cnv: rename discordant read calls arg to contigs

- make 'contigs' the primary parameter name for cnv_discordant_read_calls()\n- keep backward compatibility via deprecated 'contig' alias\n- raise TypeError if both contigs and contig are supplied\n- update tests to use contigs and add explicit deprecation-alias coverage

Author: Sharon-codes

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(

tests/anoph/test_cnv_data.py

@@ -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 +631,29 @@ 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)
+    with pytest.warns(DeprecationWarning, match="deprecated"):
+        ds = api.cnv_discordant_read_calls(contig=contig, sample_sets=sample_set)
+    assert isinstance(ds, xr.Dataset)
 
 
 def test_cnv_discordant_read_calls__sample_query(
@@ -670,13 +681,13 @@ 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 +766,14 @@ 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,