🤖 📦 Tests in Docker Image (#2404)

* Tests in docker?

* Testing docker CI

* Running with uv

* Test uv action again

* uv docker

* depreciate gdspy

* chore(github): use diff-cover for easy local diff coverage computation

* add missing permissions for the Github token

* fix fetch depth for change coverage computation and fix diff-cover args

* use fetch-depth of 0 to fetch all of the history

* move checks to local test script and add manual pre-commit hook

* Now we can run tests

* Test no vtk

* run on deploynode

* Further containerization

* Remove uv references

* Remove uv references

* Test vtk installation

* Correct python version

* Try again

* Does it work in debian

* Does it work in debian

* try if slim x11 is the issue

* coverage reports

* try

* try

* try

* remove pre-commit and keep simple local scripts for testing

* Does this work?

* remove the general coverage report due to instabilities

* fix runners

* Requires right fetchdept

* does this fix it

* does it skip properly

* Think  we're in business

* Gonna get tests running and then fix diff

* Try again

* final touches from review

---------

Co-authored-by: Frederik Schubert <[email protected]>

Author: daquinteroflex

.github/workflows/run_tests.yml

@@ -24,7 +24,7 @@ on:
 
 jobs:
   determine-test-scope:
-    runs-on: [ inhouse ]
+    runs-on: [ deploynode ]
     if: |
       github.event.pull_request.draft == false ||
       github.ref == 'refs/heads/develop' ||
@@ -115,7 +115,8 @@ jobs:
     needs: determine-test-scope
     if: ( needs.determine-test-scope.outputs.local_tests == 'true' ) || ( needs.determine-test-scope.outputs.remote_tests == 'true' )
     name: Run linting
-    runs-on: [ inhouse ]
+    runs-on: [ deploynode ] 
+    container: ghcr.io/astral-sh/uv:debian 
     steps:
       - uses: actions/checkout@v4
         with:
@@ -132,8 +133,9 @@ jobs:
     # Run on open PRs OR when manually triggered with local_tests=true
     needs: determine-test-scope
     if: needs.determine-test-scope.outputs.local_tests == 'true'
-    name: Python ${{ matrix.python-version }} - self-hosted-runner
-    runs-on: [ inhouse ]
+    name: Python ${{ matrix.python-version }} - self-hosted-runner 
+    runs-on: [ deploynode ]
+    container: ghcr.io/astral-sh/uv:debian 
     strategy:
       matrix:
         python-version: ['3.9', '3.13']
@@ -147,83 +149,95 @@ jobs:
     steps:
     - uses: actions/checkout@v4
       with:
-        fetch-depth: 1
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+        fetch-depth: 0
 
     - name: Install project
+      env:
+        PYTHON_VERSION: ${{ matrix.python-version }}
       run: |
-        python -m venv ${GITHUB_WORKSPACE}/.venv
+        if [ -f /.dockerenv ]; then
+          echo "Running inside a Docker container (detected via /.dockerenv)"
+        else
+          echo "Not running inside a Docker container (/.dockerenv not found)"
+        fi
+        uv venv -p $PYTHON_VERSION ${GITHUB_WORKSPACE}/.venv
         source ${GITHUB_WORKSPACE}/.venv/bin/activate
-        python --version
         which python
-        which pip
-        pip list
-        pip install --upgrade pip wheel setuptools
-        pip install gdstk --only-binary gdstk
-        pip install -e ".[dev]"
+        which uv
+        python --version
+        uv pip list
+        uv pip install gdstk --only-binary gdstk
+        uv pip install -e ".[dev]"
+
+        echo "Testing vtk is correctly installed."
+        python -c "import vtk"
 
     - name: Run tests with coverage
       env:
         PYTHONUNBUFFERED: "1"
       run: |
         source ${GITHUB_WORKSPACE}/.venv/bin/activate
-        pytest --cov=tidy3d -rF --tb=short tests/_test_data/_test_datasets_no_vtk.py
+        # pytest --cov=tidy3d -rF --tb=short tests/_test_data/_test_datasets_no_vtk.py
         pytest --cov=tidy3d -rF --tb=short tests
         coverage report -m
-        coverage xml -o coverage.xml
+        coverage xml -o ${GITHUB_WORKSPACE}/coverage.xml
         TOTAL_COVERAGE=$(coverage report --format=total)
         echo "total=$TOTAL_COVERAGE" >> "$GITHUB_ENV"
         echo "### Total coverage: ${TOTAL_COVERAGE}%"
 
-    - name: Produce the coverage report
-      uses: insightsengineering/coverage-action@v2
-      with:
-        path: ./coverage.xml
-        threshold: 90.0
-        fail: false
-        publish: true
-        diff: true
-        diff-branch: develop
-        diff-storage: _xml_coverage_reports
-        coverage-summary-title: "Code Coverage Summary"
-        togglable-report: true
-
-    - name: Changed files
-      id: diff
-      uses: step-security/changed-files@v46
-      with:
-        files: '**/*.py'
+    - name: verify-coverage-report-location
+      run: |
+        ls $GITHUB_WORKSPACE
 
-    - name: Slice report down to changed files
-      if: ${{ steps.diff.outputs.all_changed_files != '' }}
-      env:
-        CHANGED: ${{ steps.diff.outputs.all_changed_files }}
+    - name: Produce the diff coverage report
+      if: matrix.python-version == '3.13'
       run: |
-        echo $CHANGED
         source ${GITHUB_WORKSPACE}/.venv/bin/activate
-        include=$(printf '%s\n' $CHANGED | sed 's|^|**/|' | paste -sd, -)
-        coverage xml -i -o changed.xml --include="$include"
+        git config --global --add safe.directory ${GITHUB_WORKSPACE}
+        diff-cover ${GITHUB_WORKSPACE}/coverage.xml \
+          --compare-branch origin/${{ github.event.pull_request.base.ref }} \
+          --format markdown:diff-coverage.md
 
-    - name: Produce the changed files coverage report
-      uses: insightsengineering/coverage-action@v2
-      if: ${{ steps.diff.outputs.all_changed_files != '' }}
+    - uses: actions/github-script@v7
+      if: matrix.python-version == '3.13'
       with:
-        path: ./changed.xml
-        threshold: 90.0
-        publish: true
-        fail: false
-        coverage-summary-title: "Changed Files Coverage"
+        result-encoding: string
+        script: |
+          const fs = require('fs');
+          const marker = '<!-- diff-cover-report -->';
+          const body = fs.readFileSync('diff-coverage.md','utf8');
+          const report = `${marker}\n${body}`;
+          const {data:comments}=await github.rest.issues.listComments({
+            owner:context.repo.owner,
+            repo:context.repo.repo,
+            issue_number:context.issue.number,
+          });
+          const existing = comments.find(c=>c.body.startsWith(marker));
+          if(existing) {
+            await github.rest.issues.updateComment({
+              owner:context.repo.owner,
+              repo:context.repo.repo,
+              comment_id:existing.id,
+              body:report,
+            });
+          } else {
+            await github.rest.issues.createComment({
+              owner:context.repo.owner,
+              repo:context.repo.repo,
+              issue_number:context.issue.number,
+              body:report,
+            });
+          }
 
   remote-tests:
     # Run tests on a push event OR a workflow dispatch with remote_tests
     needs: determine-test-scope
     if: needs.determine-test-scope.outputs.remote_tests == 'true'
     name: Python ${{ matrix.python-version }} - ${{ matrix.platform }}
     runs-on: ${{ matrix.platform }}
+    permissions:
+      contents: read
+      pull-requests: write
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
@@ -234,7 +248,7 @@ jobs:
     env:  # Set environment variables for the whole job
       PIP_ONLY_BINARY: gdstk
       MPLBACKEND: agg
-    
+
     concurrency:
       group: ${{ github.workflow }}-${{ github.event.pull_request.number }}-${{ matrix.platform }}-${{ matrix.python-version }}-remote
       cancel-in-progress: true
@@ -299,7 +313,7 @@ jobs:
     name: pr-requirements-pass
     if: ( needs.determine-test-scope.outputs.local_tests == 'true' ) || ( needs.determine-test-scope.outputs.remote_tests == 'true' )
     needs: [local-tests, remote-tests, lint]
-    runs-on: [ inhouse ]
+    runs-on: [ deploynode ]
     steps:
       - name: check-passing-remote-tests
         run: |