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‎LINUX_SETUP.md‎

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# Developer setup (Linux)
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To get setup for development, see [this video if you prefer VS Code](https://youtu.be/zddl3n1DCFM), or [this older video if you prefer PyCharm](https://youtu.be/QniQi-Hoo9A), and the instructions below.
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## 1. Install Git
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Choose the command for your Linux distribution:
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**Ubuntu, Debian, and Mint:**
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```bash
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sudo apt update
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sudo apt install -y git
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```
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**Fedora:**
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## 1. Fork and clone this repo
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```bash
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git clone git@github.com:[username]/malariagen-data-python.git
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sudo dnf install -y git
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```
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**Arch Linux:**
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```bash
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sudo pacman -S sudo
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sudo pacman -S git
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sudo pacman -S openssh
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```
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If your Arch install does not have `sudo` configured yet, run the commands above as `root`, then configure `sudo` for your user.
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## 2. Fork and clone this repo
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After forking the repository on GitHub, clone your fork.
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Use SSH if your SSH keys are set up:
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```bash
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git clone git@github.com:[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
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cd malariagen-data-python
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```
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## 2. Install Python
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Use HTTPS if you prefer, or if you do not have SSH keys configured (common on WSL):
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```bash
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git clone https://github.com/[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
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cd malariagen-data-python
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```
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## 3. Install pipx
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Choose the command for your Linux distribution:
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**Ubuntu, Debian, and Mint:**
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```bash
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sudo apt update
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sudo apt install -y pipx
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pipx ensurepath
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```
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**Fedora:**
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```bash
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sudo dnf install -y pipx
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pipx ensurepath
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```
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**Arch Linux:**
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```bash
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sudo add-apt-repository ppa:deadsnakes/ppa
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sudo apt install python3.10 python3.10-venv
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sudo pacman -S python-pipx
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pipx ensurepath
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```
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## 3. Install pipx and poetry
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Close and reopen your terminal to apply PATH changes.
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If you prefer to reload the shell in-place, run:
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```bash
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exec bash
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```
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## 4. Install Poetry and Python 3.12
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The package requires `>=3.10,<3.13`. We use Poetry's built-in installer to handle the Python version universally across all distributions.
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```bash
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python3.10 -m pip install --user pipx
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python3.10 -m pipx ensurepath
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pipx install poetry
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poetry python install 3.12
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```
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## 4. Create and activate development environment
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## 5. Create development environment
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```bash
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poetry install
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poetry shell
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poetry env use 3.12
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poetry install --extras dev
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```
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## 5. Install pre-commit hooks
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## 6. Install pre-commit hooks
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```bash
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pipx install pre-commit
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pre-commit install
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```
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Run pre-commit checks manually:
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```bash
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pre-commit run --all-files
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```
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## 6. Run tests
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## 7. Run tests
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Run fast unit tests using simulated data:
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```bash
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poetry run pytest -v tests/anoph
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```
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## 7. Google Cloud authentication (for legacy tests)
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## 8. Google Cloud authentication (for legacy tests)
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To run legacy tests which read data from GCS, you'll need to [request access to MalariaGEN data on GCS](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html).
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Once access has been granted, [install the Google Cloud CLI](https://cloud.google.com/sdk/docs/install):
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```bash
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./install_gcloud.sh
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```
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Then obtain application-default credentials:
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```bash
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./google-cloud-sdk/bin/gcloud auth application-default login
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```
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Once authenticated, run legacy tests:
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```bash
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poetry run pytest --ignore=tests/anoph -v tests
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```

‎docs/source/_static/images/anopheles_dirus.jpg‎

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‎docs/source/index.rst‎

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*Anopheles gambiae* complex.
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.. image:: https://upload.wikimedia.org/wikipedia/commons/0/0a/AnophelesGambiaemosquito.jpg
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.. image:: ./_static/images/anopheles_gambiae.jpg
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:alt: Anopheles gambiae mosquito
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:align: center
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:width: 100%
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.. grid-item-card:: ``Af1``
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:link: Af1
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:link-type: doc
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*Anopheles funestus* subgroup.
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.. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/f/ff/Anopheles_Funetus.jpg/640px-Anopheles_Funetus.jpg
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.. image:: ./_static/images/anopheles_funestus.jpg
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:alt: Anopheles funestus mosquito
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:align: center
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:width: 100%
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.. grid-item-card:: ``Amin1``
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:link: Amin1
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:link-type: doc
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*Anopheles minimus*.
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.. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Anopheles_minimus_1.jpg/640px-Anopheles_minimus_1.jpg
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.. image:: ./_static/images/anopheles_minimus.jpg
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:alt: Anopheles minimus mosquito
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:align: center
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:width: 100%
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.. grid-item-card:: ``Adir1``
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:link: Adir1
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:link-type: doc
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*Anopheles dirus* complex.
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.. image:: https://phil.cdc.gov//PHIL_Images/8777/8777_lores.jpg
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.. image:: ./_static/images/anopheles_dirus.jpg
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:alt: Anopheles dirus mosquito
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:align: center
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:width: 100%
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Documentation for the `Pf7 <https://malariagen.github.io/parasite-data/pf7/api.html>`_ (*Plasmodium falciparum*)
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and `Pv4 <https://malariagen.github.io/parasite-data/pv4/api.html>`_ (*Plasmodium vivax*) APIs is also available,

‎malariagen_data/adar1.py‎

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Data releases available
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</th>
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<td>{', '.join(self._available_releases)}</td>
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</tr>
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<tr>
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Relevant data releases
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<td>{', '.join(self.releases)}</td>
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<td>{", ".join(self.releases)}</td>
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</tr>
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</table>

‎malariagen_data/adir1.py‎

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‎malariagen_data/af1.py‎

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‎malariagen_data/ag3.py‎

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<td>{", ".join(self.releases)}</td>
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