Merge pull request NationalGenomicsInfrastructure#429 from kedhammar/…

…improve-ci

Improve ci

.github/workflows/lint-code.yml

@@ -69,20 +69,26 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Install pipreqs
-        run: pip install pipreqs
-
-      - name: Install requirements
-        run: pip install -r requirements.txt
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
 
       - name: Run pipreqs
-        run: pipreqs --savepath pipreqs.txt taca
+        run: |
+          pipreqs --savepath pipreqs.txt taca 2>&1 | tee pipreqs_output.log
+          if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
+            missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
+            echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
+            exit 1
+          fi
 
       - name: Compare requirements
         run: |
           # Extract and sort package names
-          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | sort -u > requirements.compare
-          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | sort -u > pipreqs.compare
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
 
           # Compare package lists
           if cmp -s requirements.compare pipreqs.compare

.github/workflows/test-code.yml

@@ -22,11 +22,8 @@ jobs:
         run: pip install -e .
       - name: pytest
         # Options are configured in pyproject.toml
-        run: pytest
+        run: pytest --cov=genologics --cov-report=xml
       - name: CodeCov
-        run: |
-          # Replace `linux` below with the appropriate OS
-          # Options are `alpine`, `linux`, `macos`, `windows`
-          curl -Os https://uploader.codecov.io/latest/linux/codecov
-          chmod +x codecov
-          ./codecov -t ${{ secrets.CODECOV_TOKEN }}
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20240701.1
+
+Improve CI for pipreqs check and pytest/codecov
+
 ## 20240617.1
 
 Run mypy for entire repo regardless of depth.