chore: adapt the project to GitHub

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# Copyright © Idiap Research Institute <[email protected]>
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+# dependabot.yaml reference: https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Maintain dependencies in our GitHub Workflows
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+      time: "05:00"
+      timezone: CET

.github/workflows/coverage.yml

@@ -0,0 +1,42 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <[email protected]>
+# SPDX-FileContributor: Yannick Dayer <[email protected]>
+
+# SPDX-License-Identifier: BSD-3-Clause
+
+# Inspired from https://github.com/py-cov-action/python-coverage-comment-action
+
+name: Add a coverage comment to the Pull Request
+
+on:
+  workflow_run:
+    workflows: ["tests"]
+    types:
+      - completed
+
+jobs:
+  coverage-comment:
+    name: Send (or modify) a coverage comment to the PR
+    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/deploy_pypi.yml

@@ -0,0 +1,74 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <[email protected]>
+# SPDX-FileContributor: Yannick Dayer <[email protected]>
+
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: Publish package to Pypi
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release-packaging:
+    name: Package the project into a deploy-ready state
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout project
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install build dependencies
+        run: |
+          pip install --upgrade pip
+          pip install build
+      - name: Package the project
+        run: python -m build
+      - name: Produce a GitHub actions artifact (the package)
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dist
+          path: dist/
+          if-no-files-found: error
+
+  pypi-publish:
+    name: Upload the release package to PyPI
+    needs:
+      - release-packaging
+    runs-on: ubuntu-22.04
+    environment:
+      name: pypi
+      url: https://pypi.org/p/clapper
+    permissions:
+      id-token: write  # This permission is mandatory for trusted publishing
+    steps:
+      - name: Retrieve the package from GitHub actions artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dist
+          path: dist
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Upload the release package to GitHub Release
+    needs:
+      - pypi-publish
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+    steps:
+      - name: Retrieve the package from GitHub actions artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dist
+          path: dist
+      - name: Upload the release package to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        run: gh release upload '${{ github.ref_name }}' dist/** --repo '${{ github.repository }}'

.github/workflows/doc-preview.yaml

@@ -0,0 +1,25 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <[email protected]>
+# SPDX-FileContributor: Yannick Dayer <[email protected]>
+
+# SPDX-License-Identifier: BSD-3-Clause
+
+# Inspired from https://github.com/readthedocs/actions/tree/v1/preview
+
+name: Documentation preview on readthedocs for Pull Requests
+
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Modify the PR with a link to the new docs
+        uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "clapper"

.github/workflows/qa.yml

@@ -0,0 +1,26 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <[email protected]>
+# SPDX-FileContributor: Yannick Dayer <[email protected]>
+
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: Check the project is up to our quality standards
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  pre-commit:
+    name: Run pre commit on all modified files
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout project
+        uses: actions/checkout@v4
+      - name: Install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]
+        env:
+          SKIP: pixi

.github/workflows/tests.yaml

@@ -0,0 +1,94 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <[email protected]>
+# SPDX-FileContributor: Yannick Dayer <[email protected]>
+
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: Execute code tests
+
+on:
+  push:
+    branches: [ "main" ]
+    tags: ["*"]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-14]
+        pixi_environment: [test, test-alternative]  # latest and previous python
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Pixi
+        uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.25.0
+          environments: ${{ matrix.pixi_environment }}
+      - name: Run Tests
+        run: pixi run test-ci
+        env:
+          COVERAGE_FILE: ".coverage.${{ matrix.pixi_environment }}-${{ matrix.os }}"
+      - name: Store coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          # File renamed for thix matrix element
+          name: coverage-${{ matrix.pixi_environment }}-${{ matrix.os }}
+          path: .coverage.${{ matrix.pixi_environment }}-${{ matrix.os }}
+
+
+  merge-coverage:
+    name: Merge the coverage reports from multiple coverages
+    needs: 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 editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Retrieve coverage artifacts
+        uses: actions/download-artifact@v4
+        id: download
+        with:
+          pattern: coverage-*
+          merge-multiple: true
+      - name: Coverage comment
+        id: coverage_comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+          MERGE_COVERAGE_FILES: true
+      - name: Store Pull Request comment to be posted
+        uses: actions/upload-artifact@v4
+        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
+        with:
+          name: python-coverage-comment-action
+          path: python-coverage-comment-action.txt
+
+  doc:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout repository
+        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: Build docs
+        run: pixi run doc
+      - name: Run doctests
+        run: pixi run doctest

.pre-commit-config.yaml

@@ -4,7 +4,15 @@
 
 # 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: v0.4.3
     hooks:
@@ -33,8 +41,10 @@ repos:
     rev: v3.0.2
     hooks:
       - id: reuse
-        exclude: |
-          (?x)(
-              ^.pixi/|
-              ^.pixi.lock|
-              )
+  - repo: local
+    hooks:
+      - id: pixi
+        name: Check outdated pixi.lock
+        language: system
+        entry: pixi list --locked
+        pass_filenames: false

.reuse/dep5

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

LICENSES/BSD-3-Clause.txt

@@ -1,4 +1,4 @@
-Copyright (c) <year> <owner>.
+Copyright © 2024 Idiap Research Institute <[email protected]>.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

README.md

@@ -5,10 +5,9 @@ SPDX-License-Identifier: BSD-3-Clause
 -->
 
 [![latest-docs](https://img.shields.io/badge/docs-latest-orange.svg)](https://clapper.readthedocs.io/en/latest/)
-[![build](https://gitlab.idiap.ch/software/clapper/badges/main/pipeline.svg)](https://gitlab.idiap.ch/software/clapper/commits/main)
-[![coverage](https://gitlab.idiap.ch/software/clapper/badges/main/coverage.svg)](https://www.idiap.ch/software/biosignal/docs/software/clapper/main/coverage/index.html)
-[![repository](https://img.shields.io/badge/gitlab-project-0000c0.svg)](https://gitlab.idiap.ch/software/clapper)
-
+[![tests](https://github.com/idiap/clapper/main/actions/workflows/tests.svg)](https://github.com/idiap/clapper/actions)
+[![coverage](https://raw.githubusercontent.com/idiap/clapper/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/idiap/clapper/python-coverage-comment-action-data/htmlcov/index.html)
+[![repository](https://img.shields.io/badge/github-latest-darkblue.svg)](https://github.com/idiap/clapper)
 
 # Configuration Support for Python Packages and CLIs
 

doc/conf.py

@@ -99,7 +99,7 @@
 html_theme = "furo"
 
 html_theme_options = {
-    "source_edit_link": f"https://gitlab.idiap.ch/software/{project}/-/edit/main/doc/{{filename}}",
+    "source_edit_link": f"https://github.com/idiap/{project}/edit/main/doc/{{filename}}",
 }
 
 html_title = f"{project} {release}"

doc/install.rst

@@ -27,7 +27,7 @@ relevant tab for details on each of those installation paths.
 
    .. code:: sh
 
-      pip install git+https://gitlab.idiap.ch/software/clapper@main
+      pip install git+https://github.com/idiap/clapper@main
 
 
 .. tab:: Deployment (pixi)
@@ -46,7 +46,7 @@ relevant tab for details on each of those installation paths.
 
    .. code:: sh
 
-      git clone git@gitlab.idiap.ch:software/clapper
+      git clone git@github.com:idiap/clapper
       pixi install --frozen
 
    .. tip::