ci: Add coverage reports

Fix coverage badge based on that
Also fix other urls pointing to gitlab still

.github/workflows/coverage.yml

@@ -0,0 +1,35 @@
+name: Post coverage comment
+
+on:
+  workflow_run:
+    workflows: ["pixi"]
+    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/pixi.yml

@@ -34,6 +34,14 @@ jobs:
 
   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:
@@ -45,6 +53,19 @@ jobs:
           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

README.md

@@ -6,7 +6,7 @@ SPDX-License-Identifier: GPL-3.0-or-later
 
 [![latest-docs](https://img.shields.io/badge/docs-latest-orange.svg)](https://gridtk.readthedocs.io/en/latest/)
 [![build](https://github.com/idiap/gridtk/actions/workflows/pixi.yml/badge.svg)](https://github.com/idiap/gridtk/actions/workflows/pixi.yml)
-[![coverage](https://gitlab.idiap.ch/software/gridtk/badges/main/coverage.svg)](https://www.idiap.ch/software/biosignal/docs/software/gridtk/main/coverage/index.html)
+[![coverage](https://raw.githubusercontent.com/idiap/gridtk/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/idiap/gridtk/blob/python-coverage-comment-action-data/htmlcov/index.html)
 [![repository](https://img.shields.io/badge/github-project-0000c0.svg)](https://github.com/idiap/gridtk)
 
 # GridTK: SLURM Job Managetment for Humans
@@ -35,7 +35,7 @@ To install GridTK, open your terminal and run the following command:
 ```bash
 $ pixi global install pipx
 $ pixi global install python=3.12
-$ pipx install --force --python python3.12 'git+https://gitlab.idiap.ch/software/gridtk.git'
+$ pipx install --force --python python3.12 'git+https://github.com/idiap/gridtk.git'
 ```
 It is **not recommennded** to install GridTK using `pip install gridtk` in the
 same environment as your expeirments. GirdTK does not need to be installed in

pyproject.toml

@@ -67,7 +67,7 @@ doctest = "sphinx-build -aEb doctest doc html/doctest"
 
 [tool.pixi.feature.test.tasks]
 test = "pytest -sv tests/"
-test-ci = "pytest -sv --cov-report 'html:html/coverage' --cov-report 'xml:coverage.xml' --junitxml 'junit-coverage.xml' --ignore '.profile' tests/"
+test-ci = "pytest -sv --cov-branch --cov-report xml --ignore '.profile' tests/"
 
 [tool.pixi.environments]
 default = { features = ["doc", "test"], solve-group = "default" }
@@ -165,5 +165,8 @@ addopts = ["--cov=gridtk", "--cov-report=term-missing", "--import-mode=append"]
 junit_logging = "all"
 junit_log_passing_tests = false
 
+[tool.coverage.run]
+relative_files = true
+
 [tool.mypy]
 python_version = "3.12"