Merge branch 'master' into tests_dwi

.coveragerc

@@ -1,10 +1,11 @@
 [run]
 branch = True
 concurrency = multiprocessing
-data_file = .test_reports/.coverage
-source =
-    scilpy/
-    scripts/
+data_file = .coverage
+source_pkgs = 
+    scilpy
+    scripts
+relative_files = True
 omit =
     scripts/tests/*.py
     scilpy/tests/**/*.py
@@ -15,6 +16,11 @@ omit =
 
 [report]
 skip_empty = True
+skip_covered = True
 
 [html]
 title = Scilpy Coverage Report
+directory = .test_reports/coverage.html
+
+[xml]
+output = .test_reports/coverage.xml

.github/workflows/test.yml

@@ -56,16 +56,14 @@ jobs:
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        uses: codecov/codecov-action@v4
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests
           name: scilpy-unittests-${{ github.run_id }}
           verbose: true
-          directory: .test_reports/
           fail_ci_if_error: true
-          root_dir: $GITHUB_WORKSPACE/scilpy/
+          plugin: pycoverage
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/[email protected]

pytest.ini

@@ -33,8 +33,7 @@ junit_logging = out-err
 
 addopts =
     --html=.test_reports/pytest.html
-    --cov-report=html:.test_reports/coverage.html
     --junit-xml=.test_reports/junit.xml
-    --cov-report=xml:.test_reports/coverage.xml
-    --cov=scilpy/
-    --cov=scripts/    
+    --cov
+    --cov-report html
+    --cov-report xml