [0.6e-6, 1e-6, 2e-6, 3e-6]:
-        psfs[wave] = nspec.calc_psf(monochromatic=wave, oversamp=4)
+        psfs[wave] = nspec.calc_psf(monochromatic=wave, oversample=4)
 
     for i, wave in enumerate([0.6e-6, 1e-6, 2e-6, 3e-6]):
         plt.subplot(1, 4, i+1)
@@ -159,7 +159,7 @@ NIRSpec MSA
     ns.image_mask='MSA all open'
     ns.display()
     plt.savefig('example_nirspec_msa_optics.png')
-    msapsf = ns.calc_psf(monochromatic=2e-6, oversample=8, rebin=True)
+    msapsf = ns.calc_psf(monochromatic=2e-6, oversample=8)
     webbpsf.display_psf(msapsf, ext='DET_SAMP')
 
 .. image:: ./fig_example_nirspec_msa_optics.png
@@ -215,7 +215,7 @@ NIRCam coronagraphy with an offset source
                                                # (note that this is MUCH larger than expected acq
                                                # offsets. This size displacement is just for show)
     nc.options['source_offset_theta'] = 45     # at a position angle of 45 deg
-    nc.calc_psf('coronagraphic.fits', oversample=4, clobber=True)   # create highly oversampled output image
+    nc.calc_psf('coronagraphic.fits', oversample=4)   # create highly oversampled output image
 
 
     plt.figure(figsize=(12,4))
@@ -332,7 +332,7 @@ Make plots of encircled energy in PSFs at various wavelengths
 
                 outname = "PSF_MIRI_%.1fum_wfe%d.fits" % (wave, i)
                 psf = miri.calc_psf(outname, monochromatic=wave*1e-6,
-                        oversample=4, fov_arcsec=fov, rebin=True, display=True)
+                        oversample=4, fov_arcsec=fov, display=True)
 
 
 
@@ -414,7 +414,7 @@ There are two functions here, one that creates a simulated PSF for a given amoun
                     return
 
                 psf, intermediates = miri.calc_psf(oversample=4, fov_arcsec=fov,
-                        rebin=True, display=display, return_intermediates=True, \*\*kwargs)
+                        display=display, return_intermediates=True, \*\*kwargs)
 
                 lyot_intensity = intermediates[4]
 

docs/release.rst

@@ -5,38 +5,33 @@ Developer Notes: Releasing a new version of WebbPSF
 Prerequisites
 =============
 
- * Is the `develop` build `passing on Travis? <https://travis-ci.org/spacetelescope/webbpsf>`_ with all desired release items included?
+ * Is the `develop` build `passing on Github Actions? <https://github.com/spacetelescope/webbpsf/actions>`_ with all desired release items included?
 
 Releasing new data packages
 ===========================
 
- #. Run ``dev_utils/make-data-sdist.sh`` (details below) to make a gzipped tarred archive of the WebbPSF data
+ #. Run ``dev_utils/master_data_release.sh`` (details below) to make a gzipped tarred archive of the WebbPSF data
  #. If the new data package is **required** (meaning you can't run WebbPSF without it, or you can run but may get incorrect results), you must bump ``DATA_VERSION_MIN`` in ``__init__.py`` to ``(0, X, Y)``
  #. Extract the resulting data archive and check that you can run the WebbPSF tests with ``WEBBPSF_PATH`` pointing to it
- #. Copy the data archive into public web space.
-
-     #. This now means on Box. Upload to Box in the webbpsf shared data folder. Get the Box shared file URL.
-     #. Update ``docs/installation.rst`` to have that new URL and updated filename in the appropriate location.
-
- #. Update the shared copy on STScI Central Store:
-
-    #. ``cd`` to ``/grp/jwst/ote`` and remove the ``webbpsf-data`` symlink
-    #. Copy the archive into ``/grp/jwst/ote/`` and extract it to ``/grp/jwst/ote/webbpsf-data``
-    #. Rename the folder to ``webbpsf-data-0.x.y``
-    #. Create a symbolic link at ``/grp/jwst/ote/webbpsf-data`` to point to the new folder
-
+ #. Copy the data archive into public web space. This now means on Box. The following steps need to be performed in this sequence in order to preserve the naming conventions.
+     #. Find webbpsf-data-LATEST.tar.gz, and click on "more options" and "Update Version".  Choose the newest version of webbpsf-data-#.#.#.tar.gz
+     #. This will change the name of webbpsf-data-LATEST.tar.gz to be what you just uploaded, rename the file back to "webbpsf-data-LATEST.tar.gz"
+     #. Upload to Box a separate version of webbpsf-data-#.#.#.tar.gz shared data folder for future storage.
+     #. Upload to Box the minimal-webbpsf-data-#.#.#.tar.gz shared data folder.
+     #. Verify the shared link of webbpsf-data-latest.tar.gz is the same that exists in ``docs/installation.rst`` ("copy shared link" then "link settings")
+
+ #. A shared copy will be automatically configured in STScI Central Store with updated symlink ``/grp/jwst/ote/webbpsf-data``
  #. Update the URL in ``installation.rst`` under :ref:`data_install`
 
-Details for using `make-data-sdist.sh`:
+Details for using `master_data_release.sh`:
 -------------------------------------
 
-Invoke ``dev_utils/make-data-sdist.sh`` one of the following ways to make a gzipped tarred archive of the WebbPSF data suitable for distribution.
+Invoke ``dev_utils/master_data_release.sh`` one of the following ways to make a gzipped tarred archive of the WebbPSF data suitable for distribution.
 
 **If you are on the Institute network:** ::
 
    $ cd webbpsf/dev_utils/
-   $ ./make-data-sdist.sh 0.X.Y
-   $ cp ./webbpsf-data-0.X.Y.tar.gz /path/to/public/web/directory/
+   $ ./master_data_release.sh 0.X.Y
 
 **If you're working from a local data root:** ::
 
@@ -52,7 +47,7 @@ Update the dependency requirement to the new version of poppy, in ``webbpsf/pypr
 
 When you are ready, proceed with the WebbPSF release as follows:
 
-#. Get the `develop` branch into the state that you want, including all PRs merged, updated release notes. This includes all tests passing both locally and on Travis.
+#. Get the `develop` branch into the state that you want, including all PRs merged, updated release notes. This includes all tests passing both locally and on GitHub Actions.
 #. Tag the commit with `v<version>`, being sure to sign the tag with the `-s` option.
    * ``git tag -s v<version> -m "Release v<version>"``