Fix lint

.pre-commit-config.yaml

@@ -7,29 +7,29 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.8.0
     hooks:
     -   id: black
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.18.0
     hooks:
     -   id: blacken-docs
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.3.0
+    rev: v2.14.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4']
 -   repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.6.0
+    rev: v2.0.4
     hooks:
     -   id: autopep8
         args: [-i]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/yesqa
-    rev: v1.3.0
+    rev: v1.5.0
     hooks:
     -   id: yesqa
         additional_dependencies:
@@ -40,7 +40,7 @@ repos:
         -   flake8-bugbear
         -   flake8-blind-except
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.6.0
     hooks:
     -   id: detect-private-key
     -   id: check-ast
@@ -51,7 +51,7 @@ repos:
         exclude: setup.cfg
     -   id: check-case-conflict
 -   repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v2.3.1
     hooks:
     -   id: autoflake
         args:
@@ -60,7 +60,7 @@ repos:
         -   --remove-unused-variable
         -   --ignore-init-module-imports
 -   repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.1.1
     hooks:
     -   id: flake8
         additional_dependencies:
@@ -71,7 +71,7 @@ repos:
         -   flake8-bugbear
         -   flake8-blind-except
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus, --keep-runtime-typing]

setup.py

@@ -9,9 +9,7 @@
     )
     sys.stdout.write("Compile knn_graph C++ code for LISI metric...\n")
     sys.stdout.flush()
-    subprocess.check_output(
-        cmd, stderr=subprocess.STDOUT, shell=True, universal_newlines=True
-    )
+    subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True, text=True)
 except subprocess.CalledProcessError as exc:
     sys.stdout.write(
         f"Failed to compile knn_graph for LISI - skipping...\n{exc.returncode}\n{exc.output}"

tests/preprocessing/test_preprocessing.py

@@ -20,12 +20,8 @@ def test_merge_adatas(adata_paul15_template):
 
     # create ambiguous column names
     adata.var[["1", "2"]] = (0, 2)
-    adata.var = adata.var.rename(
-        columns={name: "ambig_var" for name in adata.var.columns.values}
-    )
-    adata.obs = adata.obs.rename(
-        columns={name: "ambig_obs" for name in adata.obs.columns.values}
-    )
+    adata.var = adata.var.rename(columns=dict.fromkeys(adata.var.columns, "ambig_var"))
+    adata.obs = adata.obs.rename(columns=dict.fromkeys(adata.obs.columns, "ambig_obs"))
 
     LOGGER.debug(adata)