Update GitHub Actions workflows

Use conda environments for better consistency

.github/workflows/coverage_report.yml

@@ -1,33 +1,33 @@
 name: Coverage Report
 on:
   pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'docs/**'
     types: [opened, reopened, synchronize]
-    paths:
-      - '**.py'
 jobs:
   pytest-coverage:
     runs-on: ubuntu-latest
     permissions:
       pull-requests: write
     steps:
-    - uses: actions/checkout@v3
+    - name: Checkout code
+      uses: actions/checkout@v4
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up conda environment with micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: "3.10"
+        cache-environment: true
+        environment-file: conda-environment-dev.yml
+        post-cleanup: all
 
     - name: Install dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install -y libsasl2-dev libldap2-dev libssl-dev
-        python -m pip install --upgrade pip
-        python -m pip install poetry --user
-        python -m poetry install --extras=tango
+      run: "${MAMBA_EXE} run --name mxcubecore poetry install --only=dev,main --extras=tango"
 
     - name: Run and write pytest
       run: |
         set -o pipefail
-        poetry run pytest --cov=mxcubecore --junitxml=pytest.xml --cov-report=term-missing:skip-covered | tee pytest-coverage.txt
+        ${MAMBA_EXE} run --name mxcubecore pytest --cov=mxcubecore --junitxml=pytest.xml --cov-report=term-missing:skip-covered | tee pytest-coverage.txt
 
     - name: Pytest coverage comment
       id: coverage-comment
@@ -40,7 +40,7 @@ jobs:
 
     - name: Check the output coverage
       run: |
-        echo "Coverage Percantage - ${{ steps.coverage-comment.outputs.coverage }}"
+        echo "Coverage Percentage - ${{ steps.coverage-comment.outputs.coverage }}"
         echo "Coverage Warnings - ${{ steps.coverage-comment.outputs.warnings }}"
         echo "Coverage Errors - ${{ steps.coverage-comment.outputs.errors }}"
         echo "Coverage Failures - ${{ steps.coverage-comment.outputs.failures }}"

.github/workflows/pages.yaml

@@ -21,31 +21,24 @@ jobs:
       - name: "Checkout"
         uses: "actions/checkout@v4"  # tested with v4.1.0
 
-      - name: "Set up Python 3.8"
-        uses: "actions/setup-python@v4"  # tested with v4.7.0
+      - name: "Setup conda environment with micromamba"
+        uses: "mamba-org/setup-micromamba@v1"
         with:
-          python-version: "3.8"
-
-      - name: "Install OpenLDAP's dev package with apt"
-        run: |
-          sudo apt-get update
-          sudo apt-get install --no-install-recommends --yes libldap2-dev libsasl2-dev
+          cache-environment: true
+          environment-file: "conda-environment-dev.yml"
+          post-cleanup: "all"
 
       - name: "Install dependencies with Poetry"
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install poetry --user
-          python -m poetry install --only=docs,main
+        run: "${MAMBA_EXE} run --name mxcubecore poetry install --only=docs,main"
 
       - name: "Build documentation with Sphinx"
-        run: |
-          poetry run make --directory=./docs/ html
+        run: "${MAMBA_EXE} run --name mxcubecore make --directory=./docs/ html"
 
       - name: "Upload artifact for GitHub Pages"
         # This could potentially be run only when we intend to deploy...
         # ...but it can be useful to have the artifact for debugging
         # if: "github.ref_name == github.event.repository.default_branch"
-        uses: "actions/upload-pages-artifact@v2"  # tested with v2.0.0
+        uses: "actions/upload-pages-artifact@v3"
         with:
           path: "docs/build/html"
 
@@ -69,11 +62,11 @@ jobs:
     steps:
 
       - name: "Setup GitHub Pages"
-        uses: "actions/configure-pages@v3"  # tested with v3.0.6
+        uses: "actions/configure-pages@v4"
 
       - name: "Deploy to GitHub Pages"
         id: "deployment"
-        uses: "actions/deploy-pages@v2"  # tested with 2.0.4
+        uses: "actions/deploy-pages@v4"
 
 
 ...  # EOF

.github/workflows/pre-commit.yml

@@ -1,29 +1,19 @@
-name: Linting & Code Quality
+name: Pre-commit hooks
 on:
   pull_request:
     types: [opened, reopened, synchronize]
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - name: Checkout
+      uses: actions/checkout@v4
 
+    # Python 3.8 because we want lowest supported version for syntax checks (format, lint)
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: "3.8"
 
-    - name: Install openldap
-      run: |
-        sudo apt-get update && sudo apt-get upgrade -y
-        sudo apt-get install -y libldap2-dev libsasl2-dev slapd ldap-utils tox lcov valgrind
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install poetry --user
-        python -m poetry install
-
-    - name: Run Pre-Commit
-      run: |
-        poetry run pre-commit run --all-files
+    - name: Run pre-commit hooks
+      uses: pre-commit/[email protected]

.github/workflows/tests.yml

@@ -1,32 +1,31 @@
 name: Pytest
 on:
   pull_request:
+    paths-ignore:
+      - "doc/**"
+      - "docs/**"
     types: [opened, reopened, synchronize]
-    paths:
-      - '**.py'
 jobs:
   Python:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout
+        uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Setup conda environment with micromamba for Python ${{ matrix.python-version }}
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install openldap
-        run: sudo apt-get update && sudo apt-get install -y libldap2-dev libsasl2-dev slapd ldap-utils tox lcov valgrind
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+          environment-file: conda-environment-dev.yml
+          post-cleanup: all
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install poetry --user
-          python -m poetry install --extras=tango
+        run: "${MAMBA_EXE} run --name mxcubecore poetry install --extras=tango --only=dev,main"
 
       - name: Test with pytest
-        run: |
-          python -m poetry run pytest --no-cov
+        run: "${MAMBA_EXE} run --name mxcubecore pytest --no-cov"