[misc] update package dependencies (#965)

* update pre-commit versions

* update package with security notice

* reformatting due to pre-commit (ruff) update

* reformatting due to pre-commit (ruff) update

* revert broken black version

* back out bad reformatting

.markdownlint.yaml

@@ -8,8 +8,7 @@ MD013:
   line_length: 1000
 
 # MD024/no-duplicate-heading/no-duplicate-header - Multiple headings with the same content
-MD024:
-  allow_different_nesting: true
+MD024: false
 
 # MD026/no-trailing-punctuation - Trailing punctuation in heading
 MD026:

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         args: ["--config", "./tools/pyproject.toml"]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.1.15
     hooks:
       - id: ruff
         name: ruff-cellxgene-census
@@ -88,6 +88,6 @@ repos:
         files: ^api/python/notebooks
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.38.0
+    rev: v0.39.0
     hooks:
     - id: markdownlint

api/python/cellxgene_census/tests/test_acceptance.py

@@ -10,6 +10,7 @@
 
 See README.md for historical data.
 """
+
 from typing import Any, Dict, Iterator, Optional, Tuple
 
 import pyarrow as pa

api/python/cellxgene_census/tests/test_lts_compat.py

@@ -5,6 +5,7 @@
 Where there are known and accepted incompatibilities, use `pytest.skip`
 to codify them.
 """
+
 from __future__ import annotations
 
 from collections import deque

tools/cellxgene_census_builder/pyproject.toml

@@ -38,7 +38,7 @@ dependencies= [
     "fsspec==2023.12.2",
     "s3fs==2023.12.2",
     "requests==2.31.0",
-    "aiohttp==3.9.1",
+    "aiohttp==3.9.3",
     "Cython", # required by owlready2
     "wheel",  # required by owlready2
     "owlready2==0.44",

tools/cellxgene_census_builder/src/cellxgene_census_builder/build_state.py

@@ -2,6 +2,7 @@
 Manage the configuration and dynamic build state for the Census build.
 
 """
+
 import functools
 import io
 import os

tools/cellxgene_census_builder/src/cellxgene_census_builder/release_manifest.py

@@ -1,6 +1,7 @@
 """
 Tools to manage the release.json manifest file.
 """
+
 import json
 from typing import Dict, Optional, Union, cast
 

tools/census_contrib/src/census_contrib/validate.py

@@ -1,6 +1,7 @@
 """
 Validate an embedding
 """
+
 from __future__ import annotations
 
 import concurrent.futures