ci: github workflows

Use pixi to run doc build and tests.
Use pre-commit action to run qa.
Use pypi action to handle release.
Use a readthedocs workflow to build a preview for docs in a PR.
Use dependabot to keep things updated.
Update gitlab urls to github
Add a conventional-pre-commit hook
Create a COPYING file to indicate the license to Github interface
Cleanup pixi settings.
Add coverage reports
Fix coverage badge based on that

Co-authored-by: Yannick-Dayer <[email protected]>

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      dependencies:
+        patterns:
+          - "*"

.github/workflows/build.yml

@@ -0,0 +1,86 @@
+name: build
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  simpletests:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Pixi
+        uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.25.0
+          environments: self
+      - name: Run Simple Tests
+        shell: pixi run -e self bash -e {0}
+        run: |
+          gridtk --help
+          gridtk submit --help
+          gridtk resubmit --help
+          gridtk stop --help
+          gridtk list --help
+          gridtk report --help
+          gridtk delete --help
+
+  tests:
+    runs-on: ubuntu-22.04
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for pushing data to the
+      # python-coverage-comment-action branch, and for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Pixi
+        uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.25.0
+          environments: test
+      - name: Run Tests
+        run: pixi run test-ci
+      - name: Coverage comment
+        id: coverage_comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+      - name: Store Pull Request comment to be posted
+        uses: actions/upload-artifact@v4
+        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
+        with:
+          # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly
+          name: python-coverage-comment-action
+          # If you use a different name, update COMMENT_FILENAME accordingly
+          path: python-coverage-comment-action.txt
+
+  doc:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Pixi
+        uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.25.0
+          environments: doc
+      - name: Clean previous docs
+        run: pixi run doc-clean
+      - name: Build docs
+        run: pixi run doc
+      - name: Run doctests
+        run: pixi run doctest

.github/workflows/coverage.yml

@@ -0,0 +1,35 @@
+name: Post coverage comment
+
+on:
+  workflow_run:
+    workflows: ["build"]
+    types:
+      - completed
+
+jobs:
+  test:
+    name: Run tests & display coverage
+    runs-on: ubuntu-22.04
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+      # Gives the action the necessary permissions for looking up the
+      # workflow that launched this workflow, and download the related
+      # artifact that contains the comment to be published
+      actions: read
+    steps:
+      # DO NOT run actions/checkout here, for security reasons
+      # For details, refer to https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+      - name: Post comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
+          # Update those if you changed the default values:
+          # COMMENT_ARTIFACT_NAME: python-coverage-comment-action
+          # COMMENT_FILENAME: python-coverage-comment-action.txt

.github/workflows/documentation-links.yml

@@ -0,0 +1,20 @@
+name: readthedocs preview
+on:
+  pull_request_target:
+    types:
+      - opened
+    # Execute this action only on PRs that touch
+    # documentation files.
+    # paths:
+    #   - "docs/**"
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "gridtk"

.github/workflows/pre-commit.yml

@@ -0,0 +1,17 @@
+name: pre-commit
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  push:
+    branches: [ "main" ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - uses: pre-commit/[email protected]

.github/workflows/publish-pypi.yml

@@ -0,0 +1,58 @@
+# From https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-pypi
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-22.04
+
+    needs:
+      - release-build
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    environment:
+      name: pypi
+      # include the PyPI project URL in the deployment status:
+      url: https://pypi.org/p/gridtk
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -24,7 +24,9 @@ _work/
 .mypy_cache/
 .pytest_cache/
 changelog.md
-.pixi/
 .vscode
 logs
 jobs.sql3
+# pixi environments
+.pixi
+*.egg-info

.pre-commit-config.yaml

@@ -6,7 +6,14 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 
+default_install_hook_types: ["pre-commit", "commit-msg"]
 repos:
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v3.2.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.4.4
     hooks:

.reuse/dep5

@@ -1,7 +1,7 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: gridtk
 Upstream-Contact: Andre Anjos <[email protected]>
-Source: https://gitlab.idiap.ch/software/gridtk/
+Source: https://github.com/idiap/gridtk/
 
 Files:
  pixi.lock