Update PR-test.yml

Author: edeno

.github/workflows/PR-test.yml

@@ -1,46 +1,108 @@
 name: PR Test
 
-on: push
+on:
+  push:
+    branches: [ main, master ]
+    paths-ignore:
+      - '**.md'
+      - 'docs/**'
+  pull_request:
+    branches: [ main, master ]
+    paths-ignore:
+      - '**.md'
+      - 'docs/**'
+
+# Auto-cancel in-progress runs for the same branch/PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# Principle of least privilege
+permissions:
+  contents: read
 
 jobs:
   run-tests:
+    name: Tests (${{ matrix.os }} • py${{ matrix.python }})
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest] #, macos-latest, windows-latest]
-    env:
-      OS: ${{ matrix.os }}
-      PYTHON: '3.11.*'
+        os: [ ubuntu-latest ] # add macos-latest, windows-latest as needed
+        python: [ "3.11" ]
+
     steps:
-    - name: Cancel Workflow Action
-      uses: styfle/[email protected]
-      with:
-        access_token: ${{ github.token }}
-    - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.11.*'
-    - name: Set up conda environment
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: '3.11.*'
-        miniforge-version: latest
-        use-mamba: true
-        channels: conda-forge,franklab,edeno
-        channel-priority: true
-        activate-environment: replay_trajectory_classification
-        environment-file: environment.yml
-    - name: Install replay_trajectory_classification
-      shell: bash -l {0}
-      run: |
-        pip install -e .
-    - name: Test notebooks
-      shell: bash -l {0}
-      run: |
-        jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute notebooks/tutorial/01-Introduction_and_Data_Format.ipynb
-        jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute notebooks/tutorial/02-Decoding_with_Sorted_Spikes.ipynb
-        jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute notebooks/tutorial/03-Decoding_with_Clusterless_Spikes.ipynb
-        jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute notebooks/tutorial/04-Classifying_with_Sorted_Spikes.ipynb
-        jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute notebooks/tutorial/05-Classifying_with_Clusterless_Spikes.ipynb
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Use Miniforge + mamba for faster, reproducible env solves
+      - name: Set up Conda (Miniforge)
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          use-mamba: true
+          auto-update-conda: false
+          auto-activate-base: false
+          channel-priority: strict
+          channels: conda-forge,franklab,edeno
+          activate-environment: replay_trajectory_classification
+          environment-file: environment.yml
+          python-version: ${{ matrix.python }}
+
+      # Cache conda packages to speed up solves
+      - name: Cache conda pkgs
+        uses: actions/cache@v4
+        with:
+          path: ~/.conda/pkgs
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+
+      - name: Show Conda info
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          python -V
+          pip install --upgrade pip
+          pip install -e .
+
+      # Execute tutorial notebooks to ensure they run end-to-end
+      - name: Test notebooks
+        shell: bash -l {0}
+        env:
+          NB_KERNEL: python3
+        run: |
+          set -euo pipefail
+          for nb in \
+            notebooks/tutorial/01-Introduction_and_Data_Format.ipynb \
+            notebooks/tutorial/02-Decoding_with_Sorted_Spikes.ipynb \
+            notebooks/tutorial/03-Decoding_with_Clusterless_Spikes.ipynb \
+            notebooks/tutorial/04-Classifying_with_Sorted_Spikes.ipynb \
+            notebooks/tutorial/05-Classifying_with_Clusterless_Spikes.ipynb
+          do
+            echo "Executing $nb"
+            jupyter nbconvert \
+              --to notebook \
+              --inplace \
+              --ExecutePreprocessor.kernel_name="$NB_KERNEL" \
+              --ExecutePreprocessor.timeout=1800 \
+              --execute "$nb"
+          done
+
+      # Always upload executed notebooks to aid debugging
+      - name: Upload executed notebooks
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: executed-notebooks-${{ matrix.os }}-py${{ matrix.python }}
+          path: |
+            notebooks/tutorial/*.ipynb
+          if-no-files-found: warn