Merge branch 'master' into GH1056-local-file-urls-escaped-paths

Author: khushthecoder

malariagen_data/anoph/dipclust.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Optional, Tuple
 
 import allel  # type: ignore
@@ -540,8 +541,9 @@ def _insert_dipclust_snp_trace(
             figures.append(snp_trace)
             subplot_heights.append(snp_row_height * n_snps_transcript)
         else:
-            print(
-                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
+            warnings.warn(
+                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot.",
+                stacklevel=2,
             )
         return figures, subplot_heights, n_snps_transcript
 
@@ -607,8 +609,9 @@ def plot_diplotype_clustering_advanced(
             cnv_colorscale = cnv_params.colorscale_default
         if cohort_size and snp_transcript:
             cohort_size = None
-            print(
-                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None."
+            warnings.warn(
+                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None.",
+                stacklevel=2,
             )
 
         res = self.plot_diplotype_clustering(