Merge branch 'master' into GH648-fix-h12-calibration-axis-flip

Author: jonbrenas

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)
+- [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/anoph/aim_data.py

@@ -341,6 +341,4 @@ def plot_aim_heatmap(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/cnv_data.py

@@ -810,9 +810,7 @@ def plot_cnv_hmm_coverage_track(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -884,9 +882,7 @@ def plot_cnv_hmm_coverage(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -1028,9 +1024,7 @@ def plot_cnv_hmm_heatmap_track(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -1100,6 +1094,4 @@ def plot_cnv_hmm_heatmap(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/dipclust.py

@@ -189,13 +189,11 @@ def plot_diplotype_clustering(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return {
-                "figure": fig,
-                "dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
-                "n_snps": n_snps_used,
-            }
+        return {
+            "figure": fig,
+            "dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
+            "n_snps": n_snps_used,
+        }
 
     def diplotype_pairwise_distances(
         self,
@@ -800,6 +798,4 @@ def plot_diplotype_clustering_advanced(
 
         if show:
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/distance.py

@@ -614,6 +614,4 @@ def plot_njt(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/frq_base.py

@@ -401,9 +401,7 @@ def plot_frequencies_heatmap(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -553,9 +551,7 @@ def plot_frequencies_time_series(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(

malariagen_data/anoph/fst.py

@@ -257,9 +257,7 @@ def plot_fst_gwss_track(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -345,9 +343,7 @@ def plot_fst_gwss(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -590,6 +586,4 @@ def plot_pairwise_average_fst(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/g123.py

@@ -421,9 +421,7 @@ def plot_g123_gwss_track(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -506,9 +504,7 @@ def plot_g123_gwss(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -607,9 +603,7 @@ def plot_g123_calibration(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
 
 def _diplotype_frequencies(gt):

malariagen_data/anoph/genome_features.py

@@ -312,9 +312,7 @@ def plot_transcript(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -514,9 +512,7 @@ def plot_genes(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     def _plot_genes_setup_data(self, *, region):
         attributes = [a for a in self._gff_default_attributes if a != "Parent"]