use uv to create virtual environment and update README

Author: reece

Makefile

@@ -40,22 +40,18 @@ 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 $@
+	
 #=> 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

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
@@ -78,6 +95,3 @@ Try it:
 * Quality tools: Code linting and reformatting with Ruff
 * GitHub Actions for testing and packaging
 
-## ToDo
-
-* Add devcontainer support

pyproject.toml

@@ -16,18 +16,20 @@ classifiers = [
     "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",