run tests with coverage

Author: reece

.pre-commit-config.yaml

@@ -38,6 +38,6 @@ repos:
     hooks:
       - id: canonicalize-pyproject
         name: Ensure pyproject.toml in canonical order and format
-        entry: uvx toml-sort --in-place pyproject.toml
+        entry: uvx toml-sort --in-place --all pyproject.toml
         language: system
         files: ^pyproject.toml$

Makefile

@@ -57,7 +57,7 @@ cqa: ## Run code quality assessments.
 .PHONY: test
 test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"
-	uv run pytest
+	uv run pytest --cov=. --cov-report=xml
 
 ############################################################################
 #= DOCUMENTATION
@@ -83,7 +83,7 @@ clean:  ## Remove temporary and backup files
 .PHONY: cleaner
 cleaner: clean  ## Remove files and directories that are easily rebuilt
 	$(call INFO_MESSAGE, "Remove files and directories that are easily rebuilt")
-	rm -frv .cache .DS_Store .pytest_cache build coverage.xml dist docs/_build site
+	rm -frv .cache .DS_Store .pytest_cache .ruff_cache build coverage.xml dist docs/_build site
 	rm -frv **/*.pyc **/__pycache__ **/*.egg-info
 	rm -frv **/*.orig **/*.rej
 

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
 build-backend = "setuptools.build_meta"
+requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
 
 [dependency-groups]
 dev = [
@@ -17,23 +17,25 @@ dev = [
 ]
 
 [project]
-name = "biocommons-example"
 authors = [
-  {name = "biocommons contributors", email = "biocommons[email protected]"}
+  {email = "biocommons[email protected]", name = "biocommons contributors"}
 ]
-dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
-description = "biocommons.example package (namespaced)"
-readme = "README.md"
-license = "Apache-2.0"
-requires-python = ">=3.10"
 classifiers = [
+  "Intended Audience :: Developers",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
-  "Operating System :: OS Independent"
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python",
+  "Topic :: Software Development :: Libraries :: Python Modules"
 ]
+dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
+description = "biocommons.example package (namespaced)"
 dynamic = ["version"]
+license = "Apache-2.0"
+name = "biocommons-example"
+readme = "README.md"
+requires-python = ">=3.10"
 
 [project.optional-dependencies]
 example = [
@@ -44,32 +46,32 @@ example = [
 marvin-quote = "biocommons.example.__main__:main"
 
 [project.urls]
+Documentation = "https://biocommons.github.io/python-package/"
 Homepage = "https://biocommons.github.io/python-package/"
 Issues = "https://github.com/biocommons/python-package/issues"
 Repository = "https://github.com/biocommons/python-package"
-Documentation = "https://biocommons.github.io/python-package/"
 
 [tool.coverage]
 
 [tool.coverage.report]
-show_missing = true
-skip_empty = true
 exclude_lines = [
-  # Have to re-enable the standard pragma
-  "pragma: no cover",
   # Don't complain about missing debug-only code:
   "def __repr__",
+  # Don't complain if non-runnable code isn't run:
+  "if __name__ == .__main__.:",
   "if self.debug",
+  # Have to re-enable the standard pragma
+  "pragma: no cover",
   # Don't complain if tests don't hit defensive assertion code:
   "raise AssertionError",
-  "raise NotImplementedError",
-  # Don't complain if non-runnable code isn't run:
-  "if __name__ == .__main__.:"
+  "raise NotImplementedError"
 ]
+show_missing = true
+skip_empty = true
 
 [tool.coverage.run]
 branch = true
-omit = ["*_test.py", "*/test/*", "*/tests/*"]
+omit = ["*/test/*", "*/tests/*", "*_test.py"]
 source = ["src"]
 
 [tool.deptry]
@@ -104,70 +106,74 @@ markers = [
   "network: tests that require network connectivity",
   "slow: slow tests that should be run infrequently"
 ]
+testpaths = ["tests"]
 
 [tool.ruff]
-src = ["src", "tests"]
+fix = true
 line-length = 100
+src = ["src", "tests"]
+target-version = "py39"
 
 [tool.ruff.format]
-quote-style = "double"
 docstring-code-format = true
+preview = true
+quote-style = "double"
 
 [tool.ruff.lint]
-select = [
-  "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
-  "E",
-  "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-  "I", # https://docs.astral.sh/ruff/rules/#isort-i
-  "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-  "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-  "YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
-  "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-  "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-  "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-  "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-  "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-  "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-  "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log
-  "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-  "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-  "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-  "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-  "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-  "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-  "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
-  "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-  "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl
-  "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try
-  "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
-  "RUF" # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
-]
 fixable = [
-  "F401",
-  "F541",
-  "I",
-  "D",
-  "UP",
   "B",
   "C4",
+  "D",
   "EM",
+  "F401",
+  "F541",
+  "I",
+  "PERF",
   "PIE",
   "PT",
-  "RSE",
   "RET",
+  "RSE",
+  "RUF",
   "SIM",
-  "PERF",
-  "RUF"
+  "UP"
 ]
 ignore = [
-  # ignore for compatibility with formatter
-  "W191",
   "E111",
   "E114",
   "E117",
+  "E501",
+  "E731",
+  "PLR0913",
   "S321",
-  # other
-  "PLR0913"
+  "W191"
+]
+select = [
+  "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
+  "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+  "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "E",
+  "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
+  "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  "I", # https://docs.astral.sh/ruff/rules/#isort-i
+  "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+  "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
+  "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl
+  "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+  "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+  "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+  "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try
+  "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+  "YTT" # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
 ]
 
 [tool.ruff.lint.per-file-ignores]
@@ -180,8 +186,8 @@ include-package-data = true
 "*" = ["*.gz", "*.json", "*.yaml"]
 
 [tool.setuptools.packages.find]
-where = ["src"]
-exclude = ["__pycache__", "*.pyc"]
+exclude = ["*.pyc", "__pycache__"]
 namespaces = true
+where = ["src"]
 
 [tool.setuptools_scm]