Merge branch 'master' into fix/veff-replace-asserts-with-exceptions

Author: jonbrenas

malariagen_data/anoph/cnv_data.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Dict, List, Optional, Tuple, Union
 
 import dask.array as da
@@ -602,7 +603,9 @@ def _cnv_discordant_read_calls_dataset(
     )
     def cnv_discordant_read_calls(
         self,
-        contig: base_params.contigs,
+        contigs: Optional[base_params.contigs] = None,
+        *,
+        contig: Optional[base_params.contigs] = None,
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
@@ -615,18 +618,29 @@ def cnv_discordant_read_calls(
         # CNV alleles have unknown start or end coordinates.
 
         debug("normalise parameters")
+        if contigs is not None and contig is not None:
+            raise TypeError("Please provide only one of 'contigs' or 'contig'.")
+        if contigs is None:
+            if contig is None:
+                raise TypeError("Missing required parameter 'contigs'.")
+            warnings.warn(
+                "Parameter 'contig' is deprecated; use 'contigs' instead.",
+                DeprecationWarning,
+            )
+            contigs = contig
+
         prepared_sample_sets = self._prep_sample_sets_param(sample_sets=sample_sets)
         prepared_sample_query = self._prep_sample_query_param(sample_query=sample_query)
-        if isinstance(contig, str):
-            contig = [contig]
+        if isinstance(contigs, str):
+            contigs = [contigs]
 
         # Delete original parameters to prevent accidental use.
         del sample_sets
         del sample_query
 
         debug("access data and concatenate as needed")
         lx = []
-        for c in contig:
+        for c in contigs:
             ly = []
             for s in prepared_sample_sets:
                 y = self._cnv_discordant_read_calls_dataset(

malariagen_data/anoph/cnv_frq.py

@@ -586,7 +586,7 @@ def _gene_cnv_frequencies_advanced(
                 nobs[:, cohort_index] = np.repeat(cohort_n_called, 2)
             else:
                 assert nobs_mode == "fixed"
-                nobs[:, cohort_index] = cohort.size * 2
+                nobs[:, cohort_index] = cohort.size
 
         debug("compute frequency")
         with np.errstate(divide="ignore", invalid="ignore"):

malariagen_data/anoph/frq_base.py

@@ -140,6 +140,9 @@ def _add_frequency_ci(*, ds, ci_method):
             frq_ci_low, frq_ci_upp = proportion_confint(
                 count=count, nobs=nobs, method=ci_method
             )
+        loc_zero = nobs == 0
+        frq_ci_low[loc_zero] = np.nan
+        frq_ci_upp[loc_zero] = np.nan
         ds["event_frequency_ci_low"] = ("variants", "cohorts"), frq_ci_low
         ds["event_frequency_ci_upp"] = ("variants", "cohorts"), frq_ci_upp
 

poetry.lock

@@ -36,10 +36,10 @@ BioPython = "*"
 scikit-allel = ">=1.3.13"
 xarray = "*"
 plotly = "*"
-# Bokeh 3.7.x causes type checking issues.
-# https://github.com/bokeh/bokeh/issues/14412
+# https://github.com/malariagen/malariagen-data-python/issues/845
 # https://github.com/malariagen/malariagen-data-python/issues/734
-bokeh = "<3.7.0"
+# https://github.com/malariagen/malariagen-data-python/issues/743
+bokeh = ">=3.7.0"
 statsmodels = ">=0.14.2"
 ipyleaflet = ">=0.17.0"
 ipywidgets = "*"
@@ -107,3 +107,10 @@ line-length = 88
 
 [tool.ruff.lint]
 extend-select = []
+
+[tool.mypy]
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = ["bokeh", "bokeh.*"]
+follow_imports = "skip"

pyproject.toml

@@ -564,7 +564,7 @@ def test_cnv_discordant_read_calls(fixture, api: AnophelesCnvData):
 
     for sample_sets in parametrize_sample_sets:
         for contig in parametrize_contig:
-            ds = api.cnv_discordant_read_calls(contig=contig, sample_sets=sample_sets)
+            ds = api.cnv_discordant_read_calls(contigs=contig, sample_sets=sample_sets)
             assert isinstance(ds, xr.Dataset)
 
             # check fields
@@ -631,18 +631,30 @@ def test_cnv_discordant_read_calls(fixture, api: AnophelesCnvData):
         match="No CNV discordant read calls data found|no CNVs available for contig",
     ):
         api.cnv_discordant_read_calls(
-            contig="foobar", sample_sets=random.choice(all_sample_sets)
+            contigs="foobar", sample_sets=random.choice(all_sample_sets)
         )
 
     # Check with a sample set that should not exist
     with pytest.raises(ValueError):
         api.cnv_discordant_read_calls(
-            contig=random.choice(api.contigs), sample_sets="foobar"
+            contigs=random.choice(api.contigs), sample_sets="foobar"
         )
 
     # Check with a contig and sample set that should not exist
     with pytest.raises(ValueError):
-        api.cnv_discordant_read_calls(contig="foobar", sample_sets="bazqux")
+        api.cnv_discordant_read_calls(contigs="foobar", sample_sets="bazqux")
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_discordant_read_calls_deprecated_contig_alias(
+    fixture, api: AnophelesCnvData
+):
+    sample_set = random.choice(api.sample_sets()["sample_set"].to_list())
+    contig = random.choice(api.contigs)
+    ds_contigs = api.cnv_discordant_read_calls(contigs=contig, sample_sets=sample_set)
+    with pytest.warns(DeprecationWarning, match="deprecated"):
+        ds_contig = api.cnv_discordant_read_calls(contig=contig, sample_sets=sample_set)
+    xr.testing.assert_identical(ds_contig, ds_contigs)
 
 
 def test_cnv_discordant_read_calls__sample_query(
@@ -670,13 +682,13 @@ def test_cnv_discordant_read_calls__sample_query(
         if len(df_samples) == 0:
             with pytest.raises(ValueError):
                 ds = api.cnv_discordant_read_calls(
-                    contig=contig,
+                    contigs=contig,
                     sample_sets=sample_sets,
                     sample_query=sample_query,
                 )
         else:
             ds = api.cnv_discordant_read_calls(
-                contig=contig,
+                contigs=contig,
                 sample_sets=sample_sets,
                 sample_query=sample_query,
             )
@@ -755,14 +767,14 @@ def test_cnv_discordant_read_calls__sample_query_options(
         if len(df_samples) == 0:
             with pytest.raises(ValueError):
                 ds = api.cnv_discordant_read_calls(
-                    contig=contig,
+                    contigs=contig,
                     sample_sets=sample_sets,
                     sample_query=sample_query,
                     sample_query_options=sample_query_options,
                 )
         else:
             ds = api.cnv_discordant_read_calls(
-                contig=contig,
+                contigs=contig,
                 sample_sets=sample_sets,
                 sample_query=sample_query,
                 sample_query_options=sample_query_options,