Merge pull request #294 from pitt-crc/development

Merge Development into Main for New Bank Deployment

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 100
+    ignore:
+      - dependency-name: "sphinx-jsonschema"  # Newer versions of sphinx-jsonschema have compatibility issues
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 100

.github/workflows/DocumentationBuild.yml

@@ -0,0 +1,44 @@
+name: Build Documentation
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  pull_request:
+
+permissions:
+  contents: read
+  packages: read
+
+jobs:
+  build:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/pitt-crc/test-env:latest
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Setup environment
+        run: /usr/local/bin/entrypoint.sh
+
+      - name: Checkout project source
+        uses: actions/checkout@v3
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
+
+      - name: Install dependencies
+        run: poetry install --with docs
+
+      - name: Build docs
+        working-directory: docs
+        run: make html SPHINXOPTS="-W"
+
+      - name: Upload docs to artifact storage
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/build/html

.github/workflows/DocumentationPublish.yml

@@ -0,0 +1,37 @@
+name: Publish Documentation
+
+on:
+  workflow_dispatch:
+    branches:
+     - "development"
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    name: Build
+    uses: ./.github/workflows/DocumentationBuild.yml
+    secrets: inherit
+    permissions:
+      contents: read
+      packages: read
+
+  deploy:
+    name: Deploy Documentation
+    needs: [ build ]
+
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/PackagePublish.yml

@@ -0,0 +1,84 @@
+name: Publish Package
+
+on:
+  release:
+    types: [ released ]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  run-tests:
+    name: Tests
+    uses: ./.github/workflows/PackageTest.yml
+    secrets: inherit
+
+  build-docs:
+    name: Docs
+    needs: run-tests
+    uses: ./.github/workflows/DocumentationBuild.yml
+    secrets: inherit
+
+  publish-package:
+    name: Publish Distribution
+    needs: build-docs
+    runs-on: ubuntu-latest
+    environment: ${{ matrix.environment }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - host: https://py00.crc.pitt.edu
+            environment: publish-h2p
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
+
+      # Get the new package version from the release tag
+      # Git release tags are expected to start with "refs/tags/v"
+      - name: Set package version
+        run: |
+          release_tag=${{github.ref}}
+          poetry version "${release_tag#refs/tags/v}"
+
+      - name: Build package
+        run: poetry build -v
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          print-hash: true
+          repository-url: ${{ matrix.host }}
+          user: ${{ secrets.REPO_USER }}
+          password: ${{ secrets.REPO_PASSWORD }}
+
+  publish-docs:
+    name: Deploy Documentation
+    needs: [ build-docs, publish-package ]
+
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/PackageTest.yml

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+name: Test Package
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  push:
+
+jobs:
+  run-tests:
+    name: Run Tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        slurm_version:
+          - 20.02.5.1
+          - 20.11.9.1
+          - 22.05.2.1
+        python_version:
+          - 3.8
+          - 3.9
+
+    container:
+      image: ghcr.io/pitt-crc/test-env:${{ matrix.slurm_version }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Setup environment
+        run: /usr/local/bin/entrypoint.sh
+
+      - name: Checkout source code
+        uses: actions/checkout@v3
+
+      - name: Install poetry
+        run: |
+          pip install poetry
+          poetry env use python${{ matrix.python_version }}
+
+      - name: Install dependencies
+        run: poetry install --with tests
+
+      - name: Run tests with coverage
+        run: |
+          poetry run coverage run -m unittest discover 
+          poetry run coverage report --omit="tests/*"
+          poetry run coverage xml --omit="tests/*" -o coverage.xml
+
+      # Report partial coverage results to codacy for the current python version
+      - name: Report partial coverage results
+        if: github.event_name != 'release'
+        shell: bash
+        run: bash <(curl -Ls https://coverage.codacy.com/get.sh) report --partial -l Python -r coverage.xml
+        env:
+          CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+
+  # Tell codacy we are done reporting test coverage
+  report-code-coverage:
+    name: Report Coverage
+    if: github.event_name != 'release'
+    needs: run-tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Finish reporting coverage
+        shell: bash
+        run: bash <(curl -Ls https://coverage.codacy.com/get.sh) final
+        env:
+          CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+
+  # Use this job for branch protection rules
+  report-test-status:
+    name: Report Test Status
+    if: always()
+    needs: run-tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check build status
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1