chore: update CI with decoupled way of running pytest

.github/workflows/tests.yml

@@ -46,11 +46,15 @@ jobs:
 
       - name: Install the project's dependencies
         shell: bash -el {0}
-        run: poetry install
+        run: poetry install -v
 
-      - name: Test the codebase
+      - name: Install the task runner poethepoet
         shell: bash -el {0}
-        run: poetry run pytest
+        run: poetry self add 'poethepoet[poetry_plugin]'
+
+      - name: Test the library
+        shell: bash -el {0}
+        run: poetry task check-all
 
       - name: Upload coverage reports to Codecov
         uses: codecov/[email protected]

CONTRIBUTING.md

@@ -0,0 +1,155 @@
+# Contributing
+
+## Installation for Local Development
+
+1. Install the environment manager [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
+2. Install the Python build tool [`poetry`](https://python-poetry.org/docs/#installing-with-the-official-installer)
+3. Create an environment with Python and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive):
+
+    ```console
+    mamba env create -y -f prymer.yml
+    ```
+
+4. Activate the environment:
+
+    ```console
+    mamba activate prymer
+    ```
+
+5. Install `prymer` and development dependencies into the activated virtual environment:
+
+    ```console
+    poetry install
+    ```
+
+## Primary Development Commands
+
+To check and resolve linting issues in the codebase, run:
+
+```console
+poetry run ruff check --fix
+```
+
+To check and resolve formatting issues in the codebase, run:
+
+```console
+poetry run ruff format
+```
+
+To check the unit tests in the codebase, run:
+
+```console
+poetry run pytest
+```
+
+To check the typing in the codebase, run:
+
+```console
+poetry run mypy
+```
+
+To generate a code coverage report after testing locally, run:
+
+```console
+poetry run coverage html
+```
+
+To check the lock file is up to date:
+
+```console
+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
+
+Use `mkdocs` to build and serve the documentation.
+
+```console
+poetry run mkdocs build && poetry run mkdocs serve
+```
+
+## Creating a Release on PyPi
+
+1. Clone the repository recursively and ensure you are on the `main` (un-dirty) branch
+2. Checkout a new branch to prepare the library for release
+3. Bump the version of the library to the desired SemVer with `poetry version #.#.#`
+4. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`
+5. Push the commit to the upstream remote, open a PR, ensure tests pass, and seek reviews
+6. Squash merge the PR
+7. Tag the new commit on the main branch of the origin repository with the new SemVer
+
+> NOTE:
+> This project follows [Semantic Versioning](https://semver.org/).
+> In brief:
+> 
+> - `MAJOR` version when you make incompatible API changes
+> - `MINOR` version when you add functionality in a backwards compatible manner
+> - `PATCH` version when you make backwards compatible bug fixes
+
+GitHub Actions will take care of the remainder of the deployment and release process with:
+
+1. Unit tests will be run for safety-sake
+2. A source distribution will be built
+3. Multi-arch multi-Python binary distributions will be built
+4. Assets will be deployed to PyPi with the new SemVer
+5. A [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/)-aware changelog will be drafted
+6. A GitHub release will be created with the new SemVer and the drafted changelog
+
+> WARNING:
+> Consider editing the changelog if there are any errors or necessary enhancements.

README.md

@@ -47,7 +47,7 @@
 
 ## Recommended Installation
 
-The package `prymer` requires installation of [Primer3](https://github.com/primer3-org/primer3) and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).
+The package `prymer` requires installation of [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).
 
 To satisfy these requirements, it is recommended to install using [bioconda](https://bioconda.github.io/):
 
@@ -59,4 +59,4 @@ mamba install -c bioconda prymer
 
 See the [developer's instructions][developers-instructions-link] for more information.
 
-[developers-instructions-link]: https://prymer.readthedocs.io/en/latest/installation-and-developers-documentation.html#installation-for-development
+[developers-instructions-link]: https://prymer.readthedocs.io/en/latest/CONTRIBUTING

docs/CONTRIBUTING.md

@@ -0,0 +1 @@
+../CONTRIBUTING.md

docs/index.md

@@ -2,9 +2,18 @@
 
 Python Primer Design Library
 
-## Documentation Contents
+## Recommended Installation
+
+The package `prymer` requires installation of [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).
+
+To satisfy these requirements, it is recommended to install `prymer` using [bioconda](https://bioconda.github.io/):
 
-* [Installation](installation-and-developers-documentation.md)
-* [Overview](overview.md)
-* [API](reference/prymer/index.md)
+```console
+mamba install -c bioconda prymer
+```
+
+## Documentation Contents
 
+- [Overview](overview.md)
+- [API](reference/prymer/index.md)
+- [Contributing](CONTRIBUTING.md)

mkdocs.yml

@@ -38,6 +38,7 @@ plugins:
             show_submodules: true
   - table-reader
 markdown_extensions:
+  - callouts
   - pymdownx.highlight:
       anchor_linenums: true
       line_spans: __span