Apply suggestions from code review

Co-authored-by: Clint Valentine <[email protected]>

Author: nh13

.github/workflows/publish_fgpyo.yml

@@ -2,7 +2,7 @@ name: publish fgpyo
 
 on:
   push:
-    tags: '\d+.\d+.\d+'
+    tags: '[0-9]+.[0-9]+.[0-9]+'
 
 env:
   POETRY_VERSION: 1.8.2

CONTRIBUTING.md

@@ -17,35 +17,35 @@ poetry install --all-extras
 
 [rtd-link]:    http://fgpyo.readthedocs.org/en/stable
 [poetry-link]: https://github.com/python-poetry/poetry
-[conda-link]:  https://docs.conda.io/en/latest/miniconda.html
+[conda-link]:  https://github.com/mamba-org/mamba
 
 ## Primary Development Commands
 
 To check and resolve linting issues in the codebase, run:
 
 ```console
-poetry run ruff check --fix
+poetry run ruff check --fix fgpyo tests
 ```
 
 To check and resolve formatting issues in the codebase, run:
 
 ```console
-poetry run ruff format
+poetry run ruff format fgpyo tests
 ```
 
 To check the unit tests in the codebase, run:
 
 ```console
-poetry run pytest
+poetry run pytest --cov=fgpyo --cov-report=html --cov-branch
 ```
 
 To check the typing in the codebase, run:
 
 ```console
-poetry run mypy
+poetry run mypy fgpyo tests
 ```
 
-To generate a code coverage report after testing locally, run:
+To re-generate a code coverage report after testing locally, run:
 
 ```console
 poetry run coverage html
@@ -57,61 +57,6 @@ To check the lock file is up to date:
 poetry check --lock
 ```
 
-## Shortcut Task Commands
-
-To be able to run shortcut task commands, first install the Poetry plugin [`poethepoet`](https://poethepoet.natn.io/index.html):
-
-```console
-poetry self add 'poethepoet[poetry_plugin]'
-```
-
-> NOTE:
-> Upon the release of Poetry [v2.0.0](https://github.com/orgs/python-poetry/discussions/9793#discussioncomment-11043205), Poetry will automatically support bootstrap installation of [project-specific plugins](https://github.com/python-poetry/poetry/pull/9547) and installation of the task runner will become automatic for this project.
-> The `pyproject.toml` syntax will be:
-> 
-> ```toml
-> [tool.poetry]
-> requires-poetry = ">=2.0"
-> 
-> [tool.poetry.requires-plugins]
-> poethepoet = ">=0.29"
-> ```
-
-###### For Running Individual Checks
-
-```console
-poetry task check-lock
-poetry task check-format
-poetry task check-lint
-poetry task check-tests
-poetry task check-typing
-```
-
-###### For Running All Checks
-
-```console
-poetry task check-all
-```
-
-###### For Running Individual Fixes
-
-```console
-poetry task fix-format
-poetry task fix-lint
-```
-
-###### For Running All Fixes
-
-```console
-poetry task fix-all
-```
-
-###### For Running All Fixes and Checks
-
-```console
-poetry task fix-and-check-all
-```
-
 
 ## Building the Documentation
 

README.md

@@ -53,8 +53,6 @@ Quality of life improvements for Bioinformatics in Python.
 See documentation on [fgpyo.readthedocs.org](http://fgpyo.readthedocs.org/en/stable).
 
 
-# Getting Setup
-
 ## Development and Testing
 
 See the [developer's instructions](CONTRIBUTING.md) for more information.