minor doc updates

Author: reece

.mailmap

@@ -1,13 +1,13 @@
-# I pick the account with the most modified files in git shortlog -sne
-# This is used by Git to consolidate the users who used multiple accounts
 Andreas Prlic <[email protected]> Andreas Prlic <[email protected]>
 Andreas Prlic <[email protected]> Andreas Prlic <[email protected]>
 Caitlin Gong <[email protected]> Caitlin Gong <[email protected]>
+# I pick the account with the most modified files in git shortlog -sne
 Katie Stahl <[email protected]> katie stahl <[email protected]>
 Manuel Holtgrewe <[email protected]> Manuel Holtgrewe <[email protected]>
 Meng <[email protected]> Meng Wang <[email protected]>
 Reece Hart <[email protected]> Reece Hart <[email protected]>
 Reece Hart <[email protected]> Reece Hart <[email protected]>
-Reece Hart <[email protected]> Reece Hart <[email protected]>
 Reece Hart <[email protected]> Reece Hart <[email protected]>
+Reece Hart <[email protected]> Reece Hart <[email protected]>
 Rudy Rico <[email protected]> Rudolph Rico <[email protected]>
+# This is used by Git to consolidate the users who used multiple accounts

Makefile

@@ -21,20 +21,20 @@ help: ## Display help message
 install: devready
 .PHONY: devready
 devready: ## 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)
+	$(call INFO_MESSAGE, "⚙️ Prepare local dev env: Create virtual env and install the pre-commit hooks")
 	uv sync --dev
 	uv run pre-commit install
-	@echo '⚠️ You must activate the virtual env with `source .venv/bin/activate`'
+	@echo '⚠️ Activate the virtual env with `source .venv/bin/activate`'
 
 .PHONY: build
 build: ## Build package
-	$(call INFO_MESSAGE, "Building package")
+	$(call INFO_MESSAGE, "🛠️ Build package")
 	rm -fr dist
 	uv build
 
 .PHONY: publish
-publish: build ## publish package to PyPI
-	$(call INFO_MESSAGE, "Publishing package")
+publish: build ## Publish package to PyPI
+	$(call INFO_MESSAGE, "Publish package to PyPI")
 	uv publish  # Requires UV_PUBLISH_TOKEN or Trusted Publishing setup
 
 ############################################################################
@@ -72,20 +72,20 @@ docs-test: ## Test if documentation can be built without warnings or errors
 
 .PHONY: clean
 clean:  ## Remove temporary and backup files
-	$(call INFO_MESSAGE, "Remove temporary and backup files")
+	$(call INFO_MESSAGE, "🧹 Remove temporary and backup files")
 	find . \( -name "*~" -o -name "*.bak" \) -exec rm -frv {} +
 
 .PHONY: cleaner
 cleaner: clean  ## Remove files and directories that are easily rebuilt
-	$(call INFO_MESSAGE, "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 .ruff_cache build coverage.xml dist docs/_build site
 	find . \( -name __pycache__ -type d \) -exec rm -frv {} +
 	find . \( -name "*.pyc" -o -name "*.egg-info" \) -exec rm -frv {} +
 	find . \( -name "*.orig" -o -name "*.rej" \) -exec rm -frv {} +
 
 .PHONY: cleanest
-cleanest: cleaner  ## Remove all files that can be rebuilt
-	$(call INFO_MESSAGE, "Remove files and directories that can be rebuilt")
+cleanest: cleaner  ## 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

pyproject.toml

@@ -23,22 +23,27 @@ authors = [
   {email = "[email protected]", name = "biocommons contributors"}
 ]
 classifiers = [
+  "Development Status :: 5 - Production/Stable",
   "Intended Audience :: Developers",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Medical Science Apps.",
   "Topic :: Software Development :: Libraries :: Python Modules"
 ]
 dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
 description = "biocommons.example package (namespaced)"
 dynamic = ["version"]
 keywords = [
-  "HGVS",
   "biocommons",
   "bioinformatics",
+  "computational biology",
+  "genome variation",
   "genomics",
+  "hgvs",
   "variation"
 ]
 license = "Apache-2.0"
@@ -192,10 +197,13 @@ select = [
 
 [tool.setuptools]
 include-package-data = true
+package-dir = {"" = "src"}
+zip-safe = true
 
 [tool.setuptools.package-data]
 # "*" = ["_data/*/*.json.gz"]
 # "*" = ["*.gz", "*.json", "*.yaml"]
+# hgvs = ["_data/*"]
 
 [tool.setuptools.packages.find]
 exclude = ["*.pyc", "__pycache__"]

sbin/makefile-extract-documentation

@@ -10,18 +10,24 @@
 import fileinput
 import re
 
-BOLD = "\033[1m"
-COMMAND_COLOR = "\033[36m"
-HEADER_COLOR = "\033[32m"
-RESET = "\033[0m"
-SECTION_COLOR = "\033[93m"
-UNDERLINE = "\033[4m"
+CSI = "\033["
+BOLD = CSI + "1m"
+COMMAND_COLOR = CSI + "36m"
+HEADER_COLOR = CSI + "32m"
+RESET = CSI + "0m"
+SECTION_COLOR = CSI + "95m"
+UNDERLINE = CSI + "4m"
 
-print(f"""🌟🌟 {BOLD}{HEADER_COLOR}{UNDERLINE}biocommons conventional make targets{RESET} 🌟🌟
+print(f"""🌟🌟 {BOLD}{HEADER_COLOR}{UNDERLINE}MAKE TARGETS{RESET} 🌟🌟
 
-Using these targets promots consistency between local development and ci/cd commands.
+usage: make [target ...]
 
-usage: make [target ...]""")
+biocommons packages consolidate command invocations in make targets to promote
+consistency across developers and environments (including GitHub actions). Using
+other invocations is not supported and will be ignored in bug reports.
+
+This makefile supports the following targets:
+""")
 
 for line in fileinput.input():  # noqa: SIM115
     if m := re.match(r"#= (.+)", line):

tox.ini

@@ -9,9 +9,9 @@ python =
     3.13: py313
 
 [testenv]
-passenv = PYTHON_VERSION
 allowlist_externals = uv
 commands =
     uv sync --python {envpython}
     uv run python -m pytest --doctest-modules tests --cov --cov-config=pyproject.toml --cov-report=xml
     ty check
+passenv = PYTHON_VERSION