Merge branch 'master' into issue-848-numpy-matrix

Author: jonbrenas

malariagen_data/anoph/h12.py

@@ -558,6 +558,8 @@ def plot_h12_gwss_multi_overlay_track(
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.optional_figure:
         cohort_queries = self._setup_cohort_queries(
             cohorts=cohorts,
@@ -585,8 +587,11 @@ def plot_h12_gwss_multi_overlay_track(
                 min_cohort_size=min_cohort_size,
                 max_cohort_size=max_cohort_size,
                 sample_query=cohort_query,
+                sample_query_options=sample_query_options,
                 sample_sets=sample_sets,
                 random_seed=random_seed,
+                chunks=chunks,
+                inline_array=inline_array,
             )
 
         # Determine X axis range.
@@ -679,6 +684,8 @@ def plot_h12_gwss_multi_overlay(
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
         gene_labelset: Optional[gplt_params.gene_labelset] = None,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.optional_figure:
         # Plot GWSS track.
         fig1 = self.plot_h12_gwss_multi_overlay_track(
@@ -700,6 +707,8 @@ def plot_h12_gwss_multi_overlay(
             height=track_height,
             show=False,
             output_backend=output_backend,
+            chunks=chunks,
+            inline_array=inline_array,
         )
 
         fig1.xaxis.visible = False
@@ -764,6 +773,8 @@ def plot_h12_gwss_multi_panel(
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
         gene_labelset: Optional[gplt_params.gene_labelset] = None,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.optional_figure:
         cohort_queries = self._setup_cohort_queries(
             cohorts=cohorts,
@@ -789,6 +800,7 @@ def plot_h12_gwss_multi_panel(
                 window_size=window_size[cohort_label],
                 sample_sets=sample_sets,
                 sample_query=cohort_query,
+                sample_query_options=sample_query_options,
                 cohort_size=cohort_size,
                 min_cohort_size=min_cohort_size,
                 max_cohort_size=max_cohort_size,
@@ -799,6 +811,8 @@ def plot_h12_gwss_multi_panel(
                 height=track_height,
                 show=False,
                 output_backend=output_backend,
+                chunks=chunks,
+                inline_array=inline_array,
             )
             if i > 0:
                 track = self.plot_h12_gwss_track(x_range=figs[0].x_range, **params)

tests/anoph/test_h12.py

@@ -330,6 +330,36 @@ def test_h12_gwss_multi_with_analysis(fixture, api: AnophelesH12Analysis):
                 api.plot_h12_gwss_multi_panel(**params)
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_h12_gwss_multi_param_forwarding(fixture, api: AnophelesH12Analysis):
+    """Verify sample_query_options, chunks, and inline_array are
+    forwarded through multi-cohort H12 plotting functions."""
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    all_countries = api.sample_metadata()["country"].unique().tolist()
+    country1, country2 = random.sample(all_countries, 2)
+    cohort1_query = f"country == '{country1}'"
+    cohort2_query = f"country == '{country2}'"
+
+    h12_params = dict(
+        contig=random.choice(api.contigs),
+        sample_sets=all_sample_sets,
+        window_size=200,
+        min_cohort_size=1,
+        cohorts={"cohort1": cohort1_query, "cohort2": cohort2_query},
+        sample_query_options={"engine": "python"},
+        chunks="auto",
+        inline_array=False,
+    )
+
+    # Test multi-overlay — should not raise.
+    fig = api.plot_h12_gwss_multi_overlay(**h12_params, show=False)
+    assert isinstance(fig, bokeh.models.GridPlot)
+
+    # Test multi-panel — should not raise.
+    fig = api.plot_h12_gwss_multi_panel(**h12_params, show=False)
+    assert isinstance(fig, bokeh.models.GridPlot)
+
+
 def test_garud_h12_empty_window():
     import numpy as np
     from malariagen_data.anoph.h12 import _garud_h12