From c0e6553b26ccd432b5b586e5fdedae22c7a8e259 Mon Sep 17 00:00:00 2001
From: JosePizarro3 <jose.pizarro@physik.hu-berlin.de>
Date: Thu, 6 Jun 2024 11:14:59 +0200
Subject: [PATCH] Added Ahmed changes to the pipeline for comment on pr from
 coverage

---
 .github/workflows/actions.yaml | 77 ++++++++++++++++++----------------
 pyproject.toml                 |  6 +--
 2 files changed, 45 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/actions.yaml b/.github/workflows/actions.yaml
index 37849864..83efb9a0 100644
--- a/.github/workflows/actions.yaml
+++ b/.github/workflows/actions.yaml
@@ -1,47 +1,54 @@
 name: install-and-test
 on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-        pip install coverage coveralls
-    - name: mypy
-      run: |
-        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_simulations tests
-    - name: Test with pytest
-      run: |
-        python -m coverage run -m pytest -sv tests
-    - name: Submit to coveralls
-      continue-on-error: true
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        coveralls --service=github
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          pip install uv
+          uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
+      - name: mypy
+        run: |
+          python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_simulations tests
+      - name: Build coverage file
+        run: |
+          pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests/ | tee pytest-coverage.txt
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
   build-and-install:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Build the package
-      run: |
-        pip install --upgrade pip
-        pip install build
-        python -m build --sdist
-    - name: Install the package
-      run: |
-        pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Build the package
+        run: |
+          pip install --upgrade pip
+          pip install build
+          python -m build --sdist
+      - name: Install the package
+        run: |
+          pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
   ruff-linting:
       runs-on: ubuntu-latest
       steps:
diff --git a/pyproject.toml b/pyproject.toml
index d09f6427..3a596817 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,9 +31,9 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     'mypy==1.0.1',
-    'pytest==3.10.0',
-    'pytest-timeout==1.4.2',
-    'pytest-cov==2.7.1',
+    'pytest',
+    'pytest-timeout',
+    'pytest-cov',
     'ruff',
     "structlog==22.3.0",
     "lxml_html_clean>=0.1.0",