Minor CI Improvements (#235)

* pre-commit now always dumps the test coverage report to the console. All other pre-commit stages do not have this behavior as they will spam the logs.

* Minor documentation changes to the Makefile

* Pytest will now error on warnings.

* Adds some notes in the pytest config file

* Adds Python 3.13 test; removes redundant check on 3.11

* Removes 3.13 test and adds deprecation warning notes for deadlock warning in 3.12

* Adds note about Pytest Unraisable warning

.github/workflows/commit_checks.yaml

@@ -25,7 +25,8 @@ jobs:
       name: Test on ${{ matrix.python-version }}
       strategy:
         matrix:
-          python-version: ["3.11", "3.12"]
+          # NOTE: 3.11 is skipped as it is covered by the `pre-commit` job.
+          python-version: ["3.12"]
       steps:
         - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
         - uses: ./.github/actions/setup-env

.pre-commit-config.yaml

@@ -63,3 +63,4 @@ repos:
     always_run: true
     pass_filenames: false
     entry: make test-cov
+    verbose: true

.pytest.ini

@@ -1,6 +1,17 @@
 # This surpresses deprecation `pytest` warnings related to using `conda.*` packages.
 [pytest]
 filterwarnings =
+    # Turns warnings into errors so we are alerted in the CI pipeline
+    error
+    # Further investigation needed, but this seems tied to the complex mockers used in the `fetcher` module. Tracked in
+    # Issue #237
+    #   - https://docs.pytest.org/en/stable/reference/reference.html#pytest.PytestUnraisableExceptionWarning
+    ignore::pytest.PytestUnraisableExceptionWarning
+    # Root cause unclear, may be caused by `xdist` implementation for Linux. Tracked in  Issue #236
+    #   - https://github.com/python/cpython/issues/100228
+    #   - https://github.com/python/cpython/pull/100229
+    ignore::DeprecationWarning:multiprocessing.popen_fork
+    # Deprecation warnings from `conda`
     ignore::DeprecationWarning:boltons.*
     ignore::DeprecationWarning:xdist.*
 addopts = --ignore=tests/test_aux_files

Makefile

@@ -38,9 +38,9 @@ export PRINT_HELP_PYSCRIPT
 
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
-clean: clean-test clean-build clean-env clean-docs ## remove all build, test, coverage, and Python artifacts
+clean: clean-test clean-build clean-env clean-docs ## Removes all build, test, coverage, and Python artifacts
 
-clean-build: ## remove build and Python artifacts
+clean-build: ## Removes build and Python artifacts
 	rm -fr build/
 	rm -fr dist/
 	rm -fr .eggs/
@@ -54,7 +54,7 @@ clean-build: ## remove build and Python artifacts
 clean-env:					## remove conda environment
 	conda remove -y -n $(CONDA_ENV_NAME) --all
 
-clean-test: ## remove test, coverage, and profiler artifacts
+clean-test: ## Removes test, coverage, and profiler artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
@@ -72,33 +72,33 @@ clean-docs:	## Removes temporary and auto-generated static doc files
 help:
 	$(PYTHON3) -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-dev: clean		## install the package's development version to a fresh environment
+dev: clean		## Installs the package's development version to a fresh environment
 	conda env create -f environment.yaml --name $(CONDA_ENV_NAME) --yes
 	conda run --name $(CONDA_ENV_NAME) pip install -e .
 	$(CONDA_ACTIVATE) $(CONDA_ENV_NAME) && pre-commit install
 
-pre-commit:     ## runs pre-commit against files. NOTE: older files are disabled in the pre-commit config.
+pre-commit:     ## Runs pre-commit against files.
 	pre-commit run --all-files
 
-test:			## runs test cases
+test:			## Runs test cases
 	$(PYTHON3) -m pytest -n auto --capture=no $(TEST_DIR)
 
-test-cov:		## checks test coverage requirements
+test-cov:		## Checks test coverage requirements
 	$(PYTHON3) -m pytest -n auto --cov-config=.coveragerc --cov=$(SRC_DIR) \
 		$(TEST_DIR) --cov-fail-under=80 --cov-report term-missing
 
-lint:			## runs the linter against the project
+lint:			## Runs the linter against the project
 	pylint --rcfile=.pylintrc $(SRC_DIR) $(TEST_DIR)
 
-format:			## runs the code auto-formatter
+format:			## Runs the code auto-formatter
 	isort --profile black --line-length=120 $(SRC_DIR) $(TEST_DIR) $(SCRIPTS_DIR)
 	black --line-length=120 $(SRC_DIR) $(TEST_DIR) $(SCRIPTS_DIR)
 
-format-docs:	## runs the docstring auto-formatter. NOTE: this requires manually installing `docconvert` with `pip`
+format-docs:	## Runs the docstring auto-formatter. NOTE: this requires manually installing `docconvert` with `pip`
 	docconvert --in-place --config .docconvert.json $(SRC_DIR)
 
-analyze:		## runs static analyzer on the project
+analyze:		## Runs static analyzer on the project
 	mypy --config-file=.mypy.ini --cache-dir=/dev/null $(SRC_DIR) $(TEST_DIR) $(SCRIPTS_DIR)
 
-docs: clean-docs	## generates static html documentation
+docs: clean-docs	## Generates static html documentation
 	$(MAKE) -C docs html