malariagen_data - access MalariaGEN data from Python

This Python package provides convenience methods for accessing data from MalariaGEN.

Installation

The malariagen_data Python package is available from the Python package index (PyPI) and can be installed via pip, e.g.:

$ pip install malariagen-data

Documentation

Documentation of classes and methods in the public API are available from the following locations:

• Ag3 API docs

• Amin1 API docs

• Pf7 API docs

• Pv4 API docs

Release notes (change log)

See GitHub releases for release notes.

Developer setup

To get setup for development, see this video and the instructions below.

Fork and clone this repo:

$ git clone git@github.com:[username]/malariagen-data-python.git

Install poetry 1.3.1 somehow, e.g.:

$ sudo apt install python3.7-venv
$ python3.7 -m pip install --user pipx
$ python3.7 -m pipx ensurepath
$ pipx install poetry==1.3.1

Create development environment:

$ cd malariagen-data-python
$ poetry install

Activate development environment:

$ poetry shell

Install pre-commit hooks:

$ pre-commit install

Run pre-commit checks (isort, black, blackdoc, flake8, ...) manually:

$ pre-commit run --all-files

Run tests:

$ poetry run pytest -v

Tests will run slowly the first time, as data required for testing will be read from GCS. Subsequent runs will be faster as data will be cached locally in the "gcs_cache" folder.

Release process

Create a new GitHub release. That's it. This will automatically trigger publishing of a new release to PyPI via GitHub actions.