[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.10
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -34,6 +34,7 @@ The `list_datasets()` function will display all available datasets along with th
 
 ```python
 import scrnaseq
+
 datasets = scrnaseq.list_datasets()
 print(datasets[["name", "version"]].head(3))
 
@@ -57,11 +58,8 @@ res = scrnaseq.search_datasets("pancreas")
 from gypsum_client import define_text_query
 
 res = scrnaseq.search_datasets(
-     define_text_query("GRCm38", field="genome")
-     & (
-          define_text_query("neuro%", partial=True)
-          | define_text_query("pancrea%", partial=True)
-     )
+    define_text_query("GRCm38", field="genome")
+    & (define_text_query("neuro%", partial=True) | define_text_query("pancrea%", partial=True))
 )
 print(res[["name", "version"]].head(3))
 
@@ -169,9 +167,9 @@ Want to contribute your own dataset to this package? It's easy! Just follow thes
      row_names = [f"GENE_{i}" for i in range(mat.shape[0])]
      col_names = list("ABCDEFGHIJ")
      sce = SingleCellExperiment(
-          assays={"counts": mat},
-          row_data=BiocFrame(row_names=row_names),
-          column_data=BiocFrame(row_names=col_names),
+         assays={"counts": mat},
+         row_data=BiocFrame(row_names=row_names),
+         column_data=BiocFrame(row_names=col_names),
      )
      ```
 
@@ -187,13 +185,13 @@ Want to contribute your own dataset to this package? It's easy! Just follow thes
 
      ```python
      meta = {
-          "title": "My dataset forked from ziesel brain",
-          "description": "This is a copy of the ziesel",
-          "taxonomy_id": ["10090"],  # NCBI ID
-          "genome": ["GRCh38"],  # genome build
-          "sources": [{"provider": "GEO", "id": "GSE12345"}],
-          "maintainer_name": "Shizuka Mogami",
-          "maintainer_email": "mogami.shizuka@765pro.com",
+         "title": "My dataset forked from ziesel brain",
+         "description": "This is a copy of the ziesel",
+         "taxonomy_id": ["10090"],  # NCBI ID
+         "genome": ["GRCh38"],  # genome build
+         "sources": [{"provider": "GEO", "id": "GSE12345"}],
+         "maintainer_name": "Shizuka Mogami",
+         "maintainer_email": "mogami.shizuka@765pro.com",
      }
      ```
 

setup.py

@@ -10,7 +10,7 @@
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/scrnaseq/list_versions.py

@@ -1,13 +1,11 @@
-from typing import List
-
 import gypsum_client as gypc
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
 __license__ = "MIT"
 
 
-def list_versions(name: str) -> List[str]:
+def list_versions(name: str) -> list[str]:
     """List all available versions for a dataset.
 
     Example:

src/scrnaseq/polish_dataset.py

@@ -1,5 +1,3 @@
-from typing import Type
-
 import numpy as np
 from singlecellexperiment import SingleCellExperiment
 from summarizedexperiment import SummarizedExperiment
@@ -10,12 +8,12 @@
 
 
 def polish_dataset(
-    x: Type[SummarizedExperiment],
+    x: type[SummarizedExperiment],
     reformat_assay_by_density: float = 0.3,
     attempt_integer_conversion: bool = True,
     remove_altexp_coldata: bool = True,
     forbid_nested_altexp: bool = True,
-) -> Type[SummarizedExperiment]:
+) -> type[SummarizedExperiment]:
     """Optimize dataset for saving.
 
     Prepare a
@@ -68,7 +66,7 @@ def polish_dataset(
 
 
 def _polish_dataset(
-    x: Type[SummarizedExperiment],
+    x: type[SummarizedExperiment],
     reformat_assay_by_density: float,
     attempt_integer_conversion: bool,
     remove_altexp_coldata: bool,

src/scrnaseq/search_datasets.py

@@ -1,6 +1,5 @@
 import sqlite3
 from functools import lru_cache
-from typing import Union
 
 from biocframe import BiocFrame
 from gypsum_client import cache_directory, fetch_metadata_database
@@ -18,7 +17,7 @@
 
 @lru_cache
 def search_datasets(
-    query: Union[str, GypsumSearchClause],
+    query: str | GypsumSearchClause,
     cache_dir: str = cache_directory(),
     overwrite: bool = False,
     latest: bool = True,