Merge branch 'main' into cubeviz-spec-extract-through-plugin

.github/workflows/standalone.yml

@@ -8,17 +8,79 @@ on:
     tags:
     - 'v*'
   workflow_dispatch:
+  pull_request:
 
 defaults:
   run:
     shell: bash {0}
 
 jobs:
-  build_binary:
+  build_binary_not_osx:
     runs-on: ${{ matrix.os }}-latest
+    if: (github.repository == 'spacetelescope/jdaviz' && (github.event_name == 'push' || github.event_name == 'workflow_dispatch' || contains(github.event.pull_request.labels.*.name, 'Build standalone')))
     strategy:
       matrix:
-        os: [ubuntu, windows, macos]
+        os: [ubuntu, windows]
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install jdaviz
+      run: pip install .[test]
+
+    - name: Install pyinstaller
+      run: pip install pyinstaller==6.6
+
+    - name: Create standalone binary
+      env:
+        DEVELOPER_ID_APPLICATION: ${{ secrets.DEVELOPER_ID_APPLICATION }}
+      run: (cd standalone; pyinstaller ./jdaviz.spec)
+
+    - name: Run jdaviz cmd in background
+      run: ./standalone/dist/jdaviz/jdaviz-cli imviz&
+
+    - name: Install playwright
+      run: (pip install playwright; playwright install chromium)
+
+    - name: Install pytest
+      run: pip install pytest-playwright
+
+    - name: Wait for Voila to get online
+      uses: ifaxity/wait-on-action@a7d13170ec542bdca4ef8ac4b15e9c6aa00a6866  # v1.2.1
+      with:
+        resource: tcp:8866
+        timeout: 60000
+
+    - name: Test standalone
+      run: (cd standalone; touch pytest.ini; JUPYTER_PLATFORM_DIRS=1 pytest test_standalone.py --video=on)
+
+    - name: Upload Test artifacts
+      if: github.event_name != 'pull_request'
+      uses: actions/upload-artifact@v3
+      with:
+        name: test-results-${{ matrix.os }}
+        path: standalone/test-results
+
+    - name: Upload jdaviz standalone (non-OSX)
+      if: github.event_name != 'pull_request'
+      uses: actions/upload-artifact@v3
+      with:
+        name: jdaviz-standlone-${{ matrix.os }}
+        path: |
+          standalone/dist/jdaviz
+
+  # Do not want to deal with OSX certs in pull request builds.
+  build_binary_osx:
+    runs-on: ${{ matrix.os }}-latest
+    if: (github.repository == 'spacetelescope/jdaviz' && (github.event_name == 'push' || github.event_name == 'workflow_dispatch'))
+    strategy:
+      matrix:
+        os: [macos]
     steps:
     # osx signing based on https://melatonin.dev/blog/how-to-code-sign-and-notarize-macos-audio-plugins-in-ci/
     - name: Import Certificates (macOS)
@@ -27,19 +89,20 @@ jobs:
       with:
         p12-file-base64: ${{ secrets.DEV_ID_APP_CERT }}
         p12-password: ${{ secrets.DEV_ID_APP_PASSWORD }}
+
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - name: Install jdaviz
       run: pip install .[test]
 
     - name: Install pyinstaller
-      run: pip install pyinstaller==5.11
+      run: pip install pyinstaller==6.6
 
     - name: Create standalone binary
       env:
@@ -59,6 +122,8 @@ jobs:
         rm -rf standalone/dist/jdaviz.app/Contents/Resources/skimage/.dylibs
         rm -rf standalone/dist/jdaviz.app/Contents/MacOS/shapely/.dylibs
         rm -rf standalone/dist/jdaviz.app/Contents/Resources/shapely/.dylibs
+        rm -rf standalone/dist/jdaviz.app/Contents/MacOS/scipy/.dylibs
+        rm -rf standalone/dist/jdaviz.app/Contents/Resources/scipy/.dylibs
 
     - name: Codesign (OSX)
       if: ${{ matrix.os == 'macos' }}
@@ -101,18 +166,14 @@ jobs:
       if: ${{ matrix.os == 'macos' }}
       run: ./standalone/dist/jdaviz.app/Contents/MacOS/jdaviz-cli imviz&
 
-    - name: Run jdaviz cmd in background
-      if: ${{ matrix.os != 'macos' }}
-      run: ./standalone/dist/jdaviz/jdaviz-cli imviz&
-
     - name: Install playwright
       run: (pip install playwright; playwright install chromium)
 
     - name: Install pytest
       run: pip install pytest-playwright
 
     - name: Wait for Voila to get online
-      uses: ifaxity/wait-on-action@df89d0cf8089bb0c38e25279c74848ef313da53b  # v1.2.0
+      uses: ifaxity/wait-on-action@a7d13170ec542bdca4ef8ac4b15e9c6aa00a6866  # v1.2.1
       with:
         resource: tcp:8866
         timeout: 60000
@@ -127,14 +188,6 @@ jobs:
         name: test-results-${{ matrix.os }}
         path: standalone/test-results
 
-    - name: Upload jdaviz standalone (non-OSX)
-      if: ${{ always() && (matrix.os != 'macos') }}
-      uses: actions/upload-artifact@v3
-      with:
-        name: jdaviz-standlone-${{ matrix.os }}
-        path: |
-          standalone/dist/jdaviz
-
     - name: Upload jdaviz standalone (OSX)
       if: ${{ always() && (matrix.os == 'macos') }}
       uses: actions/upload-artifact@v3

CHANGES.rst

@@ -1,23 +1,15 @@
-3.10 (unreleased)
-=================
+4.0 (unreleased)
+================
 
 New Features
 ------------
 
-- The filename entry in the export plugin is now automatically populated based on the selection. [#2824]
-
-- Adding Data Quality plugin for Imviz and Cubeviz. [#2767, #2817, #2844]
-
-- Enable exporting spectral regions to ECSV files readable by ``astropy.table.QTable`` or
-  ``specutils.SpectralRegion`` [#2843]
+- Adding flux/surface brightness translation and surface brightness
+  unit conversion in Cubeviz and Specviz. [#2781]
 
 Cubeviz
 ^^^^^^^
 
-- Enable spectral unit conversion in cubeviz. [#2758, #2803]
-
-- Enable spectral extraction for composite subsets. [#2837]
-
 Imviz
 ^^^^^
 
@@ -36,9 +28,6 @@ API Changes
 Cubeviz
 ^^^^^^^
 
-- ERROR and DATA_QUALITY extension names are now recognized as
-  uncertainty and mask, respectively. [#2840]
-
 Imviz
 ^^^^^
 
@@ -69,27 +58,77 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
-- Loading a specific extension with ``ext`` keyword no longer crashes. [#2830]
-
 Other Changes and Additions
 ---------------------------
 
-- Bump required Python version to 3.10. [#2757]
+3.11 (unreleased)
+=================
 
-- Line menu in Redshift from Centroid section of Line Analysis now shows values in current units. [#2816, #2831]
+New Features
+------------
 
-- Bump required specutils version to 1.15. [#2843]
+Cubeviz
+^^^^^^^
 
-3.9.2 (unreleased)
-==================
+Imviz
+^^^^^
+
+Mosviz
+^^^^^^
+
+Specviz
+^^^^^^^
+
+Specviz2d
+^^^^^^^^^
+
+API Changes
+-----------
+
+Cubeviz
+^^^^^^^
+
+Imviz
+^^^^^
+
+Mosviz
+^^^^^^
+
+Specviz
+^^^^^^^
+
+Specviz2d
+^^^^^^^^^
 
 Bug Fixes
 ---------
 
 Cubeviz
 ^^^^^^^
 
-- Re-enable support for exporting spectrum-viewer. [#2825]
+Imviz
+^^^^^
+
+Mosviz
+^^^^^^
+
+Specviz
+^^^^^^^
+
+Specviz2d
+^^^^^^^^^
+
+Other Changes and Additions
+---------------------------
+
+3.10.1 (unreleased)
+===================
+
+Bug Fixes
+---------
+
+Cubeviz
+^^^^^^^
 
 Imviz
 ^^^^^
@@ -103,6 +142,58 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
+3.10 (2024-05-03)
+=================
+
+New Features
+------------
+
+- The filename entry in the export plugin is now automatically populated based on the selection. [#2824]
+
+- Adding Data Quality plugin for Imviz and Cubeviz. [#2767, #2817, #2844]
+
+- Enable exporting spectral regions to ECSV files readable by ``astropy.table.QTable`` or
+  ``specutils.SpectralRegion`` [#2843]
+
+Cubeviz
+^^^^^^^
+
+- Enable spectral unit conversion in cubeviz. [#2758, #2803]
+
+- Enable spectral extraction for composite subsets. [#2837]
+
+API Changes
+-----------
+
+Cubeviz
+^^^^^^^
+
+- ERROR and DATA_QUALITY extension names are now recognized as
+  uncertainty and mask, respectively. [#2840]
+
+Bug Fixes
+---------
+
+Cubeviz
+^^^^^^^
+
+- Re-enable support for exporting spectrum-viewer. [#2825]
+
+
+Specviz2d
+^^^^^^^^^
+
+- Loading a specific extension with ``ext`` keyword no longer crashes. [#2830]
+
+Other Changes and Additions
+---------------------------
+
+- Bump required Python version to 3.10. [#2757]
+
+- Line menu in Redshift from Centroid section of Line Analysis now shows values in current units. [#2816, #2831]
+
+- Bump required specutils version to 1.15. [#2843]
+
 3.9.1 (2024-04-19)
 ==================
 

CITATION.cff

@@ -73,9 +73,9 @@ authors:
 - family-names: "Volfman"
   given-names: "Sabrina"
 title: "Jdaviz"
-version: 3.9.1
+version: 3.10
 doi: https://doi.org/10.5281/zenodo.5513927
-date-released: 2024-04-19
+date-released: 2024-05-03
 url: "https://github.com/spacetelescope/jdaviz"
 
 # see a full list of contributors here: https://github.com/spacetelescope/jdaviz/graphs/contributors

docs/mosviz/displayspectra.rst

@@ -23,9 +23,6 @@ Synchronous Spectral Pan/Zoom
 -----------------------------
 Mosviz assumes the 1D and 2D spectra objects share a relationship in spectral space. As a result, the 1D and 2D spectral viewers have their spectral axes (the horizontal x-axis) linked. As you pan and zoom in spectral space (horizontally) in either of the two spectral viewers, the other will follow, simultaneously panning and zooming by the same amounts.
 
-.. warning::
-    If you pan too far away from the bounds of the dataset provided in the 1D or 2D spectral viewers, a warning will be displayed to notify the user. If you go too far, there is a risk of desynchronizing the two viewers.
-
 Defining Spectral Regions
 =========================
 

docs/mosviz/navigation.rst

@@ -23,19 +23,16 @@ Clicking on a row in the table viewer populates the other viewers with the data
 corresponding to that row. Note that the checkbox at the far left of the row does
 not need to be checked to display the data - that checkbox is related to selecting
 subsets of rows. By default, 10 rows are shown at a time but this can be changed
-with the selector at the bottom right of the table viewer. To the right of the 
+with the selector at the bottom right of the table viewer. To the right of the
 rows-per-page selector are left and right arrows that are used to move between
-pages of the table, if there is more data than fits on a single page. 
+pages of the table, if there is more data than fits on a single page.
 
 
 .. _slit-overlay:
 
 Using the Slit Overlay
 ======================
 
-Currently, the option to overlay slit geometry is enabled by default if the 
+Currently, the option to overlay slit geometry is enabled by default if the
 required information is present. The option to toggle whether slits are displayed
-is located in the top right tool menu under the "Slit Overlay" heading, as seen
-in the screenshot below.
-
-.. image:: ../img/slit_overlay.png
+is located in the top right tool menu under the "Slit Overlay" heading.

docs/mosviz/notebook.rst

@@ -1,8 +1,8 @@
 .. _mosviz-notebook:
 
-***********************************
-Using Mosviz in a Jupyter Notebook 
-***********************************
+***************************
+Exporting data from Mosviz
+***************************
 
 To initialize an instance of the Mosviz app in a Jupyter notebook, simply run
 the following code in a cell of the notebook:
@@ -13,7 +13,7 @@ the following code in a cell of the notebook:
     mosviz = Mosviz()
     mosviz.show()
 
-After running the code above, you can interact with the Mosviz application from 
+After running the code above, you can interact with the Mosviz application from
 subsequent notebook cells via the API methods attached to the
 :class:`~jdaviz.configs.mosviz.helper.Mosviz` object,
 for example loading data into the app as described in :ref:`mosviz-import-api`.