Fix notebook tests

.github/workflows/notebooks_dispatch.yml

@@ -0,0 +1,51 @@
+name: Notebooks Dispatch
+
+on:
+  # Allows wourkflow to be called by other workflows
+  workflow_call:
+    inputs:
+      clone-irdb:
+        type: boolean
+        description: If True, use clone of IRDB repo instead of package download.
+
+jobs:
+  run_notebooks:
+    strategy:
+      matrix:
+        # Run all operating systems, because this is the first interaction
+        # that users have with ScopeSim / IRDB.
+        # However, only use minimum and maximum supported Python version,
+        # as the IRDB download often fails.
+        # As of 2023/07/19, this test still often fails. See
+        # https://github.com/AstarVienna/ScopeSim/issues/254
+        # For now, only run on one configuration, as having one green test
+        # is more useful than 5 green and one red. The others can be enabled
+        # once we fix the problem properly.
+        # os: [ubuntu-latest, windows-latest, macos-latest]
+        # python-version: ['3.8', '3.11']
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: "1.7.1"
+
+      - name: Install dependencies
+        run: |
+          poetry install --with test --with dev --all-extras
+
+      - name: Run notebooks
+        env:
+          TQDM_MININTERVAL: 10
+          CLONE:  ${{ inputs.clone-irdb && '--clone-irdb' || '' }}
+        run: ./runnotebooks.sh $CLONE --delete

.github/workflows/notebooks_with_irdb_clone.yml

@@ -5,12 +5,10 @@ on:
     branches:
       - master
       - dev_master
-      - dev_spectroscopy
   pull_request:
     branches:
       - master
       - dev_master
-      - dev_spectroscopy
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -21,31 +19,7 @@ on:
 
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Run only on a minimal subset of the matrix, as this is ran on many
-        # commits.
-        os: [ubuntu-latest]
-        python-version: ['3.11']
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          # Install this version of ScopeSim. Otherwise the PyPI version of
-          # ScopeSim will be installed when the test-requriments
-          # are installed, because ScopeSim is a dependency of
-          # ScopeSim_Templates.
-          pip install .
-          pip install .[dev,test]
-      - name: Run notebooks
-        env:
-          TQDM_MININTERVAL: 10
-        run: ./runnotebooks.sh --checkout-irdb --delete
+  call-notebooks-with-clone:
+    uses: ./.github/workflows/notebooks_dispatch.yml
+    with:
+      clone-irdb: true

.github/workflows/notebooks_with_irdb_download.yml

@@ -10,39 +10,5 @@ on:
 
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Run all operating systems, because this is the first interaction
-        # that users have with ScopeSim / IRDB.
-        # However, only use minimum and maximum supported Python version,
-        # as the IRDB download often fails.
-        # As of 2023/07/19, this test still often fails. See
-        # https://github.com/AstarVienna/ScopeSim/issues/254
-        # For now, only run on one configuration, as having one green test
-        # is more useful than 5 green and one red. The others can be enabled
-        # once we fix the problem properly.
-        # os: [ubuntu-latest, windows-latest, macos-latest]
-        # python-version: ['3.8', '3.11']
-        os: [ubuntu-latest]
-        python-version: ['3.11']
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          # Install this version of ScopeSim. Otherwise the PyPI version of
-          # ScopeSim will be installed when the test-requriments
-          # are installed, because ScopeSim is a dependency of
-          # ScopeSim_Templates.
-          pip install .
-          pip install .[dev,test]
-      - name: Run notebooks
-        # No --checkout-irdb to download the IRDB as a normal end user would.
-        run: ./runnotebooks.sh --delete
+  call-notebooks-without-clone:
+    uses: ./.github/workflows/notebooks_dispatch.yml

pyproject.toml

@@ -98,6 +98,9 @@ filterwarnings = [
     "ignore:'cgi'*:DeprecationWarning",
     "ignore:The py23*:DeprecationWarning",
     "ignore:datetime.datetime.utcfromtimestamp()*:DeprecationWarning",
+    # Pytest Notebook stuff
+    "ignore:The*:pytest.PytestRemovedIn8Warning",
+    "ignore:Proactor*:RuntimeWarning"
 ]
 
 [tool.coverage.report]

runnotebooks.sh

@@ -1,53 +1,56 @@
 #!/usr/bin/env bash
 
-echo "# Running Notebooks Tests" >> $GITHUB_STEP_SUMMARY
+# https://betterdev.blog/minimal-safe-bash-script-template/
+set -Eeuo pipefail
+
+# Set stdout as default so the script can be ran on the commandline.
+STEP_SUMMARY="${GITHUB_STEP_SUMMARY:-/dev/stdout}"
+
+echo "# Running Notebooks Tests" >> $STEP_SUMMARY
 
 if [[ "x${1}" == "x--clone-irdb" ]] ; then
   # Cloning IRDB
-  if [[ ! -e irdb ]] ; then
-    echo "_Cloning IRDB_" >> $GITHUB_STEP_SUMMARY
-    git clone https://github.com/AstarVienna/irdb.git
+  if [[ ! -e inst_pkgs ]] ; then
+    echo "_Cloning IRDB_" >> $STEP_SUMMARY
+    git clone https://github.com/AstarVienna/irdb.git inst_pkgs
   fi
 
-  echo "## Symlinks" >> $GITHUB_STEP_SUMMARY
+  echo "## Patch notebooks" >> $STEP_SUMMARY
   # https://github.com/koalaman/shellcheck/wiki/SC2044
-  find . -iname "*.ipynb" -printf '%h\0' | sort -z | uniq -z | while IFS= read -r -d '' dirnotebooks; do
+  find ./docs -iname "*.ipynb" -printf '%h\0' | sort -z | uniq -z | while IFS= read -r -d '' dirnotebooks; do
     echo "${dirnotebooks}"
-    echo "- ${dirnotebooks}" >> $GITHUB_STEP_SUMMARY
-    dirinstpkgs="${dirnotebooks}/inst_pkgs"
-    if [[ (! -e ./docs/source/examples/inst_pkgs) && (! -L ./docs/source/examples/inst_pkgs) ]] ; then
-      echo "Creating symlink to irdb: ${dirinstpkgs}" >> $GITHUB_STEP_SUMMARY
-      ln -s irdb "${dirinstpkgs}"
-    else
-      echo "Directory exists, not creating symlink: ${dirinstpkgs}" >> $GITHUB_STEP_SUMMARY
-    fi
-
-    # Comment out any download_package[s] in the notebooks.
-    pushd "${dirnotebooks}" || exit 1
+    echo "- ${dirnotebooks}" >> $STEP_SUMMARY
+    pushd "${dirnotebooks}"
+      # Comment out any download_package[s] in the notebooks.
       sed -i -E 's|"(.*\.download_package)|"#\1|g' -- *.ipynb
-    popd || exit 1
+      # Comment out explicitly setting the local_packages_path to somewhere.
+      sed -i -E 's|"(.*__config__\[\\"!SIM.file.local_packages_path)|"#\1|g' -- *.ipynb
+    popd
   done
 fi
 
 
-echo "## Notebooks tested" >> $GITHUB_STEP_SUMMARY
+echo "## Notebooks tested" >> $STEP_SUMMARY
 # https://github.com/koalaman/shellcheck/wiki/SC2044
-find . -iname "*.ipynb" -print0 | while IFS= read -r -d '' fnnotebook
+find ./docs -iname "*.ipynb" -print0 | while IFS= read -r -d '' fnnotebook
 do
   echo "Testing ${fnnotebook} ..."
   fnpy="${fnnotebook%.ipynb}.py"
 
   # Convert .ipynb file to .py.
-  jupytext --to py "${fnnotebook}"
+  poetry run jupytext --to py "${fnnotebook}"
 
   # Run the python script and quit on first error.
-  python "${fnpy}" || exit 1
-  echo "- ${fnnotebook}" >> $GITHUB_STEP_SUMMARY
+  poetry run python "${fnpy}"
+  echo "- ${fnnotebook}" >> $STEP_SUMMARY
 
   # Delete generated files if --delete is specified.
   # By default do not delete any files.
+  # The delete functionality is intended to make it easy for developers to test
+  # all the notebooks on their own machine.
   if [ "x$1" = "x--delete" ]
   then
+    echo "Removing ${fnpy}"
     rm "${fnpy}"
   fi