POC: Attempt to package jdaviz in Pyinstaller (take 2) (#1960)

* feat: pyinstaller * codesign osx * debug: try without codesign * does not need arguments * use hooks * also download the app * use branch of pyinstaller * better hooks * pin to 5.11 Otherwise we need to do at least: + rm -rf standalone/dist/jdaviz.app/Contents/MacOS/jedi/third_party/typeshed/stdlib/ + rm -rf standalone/dist/jdaviz.app/Contents/MacOS/**/*.dist-info * fix: maintain symlinks by zipping, upload-artifact does not support it * GHA logic? * code sign on gha * run notary tool on gha * fix: redo codesign after modifications * fix: reorder zipping and notary step * remove invalid symlink * make sure the program executes * fix path of entitlements file * add comment for hint with the osx fix * gpt assisted way of running the log tool on failure * fix syntax error * fix path * comments for the future * fix uuid parsing and re-zip the app after notary step * fix: use ditto instead of zip from https://developer.apple.com/forums/thread/116831 zip might cause issues with utf8 or metadata. * comments for the future * fix uuid for notary step * upload different artifact for osx * cleanup spec file and hooks, no more __pycache__ files should be included * ci: do not cancel on failure * fix: mistune 3.0 needs this * make dmg instead of zip for osx * BUG: Fix mouseover behavior in Cubeviz spectrum viewer when spatial subset is present. Co-authored-by: Duy Nguyen <[email protected]> * Remove change log from #2258 because the bug only affects unreleased code [ci skip] [rtd skip] * Deprecate get_subsets_from_viewer * Missing region index * Fix subset args * Remove get_data_from_viewer from imviz viewer tests * Remove get_data_from_viewer from mosviz data loading test and sub hardcoded viewer ref names * Mosviz test update image truth class * Fix incorrect viewer ref * Set Mos2Dviewer data statistic to None by default * Non-existent data check * Properly deprecate getters * Properly check for valueError on non-existent label * Update Specviz get_data_from_viewer test * Rename "subset_to_apply" to "spectral_subset * Codestyle * Fix docs wording Co-authored-by: Jesse Averbukh <[email protected]> * Catch missed code, fix bug * Retain Mosviz get_data behavior and fix change log * Undo bad diff * MNT: Add .mailmap so git shortlog -es gives sane listing. * DOC: Add warning about surface brightness in Simple Aperture Photometry plugin (#2261) * DOC: Add warning about surface brightness in Simple Aperture Photometry plugin. I am beginning to think the Simple in plugin name no longer applies. * DOC: Improve verbiage. Co-authored-by: Camilla Pacifici <[email protected]> --------- Co-authored-by: Camilla Pacifici <[email protected]> * FEAT: Annulus draw tool for Imviz (#2240) * FEAT: Annulus draw tool for Imviz. TODO: Need to fix icon. TST: Add tests. [ci skip] [rtd skip] * Pull in #2204 into this PR and bump upstream pins * Changed function name upstream in glue-astronomy during review process * Proper annulus icon from J. Kotler Co-authored-by: Jennifer Kotler <[email protected]> * Avoid error traceback with bad annulus radii * Disable recentering for annulus * Fix test failure because not sure why spectral region is using Imviz centering method but okay. --------- Co-authored-by: Jennifer Kotler <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> * MNT: Temporarily pin voila<0.5 (#2269) * MNT: Temp pin voila<0.5 because voila-template is incompatible, see #2268 * TST: Disable voila dev in test matrix * TST: Ignore DeprecationWarning from asteval (#2274) * TST: Ignore DeprecationWarning from asteval. For example https://github.com/newville/asteval/issues/120 * Also ignore FutureWarning from asteval * Add doc for windows latency issue * Deprecate load_spectrum * Update tests and docs from load_spectrum * Docstring suggestions Co-authored-by: P. L. Lim <[email protected]> * Changelog * Changelog * Button to export Cubeviz movie (#2264) * WIP: Backend API to write movie file but got stuck with bqplot not cooperating after first frame. [ci skip] [rtd skip] * fix: bqplot stuck after the first frame of the movie We have to run the loop outside the main thread; otherwise, the processing of messages from the frontend is blocked, causing the message with the first image to never be received. The "save_image" method can only save the next image after the previous image is received. * Fix typo, this works now from the API. [ci skip] [rtd skip] * Add frontend and tests * Add user doc * DOC: Add note about standalone app saving file into weird places. * Address some review comments * Expose FPS and fix test * DOC: Baby Shark roundtrip as promised. * DOC: Ellie said more shark! * Vue.js style improvements [ci skip] [rtd skip] Co-authored-by: Kyle Conroy <[email protected]> * Display pls install msg in plugin * Address review comments * Fix test * Fix path resolution in standalone app * Improve frontend validation and access. Co-authored-by: Kyle Conroy <[email protected]> * Disable video for spectrum-viewer in GUI and add comment to Slice. * Add tooltip to kill switch but it only shows when activated * Rename kill with something less scary * Hide stop button since disabling is not obvious enough, also moar tooltip * Disable the whole movie menu for spectrum viewer in Cubeviz [ci skip] [rtd skip] Co-authored-by: Ricky O'Steen <[email protected]> * Fix RTD warnings about invalid prop and remove unnecessary frontend check now that Ricky's suggestion is accepted. --------- Co-authored-by: Mario Buikhuizen <[email protected]> Co-authored-by: Kyle Conroy <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> * Add functional but ugly launcher * Use launcher notebook if neither config nor filepath is specified * Codestyle * Add margins on left and right to avoid cutoff in notebook * Support launcher from cli * Codestyle * Remove URI from path text until implemented * Fix standalone bug * Specify --layout= as new required cli syntax * Remove unused import Co-authored-by: P. L. Lim <[email protected]> * Update readme to show required layout flag * Changelog * Changelog Co-authored-by: P. L. Lim <[email protected]> * Changelog * Update .github/workflows/standalone.yml Co-authored-by: P. L. Lim <[email protected]> * Update .github/workflows/standalone.yml * Update to use config launcher * Moved changelog entry to new section --------- Co-authored-by: Duy Nguyen <[email protected]> Co-authored-by: Pey Lian Lim <[email protected]> Co-authored-by: Duy Tuong Nguyen <[email protected]> Co-authored-by: Jesse Averbukh <[email protected]> Co-authored-by: Camilla Pacifici <[email protected]> Co-authored-by: Jennifer Kotler <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> Co-authored-by: Mario Buikhuizen <[email protected]> Co-authored-by: Kyle Conroy <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]>
spacetelescope · Jul 5, 2023 · 46be84f · 46be84f
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diff --git a/.github/workflows/standalone.yml b/.github/workflows/standalone.yml
@@ -0,0 +1,141 @@
+name: Build standalone
+
+on:
+  push:
+    branches:
+    - main
+    - 'v*'
+    tags:
+    - 'v*'
+
+defaults:
+  run:
+    shell: bash {0}
+
+
+jobs:
+  build_binary:
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os: [ubuntu, windows, 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)
+      uses: apple-actions/import-codesign-certs@v1
+      if: ${{ matrix.os == 'macos' }}
+      with:
+        p12-file-base64: ${{ secrets.DEV_ID_APP_CERT }}
+        p12-password: ${{ secrets.DEV_ID_APP_PASSWORD }}
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+
+    - name: Install jdaviz
+      run: pip install .
+
+    - name: Install pyinstaller
+      run: pip install pyinstaller==5.11
+
+    - name: Create standalone binary
+      env:
+        DEVELOPER_ID_APPLICATION: ${{ secrets.DEVELOPER_ID_APPLICATION }}
+      run: (cd standalone; pyinstaller ./jdaviz.spec)
+
+    - name: Remove invalid files for OSX
+      # hopefully we can improve this in the future
+      # by using good hooks
+      # i think the issue is that we have a . in the name, there are many
+      # google hits on pyqt having the same issue
+      # and we might be able to remove it after https://github.com/pyinstaller/pyinstaller/pull/7619
+      # is released (pyinstaller 5.13 probably)
+      if: ${{ matrix.os == 'macos' }}
+      run: |
+        rm -rf standalone/dist/jdaviz.app/Contents/MacOS/skimage/.dylibs
+        rm -rf standalone/dist/jdaviz.app/Contents/Resources/skimage/.dylibs
+
+    - name: Codesign (OSX)
+      if: ${{ matrix.os == 'macos' }}
+      run: |
+        cd standalone/dist
+        codesign --deep --force --options=runtime --entitlements ../entitlements.plist --sign ${{ secrets.DEVELOPER_ID_APPLICATION }} --timestamp jdaviz.app
+
+    - name: Create dmg (OSX)
+      # if we do not call always() GHA will && with success()
+      if: ${{ always() && (matrix.os == 'macos') }}
+      # it seems ditto (not zip) should be used in combination with notarization
+      # see https://developer.apple.com/forums/thread/116831
+      # but dmg also works
+      # see https://github.com/glue-viz/glue-standalone-apps/blob/main/.github/workflows/build_stable.yml
+      run: |
+        rm -rf standalone/dist/jdaviz
+        hdiutil create -volname "Jdaviz" -srcfolder standalone/dist -ov -format UDZO standalone/dist/jdaviz.dmg
+
+    - name: Notary step + stapling (OSX)
+      if: ${{ matrix.os == 'macos' }}
+      run: |
+        output=$(xcrun notarytool submit standalone/dist/jdaviz.dmg --apple-id ${{ secrets.NOTARIZATION_USERNAME }} --team-id ${{ secrets.TEAM_ID }} --wait --password ${{ secrets.NOTARIZATION_PASSWORD }}) || true
+        echo "$output"
+        uuid=$(echo "$output" | awk -F '[ :]+' '/id:/ {print $3; exit}')
+        echo "UUID: $uuid"
+        if [[ $output == *"status: Accepted"* ]]; then
+          echo "Great, notarization succeeded, staple it!"
+          xcrun stapler staple standalone/dist/jdaviz.dmg
+        else
+          echo "Log output for failed notarization: $uuid"
+          xcrun notarytool log --apple-id ${{ secrets.NOTARIZATION_USERNAME }} --team-id ${{ secrets.TEAM_ID }} --password ${{ secrets.NOTARIZATION_PASSWORD }} $uuid || true
+        fi
+
+    - name: Validate app (OSX)
+      if: ${{ matrix.os == 'macos' }}
+      run: |
+        spctl -a -vvv -t execute standalone/dist/jdaviz.app
+
+    - name: Run jdaviz cmd in background
+      if: ${{ matrix.os == 'macos' }}
+      run: ./standalone/dist/jdaviz.app/Contents/MacOS/jdaviz-cli imviz&
+
+    - name: Run jdaviz cmd in background
+      if: ${{ matrix.os != 'macos' }}
+      run: ./standalone/dist/jdaviz/jdaviz-cli imviz&
+
+    - name: Install playwright
+      run: (pip install playwright; playwright install chromium)
+
+    - name: Install pytest
+      run: pip install pytest-playwright
+
+    - name: Wait for Voila to get online
+      uses: ifaxity/wait-on-action@v1
+      with:
+        resource: tcp:8866
+        timeout: 60000
+
+    - name: Test standalone
+      run: (cd standalone; touch pytest.ini; JUPYTER_PLATFORM_DIRS=1 pytest test.py --video=on)
+
+    - name: Upload Test artifacts
+      if: always()
+      uses: actions/upload-artifact@v3
+      with:
+        name: test-results-${{ 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: ${{ always() && (matrix.os == 'macos') }}
+      uses: actions/upload-artifact@v3
+      with:
+        name: jdaviz-standlone-${{ matrix.os }}
+        path: standalone/dist/jdaviz.dmg
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -105,6 +105,10 @@ Other Changes and Additions
 - Gaussian smooth plugin excludes results from the gaussian smooth plugin from the input
   dataset dropdown. [#2239]
 
+- CLI launchers no longer require data to be specified [#1960]
+
+- Added direct launchers for each config (e.g. ``specviz``) [#1960]
+
 3.5.1 (unreleased)
 ==================
 

diff --git a/jdaviz/_astropy_init.py b/jdaviz/_astropy_init.py
@@ -0,0 +1,23 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+import os
+import sys
+
+if not hasattr(sys.modules["__main__"], "__file__"):
+    # this happens under pyinstaller when running jdaviz cli
+    # which triggers an error in astropy, so we set it to the
+    # executable path of the cli executable
+    sys.modules["__main__"].__file__ = sys.executable
+
+
+from astropy.tests.runner import TestRunner
+
+__all__ = ['__version__', 'test']
+
+try:
+    from .version import version as __version__
+except ImportError:
+    __version__ = ''
+
+# Create the test function for self test
+test = TestRunner.make_test_runner_in(os.path.dirname(__file__))
+test = TestRunner.make_test_runner_in(os.path.dirname(__file__))
diff --git a/jdaviz/cli.py b/jdaviz/cli.py
@@ -1,5 +1,6 @@
 # Command-line interface for jdaviz
 
+import inspect
 import os
 import pathlib
 import sys
@@ -10,9 +11,11 @@
 
 from jdaviz import __version__
 from jdaviz.app import _verbosity_levels
+from jdaviz import configs
 
 __all__ = ['main']
 
+CONFIGS_DIR = str(pathlib.Path(inspect.getfile(configs)).parent)
 JDAVIZ_DIR = pathlib.Path(__file__).parent.resolve()
 DEFAULT_VERBOSITY = 'warning'
 DEFAULT_HISTORY_VERBOSITY = 'info'
@@ -151,3 +154,27 @@ def _main(config=None):
     main(filepaths=args.filepaths, layout=layout, instrument=args.instrument, browser=args.browser,
          theme=args.theme, verbosity=args.verbosity, history_verbosity=args.history_verbosity,
          hotreload=args.hotreload)
+
+
+def _specviz():
+    _main(config='specviz')
+
+
+def _specviz2d():
+    _main(config='specviz2d')
+
+
+def _imviz():
+    _main(config='imviz')
+
+
+def _cubeviz():
+    _main(config='cubeviz')
+
+
+def _mosviz():
+    _main(config='mosviz')
+
+
+if __name__ == "__main__":
+    _main()
diff --git a/jdaviz/configs/cubeviz/cubeviz.ipynb b/jdaviz/configs/cubeviz/cubeviz.ipynb
@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# PREFIX\n",
+    "from jdaviz import Cubeviz\n",
+    "\n",
+    "cubeviz = Cubeviz(verbosity='JDAVIZ_VERBOSITY', history_verbosity='JDAVIZ_HISTORY_VERBOSITY')\n",
+    "data_path = 'DATA_FILENAME'\n",
+    "if data_path:\n",
+    "    cubeviz.load_data('DATA_FILENAME')\n",
+    "cubeviz.app"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6-final"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/jdaviz/configs/default/default.ipynb b/jdaviz/configs/default/default.ipynb
@@ -0,0 +1,50 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "from jdaviz.app import Application\n",
+    "app = Application(configuration='default')\n",
+    "app.verbosity = 'JDAVIZ_VERBOSITY'\n",
+    "app.history_verbosity = 'JDAVIZ_HISTORY_VERBOSITY'\n",
+    "data_path = 'DATA_FILENAME'\n",
+    "if data_path:\n",
+    "    app.load_data('DATA_FILENAME')\n",
+    "app"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/jdaviz/configs/imviz/imviz.ipynb b/jdaviz/configs/imviz/imviz.ipynb
@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# PREFIX\n",
+    "from jdaviz import Imviz\n",
+    "\n",
+    "imviz = Imviz(verbosity='JDAVIZ_VERBOSITY', history_verbosity='JDAVIZ_HISTORY_VERBOSITY')\n",
+    "data_path = 'DATA_FILENAME'\n",
+    "if data_path:\n",
+    "    imviz.load_data('DATA_FILENAME')\n",
+    "imviz.app"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}