Merge pull request #860 from BradleySappington/v1.3.0.rc1

V1.3.0.rc1
spacetelescope · May 28, 2024 · ca25062 · ca25062
2 parents 2140f3c + 49cd483
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diff --git a/dev_utils/master_data_release.sh b/dev_utils/master_data_release.sh
@@ -21,9 +21,10 @@ 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"
+mkdir "$new_directory"
+tar -xzf "$PWD/webbpsf-data-$VER.tar.gz" -C "$new_directory"
+rm "$symlink_directory"
+ln -s "$new_directory/webbpsf-data" "$symlink_directory"
 
 ./make-minimal-datafiles.py  ${PWD}/webbpsf-data-${VER}.tar.gz $VER
 

diff --git a/docs/README figure.ipynb b/docs/README figure.ipynb
@@ -701,8 +701,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "pygments_lexer": "python",
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/available_opds.rst b/docs/available_opds.rst
@@ -5,31 +5,31 @@ Appendix: Available Optical Path Difference (OPD) files
 On-Orbit OPD Measurements
 -------------------------
 
-The default OPD in WebbPSF is now an on-orbit measured OPD from early in cycle 1 science operations: 
+The default OPD in WebbPSF is now an on-orbit measured OPD from early in cycle 1 science operations:
 
- * `JWST_OTE_OPD_cycle1_example_2022-07-30.fits`: The specific OPD measurement selected, from 2022 July 30, intentionally represents a slightly conservative alignment state (after a couple weeks of relative stability, shortly before a next wavefront correction). This is about a 75th percentile  performance level, based on operational experience during the first few months of cycle 1. Most observations will have OPDs similar to this, or slightly better; a smaller number will have not quite as good. 
+ * `JWST_OTE_OPD_cycle1_example_2022-07-30.fits`: The specific OPD measurement selected, from 2022 July 30, intentionally represents a slightly conservative alignment state (after a couple weeks of relative stability, shortly before a next wavefront correction). This is about a 75th percentile  performance level, based on operational experience during the first few months of cycle 1. Most observations will have OPDs similar to this, or slightly better; a smaller number will have not quite as good.
 
-This intentionally-slightly-conservative OPD was chosen for use in the cycle 2 ETC and is set as the default here for consistency. 
-For modeling PSFs of science observations, it is generally best to retrieve and use the 
-`measured in-flight wavefronts <https://webbpsf.readthedocs.io/en/latest/jwst_measured_opds.html>`_ based on the date of 
-the science observation. 
+This intentionally-slightly-conservative OPD was chosen for use in the cycle 2 ETC and is set as the default here for consistency.
+For modeling PSFs of science observations, it is generally best to retrieve and use the
+`measured in-flight wavefronts <https://webbpsf.readthedocs.io/en/latest/jwst_measured_opds.html>`_ based on the date of
+the science observation.
 
 
 
 
 Pre-Launch Model OPDs (Obsolete)
 ---------------------------------
 
-Prior versions of this page documented the _pre-flight_ models for JWST wavefronts. These models are now happily obsolete, and can be replaced by 
+Prior versions of this page documented the `_pre-flight_` models for JWST wavefronts. These models are now happily obsolete, and can be replaced by
 `actual measured in-flight wavefronts <https://webbpsf.readthedocs.io/en/latest/jwst_measured_opds.html>`_.
-    
+
 
 Most pre-launch predicted OPDs are no longer included in the WebbPSF data files distribution. The only such files still
 included are
 
- * `JWST_OTE_OPD_RevAA_prelaunch_predicted.fits.gz`:  This contains predicted OPDs based on the best available optical models at the time of launch, including the calibrated, known surface figures of each mirror as measured in ground testing. For most purposes this is superceded by the on-orbit measurements. It is retained for back-compatibility mostly. 
-    
-    
-For any cases in which you may need further information about the other pre-launch predicted OPD files, 
-consult the `older versions of this page hosted on readthedocs<https://webbpsf.readthedocs.io/en/v0.9.0/available_opds.html>`_.
-    
+ * `JWST_OTE_OPD_RevAA_prelaunch_predicted.fits.gz`:  This contains predicted OPDs based on the best available optical models at the time of launch, including the calibrated, known surface figures of each mirror as measured in ground testing. For most purposes this is superceded by the on-orbit measurements. It is retained for back-compatibility mostly.
+
+
+For any cases in which you may need further information about the other pre-launch predicted OPD files,
+consult the `older versions of this page hosted on readthedocs <https://webbpsf.readthedocs.io/en/v0.9.0/available_opds.html>`_.
+
diff --git a/docs/conf.py b/docs/conf.py
@@ -70,6 +70,7 @@
 extensions = [
     "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
+    "sphinx.ext.graphviz",
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
     "sphinx.ext.inheritance_diagram",
@@ -80,11 +81,12 @@
     "sphinx_issues",
     "nbsphinx",
     "numpydoc",
-    "astroquery",
 ]
 
 numpydoc_show_class_members = False
 
+autosummary_generate = True
+graphviz_dot = "dot"
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

diff --git a/docs/field_dependence/multifield_documentation.ipynb b/docs/field_dependence/multifield_documentation.ipynb
@@ -522,8 +522,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "pygments_lexer": "python",
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/index.rst b/docs/index.rst
@@ -19,7 +19,7 @@ WebbPSF is a Python package that computes simulated point spread functions (PSFs
 
 
 **Contributors:**
-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>`_. 
+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
 ----------------------------
@@ -77,7 +77,6 @@ Contents
 
    api_reference.rst
    help.rst
-   performance.rst
    sampling.rst
    fft_optimization.rst
    poppy.rst

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -73,7 +73,7 @@ Files containing such information as the JWST pupil shape, instrument throughput
 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=$HOME/data/webbpsf-data
+    export WEBBPSF_PATH=$HOME/data/webbpsf-data
 
 for bash. (You will probably want to add this to your ``.bashrc``.)
 

diff --git a/docs/jwst_detector_effects.ipynb b/docs/jwst_detector_effects.ipynb
@@ -39,7 +39,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import webbpsf \n",
+    "import webbpsf\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"
    ]
@@ -275,7 +275,7 @@
    ],
    "source": [
     "wave_arr = np.array([])\n",
-    "fwhm_fun_arr_no_effects = np.array([]) \n",
+    "fwhm_fun_arr_no_effects = np.array([])\n",
     "for filters in niriss.filter_list[:-1]:\n",
     "    niriss = webbpsf.NIRISS()\n",
     "    niriss.filter = filters\n",
@@ -286,8 +286,7 @@
     "    single_webbpsf_niriss_no_effects = niriss.calc_psf(fov_pixels=fov_pixels)\n",
     "    wave_arr = np.append(wave_arr, single_webbpsf_niriss_no_effects[3].header['WAVELEN'])\n",
     "    fitted_psf = measure_fwhm(single_webbpsf_niriss_no_effects[3].data)\n",
-    "    fwhm_fun_arr_no_effects = np.append(fwhm_fun_arr_no_effects,np.sqrt(fitted_psf.x_fwhm * fitted_psf.y_fwhm)*niriss.pixelscale)\n",
-    "    "
+    "    fwhm_fun_arr_no_effects = np.append(fwhm_fun_arr_no_effects,np.sqrt(fitted_psf.x_fwhm * fitted_psf.y_fwhm)*niriss.pixelscale)\n"
    ]
   },
   {
@@ -325,7 +324,7 @@
    ],
    "source": [
     "wave_arr = np.array([])\n",
-    "fwhm_fun_arr = np.array([]) \n",
+    "fwhm_fun_arr = np.array([])\n",
     "for filters in niriss.filter_list[:-1]:\n",
     "    niriss = webbpsf.NIRISS()\n",
     "    niriss.filter = filters\n",
@@ -334,8 +333,7 @@
     "    single_webbpsf_niriss = niriss.calc_psf(fov_pixels=fov_pixels)\n",
     "    wave_arr = np.append(wave_arr, single_webbpsf_niriss[3].header['WAVELEN'])\n",
     "    fitted_psf = measure_fwhm(single_webbpsf_niriss[3].data)\n",
-    "    fwhm_fun_arr = np.append(fwhm_fun_arr,np.sqrt(fitted_psf.x_fwhm * fitted_psf.y_fwhm)*niriss.pixelscale)\n",
-    "        "
+    "    fwhm_fun_arr = np.append(fwhm_fun_arr,np.sqrt(fitted_psf.x_fwhm * fitted_psf.y_fwhm)*niriss.pixelscale)\n"
    ]
   },
   {
@@ -379,10 +377,9 @@
     "\n",
     "for fn in stdpsf:\n",
     "    hd = fits.open(fn)\n",
-    "    eps_data = ndimage.zoom(hd[0].data[12],0.25) # the ePSF is binned down to detector-sampled \n",
+    "    eps_data = ndimage.zoom(hd[0].data[12],0.25) # the ePSF is binned down to detector-sampled\n",
     "    fitted_psf_epsf = measure_fwhm(eps_data)\n",
-    "    fwhm_fun_arr_epsf = np.append(fwhm_fun_arr_epsf,np.sqrt(fitted_psf_epsf.x_fwhm * fitted_psf_epsf.y_fwhm)*niriss.pixelscale)\n",
-    "   "
+    "    fwhm_fun_arr_epsf = np.append(fwhm_fun_arr_epsf,np.sqrt(fitted_psf_epsf.x_fwhm * fitted_psf_epsf.y_fwhm)*niriss.pixelscale)\n"
    ]
   },
   {
@@ -466,6 +463,14 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "575dd903",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "id": "89334f7b",
@@ -502,7 +507,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
+   "pygments_lexer": "python",
    "version": "3.11.7"
   }
  },

diff --git a/docs/jwst_matching_psfs_to_data.ipynb b/docs/jwst_matching_psfs_to_data.ipynb
@@ -226,7 +226,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
+   "pygments_lexer": "python",
    "version": "3.11.7"
   }
  },

diff --git a/docs/jwst_measured_opds.ipynb b/docs/jwst_measured_opds.ipynb
@@ -722,7 +722,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
+   "pygments_lexer": "python",
    "version": "3.11.7"
   }
  },

diff --git a/docs/jwst_optical_budgets.ipynb b/docs/jwst_optical_budgets.ipynb
@@ -303,8 +303,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "pygments_lexer": "python",
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/jwst_psf_subtraction.ipynb b/docs/jwst_psf_subtraction.ipynb
@@ -630,7 +630,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
+   "pygments_lexer": "python",
    "version": "3.11.7"
   }
  },

diff --git a/docs/jwst_wavefront_deltas.ipynb b/docs/jwst_wavefront_deltas.ipynb
@@ -103,8 +103,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.10"
+   "pygments_lexer": "python",
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/release.rst b/docs/release.rst
@@ -24,7 +24,7 @@ Releasing new data packages
  #. Update the URL in ``installation.rst`` under :ref:`data_install`
 
 Details for using `master_data_release.sh`:
--------------------------------------
+-------------------------------------------
 
 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.
 
@@ -43,25 +43,25 @@ Releasing new versions
 ======================
 
 If you are making a release for `poppy` at the same time as a release in WebbPSF, do that first.
-Update the dependency requirement to the new version of poppy, in ``webbpsf/pyproject.toml`.
+Update the dependency requirement to the new version of poppy, in ``webbpsf/pyproject.toml``.
 
 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 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>"``
+ #. 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>"``
 
-#. Push tag to github, on `develop`
-#. On github, make a PR from `develop` to `stable` (this can be done ahead of time and left open, until all individual PRs are merged into `develop`.).
-#. After verifying that PR is complete and tests pass, merge it. (Once merged, both the `stable` and `develop` branches should match).
-#. Release on Github:
+ #. Push tag to github, on `develop`
+ #. On github, make a PR from `develop` to `stable` (this can be done ahead of time and left open, until all individual PRs are merged into `develop`.).
+ #. After verifying that PR is complete and tests pass, merge it. (Once merged, both the `stable` and `develop` branches should match).
+ #. Release on Github:
 
-   #. On Github, click on "[N] Releases".
-   #. Select "Draft a new release".
-   #. Specify the version number, title, and brief description of the release.
-   #. Press "Publish Release".
+     #. On Github, click on "[N] Releases".
+     #. Select "Draft a new release".
+     #. Specify the version number, title, and brief description of the release.
+     #. Press "Publish Release".
 
-#. Release to PyPI. This should now happen automatically on GitHub Actions. This will be triggered by a GitHub Actions build of a tagged commit on the `stable` branch, so it will happen automatically on the prior step for the PR into `stable`.
+ #. Release to PyPI. This should now happen automatically on GitHub Actions. This will be triggered by a GitHub Actions build of a tagged commit on the `stable` branch, so it will happen automatically on the prior step for the PR into `stable`.
 
 .. note::