For some reason, api.genome_features(region=contig).query("type == api._gff_gene_type") doesn't find any gene for api == af1 in test_genomes_features.py. Somewhere else in the same file api.genome_features(region=contig).query("type == 'gene'") is used even for api == af1, which shouldn't return anything (but absence of genes is handled differently in this case).