Remove taxon_by param optionality and None check in frq advanced funcs

Author: leehart

malariagen_data/anoph/cnv_frq.py

@@ -445,15 +445,8 @@ def gene_cnv_frequencies_advanced(
         ci_method: Optional[frq_params.ci_method] = frq_params.ci_method_default,
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
-        taxon_by: Optional[frq_params.taxon_by] = frq_params.taxon_by_default,
+        taxon_by: frq_params.taxon_by = frq_params.taxon_by_default,
     ) -> xr.Dataset:
-        # Check that the taxon_by default hasn't been subverted, e.g. via `taxon_by=None`.
-        # This also satisfies type-checking, e.g. with `getattr`.
-        if taxon_by is None:
-            raise ValueError(
-                f"`taxon_by` cannot be set to `None`. The default would be {frq_params.taxon_by_default!r}."
-            )
-
         regions: List[Region] = parse_multi_region(self, region)
         del region
 

malariagen_data/anoph/hap_frq.py

@@ -153,15 +153,8 @@ def haplotypes_frequencies_advanced(
         ci_method: Optional[frq_params.ci_method] = frq_params.ci_method_default,
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
-        taxon_by: Optional[frq_params.taxon_by] = frq_params.taxon_by_default,
+        taxon_by: frq_params.taxon_by = frq_params.taxon_by_default,
     ) -> xr.Dataset:
-        # Check that the taxon_by default hasn't been subverted, e.g. via `taxon_by=None`.
-        # This also satisfies type-checking, e.g. with `getattr`.
-        if taxon_by is None:
-            raise ValueError(
-                f"`taxon_by` cannot be set to `None`. The default would be {frq_params.taxon_by_default!r}."
-            )
-
         # Load sample metadata.
         df_samples = self.sample_metadata(
             sample_sets=sample_sets,

malariagen_data/anoph/snp_frq.py

@@ -451,15 +451,8 @@ def snp_allele_frequencies_advanced(
         ci_method: Optional[frq_params.ci_method] = frq_params.ci_method_default,
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
-        taxon_by: Optional[frq_params.taxon_by] = frq_params.taxon_by_default,
+        taxon_by: frq_params.taxon_by = frq_params.taxon_by_default,
     ) -> xr.Dataset:
-        # Check that the taxon_by default hasn't been subverted, e.g. via `taxon_by=None`.
-        # This also satisfies type-checking, e.g. with `getattr`.
-        if taxon_by is None:
-            raise ValueError(
-                f"`taxon_by` cannot be set to `None`. The default would be {frq_params.taxon_by_default!r}."
-            )
-
         # Load sample metadata.
         df_samples = self.sample_metadata(
             sample_sets=sample_sets,
@@ -687,15 +680,8 @@ def aa_allele_frequencies_advanced(
         ci_method: Optional[frq_params.ci_method] = "wilson",
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
-        taxon_by: Optional[frq_params.taxon_by] = frq_params.taxon_by_default,
+        taxon_by: frq_params.taxon_by = frq_params.taxon_by_default,
     ) -> xr.Dataset:
-        # Check that the taxon_by default hasn't been subverted, e.g. via `taxon_by=None`.
-        # This also satisfies type-checking, e.g. with `getattr`.
-        if taxon_by is None:
-            raise ValueError(
-                f"`taxon_by` cannot be set to `None`. The default would be {frq_params.taxon_by_default!r}."
-            )
-
         # Begin by computing SNP allele frequencies.
         ds_snp_frq = self.snp_allele_frequencies_advanced(
             transcript=transcript,

notebooks/plot_frequencies_space_time.ipynb

@@ -573,6 +573,14 @@
    "source": [
     "ag3.plot_frequencies_interactive_map(ds)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d22d6d58",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {