lint part 1

api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py

@@ -12,9 +12,8 @@
 import tiledbsoma as soma
 from somacore.options import SparseDFCoord
 
-from ._util import _extract_census_version
-
 from ._experiment import _get_experiment
+from ._util import _extract_census_version
 
 CENSUS_EMBEDDINGS_LOCATION_BASE_URI = "s3://cellxgene-contrib-public/contrib/cell-census/soma"
 
@@ -103,13 +102,14 @@ def get_anndata(
             column_names=column_names,
             X_layers=X_layers,
             obsm_layers=obsm_layers,
-            varm_layers=varm_layers
+            varm_layers=varm_layers,
         )
 
         # If add_obs_embeddings or add_var_embeddings are defined, inject them in the appropriate slot
-        if add_obs_embeddings or add_var_embeddings:
+        if add_obs_embeddings is not None:
             obs_soma_joinids = query.obs_joinids()
             from cellxgene_census.experimental import get_embedding, get_embedding_metadata_by_name
+
             census_version = _extract_census_version(census)
             for emb in add_obs_embeddings:
                 emb_metadata = get_embedding_metadata_by_name(emb, organism, census_version, "obs_embedding")
@@ -118,5 +118,3 @@ def get_anndata(
                 adata.obsm[emb] = embedding
 
         return adata
-
-

api/python/cellxgene_census/src/cellxgene_census/_util.py

@@ -1,4 +1,5 @@
 import urllib.parse
+
 import tiledbsoma as soma
 
 
@@ -20,6 +21,7 @@ def _uri_join(base: str, url: str) -> str:
     ]
     return urllib.parse.urlunparse(parts)
 
-def _extract_census_version(census: soma.Collection):
+
+def _extract_census_version(census: soma.Collection) -> str:
     """Extract the Census version from the given Census object."""
-    return urllib.parse.urlparse(census.uri).path.split("/")[2]
+    return urllib.parse.urlparse(census.uri).path.split("/")[2]

api/python/cellxgene_census/src/cellxgene_census/experimental/__init__.py

@@ -1,6 +1,12 @@
 """Experimental API for the CELLxGENE Discover Census."""
 
-from ._embedding import get_embedding, get_embedding_metadata, get_embedding_metadata_by_name, get_all_available_embeddings, get_all_census_versions_with_embedding 
+from ._embedding import (
+    get_all_available_embeddings,
+    get_all_census_versions_with_embedding,
+    get_embedding,
+    get_embedding_metadata,
+    get_embedding_metadata_by_name,
+)
 
 __all__ = [
     "get_embedding",

api/python/cellxgene_census/src/cellxgene_census/experimental/_embedding.py

@@ -13,8 +13,8 @@
 import numpy.typing as npt
 import pandas as pd
 import pyarrow as pa
-import tiledbsoma as soma
 import requests
+import tiledbsoma as soma
 
 from .._open import get_default_soma_context, open_soma
 from .._release_directory import get_census_version_directory
@@ -140,8 +140,11 @@ def get_embedding(
 
     return embedding
 
-def get_embedding_metadata_by_name(embedding_name: str, organism: str, census_version: str, embedding_type: str | None = "obs_embedding") -> dict[str, Any]:
-    """Return metadata for a specific embedding. If more embeddings match the query parameters, 
+
+def get_embedding_metadata_by_name(
+    embedding_name: str, organism: str, census_version: str, embedding_type: str | None = "obs_embedding"
+) -> dict[str, Any]:
+    """Return metadata for a specific embedding. If more embeddings match the query parameters,
     the most recent one will be returned.
 
     Args:
@@ -167,14 +170,20 @@ def get_embedding_metadata_by_name(embedding_name: str, organism: str, census_ve
     manifest = response.json()
     embeddings = []
     for _, obj in manifest.items():
-        if obj["embedding_name"] == embedding_name and obj["experiment_name"] == organism and obj["data_type"] == embedding_type and obj["census_version"] == census_version:
+        if (
+            obj["embedding_name"] == embedding_name
+            and obj["experiment_name"] == organism
+            and obj["data_type"] == embedding_type
+            and obj["census_version"] == census_version
+        ):
             embeddings.append(obj)
 
     if len(embeddings) == 0:
         raise ValueError(f"No embeddings found for {embedding_name}, {organism}, {census_version}, {embedding_type}")
-    
+
     return sorted(embeddings, key=lambda x: x["submission_date"])[-1]
 
+
 def get_all_available_embeddings(census_version: str) -> list[dict[str, Any]]:
     """Return a dictionary of all available embeddings for a given Census version.
 
@@ -188,19 +197,19 @@ def get_all_available_embeddings(census_version: str) -> list[dict[str, Any]]:
     Examples:
         >>> get_all_available_embeddings('2023-12-15')
         [{
-            'experiment_name': 'experiment_1', 
-            'measurement_name': 'RNA', 
-            'organism': "homo_sapiens", 
-            'census_version': '2023-12-15', 
-            'n_embeddings': 1000, 
-            'n_features': 200, 
+            'experiment_name': 'experiment_1',
+            'measurement_name': 'RNA',
+            'organism': "homo_sapiens",
+            'census_version': '2023-12-15',
+            'n_embeddings': 1000,
+            'n_features': 200,
             'uri': 's3://bucket/embedding_1'
         }]
 
     """
     response = requests.get(CELL_CENSUS_EMBEDDINGS_MANIFEST_URL)
     response.raise_for_status()
-    
+
     embeddings = []
     manifest = response.json()
     for _, obj in manifest.items():
@@ -209,28 +218,34 @@ def get_all_available_embeddings(census_version: str) -> list[dict[str, Any]]:
 
     return embeddings
 
-def get_all_census_versions_with_embedding(embedding_name: str, organism: str, embedding_type: str | None = "obs_embedding") -> list[str]:
-    """
-    Get a list of all census versions that contain a specific embedding.
+
+def get_all_census_versions_with_embedding(
+    embedding_name: str, organism: str, embedding_type: str | None = "obs_embedding"
+) -> list[str]:
+    """Get a list of all census versions that contain a specific embedding.
 
     Args:
-        embedding_name: 
+        embedding_name:
             The name of the embedding, e.g. "scvi".
-        organism: 
+        organism:
             The organism for which the embedding is associated.
-        embedding_type: 
+        embedding_type:
             The type of embedding. Defaults to "obs_embedding".
 
     Returns:
         A list of census versions that contain the specified embedding.
     """
     response = requests.get(CELL_CENSUS_EMBEDDINGS_MANIFEST_URL)
     response.raise_for_status()
-    
+
     versions = set()
     manifest = response.json()
     for _, obj in manifest.items():
-        if obj["embedding_name"] == embedding_name and obj["experiment_name"] == organism and obj["data_type"] == embedding_type:
+        if (
+            obj["embedding_name"] == embedding_name
+            and obj["experiment_name"] == organism
+            and obj["data_type"] == embedding_type
+        ):
             versions.add(obj["census_version"])
 
-    return sorted(list(versions))
+    return sorted(versions)

api/python/cellxgene_census/tests/experimental/test_embeddings.py

@@ -1,8 +1,11 @@
 import pytest
 import requests_mock as rm
 
-from cellxgene_census.experimental import get_all_available_embeddings, get_all_census_versions_with_embedding, get_embedding_metadata_by_name
-
+from cellxgene_census.experimental import (
+    get_all_available_embeddings,
+    get_all_census_versions_with_embedding,
+    get_embedding_metadata_by_name,
+)
 from cellxgene_census.experimental._embedding import CELL_CENSUS_EMBEDDINGS_MANIFEST_URL
 
 
@@ -16,7 +19,7 @@ def test_get_embedding_metadata_by_name(requests_mock: rm.Mocker) -> None:
             "experiment_name": "homo_sapiens",
             "data_type": "obs_embedding",
             "census_version": "2023-12-15",
-            "submission_date": "2023-11-15"
+            "submission_date": "2023-11-15",
         },
         "embedding-id-2": {
             "id": "embedding-id-2",
@@ -42,23 +45,34 @@ def test_get_embedding_metadata_by_name(requests_mock: rm.Mocker) -> None:
     requests_mock.real_http = True
     requests_mock.get(CELL_CENSUS_EMBEDDINGS_MANIFEST_URL, json=mock_embeddings)
 
-    embedding = get_embedding_metadata_by_name("emb_1", organism = "homo_sapiens", census_version = "2023-12-15", embedding_type = "obs_embedding")
+    embedding = get_embedding_metadata_by_name(
+        "emb_1", organism="homo_sapiens", census_version="2023-12-15", embedding_type="obs_embedding"
+    )
     assert embedding is not None
-    assert embedding["id"] == "embedding-id-2" # most recent version
+    assert embedding["id"] == "embedding-id-2"  # most recent version
     assert embedding == mock_embeddings["embedding-id-2"]
 
-    embedding = get_embedding_metadata_by_name("emb_3", organism = "homo_sapiens", census_version = "2023-12-15", embedding_type = "obs_embedding")
+    embedding = get_embedding_metadata_by_name(
+        "emb_3", organism="homo_sapiens", census_version="2023-12-15", embedding_type="obs_embedding"
+    )
     assert embedding is not None
-    assert embedding["id"] == "embedding-id-3" 
+    assert embedding["id"] == "embedding-id-3"
     assert embedding == mock_embeddings["embedding-id-3"]
 
     with pytest.raises(ValueError):
-        get_embedding_metadata_by_name("emb_2", organism = "homo_sapiens", census_version = "2023-12-15", embedding_type = "obs_embedding")
-        get_embedding_metadata_by_name("emb_1", organism = "mus_musculus", census_version = "2023-12-15", embedding_type = "obs_embedding")
-        get_embedding_metadata_by_name("emb_1", organism = "homo_sapiens", census_version = "2023-10-15", embedding_type = "obs_embedding")
-        get_embedding_metadata_by_name("emb_1", organism = "mus_musculus", census_version = "2023-12-15", embedding_type = "var_embedding")
+        get_embedding_metadata_by_name(
+            "emb_2", organism="homo_sapiens", census_version="2023-12-15", embedding_type="obs_embedding"
+        )
+        get_embedding_metadata_by_name(
+            "emb_1", organism="mus_musculus", census_version="2023-12-15", embedding_type="obs_embedding"
+        )
+        get_embedding_metadata_by_name(
+            "emb_1", organism="homo_sapiens", census_version="2023-10-15", embedding_type="obs_embedding"
+        )
+        get_embedding_metadata_by_name(
+            "emb_1", organism="mus_musculus", census_version="2023-12-15", embedding_type="var_embedding"
+        )
 
-
 
 def test_get_all_available_embeddings(requests_mock: rm.Mocker) -> None:
     mock_embeddings = {

api/python/cellxgene_census/tests/test_get_anndata.py

@@ -194,6 +194,7 @@ def test_get_anndata_obsm_two_layers(census: soma.Collection, obsm_layers: List[
         assert obsm_layer in ad.obsm.keys()
         assert ad.obsm[obsm_layer].shape[0] == 100
 
+
 @pytest.mark.live_corpus
 @pytest.mark.parametrize("add_obs_embeddings", [["scvi", "geneformer"]])
 def test_get_anndata_add_obs_embeddings(census: soma.Collection, add_obs_embeddings: List[str]) -> None:

api/python/cellxgene_census/tests/test_util.py

@@ -1,8 +1,10 @@
-from cellxgene_census._util import _uri_join, _extract_census_version
-import cellxgene_census
-import pytest
 import re
 
+import pytest
+
+import cellxgene_census
+from cellxgene_census._util import _extract_census_version, _uri_join
+
 
 def test_uri_join() -> None:
     assert _uri_join("https://foo/", "bar") == "https://foo/bar"
@@ -23,11 +25,12 @@ def test_uri_join() -> None:
 
     assert _uri_join("https://foo/bar", "https://a/b") == "https://a/b"
 
+
 @pytest.mark.live_corpus
 def test_extract_census_version() -> None:
     """Ensures that extracting the Census version from a Collection object does not break"""
 
-    pattern = r'^\d{4}-\d{2}-\d{2}$'
+    pattern = r"^\d{4}-\d{2}-\d{2}$"
 
     with cellxgene_census.open_soma(census_version="stable") as census:
         assert census is not None
@@ -37,4 +40,4 @@ def test_extract_census_version() -> None:
     with cellxgene_census.open_soma(census_version="latest") as census:
         assert census is not None
         version = _extract_census_version(census)
-        assert re.match(pattern, version)
+        assert re.match(pattern, version)

tools/census_contrib/src/census_contrib/metadata.py

@@ -144,7 +144,7 @@ def validate_metadata(args: Arguments, metadata: EmbeddingMetadata) -> Embedding
 
     # 7. Name must have length < 128 characters
     MAX_NAME_LENGTH = 128
-    if not metadata.name or len(metadata.name) > MAX_NAME_LENGTH:
+    if not metadata.embedding_name or len(metadata.embedding_name) > MAX_NAME_LENGTH:
         raise ValueError(
             f"Metadata: name must be string between 1 and {MAX_NAME_LENGTH} characters in length",
         )