run coverage in better way

.github/workflows/base_test_workflow.yml

@@ -1,3 +1,5 @@
+name: Base Test Workflow
+
 on:
   workflow_call:
     inputs:
@@ -97,25 +99,10 @@ jobs:
             ./report-*.json
           retention-days: 7
 
-      - name: Upload coverage report ${{ inputs.tox_args }}
+      - name: Upload coverage data
         uses: actions/upload-artifact@v3
         if: ${{ inputs.coverage }}
         with:
-          name: coverage_report ${{ inputs.tox_args }}
+          name: coverage reports
           path: |
-            ./htmlcov
-          retention-days: 7
-
-      - name: Upload coverage raw data
-        uses: actions/upload-artifact@v3
-        with:
-          name: coverage_raw ${{ inputs.tox_args }}
-          path: ./coverage.xml
-          retention-days: 7
-
-      - uses: codecov/codecov-action@v3
-        if: ${{ inputs.coverage }}
-        with:
-          file: ./coverage.xml
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+            ./.coverage.*

.github/workflows/reusable_coverage_upload.yml

@@ -0,0 +1,43 @@
+name: Coverage Upload
+
+on:
+  workflow_call:
+
+
+jobs:
+  upload_coverage:
+    name: Upload coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+          cache-dependency-path: setup.cfg
+          cache: 'pip'
+
+      - name: Install Dependencies
+        run: |
+          pip install --upgrade pip
+          pip install codecov
+
+      - name: Download coverage data
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage reports
+          path: coverage
+
+      - name: combine coverage data
+        run: |
+          python -Im coverage combine coverage
+          python -Im coverage xml -o coverage.xml
+
+          # Report and write to summary.
+          python -Im coverage report --format=markdown --skip-empty --skip-covered >> $GITHUB_STEP_SUMMARY
+
+      - name: Upload coverage data
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tests.yml

@@ -116,6 +116,11 @@ jobs:
       tox_args: "-e py38-PyQt5-minimal"
       coverage: true
 
+  coverage_upload:
+    name: Upload coverage
+    needs: [test_coverage, test_minimal]
+    uses: ./.github/workflows/reusable_coverage_upload.yml
+
   test_conda:
     name: Test PartSeg conda
     runs-on: ubuntu-20.04

setup.cfg

@@ -79,7 +79,6 @@ package_dir =
     =package
 tests_require =
     pytest
-    pytest-cov
     pytest-qt
     lxml
 
@@ -120,9 +119,9 @@ pyside2 =
 pyside6 =
     PySide6
 test =
+    coverage
     lxml
     pytest>=7.0.0
-    pytest-cov
     pytest-qt
     pytest-timeout
     scikit-image
@@ -166,7 +165,10 @@ source =
     PartSeg
     PartSegCore
     PartSegImage
-omit = .tox/*
+omit =
+    .tox/*
+    package/PartSeg/changelog.py
+    package/ParsSeg/version.py
 parallel = True
 
 [coverage:report]

tox.ini

@@ -83,11 +83,11 @@ commands =
     !repo: python -m pytest -v package/tests/test_PartSeg/test_napari_widgets.py  --no-cov --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json
     repo: python -m pytest --no-cov --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json
 
-[testenv:py{38,39,310,311s}-PyQt5-coverage]
+[testenv:py{38,39,310,311}-PyQt5-coverage]
 deps =
     {[testenv]deps}
 commands =
-    python -m pytest --cov-report=xml --cov-report html --cov-append --cov {envsitepackagesdir}/PartSeg --cov {envsitepackagesdir}/PartSegCore --cov {envsitepackagesdir}/PartSegImage --cov package/tests  --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json
+    coverage run -m pytest --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json
 
 [testenv:py38-PyQt5-minimal]
 min_req = 1