CI Upgrade (#11)

* Removed broken zenodo for now * bump version to 0.2.0 * bump version to 0.1.3 * Codecov v4 * lsbi continuous integration copied across * Updated documentation * Added double-check for previously different formatted version
handley-lab · Apr 9, 2024 · 0d54adb · 0d54adb
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -1,17 +1,26 @@
-name: Build and push to PyPI on merging to master
+name: Build
 on:
   push:
     branches:
       - master
 jobs:
-  git-tag-and-release:
+  get-version:
     runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.step1.outputs.v }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Get version number
-        run: |
-          VERSION="$(grep ':Version:' README.rst | awk '{print $2}')"
-          echo "DIST_VERSION=v${VERSION}" >> $GITHUB_ENV
+        id: step1 
+        run: echo "v=$(grep ':Version:' README.rst | awk '{print $2}')" >> $GITHUB_OUTPUT
+
+  git-tag-and-release:
+    runs-on: ubuntu-latest
+    needs: get-version
+    steps:
+      - uses: actions/checkout@v4
+      - name: set version number
+        run: echo "DIST_VERSION=v${{ needs.get-version.outputs.version }}" >> $GITHUB_ENV
       - name: Create Tag
         uses: actions/github-script@v6
         with:
@@ -34,11 +43,11 @@ jobs:
   pypi-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.9'
       - name: Install pypa/build
         run: python -m pip install build --user
       - name: Build a binary wheel and a source tarball
@@ -48,32 +57,35 @@ jobs:
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
 
+  pypi-public:
+    needs: 
+      - get-version
+      - pypi-release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Wait for PyPi
+        uses: nev7n/wait_for_response@v1
+        with:
+          url: "https://files.pythonhosted.org/packages/source/u/unimpeded/unimpeded-${{ needs.get-version.outputs.version }}.tar.gz"
+          responseCode: 200
+          timeout: 600000
+          interval: 10000
+
   aur-release:
-    needs: pypi-release
+    needs: pypi-public
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.9'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install tomli
       - name: Generate PKGBUILD
         run: python ./bin/gen_PKGBUILD.py > ./PKGBUILD
-      - name: Get version number
-        run: |
-          VERSION="$(cat ./PKGBUILD | grep pkgver= | awk -F= '{print $2}')"
-          echo "DIST_VERSION=${VERSION}" >> $GITHUB_ENV
-      - name: Wait for PyPi
-        uses: nev7n/wait_for_response@v1
-        with:
-          url: "https://files.pythonhosted.org/packages/source/u/unimpeded/unimpeded-${{ env.DIST_VERSION }}.tar.gz"
-          responseCode: 200
-          timeout: 600000
-          interval: 10000
       - name: Publish AUR package
         uses: KSXGitHub/[email protected]
         with:
@@ -83,3 +95,74 @@ jobs:
           commit_username: ${{ secrets.AUR_USERNAME }}
           commit_email: ${{ secrets.AUR_EMAIL }}
           ssh_private_key: ${{ secrets.AUR_SSH_PRIVATE_KEY }}
+
+  conda-release:
+    needs: pypi-public
+    name: Build and deploy to conda
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.9'
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: install dependencies
+        shell: bash -el {0}
+        run: conda install grayskull conda-build anaconda-client
+      - name: Generate meta.yaml from grayskull
+        shell: bash -el {0}
+        run: grayskull pypi --strict-conda-forge unimpeded
+      - name: Build and upload the conda packages
+        uses: uibcdf/[email protected]
+        with:
+          meta_yaml_dir: unimpeded
+          python-version: '3.9'
+          user: handley-lab
+          label: 'main'
+          token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret
+
+  conda-build:
+    needs: 
+      - conda-release
+      - get-version
+    name: test installation from conda
+    runs-on: ubuntu-latest
+    steps:
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.9'
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: install from conda
+        shell: bash -el {0}
+        run: conda install -c handley-lab unimpeded
+      - name: get install version
+        shell: bash -el {0}
+        run: echo "install_version=$(python -c 'import unimpeded; print(unimpeded.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1
+
+  pypi-build:
+    needs: 
+      - pypi-public
+      - get-version
+    name: test installation from pypi
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install from pypi
+        run: pip install unimpeded
+      - name: get install version
+        run: echo "install_version=$(python -c 'import unimpeded; print(unimpeded.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1
diff --git a/.github/workflows/code_style.yaml b/.github/workflows/code_style.yaml
@@ -0,0 +1,49 @@
+name: Code style
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install black
+        run: pip install black
+      - name: Run black
+        run: black . --check
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install isort
+        run: pip install isort
+      - name: Run isort
+        run: isort . --check-only
+
+  pydocstyle:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install pydocstyle
+        run: pip install pydocstyle
+      - name: run pydocstyle
+        run: python -m pydocstyle --convention=numpy anesthetic
diff --git a/.github/workflows/pr_checks.yaml b/.github/workflows/pr_checks.yaml
@@ -0,0 +1,58 @@
+name: PR checks
+
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  version-is-unit-incremented:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Upgrade pip and install linters
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install packaging
+      - name: Check version number
+        run: python ./bin/check_version.py
+
+  sphinx:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Upgrade pip and install doc requirements
+        run: pip install -e ".[all,docs]"
+      - name: build documentation
+        run: |
+          cd docs
+          make clean
+          make html SPHINXOPTS="-W --keep-going -n"
+
+  test-pypi-release:
+    name: Build and deploy to test PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install pypa/build
+        run: pip install build --user
+      - name: Build a binary wheel and a source tarball
+        run: python -m build --sdist --wheel --outdir dist/
+      - name: Publish to Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        continue-on-error: true
+        with:
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
diff --git a/.github/workflows/unittests.yaml b/.github/workflows/unittests.yaml
@@ -0,0 +1,29 @@
+name: Unit tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  pip:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install dependencies
+        run: pip install -e ".[test]"
+
+      - name: Test with pytest
+        run: pytest --cov=unimpeded tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}