ci(5): run the Job tester (jote) against every job submodule

.github/workflows/test-jobs.yaml

@@ -0,0 +1,85 @@
+---
+name: test-jobs
+
+# Runs the Data Manager Job Tester ("jote") against every job-based submodule.
+#
+# For each job repository we run 'jote --dry-run' (which does not execute any
+# tests) against every manifest found in its 'data-manager' directory. A
+# dry-run validates the Job Definition and Manifest files against the decoder
+# schemas and lint rules without needing Docker or any running containers.
+#
+# jote is installed from PyPI (https://pypi.org/project/im-jote/) at the version
+# pinned by the JOTE_VERSION variable below, so the check is reproducible; bump
+# that single value to test against a newer tester and its schemas.
+
+env:
+  # The version of the im-jote package (https://pypi.org/project/im-jote/) to
+  # install and run. Change this in one place to move every matrix leg.
+  JOTE_VERSION: '0.13.0'
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+  schedule:
+  # Weekly (Monday 06:24 UTC) so a new jote/schema release that changes
+  # validation is caught even without a repository change.
+  - cron: '24 6 * * 1'
+  workflow_dispatch:
+
+jobs:
+  jote:
+    runs-on: ubuntu-latest
+    strategy:
+      # Test every repository even if one fails, so a single non-compliant
+      # repository does not hide the status of the others.
+      fail-fast: false
+      matrix:
+        repo:
+        - virtual-screening
+        - squonk2-cdk
+        - squonk2-chemaxon
+        - squonk2-fragmenstein
+        - squonk2-jaqpot
+        - squonk2-smartcyp
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v7
+
+    - name: Checkout the ${{ matrix.repo }} submodule
+      run: |
+        # The submodules are declared with SSH URLs; rewrite to anonymous
+        # HTTPS so the (public) job repository can be fetched without a key.
+        git config --global url."https://github.com/".insteadOf "git@github.com:"
+        git submodule update --init -- "${{ matrix.repo }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.10'
+
+    - name: Install jote
+      run: |
+        python -m pip install --upgrade pip
+        pip install "im-jote==${JOTE_VERSION}"
+
+    - name: Dry-run jote against every manifest
+      working-directory: ${{ matrix.repo }}
+      run: |
+        shopt -s nullglob
+        manifests=(data-manager/manifest*.yaml data-manager/manifest*.yml)
+        if [ ${#manifests[@]} -eq 0 ]; then
+          echo "No manifests found in ${{ matrix.repo }}/data-manager"
+          exit 1
+        fi
+        rc=0
+        for manifest in "${manifests[@]}"; do
+          name="$(basename "${manifest}")"
+          echo "::group::jote --manifest ${name} --dry-run"
+          # --allow-no-tests keeps this a pure definition/schema check: a
+          # manifest whose jobs have no tests must not fail the dry-run.
+          jote --manifest "${name}" --dry-run --allow-no-tests || rc=1
+          echo "::endgroup::"
+        done
+        exit ${rc}