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merge: resolve conflicts with master in anopheles.py
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‎.gitignore‎

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.idea
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.vscode
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__pycache__
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.mypy_cache
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*.pyc
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dist
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.venv/
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.coverage
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coverage.xml
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.ipynb_checkpoints/

‎README.md‎

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@@ -49,6 +49,8 @@ To get setup for development, see [this video if you prefer VS Code](https://you
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For detailed setup instructions, see:
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- [Linux setup guide](LINUX_SETUP.md)
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- [macOS setup guide](MACOS_SETUP.md)
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- [Windows setup guide](WINDOWS_SETUP.md)
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- [Google Colab (TPU) setup guide](docs/source/colab_tpu_runtime.rst)
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Detailed instructions can be found in the [Contributors guide](https://github.com/malariagen/malariagen-data-python/blob/master/CONTRIBUTING.md).
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## AI use policy and guidelines

‎WINDOWS_SETUP.md‎

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# Windows Setup Guide
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To get setup for development on Windows, see
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[this video if you prefer VS Code](https://youtu.be/zddl3n1DCFM),
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or [this older video if you prefer PyCharm](https://youtu.be/QniQi-Hoo9A),
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and the instructions below.
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## 1. Fork and clone this repo
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```bash
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git clone https://github.com/[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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Download and install Python 3.10 from the official website:
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https://www.python.org/downloads/windows/
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During installation, check the box that says Add Python to PATH
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before clicking Install.
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Verify the installation worked:
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```bash
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python --version
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```
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## 3. Install pipx and poetry
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```bash
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python -m pip install --user pipx
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python -m pipx ensurepath
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pipx install poetry
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```
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After running ensurepath, close and reopen PowerShell before continuing.
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## 4. Create and activate development environment
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```bash
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poetry install
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poetry shell
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```
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## 5. 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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## 6. Add upstream remote and get latest code
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```bash
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git remote add upstream https://github.com/malariagen/malariagen-data-python
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git pull upstream master
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```
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Note: On Windows the default branch is called master, not main.
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## 7. Verify everything works
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```bash
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python -c "import malariagen_data; print('Setup successful!')"
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```
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## Common Issues on Windows
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**poetry not found after install**
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Close and reopen PowerShell, then try again.
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**git not recognized**
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Install Git from https://git-scm.com/download/win
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and restart PowerShell.
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**python not recognized**
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Reinstall Python and make sure to check
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Add Python to PATH during installation.
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**fatal: not a git repository**
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Make sure you are inside the malariagen-data-python
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folder before running any git commands.
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```bash
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cd malariagen-data-python
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```
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**error: pathspec main did not match**
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On Windows use master instead of main.
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```bash
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git checkout master
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```

‎docs/source/colab_tpu_runtime.rst‎

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Google Colab Installation Guide
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===============================
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Prerequisites
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-------------
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Before installing the package, configure the runtime environment
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correctly:
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1. Open a new notebook in Google Colab.
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2. Navigate to ``Runtime → Change runtime type``.
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3. Set the runtime configuration as follows:
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- **Runtime type:** Python 3
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- **Hardware accelerator:** TPU
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- **TPU type:** v2-8
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4. Click **Save** to apply the configuration.
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Using the recommended TPU configuration ensures compatibility with
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workflows that may require TPU-based computation.
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Installation Procedure
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----------------------
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In a new notebook cell, install the package:
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.. code-block:: bash
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!pip install malariagen_data
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After installation completes, verify that the package is available:
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.. code-block:: python
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import malariagen_data
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If the import executes without errors, the installation was successful.
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If dependency-related warnings or conflicts occur, follow one of the
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resolution options described below.
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Resolution Options
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------------------
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Resolution Option 1: Uninstall Panel
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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If your notebook does not require ``panel``, uninstall it before
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installing ``malariagen_data``.
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.. code-block:: bash
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!pip uninstall -y panel
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!pip install malariagen_data
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Verify installation:
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.. code-block:: python
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import malariagen_data
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Resolution Option 2: Install Compatible Panel Version
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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If your workflow depends on ``panel``, install a compatible version:
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.. code-block:: bash
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!pip install panel==1.7.0
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!pip install malariagen_data
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Restart the runtime:
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``Runtime → Restart runtime``
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Then verify:
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.. code-block:: python
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import malariagen_data
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Resolution Option 3: Install Required Blinker Version
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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If a ``blinker`` version conflict occurs:
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.. code-block:: bash
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!pip install blinker==1.9.0 --ignore-installed
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!pip install malariagen_data
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Restart the runtime and verify:
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.. code-block:: python
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import malariagen_data
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Final Verification
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------------------
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After completing any of the procedures above:
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- Ensure that ``malariagen_data`` installs without dependency errors.
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- Confirm that ``import malariagen_data`` runs successfully.
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- Restart the runtime whenever core dependencies are modified.
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- Avoid mixing incompatible package versions within the same Colab session.

‎malariagen_data/adar1.py‎

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tqdm_class=tqdm_class,
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taxon_colors=TAXON_COLORS,
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virtual_contigs=None,
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gene_names=None,
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inversion_tag_path=None,
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unrestricted_use_only=unrestricted_use_only,
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surveillance_use_only=surveillance_use_only,
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<th style="text-align: left">
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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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<td>{", ".join(self._available_releases)}</td>
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</tr>
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<tr>
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<th style="text-align: left">
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<th style="text-align: left">
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Relevant data releases
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</th>
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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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</tbody>
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</table>

‎malariagen_data/adir1.py‎

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tqdm_class=tqdm_class,
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virtual_contigs=None,
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unrestricted_use_only=unrestricted_use_only,
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surveillance_use_only=surveillance_use_only,
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<th style="text-align: left">
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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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<td>{", ".join(self._available_releases)}</td>
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</tr>
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<tr>
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<th style="text-align: left">
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<th style="text-align: left">
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Relevant data releases
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</th>
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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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</tbody>
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</table>

‎malariagen_data/af1.py‎

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tqdm_class=tqdm_class,
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taxon_colors=TAXON_COLORS,
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virtual_contigs=None,
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gene_names=None,
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inversion_tag_path=None,
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unrestricted_use_only=unrestricted_use_only,
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surveillance_use_only=surveillance_use_only,
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<th style="text-align: left">
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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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<td>{", ".join(self._available_releases)}</td>
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</tr>
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<tr>
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<th style="text-align: left">
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<th style="text-align: left">
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Relevant data releases
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</th>
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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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</tbody>
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</table>

‎malariagen_data/ag3.py‎

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Data releases available
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<td>{', '.join(self._available_releases)}</td>
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<td>{", ".join(self._available_releases)}</td>
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</tr>
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<tr>
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<th style="text-align: left">
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<th style="text-align: left">
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Relevant data releases
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</th>
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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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</tbody>
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</table>

‎malariagen_data/amin1.py‎

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inversion_tag_path=None,
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unrestricted_use_only=unrestricted_use_only,
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surveillance_use_only=surveillance_use_only,
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<th style="text-align: left">
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Data releases available
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</th>
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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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<tr>
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<th style="text-align: left">
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<th style="text-align: left">
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Relevant data releases
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</th>
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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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</tbody>
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</table>

‎malariagen_data/anoph/aim_data.py‎

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# to the superclass constructor.
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super().__init__(**kwargs)
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# Store possible values for the `aims` parameter.
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# TODO Consider moving this to data resource configuration.
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self._aim_ids = aim_ids
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self._aim_palettes = aim_palettes
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# Read AIM parameters from the JSON config, falling back to
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# constructor args for backward compatibility.
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config = self.config
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_aim_ids = config.get("AIM_IDS", None)
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if _aim_ids is not None:
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self._aim_ids: Optional[aim_params.aim_ids] = tuple(_aim_ids)
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else:
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self._aim_ids = aim_ids
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_aim_palettes = config.get("AIM_PALETTES", None)
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if _aim_palettes is not None:
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# Convert lists to tuples for each palette entry.
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self._aim_palettes: Optional[aim_params.aim_palettes] = {
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k: tuple(v)
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for k, v in _aim_palettes.items() # type: ignore
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}
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else:
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self._aim_palettes = aim_palettes
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# Set up caches.
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self._cache_aim_variants: Dict[str, xr.Dataset] = dict()
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if show: # pragma: no cover
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fig.show(renderer=renderer)
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return None
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else:
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return fig
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return fig

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