Update test_utils.py

- add docstrings
- rename test function names

tests/genomics/test_utils.py

@@ -15,6 +15,7 @@
 
 
 def test_generate_mappings_genome_id_bgc_id(tmp_path):
+    """Test generate_mappings_genome_id_bgc_id function."""
     bgc_dir = DATA_DIR / "antismash"
 
     # using default output file path
@@ -50,6 +51,7 @@ def test_generate_mappings_genome_id_bgc_id(tmp_path):
 
 
 def test_generate_mappings_genome_id_bgc_id_empty_dir(tmp_path, caplog):
+    """Test generate_mappings_genome_id_bgc_id function with empty dir."""
     # prepare dir and file
     bgc_dir = tmp_path / "GCF_1"
     bgc_file = bgc_dir / "BGC_1.gbk"
@@ -70,6 +72,7 @@ def test_generate_mappings_genome_id_bgc_id_empty_dir(tmp_path, caplog):
 
 @pytest.fixture
 def strain_collection() -> StrainCollection:
+    """Return a StrainCollection object."""
     sc = StrainCollection()
 
     strain = Strain("STRAIN_01")
@@ -89,11 +92,13 @@ def strain_collection() -> StrainCollection:
 
 @pytest.fixture
 def bgc_list() -> list[BGC]:
+    """Return a list of BGC objects."""
     return [BGC("BGC_01", "NPR"), BGC("BGC_02", "Alkaloid"), BGC("SAMPLE_BGC_03", "Polyketide")]
 
 
 @pytest.fixture
 def gcf_list() -> list[GCF]:
+    """Return a list of GCF objects."""
     gcf1 = GCF("1")
     gcf1.bgc_ids |= {"BGC_01"}
     gcf2 = GCF("2")
@@ -103,12 +108,14 @@ def gcf_list() -> list[GCF]:
 
 @pytest.fixture
 def gcf_list_error() -> list[GCF]:
+    """Return a list of GCF objects for testing errors."""
     gcf1 = GCF("1")
     gcf1.bgc_ids |= {"SAMPLE_BGC_03", "BGC_04"}
     return [gcf1]
 
 
-def test_map_strain_to_bgc(strain_collection, bgc_list):
+def test_add_strain_to_bgc(strain_collection, bgc_list):
+    """Test add_strain_to_bgc function."""
     for bgc in bgc_list:
         assert bgc.strain is None
     add_strain_to_bgc(strain_collection, bgc_list)
@@ -119,14 +126,16 @@ def test_map_strain_to_bgc(strain_collection, bgc_list):
     assert bgc_list[2].strain.id == "SAMPLE_BGC_03"
 
 
-def test_map_strain_to_bgc_error(strain_collection):
+def test_add_strain_to_bgc_error(strain_collection):
+    """Test add_strain_to_bgc function error."""
     bgcs = [BGC("BGC_04", "NPR")]
     with pytest.raises(ValueError) as e:
         add_strain_to_bgc(strain_collection, bgcs)
     assert "Strain id 'BGC_04' from BGC object 'BGC_04' not found" in e.value.args[0]
 
 
-def test_map_bgc_to_gcf(bgc_list, gcf_list):
+def test_add_bgc_to_gcf(bgc_list, gcf_list):
+    """Test add_bgc_to_gcf function."""
     assert gcf_list[0].bgc_ids == {"BGC_01"}
     assert gcf_list[1].bgc_ids == {"BGC_02", "SAMPLE_BGC_03"}
     assert len(gcf_list[0].bgcs) == 0
@@ -140,7 +149,8 @@ def test_map_bgc_to_gcf(bgc_list, gcf_list):
     assert gcf_list[1].bgcs == set(bgc_list[1:])
 
 
-def test_map_bgc_to_gcf_error(bgc_list, gcf_list_error):
+def test_add_bgc_to_gcf_error(bgc_list, gcf_list_error):
+    """Test add_bgc_to_gcf function error."""
     assert gcf_list_error[0].bgc_ids == {"SAMPLE_BGC_03", "BGC_04"}
     assert len(gcf_list_error[0].bgcs) == 0
     with pytest.raises(KeyError) as e:
@@ -149,6 +159,7 @@ def test_map_bgc_to_gcf_error(bgc_list, gcf_list_error):
 
 
 def test_get_bgcs_from_gcfs(bgc_list, gcf_list):
+    """Test get_bgcs_from_gcfs function."""
     add_bgc_to_gcf(bgc_list, gcf_list)
     bgcs = get_bgcs_from_gcfs(gcf_list)
     assert isinstance(bgcs, list)
@@ -158,6 +169,7 @@ def test_get_bgcs_from_gcfs(bgc_list, gcf_list):
 
 
 def test_get_strains_from_bgcs(strain_collection, bgc_list):
+    """Test get_strains_from_bgcs function."""
     add_strain_to_bgc(strain_collection, bgc_list)
     strains = get_strains_from_bgcs(bgc_list)
     assert isinstance(strains, StrainCollection)