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Developer setup (macOS)

The Linux setup guide is available in LINUX_SETUP.md. If you are on macOS, follow these steps instead.

1. Install Miniconda

Download and install Miniconda for macOS from https://docs.conda.io/en/latest/miniconda.html. Choose the Apple Silicon installer if you have an Apple Silicon Mac, or the Intel installer otherwise. You can check with:

uname -m
# arm64 = Apple Silicon, x86_64 = Intel

After installation, close and reopen your terminal for conda to be available.

2. Create a conda environment

The package requires Python >=3.10, <3.13. Python 3.13+ is not currently supported.

conda create -n malariagen python=3.11
conda activate malariagen

3. Fork and clone this repo

Fork the repository on GitHub, then clone your fork:

git clone git@github.com:[username]/malariagen-data-python.git
cd malariagen-data-python
pip install -e ".[dev]"

4. Install pre-commit hooks

pre-commit install

Run pre-commit checks manually:

pre-commit run --all-files

5. Run tests

Run fast unit tests using simulated data:

pytest -v tests/anoph

6. 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:

brew install google-cloud-sdk

Then authenticate:

gcloud auth application-default login

This opens a browser — log in with any Google account.

Once authenticated, run legacy tests:

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.

7. VS Code terminal integration

To use the code command from the terminal:

Open VS Code → Cmd + Shift + P → type Shell Command: Install 'code' command in PATH → press Enter.