use uv run in Makefile; make more prettier; update precommit config

Author: reece

.github/actions/setup-python-env/action.yml

@@ -7,9 +7,9 @@ repos:
       - id: check-toml
       - id: check-yaml
       - id: check-json
-        exclude: ^.devcontainer/devcontainer.json
+        exclude: ^.devcontainer/.*devcontainer.json
       - id: pretty-format-json
-        exclude: ^.devcontainer/devcontainer.json
+        exclude: ^.devcontainer/.*devcontainer.json
         args: [--autofix, --no-sort-keys]
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -20,3 +20,19 @@ repos:
       - id: ruff-check
         args: [ --exit-non-zero-on-fix ]
       - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: canonicalize-gitignore
+        name: Sort unique .gitignore
+        entry: sort -u -o .gitignore .gitignore
+        language: system
+        files: ^\.gitignore$
+
+  - repo: local
+    hooks:
+      - id: canonicalize-pyproject
+        name: Ensure pyproject.toml in canonical order and format
+        entry: uvx toml-sort --in-place pyproject.toml
+        language: system
+        files: ^pyproject.toml$

.pre-commit-config.yaml

@@ -6,11 +6,14 @@
 .DEFAULT_GOAL := help
 default: help
 
-SHELL:=/bin/bash
+ifeq ("","$(shell command -v zsh)")
+$(error "zsh not found; you must install zsh first")
+endif
+SHELL:=zsh -eu -o pipefail -o null_glob
 
 COLOR_RESET=\033[0m
 COLOR_CYAN_BOLD=\033[1;36m
-define ECHO_BANNER
+define INFO_MESSAGE
 	@echo -e "⏩$(COLOR_CYAN_BOLD)$(1)$(COLOR_RESET)"
 endef
 
@@ -20,85 +23,73 @@ endef
 .PHONY: help
 help: ## Display help message
 	@uvx python -c "import re; \
-	[[print(f'- \033[36m{m[0]:<20}\033[0m {m[1]}') for m in re.findall(r'^([\sa-zA-Z_-]+):.*?## (.*)$$', open(makefile).read(), re.M)] for makefile in ('$(MAKEFILE_LIST)').strip().split()]" | sort
-
+	[[print(f'✦ \033[36m{m[0]:<20}\033[0m {m[1]}') for m in re.findall(r'^([\sa-zA-Z_-]+):.*?## (.*)$$', open(makefile).read(), re.M)] for makefile in ('$(MAKEFILE_LIST)').strip().split()]" | sort
 
 ############################################################################
 #= SETUP, INSTALLATION, PACKAGING
 
 install: devready
 .PHONY: devready
 devready: ## Prepare local dev env: Create virtual env, install the pre-commit hooks
-	$(call ECHO_BANNER, "Prepare local dev env: Create virtual env, install the pre-commit hooks")
+	$(call INFO_MESSAGE, Prepare local dev env: Create virtual env and install the pre-commit hooks)
 	uv sync --dev
-	uvx pre-commit install
+	uv run pre-commit install
+	@echo '⚠️ You must activate the virtual env with `source .venv/bin/activate`'
 
 .PHONY: build
 build: ## Build package
-	$(call ECHO_BANNER, "Building package")
+	$(call INFO_MESSAGE, "Building package")
 	rm -fr dist
-	uvx --from build pyproject-build --installer uv
-
-.PHONY: publish
-publish: ## Publish a release to PyPI.
-	$(call ECHO_BANNER, "Publishing to PyPI.")
-	uvx publish
-
+	uv build
 
 ############################################################################
-#= TESTING AND CODE QUALITY
+#= FORMATTING, TESTING, AND CODE QUALITY
 
-.PHONY: check
-cqa check: ## Run code quality tools.
-	$(call ECHO_BANNER, "Checking lock file consistency with 'pyproject.toml'")
+.PHONY: cqa
+cqa: ## Run code quality assessments.
+	$(call INFO_MESSAGE, "Checking lock file consistency")
 	uv lock --locked
-	$(call ECHO_BANNER, "Linting code: Running pre-commit")
-	uvx pre-commit run -a
-	$(call ECHO_BANNER, "Checking for obsolete dependencies: Running deptry")
-	uvx deptry src
+	$(call INFO_MESSAGE, "Linting and reformatting files")
+	uv run pre-commit run -a
+	$(call INFO_MESSAGE, "Checking for obsolete dependencies")
+	uv run deptry src
 
 .PHONY: test
 test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"
-	pytest
-	#uvx python -m pytest # --cov --cov-config=pyproject.toml --cov-report=xml
-
+	uv run pytest
 
 ############################################################################
 #= DOCUMENTATION
 
+.PHONY: docs-serve
+docs-serve: ## Build and serve the documentation
+	$(call INFO_MESSAGE, "Build and serve docs for local development")
+	uv run mkdocs serve
+
 .PHONY: docs-test
 docs-test: ## Test if documentation can be built without warnings or errors
-	$(call ECHO_BANNER, "Testing whether docs can be build")
-	uvx mkdocs build -s
-
-.PHONY: serve
-serve: ## Build and serve the documentation
-	$(call ECHO_BANNER, "Build and serve docs for local development")
-	uvx mkdocs serve
-
+	$(call INFO_MESSAGE, "Testing whether docs can be build")
+	uv run mkdocs build -s
 
 ############################################################################
 #= CLEANUP
 
 .PHONY: clean
 clean:  ## Remove temporary and backup files
-	$(call ECHO_BANNER, "Remove temporary and backup files")
+	$(call INFO_MESSAGE, "Remove temporary and backup files")
 	rm -frv **/*~ **/*.bak
 
 .PHONY: cleaner
 cleaner: clean  ## Remove files and directories that are easily rebuilt
-	$(call ECHO_BANNER, "Remove files and directories that are easily rebuilt")
+	$(call INFO_MESSAGE, "Remove files and directories that are easily rebuilt")
 	rm -frv .cache build dist docs/_build
-	rm -frv **/__pycache__
-	rm -frv **/*.egg-info
-	rm -frv **/*.pyc
-	rm -frv **/*.orig
-	rm -frv **/*.rej
+	rm -frv **/*.pyc **/__pycache__ **/*.egg-info
+	rm -frv **/*.orig **/*.rej
 
 .PHONY: cleanest
 cleanest: cleaner  ## Remove all files that can be rebuilt
-	$(call ECHO_BANNER, "Remove files and directories that can be rebuilt")
+	$(call INFO_MESSAGE, "Remove files and directories that can be rebuilt")
 	rm -frv .eggs .tox .venv venv
 
 .PHONY: distclean

Makefile

@@ -22,6 +22,7 @@ name = "biocommons-example"
 authors = [
   {name = "biocommons contributors", email = "[email protected]"}
 ]
+dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
 description = "biocommons.example package (namespaced)"
 readme = "README.md"
 license = "Apache-2.0"
@@ -33,9 +34,13 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Operating System :: OS Independent"
 ]
-dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
 dynamic = ["version"]
 
+[project.optional-dependencies]
+example = [
+  "pyyaml"
+]
+
 [project.scripts]
 marvin-quote = "biocommons.example.__main__:main"
 
@@ -68,6 +73,8 @@ branch = true
 omit = ["*_test.py", "*/test/*", "*/tests/*"]
 source = ["src"]
 
+[tool.deptry]
+
 [tool.deptry.package_module_name_map]
 # map package name to import name
 # Making this explicit suppresses deptry notices