Ignore conftest.py in code coverage (#388)

* Ignore conftest.py in code coverage

* Configure coverage in pyproject.toml

* Do not run pytest coverage by default

Author: chuckwondo

.github/codecov.yml

@@ -3,7 +3,8 @@ coverage:
     project:
       default:
         target: 75
-        threshold: 0.1
+        # See https://json.schemastore.org/codecov.json
+        threshold: "0.1%"
     patch:
       default:
         target: 75
@@ -14,4 +15,5 @@ comment:
   branches:               # branch names that can post comment
     - "main"
 ignore:
+  - "conftest.py"
   - "virtualizarr/tests"  # ignore folders and all its contents

.github/workflows/main.yml

@@ -51,7 +51,7 @@ jobs:
 
       - name: Running Tests
         run: |
-          python -m pytest ./virtualizarr --run-network-tests --cov=./ --cov-report=xml --verbose
+          python -m pytest --run-network-tests --verbose --cov=virtualizarr --cov-report=xml
 
       - name: Upload code coverage to Codecov
         uses: codecov/[email protected]

.github/workflows/min-deps.yml

@@ -51,7 +51,7 @@ jobs:
 
       - name: Running Tests
         run: |
-          python -m pytest ./virtualizarr --cov=./ --cov-report=xml --verbose
+          python -m pytest --verbose --cov=virtualizarr --cov-report=xml
 
       - name: Upload code coverage to Codecov
         uses: codecov/[email protected]

.github/workflows/upstream.yml

@@ -51,7 +51,7 @@ jobs:
 
       - name: Running Tests
         run: |
-          python -m pytest ./virtualizarr --cov=./ --cov-report=xml --verbose
+          python -m pytest --verbose --cov=virtualizarr --cov-report=xml
 
       - name: Upload code coverage to Codecov
         uses: codecov/[email protected]

ci/environment.yml

@@ -16,7 +16,7 @@ dependencies:
   - hdf5plugin
   - numcodecs
   # Testing
-  - codecov
+  - codecov[toml]
   - pre-commit
   - mypy
   - ruff

ci/min-deps.yml

@@ -13,7 +13,7 @@ dependencies:
   - ujson
   - universal_pathlib
   # Testing
-  - codecov
+  - codecov[toml]
   - pre-commit
   - mypy
   - ruff

ci/upstream.yml

@@ -16,7 +16,7 @@ dependencies:
   - numcodecs
   - imagecodecs>=2024.6.1
   # Testing
-  - codecov
+  - codecov[toml]
   - pre-commit
   - mypy
   - ruff

docs/contributing.md

@@ -12,10 +12,30 @@ mamba activate virtualizarr-tests
 pre-commit install
 # git checkout -b new-feature
 python -m pip install -e . --no-deps
-python -m pytest ./virtualizarr --run-network-tests --cov=./ --cov-report=xml --verbose
+python -m pytest
 ```
 
-The `--run-network-tests` argument is optional - it will run additional tests that require downloading files over the network. Skip this if you want the tests to run faster or you have no internet access.
+You may also add the `--run-network-tests` option, which will run additional tests
+that require downloading files over the network.  Skip this if you want the tests to run
+faster or you have no internet access:
+
+```bash
+python -m pytest --run-network-tests
+```
+
+Further, the `pytest-cov` plugin is a test dependency, so you can generate a test
+coverage report locally, if you wish (CI will automatically do so).  Here are some
+examples:
+
+```bash
+python -m pytest --cov=.                     # Terminal (text) report (--cov=term)
+python -m pytest --cov=. --cov=term-missing  # Terminal report showing missing coverage
+python -m pytest --cov=. --cov=html          # HTML report written to htmlcov/index.html
+```
+
+To see all available `pytest` options added by the `pytest-cov` plugin, run
+`python -m pytest -h`, or see the
+[pytest-cov documentation](https://pytest-cov.readthedocs.io/en/latest/readme.html).
 
 ## Contributing documentation
 

pyproject.toml

@@ -148,6 +148,10 @@ line-ending = "auto"
 [tool.ruff.lint.isort]
 known-first-party = ["virtualizarr"]
 
+[tool.coverage.run]
+include = ["virtualizarr/"]
+omit = ["conftest.py", "virtualizarr/tests/*"]
+
 [tool.pytest.ini_options]
 # See https://pytest-asyncio.readthedocs.io/en/latest/concepts.html#asyncio-event-loops
 # Explicitly set asyncio_default_fixture_loop_scope to eliminate the following warning: