Merge pull request #13 from MDAnalysis/hmacdope-patch-2

Update gh-ci.yaml so that GitHub CI works
MDAnalysis · Jul 24, 2024 · 74f52d9 · 74f52d9
2 parents 802e09f + 3710ae4
commit 74f52d9
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Showing 3 changed files with 29 additions and 41 deletions.
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -12,41 +12,21 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * 0"
 
-concurrency:
-  # Specific group naming so CI is only cancelled
-  # within same PR or on merge to main
-  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
-  cancel-in-progress: true
+
 
 defaults:
   run:
     shell: bash  -l {0} 
 
 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 == 'lunamorrow/mda_openbabel_converter'"
-    needs: environment-config
+    if: "github.repository == 'MDAnalysis/mda-openbabel-converter'"
     runs-on: ${{ matrix.os }}
     strategy:
         fail-fast: false
         matrix:
           os: [macOS-latest, ubuntu-latest, windows-latest]
-          python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }}
+          python-version: ["3.10", "3.11", "3.12"]
           mdanalysis-version: ["latest", "develop"]
 
     steps:
@@ -61,12 +41,11 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
         add-pip-as-python-dependency: true
-        architecture: x64
 
         miniforge-variant: Mambaforge
         use-mamba: true
@@ -85,11 +64,19 @@ jobs:
         install-tests: false
         installer:  mamba 
         shell: bash  -l {0} 
-
+
+    - name: Setup Conda Environment
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: devtools/conda-envs/test_env.yaml
+        environment-name: mda-ob
+        create-args: >-
+          python==${{ matrix.python-version }}
+
     - name: Install package
       run: |
         python --version
-        python -m pip install .  --no-deps 
+        python -m pip install .  --no-deps
 
     - name: Python information
       run: |
@@ -103,29 +90,29 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest -n 2 -v --cov=mda_openbabel_converter --cov-report=xml --color=yes mda_openbabel_converter/tests/
+        pytest -n auto -v --cov=mda_openbabel_converter --cov-report=xml --color=yes mda_openbabel_converter/tests/
 
     - name: codecov
-      if: github.repository == 'lunamorrow/mda_openbabel_converter' && github.event_name != 'schedule'
+      if: github.repository == 'MDAnalysis/mda_openbabel_converter' && github.event_name != 'schedule'
       uses: codecov/codecov-action@v3
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         verbose: True
 
 
   pylint_check:
-    if: "github.repository == 'lunamorrow/mda_openbabel_converter'"
-    needs: environment-config
+    if: "github.repository == 'MDAnalysis/mda_openbabel_converter'"
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install Pylint
       run: |
@@ -141,17 +128,16 @@ jobs:
 
 
   pypi_check:
-    if: "github.repository == 'lunamorrow/mda_openbabel_converter'"
-    needs: environment-config
+    if: "github.repository == 'MDAnalysis/mda-openbabel-converter'"
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
-      uses: actions/setup-python@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -10,6 +10,9 @@ dependencies:
   # MDAnalysis
   - MDAnalysis
 
+  # OpenBabel
+  - openbabel
+
   # Testing
   - pytest
   - pytest-cov

diff --git a/mda_openbabel_converter/data/files.py b/mda_openbabel_converter/data/files.py
@@ -12,6 +12,5 @@
     "MDANALYSIS_LOGO",  # example file of MDAnalysis logo
 ]
 
-from pkg_resources import resource_filename
-
-MDANALYSIS_LOGO = resource_filename(__name__, "mda.txt")
+import importlib.resources
+MDANALYSIS_LOGO = importlib.resources.files(__name__) / "mda.txt"