more README cleanup

Author: reece

README.md

@@ -15,11 +15,25 @@ This is a [biocommons](https://biocommons.org/) project.
 
 ## Python Package Installation
 
-Install from PyPI using one or more of the following:
+Install from PyPI with `pip install biocommons.example` or `uv pip install biocommons.example`, then try it:
+
+    $ source venv/bin/activate
+
+    $ python3 -m biocommons.example
+    Marvin says:
+    There's only one life-form as intelligent as me within thirty parsecs...
+
+    $ marvin-quote
+    Marvin says:
+    You think you've got problems? What are you supposed to do if you...
+
+    $ ipython
+    >>> from biocommons.example import __version__, get_quote_from_marvin
+    >>> __version__
+    '0.1.dev8+gd5519a8.d20211123'
+    >>> get_quote()
+    "The first ten million years were the worst, ...
 
-- `pip install biocommons.example`
-- `uv pip install biocommons.example`
-- Add `biocommons.example` to dependencies in `pyproject.toml` or `requirements.txt`
 
 ## Developer Setup
 
@@ -53,101 +67,34 @@ Create a Python virtual environment, install dependencies, install pre-commit ho
 ### Development
 
 **N.B.** Developers are strongly encouraged to use `make` to invoke tools to
-ensure consistency with the CI/CD pipelines.  Type `make help` to see a list of
-supported targets.
-
-Try it:
-
-    $ source venv/bin/activate
-
-    $ python3 -m biocommons.example
-    Marvin says:
-    There's only one life-form as intelligent as me within thirty parsecs...
-
-    $ marvin-quote
-    Marvin says:
-    You think you've got problems? What are you supposed to do if you...
-
-    $ ipython
-    >>> from biocommons.example import __version__, get_quote_from_marvin
-    >>> __version__
-    '0.1.dev8+gd5519a8.d20211123'
-    >>> get_quote()
-    "The first ten million years were the worst, ...
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-## Getting started with your project
-
-### 1. Create a New Repository
-
-First, create a repository on GitHub with the same name as this project, and then run the following commands:
-
-```bash
-git init -b main
-git add .
-git commit -m "init commit"
-git remote add origin [email protected]:biocommons/python-package.git
-git push -u origin main
-```
-
-### 2. Set Up Your Development Environment
-
-Then, install the environment and the pre-commit hooks with
-
-```bash
-make install
-```
-
-This will also generate your `uv.lock` file
-
-### 3. Run the pre-commit hooks
-
-Initially, the CI/CD pipeline might be failing due to formatting issues. To resolve those run:
-
-```bash
-uv run pre-commit run -a
-```
-
-### 4. Commit the changes
-
-Lastly, commit the changes made by the two steps above to your repository.
+ensure consistency with the CI/CD pipelines.  Type `make` to see a list of
+supported targets.  A subset are listed here:
 
-```bash
-git add .
-git commit -m 'Fix formatting issues'
-git push origin main
-```
+    » make
+    🌟🌟 biocommons conventional make targets 🌟🌟
 
-You are now ready to start development on your project!
-The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+    Using these targets promots consistency between local development and ci/cd commands.
 
-To finalize the set-up for publishing to PyPI, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/publishing/#set-up-for-pypi).
-For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/mkdocs/#enabling-the-documentation-on-github).
-To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/codecov/).
+    usage: make [target ...]
 
-## Releasing a new version
+    BASIC USAGE
+    help                Display help message
 
-- Create an API Token on [PyPI](https://pypi.org/).
-- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/biocommons/python-package/settings/secrets/actions/new).
-- Create a [new release](https://github.com/biocommons/python-package/releases/new) on Github.
-- Create a new tag in the form `*.*.*`.
+    SETUP, INSTALLATION, PACKAGING
+    devready            Prepare local dev env: Create virtual env, install the pre-commit hooks
+    build               Build package
+    publish             publish package to PyPI
 
-For more details, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/cicd/#how-to-trigger-a-release).
+    FORMATTING, TESTING, AND CODE QUALITY
+    cqa                 Run code quality assessments
+    test                Test the code with pytest
 
----
+    DOCUMENTATION
+    docs-serve          Build and serve the documentation
+    docs-test           Test if documentation can be built without warnings or errors
 
-Repository initiated with [fpgmaas/cookiecutter-uv](https://github.com/fpgmaas/cookiecutter-uv).
+    CLEANUP
+    clean               Remove temporary and backup files
+    cleaner             Remove files and directories that are easily rebuilt
+    cleanest            Remove all files that can be rebuilt
+    distclean           Remove untracked files and other detritus

sbin/makefile-extract-documentation

@@ -21,7 +21,7 @@ print(f"""🌟🌟 {BOLD}{HEADER_COLOR}{UNDERLINE}biocommons conventional make t
 
 Using these targets promots consistency between local development and ci/cd commands.
 
-usage: make [target ...])""")
+usage: make [target ...]""")
 
 for line in fileinput.input():  # noqa: SIM115
     if m := re.match(r"#= (.+)", line):