updated deployment workflow

.github/actions/wait-for-pypi-version/action.yaml

@@ -0,0 +1,93 @@
+name: 'Wait for PyPI version'
+description: 'Wait for a specific package version to become available on PyPI or TestPyPI'
+inputs:
+  repository:
+    description: 'PyPI repository type: "pypi" or "testpypi"'
+    required: true
+  package:
+    description: 'Package name'
+    required: true
+  version:
+    description: 'Package version to wait for'
+    required: true
+  max_attempts:
+    description: 'Maximum number of retry attempts'
+    required: false
+    default: '30'
+  wait_seconds:
+    description: 'Seconds to wait between attempts'
+    required: false
+    default: '10'
+
+runs:
+  using: composite
+  steps:
+    - name: Install requests
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install requests
+
+    - name: Wait for version to be available
+      shell: python
+      env:
+        REPOSITORY: ${{ inputs.repository }}
+        PACKAGE: ${{ inputs.package }}
+        VERSION: ${{ inputs.version }}
+        MAX_ATTEMPTS: ${{ inputs.max_attempts }}
+        WAIT_SECONDS: ${{ inputs.wait_seconds }}
+      run: |
+        import os
+        import sys
+        import time
+
+        import requests
+
+        repository = os.environ["REPOSITORY"].strip().lower()
+        package = os.environ["PACKAGE"]
+        version = os.environ["VERSION"]
+        max_attempts = int(os.environ.get("MAX_ATTEMPTS", "30"))
+        wait_seconds = int(os.environ.get("WAIT_SECONDS", "10"))
+
+        if repository == "testpypi":
+            api_url = f"https://test.pypi.org/pypi/{package}/json"
+            repo_name = "TestPyPI"
+        elif repository == "pypi":
+            api_url = f"https://pypi.org/pypi/{package}/json"
+            repo_name = "PyPI"
+        else:
+            print(
+                f"ERROR: repository must be 'pypi' or 'testpypi', got {repository!r}",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+
+        for attempt in range(max_attempts):
+            try:
+                r = requests.get(api_url, timeout=10)
+                r.raise_for_status()
+                data = r.json()
+                versions = data.get("releases", {})
+                keys = list(versions.keys())
+                print("Available versions:", keys[-10:])  # Show last 10 versions
+                if version in versions:
+                    print(f"✓ Version {version} is available on {repo_name}")
+                    print(f"Version {version} is now available on {repo_name}")
+                    sys.exit(0)
+                print(f"✗ Version {version} is NOT available on {repo_name}")
+            except Exception as e:
+                print(f"Error checking version: {e}")
+
+            current = attempt + 1
+            print(
+                f"Attempt {current}/{max_attempts}: Version {version} not yet available "
+                f"on {repo_name}, waiting {wait_seconds} seconds..."
+            )
+            time.sleep(wait_seconds)
+
+        print(
+            f"ERROR: Version {version} did not become available on {repo_name} "
+            f"after {max_attempts} attempts",
+            file=sys.stderr,
+        )
+        sys.exit(1)

.github/workflows/deploy.yaml

@@ -1,4 +1,4 @@
-name: Build and upload to PyPi
+name: Build and upload to PyPI
 
 on:
   push:
@@ -8,52 +8,208 @@ on:
     types:
       - published
 
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
+  cancel-in-progress: false
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
-  test_pypi_push:
+  build:
+    name: Build package
+    if: github.repository == 'Becksteinlab/propkatraj'
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.extract-version.outputs.version }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install "setuptools>=61.2,<81" build twine
+
+      - name: Build package (wheel and sdist)
+        run: python -m build
+
+      - name: Check package
+        run: twine check dist/*
+
+      - name: Extract package version
+        id: extract-version
+        run: |
+          WHEEL_FILE=$(ls dist/*.whl)
+          VERSION=$(basename "$WHEEL_FILE" | sed -n 's/propkatraj-\([^-]*\)-.*/\1/p')
+          if [ -z "$VERSION" ]; then
+            pip install "$WHEEL_FILE" --quiet
+            VERSION=$(python -c "import propkatraj; print(propkatraj.__version__)")
+            pip uninstall -y propkatraj --quiet
+          fi
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+          echo "Extracted version: $VERSION"
+
+      - name: Upload dist files
+        uses: actions/upload-artifact@v7
+        with:
+          name: dist-files
+          path: dist/
+          retention-days: 1
+
+  test-pytest:
+    name: Run tests
+    if: github.repository == 'Becksteinlab/propkatraj'
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Download dist files
+        uses: actions/download-artifact@v8
+        with:
+          name: dist-files
+          path: dist/
+
+      - name: Install wheel with test extras
+        run: |
+          python -m pip install --upgrade pip
+          WHEEL_FILE=$(ls dist/*.whl)
+          pip install "${WHEEL_FILE}[test]"
+
+      - name: Test import
+        run: |
+          python -c "import propkatraj; print(f'Package {propkatraj.__version__} imported successfully')"
+
+      - name: Run tests
+        run: pytest -v --pyargs propkatraj.tests
+
+  deploy-testpypi:
+    name: Deploy to TestPyPI
+    if: |
+      github.repository == 'Becksteinlab/propkatraj' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
+    runs-on: ubuntu-latest
+    needs: [build, test-pytest]
     environment:
       name: TestPyPi
       url: https://test.pypi.org/p/propkatraj
     permissions:
       id-token: write
+    steps:
+      - name: Download dist files
+        uses: actions/download-artifact@v8
+        with:
+          name: dist-files
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+          skip-existing: true
+
+  deploy-pypi:
+    name: Deploy to PyPI
     if: |
       github.repository == 'Becksteinlab/propkatraj' &&
-      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
-    name: "TestPyPi: Build and upload pure Python wheels"
+      (github.event_name == 'release' && github.event.action == 'published')
     runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: testpypi_deploy
-        uses: MDAnalysis/pypi-deployment@main
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-        with:
-          test_submission: true
-          package_name: 'propkatraj'
-          module_name: 'propkatraj'
-          test_deps: 'pytest MDAnalysisTests'
-          tests: true
-
-  pypi_push:
+    needs: [build, test-pytest]
     environment:
       name: PyPi
       url: https://pypi.org/p/propkatraj
     permissions:
       id-token: write
+    steps:
+      - name: Download dist files
+        uses: actions/download-artifact@v8
+        with:
+          name: dist-files
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  test-deployed-testpypi:
+    name: Test deployed package (TestPyPI)
     if: |
       github.repository == 'Becksteinlab/propkatraj' &&
-      (github.event_name == 'release' && github.event.action == 'published')
-    name: "PyPi: Build and upload pure Python wheels"
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
     runs-on: ubuntu-latest
+    needs: [build, deploy-testpypi]
+    steps:
+      - name: Checkout repository for actions
+        uses: actions/checkout@v7
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Wait for version to be available on TestPyPI
+        uses: ./.github/actions/wait-for-pypi-version
+        with:
+          repository: testpypi
+          package: propkatraj
+          version: ${{ needs.build.outputs.version }}
+
+      - name: Install from TestPyPI
+        run: |
+          python -m pip install --upgrade pip
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ "propkatraj[test]==${{ needs.build.outputs.version }}"
+
+      - name: Test import
+        run: |
+          python -c "import propkatraj; print(f'Package {propkatraj.__version__} imported successfully from TestPyPI')"
+
+      - name: Run tests
+        run: pytest -v --pyargs propkatraj.tests
 
+  test-deployed-pypi:
+    name: Test deployed package (PyPI)
+    if: |
+      github.repository == 'Becksteinlab/propkatraj' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    runs-on: ubuntu-latest
+    needs: [build, deploy-pypi]
     steps:
-      - uses: actions/checkout@v4
-
-      - name: pypi_deploy
-        uses: MDAnalysis/pypi-deployment@main
-        if: github.event_name == 'release' && github.event.action == 'published'
-        with:        
-          package_name: 'propkatraj'
-          module_name: 'propkatraj'
-          test_deps: 'pytest MDAnalysisTests'     
-          tests: true
+      - name: Checkout repository for actions
+        uses: actions/checkout@v7
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Wait for version to be available on PyPI
+        uses: ./.github/actions/wait-for-pypi-version
+        with:
+          repository: pypi
+          package: propkatraj
+          version: ${{ needs.build.outputs.version }}
+
+      - name: Install from PyPI
+        run: |
+          python -m pip install --upgrade pip
+          pip install "propkatraj[test]==${{ needs.build.outputs.version }}"
+
+      - name: Test import
+        run: |
+          python -c "import propkatraj; print(f'Package {propkatraj.__version__} imported successfully from PyPI')"
+
+      - name: Run tests
+        run: pytest -v --pyargs propkatraj.tests