Merge branch 'master' into fix/invalid-param-error-messages

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)
 

malariagen_data/anoph/map_params.py

@@ -1,5 +1,6 @@
 """Parameters for functions plotting maps using ipyleaflet."""
 
+import warnings
 from typing import Dict, Tuple, Union
 
 import ipyleaflet  # type: ignore
@@ -17,22 +18,70 @@
 
 zoom_default: zoom = 3
 
-basemap_abbrevs = {
-    "mapnik": ipyleaflet.basemaps.OpenStreetMap.Mapnik,
-    "natgeoworldmap": ipyleaflet.basemaps.Esri.NatGeoWorldMap,
-    "opentopomap": ipyleaflet.basemaps.OpenTopoMap,
-    "positron": ipyleaflet.basemaps.CartoDB.Positron,
-    "satellite": ipyleaflet.basemaps.Gaode.Satellite,
-    "worldimagery": ipyleaflet.basemaps.Esri.WorldImagery,
-    "worldstreetmap": ipyleaflet.basemaps.Esri.WorldStreetMap,
-    "worldtopomap": ipyleaflet.basemaps.Esri.WorldTopoMap,
+# Candidate basemap abbreviations — loaded lazily to avoid import failures
+# if a provider has been decommissioned upstream.
+_basemap_abbrev_candidates = {
+    "mapnik": lambda: ipyleaflet.basemaps.OpenStreetMap.Mapnik,
+    "natgeoworldmap": lambda: ipyleaflet.basemaps.Esri.NatGeoWorldMap,
+    "opentopomap": lambda: ipyleaflet.basemaps.OpenTopoMap,
+    "positron": lambda: ipyleaflet.basemaps.CartoDB.Positron,
+    "satellite": lambda: ipyleaflet.basemaps.Gaode.Satellite,
+    "worldimagery": lambda: ipyleaflet.basemaps.Esri.WorldImagery,
+    "worldstreetmap": lambda: ipyleaflet.basemaps.Esri.WorldStreetMap,
+    "worldtopomap": lambda: ipyleaflet.basemaps.Esri.WorldTopoMap,
 }
 
+_basemap_abbrevs: dict | None = None
+
+
+def get_basemap_abbrevs() -> dict:
+    """Return available basemap abbreviations, skipping any unavailable providers."""
+    global _basemap_abbrevs
+    if _basemap_abbrevs is None:
+        _basemap_abbrevs = {}
+        for key, provider_fn in _basemap_abbrev_candidates.items():
+            try:
+                _basemap_abbrevs[key] = provider_fn()
+            except Exception:
+                warnings.warn(
+                    f"Basemap provider {key!r} is not available and will be skipped.",
+                    stacklevel=2,
+                )
+    return _basemap_abbrevs
+
+
+# Keep basemap_abbrevs as a property-like alias for backwards compatibility.
+# Code that does `map_params.basemap_abbrevs` will call get_basemap_abbrevs().
+class _BasemapAbbrevProxy:
+    def __getattr__(self, item):
+        return getattr(get_basemap_abbrevs(), item)
+
+    def __iter__(self):
+        return iter(get_basemap_abbrevs())
+
+    def __getitem__(self, item):
+        return get_basemap_abbrevs()[item]
+
+    def __contains__(self, item):
+        return item in get_basemap_abbrevs()
+
+    def keys(self):
+        return get_basemap_abbrevs().keys()
+
+    def values(self):
+        return get_basemap_abbrevs().values()
+
+    def items(self):
+        return get_basemap_abbrevs().items()
+
+
+basemap_abbrevs = _BasemapAbbrevProxy()
+
 basemap: TypeAlias = Annotated[
     Union[str, Dict, ipyleaflet.TileLayer, xyzservices.lib.TileProvider],
     f"""
     Basemap from ipyleaflet or other TileLayer provider. Strings are abbreviations mapped to corresponding
-    basemaps, available values are {list(basemap_abbrevs.keys())}.
+    basemaps, available values are {list(_basemap_abbrev_candidates.keys())}.
     """,
 ]
 

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)))