fix(ci): restore coverage and remove deprecated plotly usage

- restore dynamic gene attribute lookup
- replace append_trace with add_trace
- restore f-strings for style consistency

No functional changes.

Author: adilraza99

malariagen_data/plotly_dendrogram.py

@@ -166,10 +166,10 @@ def concat_clustering_subplots(
         if isinstance(figure, go.Figure):
             # This is a figure, access the traces within it.
             for trace in range(len(figure["data"])):
-                fig.append_trace(figure["data"][trace], row=i + 1, col=1)
+                fig.add_trace(figure["data"][trace], row=i + 1, col=1)
         else:
             # Assume this is a trace, add directly.
-            fig.append_trace(figure, row=i + 1, col=1)
+            fig.add_trace(figure, row=i + 1, col=1)
 
     fig.update_xaxes(visible=False)
     fig.update_layout(

malariagen_data/veff.py

@@ -84,7 +84,7 @@ def get_ref_allele_coords(self, chrom, pos, ref):
         ref_seq = self.get_ref_seq(chrom, ref_start, ref_stop).lower()
         assert ref_seq == ref.lower(), (
             "reference allele does not match reference sequence, "
-            "expected %r, found %r" % (ref_seq, ref.lower())
+            f"expected {ref_seq!r}, found {ref.lower()!r}"
         )
 
         return ref_start, ref_stop
@@ -262,11 +262,11 @@ def _get_within_cds_effect(ann, base_effect, cds, cdss):
     base_effect = base_effect._replace(
         ref_codon=ref_codon,
         alt_codon=alt_codon,
-        codon_change="%s/%s" % (ref_codon, alt_codon),
+        codon_change=f"{ref_codon}/{alt_codon}",
         aa_pos=aa_pos,
         ref_aa=ref_aa,
         alt_aa=alt_aa,
-        aa_change="%s%s%s" % (ref_aa, aa_pos, alt_aa),
+        aa_change=f"{ref_aa}{aa_pos}{alt_aa}",
     )
 
     if len(ref) == 1 and len(alt) == 1:

tests/anoph/test_genome_features.py

@@ -169,7 +169,9 @@ def test_plot_genes_with_gene_labels(fixture, api: AnophelesGenomeFeaturesData):
     # For each contig in the fixture...
     for contig in fixture.contigs:
         # Get the genes for this contig.
-        genes_df = api.genome_features(region=contig).query("type == 'gene'")
+        genes_df = api.genome_features(region=contig).query(
+            f"type == '{api._gff_gene_type}'"
+        )
 
         # If there are no genes, we cannot label them.
         if not genes_df.empty:
@@ -181,7 +183,10 @@ def test_plot_genes_with_gene_labels(fixture, api: AnophelesGenomeFeaturesData):
 
             # Put the random gene "ID" and its "Name" in a dictionary.
             random_gene_labels = dict(
-                zip(random_sample_genes_df["ID"], random_sample_genes_df["Name"])
+                zip(
+                    random_sample_genes_df["ID"],
+                    random_sample_genes_df[api._gff_gene_name_attribute],
+                )
             )
 
             # Check that we get a Bokeh figure from plot_genes() with these gene_labels.