fix: update CI to use python -m for all commands

- Changed pytest, ruff, and mypy to use 'python -m' prefix
- This ensures commands are found in the Python environment
- Removed duplicate coverage options from pyproject.toml that conflicted with CI
- Exit code 2 was likely due to pytest command not being in PATH

Author: jdrhyne

.github/workflows/ci.yml

@@ -36,14 +36,14 @@ jobs:
 
     - name: Run linting with ruff
       run: |
-        ruff check .
-        ruff format --check .
+        python -m ruff check .
+        python -m ruff format --check .
 
     - name: Run type checking with mypy
-      run: mypy src tests
+      run: python -m mypy src tests
 
     - name: Run tests with pytest
-      run: pytest -v --cov=nutrient_dws --cov-report=xml --cov-report=term
+      run: python -m pytest -v --cov=nutrient_dws --cov-report=xml --cov-report=term
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4

pyproject.toml

@@ -112,10 +112,6 @@ testpaths = ["tests"]
 addopts = [
     "-ra",
     "--strict-markers",
-    "--cov=nutrient_dws",
-    "--cov-report=term-missing",
-    "--cov-report=html",
-    "--cov-report=xml",
 ]
 markers = [
     "integration: marks tests as integration tests (deselect with '-m \"not integration\"')",