Merge branch 'master' into fix/version-switcher-dropdown-overflow

Author: Tanisha127

.gitignore

@@ -1,6 +1,7 @@
 .idea
 .vscode
 __pycache__
+.mypy_cache
 *.pyc
 dist
 .venv/

LINUX_SETUP.md

@@ -1,65 +1,138 @@
 # Developer setup (Linux)
 
-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.
+## 1. Install Git
+
+Choose the command for your Linux distribution:
+
+**Ubuntu, Debian, and Mint:**
+
+```bash
+sudo apt update
+sudo apt install -y git
+```
+
+**Fedora:**
 
-## 1. Fork and clone this repo
 ```bash
-git clone git@github.com:[username]/malariagen-data-python.git
+sudo dnf install -y git
+```
+
+**Arch Linux:**
+
+```bash
+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:
+
+```bash
+git clone git@github.com:[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
 cd malariagen-data-python
 ```
 
-## 2. Install Python
+Use HTTPS if you prefer, or if you do not have SSH keys configured (common on WSL):
+
+```bash
+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:**
+
+```bash
+sudo apt update
+sudo apt install -y pipx
+pipx ensurepath
+```
+
+**Fedora:**
+
+```bash
+sudo dnf install -y pipx
+pipx ensurepath
+```
+
+**Arch Linux:**
+
 ```bash
-sudo add-apt-repository ppa:deadsnakes/ppa
-sudo apt install python3.10 python3.10-venv
+sudo pacman -S python-pipx
+pipx ensurepath
 ```
 
-## 3. Install pipx and poetry
+Close and reopen your terminal to apply PATH changes.
+If you prefer to reload the shell in-place, run:
+
+```bash
+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.
+
 ```bash
-python3.10 -m pip install --user pipx
-python3.10 -m pipx ensurepath
 pipx install poetry
+poetry python install 3.12
 ```
 
-## 4. Create and activate development environment
+## 5. Create development environment
+
 ```bash
-poetry install
-poetry shell
+poetry env use 3.12
+poetry install --extras dev
 ```
 
-## 5. Install pre-commit hooks
+## 6. Install pre-commit hooks
+
 ```bash
 pipx install pre-commit
 pre-commit install
 ```
 
 Run pre-commit checks manually:
+
 ```bash
 pre-commit run --all-files
 ```
 
-## 6. Run tests
+## 7. Run tests
 
 Run fast unit tests using simulated data:
+
 ```bash
 poetry run pytest -v tests/anoph
 ```
 
-## 7. Google Cloud authentication (for legacy tests)
+## 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](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html).
 
 Once access has been granted, [install the Google Cloud CLI](https://cloud.google.com/sdk/docs/install):
+
 ```bash
 ./install_gcloud.sh
 ```
 
 Then obtain application-default credentials:
+
 ```bash
 ./google-cloud-sdk/bin/gcloud auth application-default login
 ```
 
 Once authenticated, run legacy tests:
+
 ```bash
 poetry run pytest --ignore=tests/anoph -v tests
 ```

README.md

@@ -49,6 +49,7 @@ To get setup for development, see [this video if you prefer VS Code](https://you
 For detailed setup instructions, see:
 - [Linux setup guide](LINUX_SETUP.md)
 - [macOS setup guide](MACOS_SETUP.md)
+- [Windows setup guide](WINDOWS_SETUP.md)
 - [Google Colab (TPU) setup guide](docs/source/colab_tpu_runtime.rst)
 Detailed instructions can be found in the [Contributors guide](https://github.com/malariagen/malariagen-data-python/blob/master/CONTRIBUTING.md).
 

WINDOWS_SETUP.md

@@ -0,0 +1,90 @@
+# Windows Setup Guide
+
+To get setup for development on Windows, 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.
+
+## 1. Fork and clone this repo
+```bash
+git clone https://github.com/[username]/malariagen-data-python.git
+cd malariagen-data-python
+```
+
+## 2. Install Python
+
+Download and install Python 3.10 from the official website:
+https://www.python.org/downloads/windows/
+
+During installation, check the box that says Add Python to PATH
+before clicking Install.
+
+Verify the installation worked:
+```bash
+python --version
+```
+
+## 3. Install pipx and poetry
+```bash
+python -m pip install --user pipx
+python -m pipx ensurepath
+pipx install poetry
+```
+
+After running ensurepath, close and reopen PowerShell before continuing.
+
+## 4. Create and activate development environment
+```bash
+poetry install
+poetry shell
+```
+
+## 5. Install pre-commit hooks
+```bash
+pipx install pre-commit
+pre-commit install
+```
+
+## 6. Add upstream remote and get latest code
+```bash
+git remote add upstream https://github.com/malariagen/malariagen-data-python
+git pull upstream master
+```
+
+Note: On Windows the default branch is called master, not main.
+
+## 7. Verify everything works
+```bash
+python -c "import malariagen_data; print('Setup successful!')"
+```
+
+## Common Issues on Windows
+
+**poetry not found after install**
+
+Close and reopen PowerShell, then try again.
+
+**git not recognized**
+
+Install Git from https://git-scm.com/download/win
+and restart PowerShell.
+
+**python not recognized**
+
+Reinstall Python and make sure to check
+Add Python to PATH during installation.
+
+**fatal: not a git repository**
+
+Make sure you are inside the malariagen-data-python
+folder before running any git commands.
+```bash
+cd malariagen-data-python
+```
+
+**error: pathspec main did not match**
+
+On Windows use master instead of main.
+```bash
+git checkout master
+```

docs/source/_static/images/anopheles_dirus.jpg

@@ -17,31 +17,43 @@ API documentation
 
       *Anopheles gambiae* complex.
 
-      .. image:: https://upload.wikimedia.org/wikipedia/commons/0/0a/AnophelesGambiaemosquito.jpg
+      .. image:: ./_static/images/anopheles_gambiae.jpg
+         :alt: Anopheles gambiae mosquito
+         :align: center
+         :width: 100%
 
    .. grid-item-card:: ``Af1``
       :link: Af1
       :link-type: doc
 
       *Anopheles funestus* subgroup.
 
-      .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/f/ff/Anopheles_Funetus.jpg/640px-Anopheles_Funetus.jpg
+      .. image:: ./_static/images/anopheles_funestus.jpg
+         :alt: Anopheles funestus mosquito
+         :align: center
+         :width: 100%
 
    .. grid-item-card:: ``Amin1``
       :link: Amin1
       :link-type: doc
 
       *Anopheles minimus*.
 
-      .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Anopheles_minimus_1.jpg/640px-Anopheles_minimus_1.jpg
+      .. image:: ./_static/images/anopheles_minimus.jpg
+         :alt: Anopheles minimus mosquito
+         :align: center
+         :width: 100%
 
    .. grid-item-card:: ``Adir1``
       :link: Adir1
       :link-type: doc
 
       *Anopheles dirus* complex.
 
-      .. image:: https://phil.cdc.gov//PHIL_Images/8777/8777_lores.jpg
+      .. image:: ./_static/images/anopheles_dirus.jpg
+         :alt: Anopheles dirus mosquito
+         :align: center
+         :width: 100%
 
 Documentation for the `Pf7 <https://malariagen.github.io/parasite-data/pf7/api.html>`_ (*Plasmodium falciparum*)
 and `Pv4 <https://malariagen.github.io/parasite-data/pv4/api.html>`_ (*Plasmodium vivax*) APIs is also available,

docs/source/_static/images/anopheles_funestus.jpg

@@ -7,6 +7,7 @@
 from .anopheles import AnophelesDataResource, Region
 from .pf7 import Pf7
 from .pf8 import Pf8
+from .pf9 import Pf9
 from .pv4 import Pv4
 from .util import SiteClass