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Developer setup (Linux)

1. Install Git

Choose the command for your Linux distribution:

Ubuntu, Debian, and Mint:

sudo apt update
sudo apt install -y git

Fedora:

sudo dnf install -y git

Arch Linux:

sudo pacman -S sudo
sudo pacman -S git
sudo pacman -S openssh

If your Arch install does not have sudo configured yet, run the commands above as root, then configure sudo for your user.

2. Fork and clone this repo

After forking the repository on GitHub, clone your fork.

Use SSH if your SSH keys are set up:

git clone git@github.com:[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
cd malariagen-data-python

Use HTTPS if you prefer, or if you do not have SSH keys configured (common on WSL):

git clone https://github.com/[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
cd malariagen-data-python

3. Install pipx

Choose the command for your Linux distribution:

Ubuntu, Debian, and Mint:

sudo apt update
sudo apt install -y pipx
pipx ensurepath

Fedora:

sudo dnf install -y pipx
pipx ensurepath

Arch Linux:

sudo pacman -S python-pipx
pipx ensurepath

Close and reopen your terminal to apply PATH changes. If you prefer to reload the shell in-place, run:

exec bash

4. Install Poetry and Python 3.12

The package requires >=3.10,<3.13. We use Poetry's built-in installer to handle the Python version universally across all distributions.

pipx install poetry
poetry python install 3.12

5. Create development environment

poetry env use 3.12
poetry install --extras dev

6. Install pre-commit hooks

pipx install pre-commit
pre-commit install

Run pre-commit checks manually:

pre-commit run --all-files

7. Run tests

Run fast unit tests using simulated data:

poetry run pytest -v tests/anoph

8. Google Cloud authentication (for legacy tests)

To run legacy tests which read data from GCS, you'll need to request access to MalariaGEN data on GCS.

Once access has been granted, install the Google Cloud CLI:

./install_gcloud.sh

Then obtain application-default credentials:

./google-cloud-sdk/bin/gcloud auth application-default login

Once authenticated, run legacy tests:

poetry run pytest --ignore=tests/anoph -v tests

Tests will run slowly the first time, as data will be read from GCS and cached locally in the gcs_cache folder.