Fix build test (#193)

* refactor pipelines
* switch to MANIFEST.in
* bump version

.github/workflows/_build-package.yml

@@ -0,0 +1,161 @@
+name: build-package
+on:
+    workflow_call:
+      inputs:
+        check-prerelease:
+          default: false
+          required: false
+          type: boolean
+        test-files:
+          default: true
+          required: false
+          type: boolean
+        test-imports:
+          default: false
+          required: false
+          type: boolean
+        cache-package:
+          default: true
+          required: false
+          type: boolean
+        upload-package:
+          default: false
+          required: false
+          type: boolean
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  build:
+    name: Build ProLIF package
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Get prerelease version tags
+      if: inputs.check-prerelease
+      id: prerelease-check
+      run: |
+        py_dirty_tag=$(awk '/__version__ = "[[:digit:]+]\.[[:digit:]+]\.[[:digit:]+]\-.+"/ {print $3}' ./prolif/_version.py)
+        py_is_pre=$(test -z "$py_dirty_tag" && echo "false" || echo "true")
+        echo "py=$py_is_pre" >> $GITHUB_OUTPUT
+
+    - name: Fail if prerelease is not correctly versioned
+      if: (inputs.check-prerelease) && !( steps.prerelease-check.outputs.py )
+      uses: actions/github-script@v3
+      with:
+        script: |
+          core.setFailed("Version is not tagged as a prerelease")
+
+    - name: Install python with pip
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: "pip"
+
+    - name: Install dependencies for packaging
+      run: |
+        pip install setuptools wheel build virtualenv
+
+    - name: Check python installation
+      run: |
+        which python
+        python --version
+        pip --version
+        pip list
+
+    - name: Build package
+      run: |
+        python -m build .
+    
+    - name: List output
+      run: |
+        ls -lah dist/*
+
+    - name: List .tar.gz content
+      run: |
+        tar -ztvf dist/prolif-*.tar.gz
+    
+    - name: Ensure tests and data included in source dist
+      if: inputs.test-files
+      run: |
+        tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/tests/.+' || exit 1
+        tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/tests/conftest.py' || exit 1
+        tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/tests/plotting/.+' || exit 1
+        tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/.+' || exit 1
+        tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/vina/.+' || exit 1
+
+    - name: Cache package
+      if: inputs.cache-package
+      uses: actions/cache/save@v3
+      with:
+        path: |
+          dist/prolif-*.whl
+          dist/prolif-*.tar.gz
+        key: prolif-${{ runner.os }}-${{ github.sha }}
+
+    - name: Expose package as artifact
+      if: inputs.upload-package
+      uses: actions/upload-artifact@v4
+      with:
+        name: prolif-package
+        path: |
+          dist/prolif-*.whl
+          dist/prolif-*.tar.gz
+        if-no-files-found: error
+        retention-days: 20
+
+  test-build:
+    name: Test ProLIF build
+    runs-on: ubuntu-latest
+    needs: [build]
+    if: (inputs.test-imports) && (inputs.cache-package)
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Install python with pip
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: "pip"
+
+    - name: Install requirements
+      run: |
+        pip install rdkit
+
+    - name: Retrieve cached package
+      uses: actions/cache/restore@v3
+      id: cache-prolif
+      with:
+        path: |
+          dist/prolif-*.whl
+          dist/prolif-*.tar.gz
+        key: prolif-${{ runner.os }}-${{ github.sha }}
+
+    - name: Install from tar.gz
+      run: |
+        pip install dist/prolif-*.tar.gz
+
+    - name: Test tar.gz install
+      working-directory: scripts/
+      run: |
+        python test_build.py
+
+    - name: Remove previous ProLIF install
+      run: |
+        pip uninstall -y prolif
+
+    - name: Install from wheel
+      run: |
+        pip install dist/prolif-*.whl
+
+    - name: Test wheel install
+      working-directory: scripts/
+      run: |
+        python test_build.py

.github/workflows/build.yml

@@ -8,52 +8,31 @@ defaults:
   run:
     shell: bash -l {0}
 
-env:
-  IS_PRERELEASE: ${{ github.event_name == 'workflow_dispatch' }}
-
 jobs:
-  build-n-publish:
-    name: Build and publish to PyPI
+  build:
+    name: Build package
+    uses: ./.github/workflows/_build-package.yml
+    with:
+      check-prerelease: ${{ github.event_name == 'workflow_dispatch' }}
+      cache-package: true
+      upload-package: true
+      test-files: true
+      test-imports: true
+
+  publish:
+    name: Publish to PyPI
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Get prerelease version tags
-      if: env.IS_PRERELEASE == 'true'
-      run: |
-        py_dirty_tag=$(awk '/__version__ = "[[:digit:]+]\.[[:digit:]+]\.[[:digit:]+]\-.+"/ {print $3}' ./prolif/_version.py)
-        py_is_pre=$(test -z "$py_dirty_tag" && echo "false" || echo "true")
-        echo "py_is_pre=$py_is_pre" >> $GITHUB_ENV
-
-    - name: Fail if prerelease is not correctly versioned
-      if: ( env.IS_PRERELEASE == 'true' ) && !( env.py_is_pre )
-      uses: actions/github-script@v3
+    - name: Retrieve cached package
+      uses: actions/cache/restore@v3
+      id: cache-prolif
       with:
-        script: |
-          core.setFailed("Versions are not tagged as a prerelease")
-
-    - name: Install python with pip
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.8
-
-    - name: Install dependencies for packaging
-      run: |
-        pip install build
-
-    - name: Check python installation
-      run: |
-        which python
-        python --version
-        pip --version
-        pip list
-
-    - name: Build package
-      run: |
-        python -m build
+        path: |
+          dist/prolif-*.whl
+          dist/prolif-*.tar.gz
+        key: prolif-${{ runner.os }}-${{ github.sha }}
 
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        password: ${{ secrets.PYPI_TOKEN }}
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/ci.yml

@@ -17,8 +17,20 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  tests:
-    name: ${{ matrix.label }}
+  build:
+    name: Build
+    # only run once if internal PR
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+    uses: ./.github/workflows/_build-package.yml
+    with:
+      check-prerelease: ${{ github.event_name == 'workflow_dispatch' }}
+      cache-package: true
+      upload-package: true
+      test-files: true
+      test-imports: true
+
+  unit-tests:
+    name: Test ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
     # only run once if internal PR
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
@@ -42,7 +54,8 @@ jobs:
             coverage: false
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout
+        uses: actions/checkout@v4
 
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -74,16 +87,6 @@ jobs:
           pip install .[dev]
           pip list
 
-      - name: Build
-        run: |
-          python -m build
-
-      - name: Ensure tests and data included in source dist
-        run: |
-          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/tests/.+' || exit 1
-          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/.+' || exit 1
-          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/vina/.+' || exit 1
-
       - name: Run tests
         run: |
           pytest --color=yes --disable-pytest-warnings --cov=prolif --cov-report=xml tests/
@@ -96,53 +99,3 @@ jobs:
           fail_ci_if_error: true
           verbose: true
           token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Build
-        run: |
-          python -m build
-
-      - name: Remove previous ProLIF install
-        run: |
-          pip uninstall -y prolif
-
-      - name: Install from tar.gz
-        run: |
-          pip install dist/prolif-*.tar.gz
-
-      - name: Test tar.gz install
-        working-directory: /
-        run: |
-          python <<EOF
-          from pathlib import Path
-          from contextlib import suppress
-          import prolif
-          print(prolif.__version__)
-          from prolif.plotting.network import LigNetwork
-          assert Path(prolif.datafiles.TOP).is_file()
-          with suppress(ImportError, ModuleNotFoundError):
-              import tests
-              assert next(Path(tests.__file__).parent.glob("test_fingerprint.py"), None) is None
-          EOF
-
-      - name: Remove previous ProLIF install
-        run: |
-          pip uninstall -y prolif
-
-      - name: Install from wheel
-        run: |
-          pip install dist/prolif-*.whl
-
-      - name: Test wheel install
-        working-directory: /
-        run: |
-          python <<EOF
-          from pathlib import Path
-          from contextlib import suppress
-          import prolif
-          print(prolif.__version__)
-          from prolif.plotting.network import LigNetwork
-          assert Path(prolif.datafiles.TOP).is_file()
-          with suppress(ImportError, ModuleNotFoundError):
-              import tests
-              assert next(Path(tests.__file__).parent.glob("test_fingerprint.py"), None) is None
-          EOF

MANIFEST.in

@@ -0,0 +1,3 @@
+graft tests
+
+global-exclude *~ *.py[cod] *.so

prolif/_version.py

@@ -1 +1 @@
-__version__ = "2.0.2"
+__version__ = "2.0.3-rc1"

pyproject.toml

@@ -85,8 +85,6 @@ include = ["prolif*"]
 [tool.setuptools.package-data]
 "prolif.data" = ["*"]
 "prolif.data.vina" = ["*"]
-"tests" = ["*"]
-"tests.plotting" = ["*"]
 
 [tool.setuptools.dynamic]
 version = { attr = "prolif._version.__version__" }

scripts/test_build.py

@@ -0,0 +1,14 @@
+from contextlib import suppress
+from pathlib import Path
+
+import prolif
+from prolif.plotting.network import LigNetwork
+
+print(prolif.__version__)
+
+assert Path(prolif.datafiles.TOP).is_file()
+
+with suppress(ImportError, ModuleNotFoundError):
+    import tests
+
+    assert next(Path(tests.__file__).parent.glob("test_fingerprint.py"), None) is None