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scverse · Apr 2, 2024 · 88ca186 · 88ca186
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Showing 3 changed files with 28 additions and 18 deletions.
diff --git a/docs/notebooks/basic_usage.ipynb b/docs/notebooks/basic_usage.ipynb
@@ -250,7 +250,7 @@
     }
    ],
    "source": [
-    "gf.ensembl.list_ensdb_annotations(species='Mmusculus')"
+    "gf.ensembl.list_ensdb_annotations(species=\"Mmusculus\")"
    ]
   },
   {
@@ -854,7 +854,8 @@
    ],
    "source": [
     "ensdb.genes(\n",
-    "    filter=gf.filters.GeneBioTypeFilter(\"lncRNA\") & gf.filters.GeneRangesFilter(\"1:10000-20000\")\n",
+    "    filter=gf.filters.GeneBioTypeFilter(\"lncRNA\")\n",
+    "    & gf.filters.GeneRangesFilter(\"1:10000-20000\")\n",
     ")"
    ]
   },
@@ -1128,6 +1129,7 @@
    "source": [
     "import pandas as pd\n",
     "import scanpy as sc\n",
+    "\n",
     "pbmc = sc.datasets.pbmc3k()"
    ]
   },
@@ -1214,19 +1216,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pbmc.var = (\n",
-    "    pd.merge(\n",
-    "        (\n",
-    "            pbmc.var\n",
-    "            .reset_index()\n",
-    "            .rename(columns={\"gene_ids\": \"gene_id\", \"index\": \"orig_gene_name\"})\n",
-    "        ),\n",
-    "        genes,\n",
-    "        on=\"gene_id\",\n",
-    "        how=\"left\",\n",
-    "    )\n",
-    "    .set_index(\"gene_id\")\n",
-    ")"
+    "pbmc.var = pd.merge(\n",
+    "    (\n",
+    "        pbmc.var.reset_index().rename(\n",
+    "            columns={\"gene_ids\": \"gene_id\", \"index\": \"orig_gene_name\"}\n",
+    "        )\n",
+    "    ),\n",
+    "    genes,\n",
+    "    on=\"gene_id\",\n",
+    "    how=\"left\",\n",
+    ").set_index(\"gene_id\")"
    ]
   },
   {

diff --git a/src/genomic_features/_core/filters.py b/src/genomic_features/_core/filters.py
@@ -252,7 +252,7 @@ class CanonicalTxFilter(AbstractFilterExpr):
     >>> ensdb.transcripts(filter=gf.filters.CanonicalTxFilter())
     >>> ensdb.exons(
     ...     cols=["tx_id", "exon_id", "seq_name", "exon_seq_start", "exon_seq_end"],
-    ...     filter=gf.filters.CanonicalTxFilter()
+    ...     filter=gf.filters.CanonicalTxFilter(),
     ... )
     """
 

diff --git a/tests/test_list_ensdb_annotations.py b/tests/test_list_ensdb_annotations.py
@@ -3,7 +3,15 @@
 
 import genomic_features as gf
 
-SPECIES = ['Scerevisiae', 'Mmusculus_nzohlltj', 'Ggallus', 'Hsapiens', 'Mmusculus', 'Celegans']
+SPECIES = [
+    "Scerevisiae",
+    "Mmusculus_nzohlltj",
+    "Ggallus",
+    "Hsapiens",
+    "Mmusculus",
+    "Celegans",
+]
+
 
 def test_ensdb_versions():
     species_versions = gf.ensembl.list_ensdb_annotations("Hsapiens")
@@ -13,16 +21,19 @@ def test_ensdb_versions():
     species_versions = gf.ensembl.list_ensdb_annotations("Rnorvegicus")
     assert isinstance(species_versions, pd.DataFrame)
 
+
 def test_missing_species():
     # test error is raised when species is not found
     with pytest.raises(ValueError):
         gf.ensembl.list_ensdb_annotations("Homo sapiens")
 
+
 def test_unique_versions():
     # Check that different mouse strains are not considered the same species
     species_versions = gf.ensembl.list_ensdb_annotations("Mmusculus")
     assert species_versions.Ensembl_version.is_unique
 
+
 def test_all_species():
     species_versions = gf.ensembl.list_ensdb_annotations()
-    assert pd.Series(SPECIES).isin(species_versions['Species']).all()
+    assert pd.Series(SPECIES).isin(species_versions["Species"]).all()