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Installation and Developer's Documentation

The package prymer requires installation of Primer3 and interactive bwa.

To satisfy these requirements, it is recommended to install using bioconda:

mamba install -c bioconda prymer

Installation for Development and Release

  1. Install the environment manager mamba
  2. Install the Python build tool poetry

  3. Create an environment with Python, Primer3, and interactive bwa:

    mamba env create -y -f prymer.yml

  4. Activate the environment:

    mamba activate prymer

  5. Configure poetry to install into pre-existing virtual environments:

    poetry config virtualenvs.create false

  6. Install prymer into the virtual environment:

    poetry install

Checking the Build

Use poetry to test your code.

poetry run pytest

Note that poetry run pytest will run mypy checks, ruff checks, pytest unit tests, and will provide a unit test coverage report. However, pytest will neither run the ruff formatter nor apply ruff's automatic lint fixes, which can be done by calling ruff directly. 

poetry run ruff format && poetry run ruff check --fix

Building the Documentation

Use mkdocs to build and serve the documentation.

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. 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-aware changelog will be drafted
  6. A GitHub release will be created with the new SemVer and the drafted changelog

[!IMPORTANT] Consider editing the changelog if there are any errors or necessary enhancements.