Merge branch 'main' into main

.github/actions/run-cookie-ci/action.yaml

@@ -20,6 +20,9 @@ inputs:
     description: email associated with GitHub user
     required: true
     default: [email protected]
+  CODECOV_TOKEN:
+    description: Codecov token
+    required: true
 
 runs:
   using: "composite"
@@ -54,4 +57,6 @@ runs:
       shell: bash
       run: |
         docker images
-        act --job main-tests --platform ubuntu-latest=act-conda
+        sed -i -e 's/fail_ci_if_error: true/fail_ci_if_error: false/g' .github/workflows/gh-ci.yaml
+        cat .github/workflows/gh-ci.yaml
+        act --job main-tests --platform ubuntu-latest=act-conda -s CODECOV_TOKEN=${{ inputs.CODECOV_TOKEN }} -p=false

.github/workflows/gh-ci.yaml

@@ -19,6 +19,7 @@ defaults:
 env:
     ARTIFACT_NAME: demo-mdakit-repos
     OUTPUT_DIRECTORY: /home/runner/example_outputs
+    OUTPUT_COOKIE_SUBDIRECTORY: TestMDAKit_with_host_MDAnalysis_condaforge-deps_and_ReadTheDocs/mdakit-cookie
     GH_USER: github-actions
     GH_EMAIL: "[email protected]"
     GH_REPOSITORY: "github.com/${{ github.repository }}.git"
@@ -60,19 +61,26 @@ jobs:
         run: |
           # --keep-test-outputs also saves the generated repositories
           if [[ ${{ matrix.os }} == "ubuntu-latest" ]] ; then
-            PYTEST_FLAGS="--keep-test-outputs $OUTPUT_DIRECTORY"
+            PYTEST_FLAGS="--keep-test-outputs ${{ env.OUTPUT_DIRECTORY }}"
           else
             PYTEST_FLAGS=""
           fi
           echo "PYTEST_FLAGS=${PYTEST_FLAGS}"
           
           pytest tests/ $PYTEST_FLAGS
 
+      - name: check cookie CI presence
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: |
+          ls -la ${{ env.OUTPUT_DIRECTORY }}/
+          ls -la ${{ env.OUTPUT_DIRECTORY }}/${{ env.OUTPUT_COOKIE_SUBDIRECTORY }}/
+
       - name: Run cookie CI
         if: ${{ matrix.os == 'ubuntu-latest' }}
         uses: ./.github/actions/run-cookie-ci
         with:
-          source-directory: ${{ env.OUTPUT_DIRECTORY }}/TestMDAKit_with_host_MDAnalysis_condaforge-deps_and_ReadTheDocs/mdakit-cookie
+          source-directory: ${{ env.OUTPUT_DIRECTORY }}/${{ env.OUTPUT_COOKIE_SUBDIRECTORY }}
+          CODECOV_TOKEN: ${{ secrets.COOKIE_CODECOV_TOKEN }}
 
       - name: Upload artifact
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.last-n-minor-python-release == 0 }}

tests/test_output.py

@@ -61,7 +61,7 @@ def test_write_outputs(
     kitter = CookiecutterMDAKit(
         project_name=project_name,
         repo_name="mdakit-cookie",
-        package_name="mdakit_cookie",
+        package_name="cookiekit",
         github_username="test-user-account",
         github_host_account=github_host_account,
         description=description,

{{cookiecutter.repo_name}}/.github/workflows/{{cookiecutter._ci_name}}.yaml

@@ -23,31 +23,21 @@ defaults:
     shell: bash {% if cookiecutter.__dependency_source != 'pip' %} -l {0} {% endif %}
 
 jobs:
-  environment-config:
-    runs-on: ubuntu-latest
-    outputs:
-      stable-python-version: {{ "${{ steps.get-compatible-python.outputs.stable-python }}" }}
-      python-matrix: {{ "${{ steps.get-compatible-python.outputs.python-versions }}" }}
-    steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-
-      - id: get-compatible-python
-        uses: MDAnalysis/mdanalysis-compatible-python@main
-        with:
-          release: "latest"
-
   main-tests:
     if: "github.repository == '{{ cookiecutter.github_host_account }}/{{ cookiecutter.repo_name }}'"
-    needs: environment-config
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-latest, ubuntu-latest, windows-latest]
-          python-version: {% raw %}${{ fromJSON(needs.environment-config.outputs.python-matrix) }}{% endraw %}
+          os: [ubuntu-latest, macOS-latest, windows-latest]
           mdanalysis-version: ["latest", "develop"]
+          python-version: ["3.10", "3.11", "3.12"]
+          exclude:
+            # Entries here exclude particular combinations of the matrix
+            # Edit or remove as particular combinations come into or out of date
+            # Below we exclude runs with the latest release and Python 3.12
+            - mdanalysis-version: "latest"
+              python-version: "3.12"
 
     steps:
     - uses: actions/checkout@v4
@@ -123,11 +113,19 @@ jobs:
         file: coverage.xml
         name: codecov-{{ '${{ matrix.os }}' }}-py{{ '${{ matrix.python-version }}' }}
         verbose: True
+        # to upload coverage reports, set a secret called CODECOV_TOKEN
+        # in the repository settings
+        # (Obtain this from the Codecov website after setting up the repository there)
+        token: {{ '${{ secrets.CODECOV_TOKEN }}' }}
+        # To fail the CI if there's an error, keep this set to true
+        # If repository forks need to run CI, you may need to set this to false
+        # Forks can't access the CODECOV_TOKEN secret,
+        # and a failed upload registers as an error
+        fail_ci_if_error: true
 
 
   pylint_check:
     if: "github.repository == '{{ cookiecutter.github_host_account }}/{{ cookiecutter.repo_name }}'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
@@ -136,7 +134,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: {{ '${{ needs.environment-config.outputs.stable-python-version }}' }}
+        python-version: "3.11"
 
     - name: Install Pylint
       run: |
@@ -153,16 +151,15 @@ jobs:
 
   pypi_check:
     if: "github.repository == '{{ cookiecutter.github_host_account }}/{{ cookiecutter.repo_name }}'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python {{ '${{ needs.environment-config.outputs.stable-python-version }}' }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: {{ '${{ needs.environment-config.outputs.stable-python-version }}' }}
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |