backport changes from bioutils implementation

Author: reece

.gitignore

@@ -1,12 +1,15 @@
 *$py.class
+*.bak
 *.cover
 *.egg
 *.egg-info/
 *.log
 *.manifest
 *.mo
+*.orig
 *.pot
 *.py.cover
+*.py[cod]
 *.py[codz]
 *.sage.py
 *.so
@@ -27,6 +30,7 @@
 .env
 .envrc
 .hypothesis/
+.idea
 .installed.cfg
 .ipynb_checkpoints
 .mypy_cache/
@@ -37,7 +41,9 @@
 .pybuilder/
 .pypirc
 .pyre/
+.pytest_cache
 .pytest_cache/
+.python-version
 .pytype/
 .ropeproject
 .ruff_cache/
@@ -55,6 +61,7 @@ __marimo__/
 __pycache__/
 __pypackages__/
 archive
+bioutils/_data/assemblies/pull
 build/
 celerybeat-schedule
 celerybeat.pid
@@ -64,6 +71,10 @@ cython_debug/
 develop-eggs/
 dist/
 dmypy.json
+doc/_build
+doc/changelog/*/.tags
+doc/changelog/*/.tags.mk
+doc/changelog/*/hg-git-remap.pl
 docs/_build/
 docs/source
 downloads/
@@ -78,6 +89,7 @@ lib64/
 local_settings.py
 marimo/_lsp/
 marimo/_static/
+misc
 nosetests.xml
 parts/
 pip-delete-this-directory.txt

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: detect-private-key
       - id: end-of-file-fixer
       - id: mixed-line-ending
-        args: [ --fix=lf ]
+        args: [--fix=lf]
       - id: pretty-format-json
         exclude: ^.devcontainer/.*devcontainer.json
         args: [--autofix, --no-sort-keys]
@@ -23,7 +23,7 @@ repos:
     rev: "v0.12.7"
     hooks:
       - id: ruff-check
-        args: [ --fix, --exit-non-zero-on-fix ]
+        args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
 
   - repo: local
@@ -33,11 +33,3 @@ repos:
         entry: sh -c 'LC_ALL=C 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 --all pyproject.toml
-        language: system
-        files: ^pyproject.toml$

Makefile

@@ -1,3 +1,5 @@
+# Makefile for Python project
+
 .DELETE_ON_ERROR:
 .PHONY: FORCE
 .PRECIOUS:
@@ -6,12 +8,6 @@
 .DEFAULT_GOAL := help
 default: help
 
-COLOR_RESET=\033[0m
-COLOR_CYAN_BOLD=\033[1;36m
-define INFO_MESSAGE
-	@echo -e "⏩$(COLOR_CYAN_BOLD)$(1)$(COLOR_RESET)"
-endef
-
 ############################################################################
 #= BASIC USAGE
 
@@ -41,7 +37,6 @@ publish: build ## publish package to PyPI
 	$(call INFO_MESSAGE, "Publishing package")
 	uv publish  # Requires UV_PUBLISH_TOKEN or Trusted Publishing setup
 
-
 ############################################################################
 #= FORMATTING, TESTING, AND CODE QUALITY
 
@@ -50,7 +45,7 @@ cqa: ## Run code quality assessments
 	$(call INFO_MESSAGE, "Checking lock file consistency")
 	uv lock --locked
 	$(call INFO_MESSAGE, "Linting and reformatting files")
-	uv run pre-commit run -a
+	uv run pre-commit run
 	$(call INFO_MESSAGE, "Checking for obsolete dependencies")
 	uv run deptry src
 

mkdocs.yml

@@ -7,15 +7,14 @@ edit_uri: edit/main/docs/
 repo_name: biocommons/python-package
 copyright: Maintained by <a href="https://biocommons.com">biocommons</a>.
 
-nav:
-  - Home: index.md
-  - Modules: modules.md
 plugins:
   - search
+  - awesome-nav
   - mkdocstrings:
       handlers:
         python:
-          paths: ["src/biocommons/example"]
+          options:
+            show_source: false
 theme:
   name: material
   feature:

pyproject.toml

@@ -5,6 +5,7 @@ requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
 [dependency-groups]
 dev = [
   "deptry>=0.23",
+  "mkdocs-awesome-nav>=3.1.2",
   "mkdocs-material>=9.6",
   "mkdocs>=1.6",
   "mkdocstrings[python]>=0.30",
@@ -13,7 +14,8 @@ dev = [
   "pytest-cov>=4.1",
   "pytest>=7.4",
   "ruff>=0.12",
-  "tox-uv>=1.28"
+  "tox-uv>=1.28",
+  "vcrpy"
 ]
 
 [project]
@@ -32,6 +34,13 @@ classifiers = [
 dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
 description = "biocommons.example package (namespaced)"
 dynamic = ["version"]
+keywords = [
+  "HGVS",
+  "biocommons",
+  "bioinformatics",
+  "genomics",
+  "variation"
+]
 license = "Apache-2.0"
 name = "biocommons-example"
 readme = "README.md"
@@ -55,16 +64,19 @@ Repository = "https://github.com/biocommons/python-package"
 
 [tool.coverage.report]
 exclude_lines = [
-  # 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"
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self.debug",
+
+    # 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__.:",
 ]
 show_missing = true
 skip_empty = true
@@ -182,11 +194,12 @@ select = [
 include-package-data = true
 
 [tool.setuptools.package-data]
-"*" = ["*.gz", "*.json", "*.yaml"]
+# "*" = ["_data/*/*.json.gz"]
+# "*" = ["*.gz", "*.json", "*.yaml"]
 
 [tool.setuptools.packages.find]
 exclude = ["*.pyc", "__pycache__"]
-namespaces = true
+# namespaces = true
 where = ["src"]
 
 [tool.setuptools_scm]