Merge branch 'master' into update-contributing-guide

Author: jonbrenas

.codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+    patch:
+      default:
+        target: 80%
+        threshold: 0%

.github/workflows/tests.yml

@@ -12,6 +12,10 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
+        numpy-spec:
+          # Keep this aligned with pyproject.toml: numpy = ">=2.0.2,<2.1"
+          - "==2.0.2"       # locked baseline
+          - ">=2.0.2,<2.1"  # latest allowed in declared range
     runs-on: ubuntu-latest
 
     steps:
@@ -23,8 +27,26 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Verify NumPy version
-        run: poetry run python -c "import numpy; print('NumPy version:', numpy.__version__)"
+      - name: Install matrix NumPy version
+        run: poetry run pip install --upgrade --no-deps "numpy${{ matrix.numpy-spec }}"
+
+      - name: Verify NumPy version and spec
+        env:
+          NUMPY_SPEC: ${{ matrix.numpy-spec }}
+        run: |
+          poetry run python - <<'PY'
+          import os
+          import numpy
+          from packaging.specifiers import SpecifierSet
+
+          spec = SpecifierSet(os.environ["NUMPY_SPEC"])
+          version = numpy.__version__
+          if version not in spec:
+              raise RuntimeError(
+                  f"NumPy version {version} does not satisfy matrix spec {spec}"
+              )
+          print("NumPy version:", version, "| spec:", spec)
+          PY
 
       - name: Run unit tests
         run: poetry run pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph

LINUX_SETUP.md

@@ -0,0 +1,67 @@
+# 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. Fork and clone this repo
+```bash
+git clone git@github.com:[username]/malariagen-data-python.git
+cd malariagen-data-python
+```
+
+## 2. Install Python
+```bash
+sudo add-apt-repository ppa:deadsnakes/ppa
+sudo apt install python3.10 python3.10-venv
+```
+
+## 3. Install pipx and poetry
+```bash
+python3.10 -m pip install --user pipx
+python3.10 -m pipx ensurepath
+pipx install poetry
+```
+
+## 4. Create and activate development environment
+```bash
+poetry install
+poetry shell
+```
+
+## 5. 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
+
+Run fast unit tests using simulated data:
+```bash
+poetry run pytest -v tests/anoph
+```
+
+## 7. 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
+```
+
+Tests will run slowly the first time, as data will be read from GCS and cached locally in the `gcs_cache` folder.

MACOS_SETUP.md

@@ -0,0 +1,77 @@
+# Developer setup (macOS)
+
+The Linux setup guide is available in [LINUX_SETUP.md](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:
+```bash
+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.
+```bash
+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:
+```bash
+git clone git@github.com:[username]/malariagen-data-python.git
+cd malariagen-data-python
+pip install -e ".[dev]"
+```
+
+## 4. Install pre-commit hooks
+```bash
+pre-commit install
+```
+
+Run pre-commit checks manually:
+```bash
+pre-commit run --all-files
+```
+
+## 5. Run tests
+
+Run fast unit tests using simulated data:
+```bash
+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](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html).
+
+Once access has been granted, install the Google Cloud CLI:
+```bash
+brew install google-cloud-sdk
+```
+
+Then authenticate:
+```bash
+gcloud auth application-default login
+```
+
+This opens a browser — log in with any Google account.
+
+Once authenticated, run legacy tests:
+```bash
+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.

README.md

@@ -44,8 +44,11 @@ for release notes.
 
 ## Developer setup
 
-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.
+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).
 
+For detailed setup instructions, see:
+- [Linux setup guide](LINUX_SETUP.md)
+- [macOS setup guide](MACOS_SETUP.md)
 Detailed instructions can be found in the [Contributors guide](https://github.com/malariagen/malariagen-data-python/blob/master/CONTRIBUTING.md).
 
 ## AI use policy and guidelines

docs/source/index.rst

@@ -92,7 +92,7 @@ Some data from MalariaGEN are subject to **terms of use** which may include an e
 public communication of any analysis results without permission from data owners. If you
 have any questions about terms of use please email support@malariagen.net.
 
-By default, this sofware package accesses data directly from the **MalariaGEN cloud data repository**
+By default, this software package accesses data directly from the **MalariaGEN cloud data repository**
 hosted in Google Cloud Storage in the US. Note that data access will be more efficient if your
 computations are also run within the same region. Google Colab provides a convenient and free
 service which you can use to explore data and run computations. If you have any questions about

malariagen_data/__init__.py

@@ -1,4 +1,5 @@
 # flake8: noqa
+from .adar1 import Adar1
 from .adir1 import Adir1
 from .af1 import Af1
 from .ag3 import Ag3