Split test workflow to fix permission issue (#2)

.github/workflows/pytest.yml

@@ -0,0 +1,70 @@
+name: PyTest
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Code tests
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        include-sigpy: [true]
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Cache pip dependencies
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install PyPulseq and dependencies
+        run: |
+          pip install --upgrade --upgrade-strategy eager .[test]
+          if [ ${{ matrix.include-sigpy }} == "true" ]; then
+            pip install sigpy
+          fi
+
+      - name: Install PyTest GitHub Annotation Plugin
+        run: pip install pytest-github-actions-annotate-failures
+
+      - name: Run PyTest and Generate Coverage Report
+        shell: bash
+        run: |
+          if [ ${{ matrix.include-sigpy }} == "true" ]; then
+            pytest --junitxml=pytest.xml \
+              --cov-report=term-missing:skip-covered --cov=pypulseq | tee pytest-coverage.txt
+          else
+            pytest -m "not sigpy" --junitxml=pytest.xml \
+              --cov-report=term-missing:skip-covered --cov=pypulseq | tee pytest-coverage.txt
+          fi
+
+      - name: Upload PyTest Coverage Report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: pytest-report-${{ matrix.python-version }}-${{ matrix.include-sigpy }}
+          path: |
+            pytest-coverage.txt
+            pytest.xml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  cancel-in-progress: true

.github/workflows/report_pytest.yml

@@ -0,0 +1,99 @@
+name: Report PyTest
+
+on:
+  workflow_run:
+    workflows:
+      - PyTest
+    types:
+      - completed
+
+jobs:
+  coverage_report_pr:
+    name: Coverage report PR
+    if: ${{ github.event.workflow_run.event == 'pull_request' }}
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      pull-requests: write
+    steps:
+      # use the results of python 3.12, consider this as target platform
+      - name: Download PyTest report artifact for Python 3.12
+        uses: actions/download-artifact@v4
+        with:
+          name: pytest-report-3.12-true
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Get PR number
+        id: pr-context
+        env:
+          # Token required for GH CLI:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # Best practice for scripts is to reference via ENV at runtime. Avoid using the expression syntax in the script content directly:
+          PR_TARGET_REPO: ${{ github.repository }}
+          # If the PR is from a fork, prefix it with `<owner-login>:`, otherwise only the PR branch name is relevant:
+          PR_BRANCH: |-
+            ${{
+              (github.event.workflow_run.head_repository.owner.login != github.event.workflow_run.repository.owner.login)
+                && format('{0}:{1}', github.event.workflow_run.head_repository.owner.login, github.event.workflow_run.head_branch)
+                || github.event.workflow_run.head_branch
+            }}
+        # Query the PR number by repo + branch, then assign to step output:
+        run: |
+          gh pr view --repo "${PR_TARGET_REPO}" "${PR_BRANCH}" \
+              --json 'number' --jq '"number=\(.number)"' \
+              >> "${GITHUB_OUTPUT}"
+
+      - name: Post PyTest Coverage Comment
+        id: coverage_comment
+        uses: MishaKav/[email protected]
+        with:
+          issue-number: ${{ steps.pr-context.outputs.number }}
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+
+      - name: Post Failure Comment if Coverage Comment failed
+        # if there is no data the comment action does not fail but has an empty output
+        if: steps.coverage_comment.outputs.coverageHtml == ''
+        uses: edumserrano/find-create-or-update-comment@v3
+        with:
+          issue-number: ${{ steps.pr-context.outputs.number }}
+          body-includes: "<!-- Pytest Coverage Comment: ${{ github.job }} -->"
+          comment-author: "github-actions[bot]"
+          body: |
+            <!-- Pytest Coverage Comment: ${{ github.job }} -->
+            ### :x: PyTest Coverage Report was not found
+
+            Check the PyTest Workflow
+          edit-mode: replace
+
+  coverage_report_push:
+    name: Coverage report PUSH
+    if: ${{ github.event.workflow_run.event == 'push' && github.event.workflow_run.head_branch == 'master' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          name: pytest-report-3.12-true
+
+      - name: Post PyTest Coverage Comment on push
+        id: coverage_comment
+        uses: MishaKav/[email protected]
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+
+      # Todo: create a GIST and GIST secret to enable badge creation
+      # - name: Create Coverage Badge on push to master
+      #   uses: schneegans/[email protected]
+      #   with:
+      #     auth: ${{ secrets.GIST_SECRET }}
+      #     gistID: xxx
+      #     filename: coverage.json
+      #     label: Coverage Report
+      #     message: ${{ steps.coverage_comment.outputs.coverage }}
+      #     color: ${{ steps.coverage_comment.outputs.color }}
+      #     namedLogo: python