#55 Modernize package template

.github/workflows/python-package.yml

@@ -50,7 +50,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

.gitignore

@@ -1,143 +1,89 @@
-# Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
+__pypackages__/
+.cache
 .coverage
 .coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
+.dmypy.json
+.DS_Store
+.eggs/
+.env
 .hypothesis/
+.idea/
+.installed.cfg
+.ipynb_checkpoints
+.mypy_cache/
+.nox/
+.pdm-build/
+.pdm-python
+.pdm.toml
+.pybuilder/
+.pyre/
 .pytest_cache/
-cover/
-
-# Translations
+.Python
+.python-version
+.pytype/
+.ropeproject
+.scrapy
+.spyderproject
+.spyproject
+.tox/
+.venv
+.vscode
+.webassets-cache
+*.bak
+*.cover
+*.egg
+*.egg-info/
+*.log
+*.manifest
 *.mo
+*.orig
 *.pot
-
-# Django stuff:
-*.log
-local_settings.py
+*.py,cover
+*.py[cod]
+*.sage.py
+*.so
+*.spec
 *.sqlite3
+**/.DS_Store
+*~
+*$py.class
+/site
+archive
+build/
+celerybeat-schedule
+celerybeat.pid
+cover/
+coverage.xml
+cython_debug/
 db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
+develop-eggs/
+dist/
+dmypy.json
 docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# package/env management
-.python-version
-.env
-.venv
+downloads/
+eggs/
 env/
-venv/
 ENV/
-*.bak
+htmlcov/
+instance/
+ipython_config.py
+lib/
+lib64/
+local_settings.py
+MANIFEST
+nosetests.xml
+parts/
+pdm.lock
+pip-delete-this-directory.txt
+pip-log.txt
 Pipfile.lock
 poetry.lock
-pdm.lock
-.pdm.toml
-.pdm-python
-.pdm-build/
+profile_default/
+sdist/
+share/python-wheels/
+target/
 uv.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# IDEs
-.idea/
-.vscode
-
-# misc
-*.orig
-archive
-*~
-**/.DS_Store
+var/
+venv/
+wheels/

.mailmap

@@ -0,0 +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]>
+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]>
+Rudy Rico <[email protected]> Rudolph Rico <[email protected]>

Makefile

@@ -12,7 +12,8 @@ endif
 SHELL:=zsh -eu -o pipefail -o null_glob
 SELF:=$(firstword $(MAKEFILE_LIST))
 
-VE_DIR=venv
+VE_DIR:=venv
+PY_VERSION:=3.13
 
 TEST_DIRS:=tests
 DOC_TESTS:=src ./README.md
@@ -40,27 +41,23 @@ devready:
 
 #=> venv: make a Python 3 virtual environment
 ${VE_DIR}:
-	python3 --version
-	python3 -mvenv $@; \
-	source $@/bin/activate; \
-	python3 -m ensurepip --upgrade; \
-	pip install --upgrade pip setuptools wheel
-
+	uv venv --python ${PY_VERSION} $@
+
 #=> develop: install package in develop mode
 .PHONY: develop
 develop:
-	pip install -e ".[dev,tests]"
+	uv pip install -e ".[dev,tests]"
 	pre-commit install
 
 #=> install: install package
 .PHONY: install
 install:
-	pip install "."
+	uv pip install "."
 
 #=> build: make sdist and wheel
 .PHONY: build
 build: %:
-	python -m build
+	uv build
 
 
 ############################################################################

README.md

@@ -2,6 +2,8 @@
 
 [![codecov](https://codecov.io/gh/biocommons/biocommons.example/graph/badge.svg?token=CCUMQQV5R6)](https://codecov.io/gh/biocommons/biocommons.example)
 
+---
+
 This repo provides a template for biocommons Python packages.  Here's how to use it:
 
 1. Click the [Use this template](https://github.com/biocommons/example/generate)
@@ -11,28 +13,43 @@ This repo provides a template for biocommons Python packages.  Here's how to use
 1. Remove this header.
 1. Commit and push.
 
+Delete this section in your generated template.
+
+---
+
 ## Installation
 
 To install from pypi: ```pip install biocommons.example```
 
 ## Developer Setup
 
-Developers must install zsh, which is required by the Makefile. zsh is included by default in MacOS, and is readily available on all modern Linux distributions.
+### Prerequisites
 
-Setup like this:
+- [GNU make](https://www.gnu.org/software/make/): Current mechanism for consistent invocation of developer tools.
+  - Mac: [Install brew](https://brew.sh/), then [install make](https://formulae.brew.sh/formula/make)
+  - Ubuntu: `sudo apt install make`
+- [uv](https://docs.astral.sh/uv/): An extremely fast Python package and project manager, written in Rust.
+  - All platforms: See the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
+- [zsh](https://www.zsh.org/): Shell used by the Makefile
+  - Mac: included by default
+  - Ubuntu: `sudo apt install zsh`
+
+### One-time developer setup
+
+Create a Python virtual environment and install dependencies:
 
     make devready
+
+### Development
+
+Activate your environment:
+
     source venv/bin/activate
 
 Code reformatting:
 
     make reformat
 
-Install pre-commit hook:
-
-    # included in `make devready`, not necessary for new installations
-    pre-commit install
-
 Test:
 
     make test   # for current environment
@@ -77,7 +94,3 @@ Try it:
 
 * Quality tools: Code linting and reformatting with Ruff
 * GitHub Actions for testing and packaging
-
-## ToDo
-
-* Add devcontainer support

pyproject.toml

@@ -3,31 +3,35 @@ name = "biocommons.example"
 authors = [
     { name = "biocommons contributors", email = "[email protected]" },
 ]
-description = "Example Package"
+description = "biocommons.example Package"
 readme = "README.md"
-license = { file = "LICENSE.txt" }
-requires-python = ">=3.10"
+license = "Apache-2.0"
+# license_files = [ "LICENSE.txt" ]
+# requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.13",
     "Operating System :: OS Independent",
 ]
 dynamic = ["version"]
-dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
+dependencies = [
+    "coloredlogs ~= 15.0",
+    "pyyaml ~= 6.0",
+]
 
 [project.optional-dependencies]
 dev = [
     "build ~= 0.8",
     "ipython ~= 8.4",
-    "pre-commit ~= 3.4",
+    "pre-commit>=3.8.0",
     "ruff == 0.4.4",
 ]
 tests = [
     "pytest-cov ~= 4.1",
-    "pytest-optional-tests",
     "pytest ~= 7.1",
     "vcrpy",
     "tox ~= 4.15",