update coverage config

.github/workflows/sonar-cloud.yml

@@ -45,7 +45,7 @@ jobs:
           python3 -m pip install .[dev]
           install-nplinker-deps --run-on-github
       - name: Run unit tests with coverage
-        run: pytest --cov --cov-report term --cov-report xml tests/unit
+        run: pytest --cov=nplinker --cov-report=xml tests/unit
       - name: SonarCloud Scan
         uses: SonarSource/sonarcloud-github-action@master
         env:

Makefile

@@ -26,7 +26,8 @@ clean-pyc:
 	find . -name '*_cache' -exec rm -fr {} +
 
 clean-test:
-	rm -f .coverage
+	rm -f .coverage*
+	rm -f coverage.xml
 
 build: clean
 	python -m build

pyproject.toml

@@ -97,7 +97,20 @@ testpaths = ["tests/unit"]
 [tool.coverage.run]
 branch = true
 source = ["src"]
-command_line = "-m pytest"
+
+[tool.coverage.report]
+omit = [
+    "src/nplinker/class_info/*",
+    "src/nplinker/data/*",
+    "src/nplinker/genomics/aa_pred.py",
+    "src/nplinker/parsers/*",
+    "src/nplinker/scoring/iokr/*",
+    "src/nplinker/scoring/rosetta/*",
+    "src/nplinker/scoring/np_class_scoring.py",
+    "src/nplinker/scoring/rosetta_scoring.py",
+    "src/nplinker/spec_clustering.py",
+    "src/nplinker/pickler.py"
+    ]
 
 # Mypy: to check static type
 # see https://mypy.readthedocs.io/en/stable/config_file.html#example-pyproject-toml