Merge branch 'master' into fix/446-guard-free-basemap-import

Author: jonbrenas

malariagen_data/anoph/frq_base.py

@@ -227,7 +227,7 @@ def plot_frequencies_heatmap(
         **kwargs,
     ) -> plotly_params.figure:
         # Check len of input.
-        if max_len and len(df) > max_len:
+        if max_len is not None and len(df) > max_len:
             raise ValueError(
                 dedent(
                     f"""

malariagen_data/anoph/g123.py

@@ -629,6 +629,9 @@ def _garud_g123(gt):
     # convert to array of sorted frequencies
     f = np.sort(np.fromiter(frq_counter.values(), dtype=float))[::-1]
 
+    if f.size == 0:
+        return np.nan
+
     # compute G123
     g123 = np.sum(f[:3]) ** 2 + np.sum(f[3:] ** 2)
 

malariagen_data/anoph/h12.py

@@ -848,6 +848,9 @@ def _garud_h12(ht):
     # Convert to array of sorted frequencies.
     f = np.sort(np.fromiter(frq_counter.values(), dtype=float))[::-1]
 
+    if f.size == 0:
+        return np.nan
+
     # Compute H12.
     h12 = np.sum(f[:2]) ** 2 + np.sum(f[2:] ** 2)
 

tests/anoph/test_g123.py

@@ -265,3 +265,10 @@ def test_g123_calibration(fixture, api: AnophelesG123Analysis):
     # Run plotting function.
     fig = api.plot_g123_calibration(**g123_params, show=False)
     assert isinstance(fig, bokeh.models.Plot)
+
+
+def test_garud_g123_empty_window():
+    import numpy as np
+    from malariagen_data.anoph.g123 import _garud_g123
+
+    assert np.isnan(_garud_g123(np.empty((0, 0), dtype=int)))

tests/anoph/test_h12.py

@@ -328,3 +328,10 @@ def test_h12_gwss_multi_with_analysis(fixture, api: AnophelesH12Analysis):
             params["min_cohort_size"] = n2 + 1
             with pytest.raises(ValueError):
                 api.plot_h12_gwss_multi_panel(**params)
+
+
+def test_garud_h12_empty_window():
+    import numpy as np
+    from malariagen_data.anoph.h12 import _garud_h12
+
+    assert np.isnan(_garud_h12(np.empty((0, 0), dtype=int)))