A package for accessing and analysing MalariaGEN data.
Project description
malariagen_data - analyse MalariaGEN data from Python
This Python package provides methods for accessing and analysing 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:
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 Python, e.g.:
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt install python3.9 python3.9-venv
Install pipx, e.g.:
python3.9 -m pip install --user pipx
python3.9 -m pipx ensurepath
Install poetry, e.g.:
pipx install poetry==1.8.2 --python=/usr/bin/python3.9
Create development environment:
cd malariagen-data-python
poetry use 3.9
poetry install
Activate development environment:
poetry shell
Install pre-commit and pre-commit hooks:
pipx install pre-commit --python=/usr/bin/python3.9
pre-commit install
Run pre-commit checks (isort, black, blackdoc, flake8, ...) manually:
pre-commit run --all-files
Run fast unit tests using simulated data:
poetry run pytest -v tests/anoph
To run legacy tests which read data from GCS, you'll need to install the Google Cloud CLI. E.g., if on Linux:
./install_gcloud.sh
You'll then need to obtain application-default credentials, e.g.:
./google-cloud-sdk/bin/gcloud auth application-default login
Once this is done, you can run legacy tests:
poetry run pytest --ignore=tests/anoph -v tests
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 and a new version of the documentation via GitHub Actions.
The version switcher for the documentation can then be updated by
modifying the docs/source/_static/switcher.json file accordingly.
Release history Release notifications | RSS feed
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