Merge branch 'master' into fix/deprecation-warning

Author: aman-dev-maker

.github/actions/setup-python/action.yaml

@@ -19,4 +19,4 @@ runs:
       shell: bash
       run: |
         poetry env use ${{ inputs.python-version }}
-        poetry install --extras dev
+        poetry install --with dev,test,docs

.gitignore

@@ -1,8 +1,10 @@
 .idea
 .vscode
 __pycache__
+.mypy_cache
 *.pyc
 dist
+.venv/
 .coverage
 coverage.xml
 .ipynb_checkpoints/

CONTRIBUTING.md

@@ -12,7 +12,7 @@ This package provides Python tools for accessing and analyzing genomic data from
 
 You'll need:
 
-- [pipx](https://python-poetry.org/) for installing Python tools
+- [pipx](https://pipx.pypa.io/) for installing Python tools
 - [git](https://git-scm.com/) for version control
 
 Both of these can be installed using your distribution's package manager or [Homebrew](https://brew.sh/) on Mac.
@@ -52,9 +52,13 @@ Both of these can be installed using your distribution's package manager or [Hom
 
    ```bash
    poetry env use 3.12
-   poetry install --extras dev
+   poetry install --with dev,test,docs
    ```
 
+   This installs the runtime dependencies along with the `dev`, `test`, and `docs`
+   [dependency groups](https://python-poetry.org/docs/managing-dependencies/#dependency-groups).
+   If you only need to run tests, `poetry install --with test` is sufficient.
+
    **Recommended**: Use `poetry run` to run commands inside the virtual environment:
 
    ```bash

README.md

@@ -50,6 +50,7 @@ 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).
 
 ## AI use policy and guidelines

docs/source/colab_tpu_runtime.rst

@@ -0,0 +1,111 @@
+Google Colab Installation Guide
+===============================
+Prerequisites
+-------------
+
+Before installing the package, configure the runtime environment
+correctly:
+
+1. Open a new notebook in Google Colab.
+2. Navigate to ``Runtime → Change runtime type``.
+3. Set the runtime configuration as follows:
+
+   - **Runtime type:** Python 3
+   - **Hardware accelerator:** TPU
+   - **TPU type:** v2-8
+
+4. Click **Save** to apply the configuration.
+
+Using the recommended TPU configuration ensures compatibility with
+workflows that may require TPU-based computation.
+
+
+Installation Procedure
+----------------------
+
+In a new notebook cell, install the package:
+
+.. code-block:: bash
+
+   !pip install malariagen_data
+
+After installation completes, verify that the package is available:
+
+.. code-block:: python
+
+   import malariagen_data
+
+If the import executes without errors, the installation was successful.
+
+If dependency-related warnings or conflicts occur, follow one of the
+resolution options described below.
+
+
+Resolution Options
+------------------
+
+Resolution Option 1: Uninstall Panel
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If your notebook does not require ``panel``, uninstall it before
+installing ``malariagen_data``.
+
+.. code-block:: bash
+
+   !pip uninstall -y panel
+   !pip install malariagen_data
+
+Verify installation:
+
+.. code-block:: python
+
+   import malariagen_data
+
+
+Resolution Option 2: Install Compatible Panel Version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If your workflow depends on ``panel``, install a compatible version:
+
+.. code-block:: bash
+
+   !pip install panel==1.7.0
+   !pip install malariagen_data
+
+Restart the runtime:
+
+``Runtime → Restart runtime``
+
+Then verify:
+
+.. code-block:: python
+
+   import malariagen_data
+
+
+Resolution Option 3: Install Required Blinker Version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If a ``blinker`` version conflict occurs:
+
+.. code-block:: bash
+
+   !pip install blinker==1.9.0 --ignore-installed
+   !pip install malariagen_data
+
+Restart the runtime and verify:
+
+.. code-block:: python
+
+   import malariagen_data
+
+
+Final Verification
+------------------
+
+After completing any of the procedures above:
+
+- Ensure that ``malariagen_data`` installs without dependency errors.
+- Confirm that ``import malariagen_data`` runs successfully.
+- Restart the runtime whenever core dependencies are modified.
+- Avoid mixing incompatible package versions within the same Colab session.

malariagen_data/adar1.py

@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            gene_names=None,
             inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,

malariagen_data/adir1.py

@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            gene_names=None,
             inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,

malariagen_data/af1.py

@@ -132,7 +132,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            gene_names=None,
             inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,

malariagen_data/amin1.py

@@ -130,7 +130,6 @@ def __init__(
             tqdm_class=tqdm_class,
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
-            gene_names=None,
             inversion_tag_path=None,
             unrestricted_use_only=unrestricted_use_only,
             surveillance_use_only=surveillance_use_only,

malariagen_data/anoph/aim_data.py

@@ -40,10 +40,24 @@ def __init__(
         # to the superclass constructor.
         super().__init__(**kwargs)
 
-        # Store possible values for the `aims` parameter.
-        # TODO Consider moving this to data resource configuration.
-        self._aim_ids = aim_ids
-        self._aim_palettes = aim_palettes
+        # Read AIM parameters from the JSON config, falling back to
+        # constructor args for backward compatibility.
+        config = self.config
+        _aim_ids = config.get("AIM_IDS", None)
+        if _aim_ids is not None:
+            self._aim_ids: Optional[aim_params.aim_ids] = tuple(_aim_ids)
+        else:
+            self._aim_ids = aim_ids
+
+        _aim_palettes = config.get("AIM_PALETTES", None)
+        if _aim_palettes is not None:
+            # Convert lists to tuples for each palette entry.
+            self._aim_palettes: Optional[aim_params.aim_palettes] = {
+                k: tuple(v)
+                for k, v in _aim_palettes.items()  # type: ignore
+            }
+        else:
+            self._aim_palettes = aim_palettes
 
         # Set up caches.
         self._cache_aim_variants: Dict[str, xr.Dataset] = dict()
@@ -341,6 +355,4 @@ def plot_aim_heatmap(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig