Bump the py-updates group across 1 directory with 78 updates

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "cloudpathlib",
     "docker",
     "pandas",
-    "polars>=1.17.1,<1.29.0",
+    "polars>=1.17.1,<1.37.0",
     "pyarrow",
     "requests>=2.32.0",
     "rich",

requirements/requirements-dev.txt

@@ -1,50 +1,50 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt
-awscli==1.40.17
+awscli==1.43.15
     # via cladetime (pyproject.toml)
 biobear==0.23.7
     # via cladetime (pyproject.toml)
-biopython==1.85
+biopython==1.86
     # via cladetime (pyproject.toml)
-boto3==1.38.18
+boto3==1.42.9
     # via
     #   cladetime (pyproject.toml)
     #   moto
-boto3-stubs==1.38.18
+boto3-stubs==1.42.9
     # via cladetime (pyproject.toml)
-botocore==1.38.18
+botocore==1.42.9
     # via
     #   awscli
     #   boto3
     #   moto
     #   s3transfer
-botocore-stubs==1.38.18
+botocore-stubs==1.42.9
     # via boto3-stubs
-certifi==2025.4.26
+certifi==2025.11.12
     # via requests
-cffi==1.17.1
+cffi==2.0.0
     # via cryptography
-charset-normalizer==3.4.2
+charset-normalizer==3.4.4
     # via requests
-cloudpathlib==0.21.1
+cloudpathlib==0.23.0
     # via cladetime (pyproject.toml)
 colorama==0.4.6
     # via awscli
-coverage==7.8.0
+coverage==7.13.0
     # via cladetime (pyproject.toml)
-cryptography==44.0.3
+cryptography==46.0.3
     # via moto
 docker==7.1.0
     # via cladetime (pyproject.toml)
-docutils==0.19
+docutils==0.22.3
     # via awscli
-freezegun==1.5.1
+freezegun==1.5.5
     # via cladetime (pyproject.toml)
-idna==3.10
+idna==3.11
     # via requests
-iniconfig==2.1.0
+iniconfig==2.3.0
     # via pytest
-jellyfish==1.2.0
+jellyfish==1.2.1
     # via us
 jinja2==3.1.6
     # via
@@ -54,49 +54,49 @@ jmespath==1.0.1
     # via
     #   boto3
     #   botocore
-markdown-it-py==3.0.0
+markdown-it-py==4.0.0
     # via rich
-markupsafe==3.0.2
+markupsafe==3.0.3
     # via
     #   jinja2
     #   werkzeug
 mdurl==0.1.2
     # via markdown-it-py
-moto==5.1.4
+moto==5.1.18
     # via cladetime (pyproject.toml)
-mypy==1.15.0
+mypy==1.19.0
     # via cladetime (pyproject.toml)
-mypy-boto3-s3==1.38.0
+mypy-boto3-s3==1.42.3
     # via boto3-stubs
 mypy-extensions==1.1.0
     # via mypy
-numpy==2.2.5
+numpy==2.3.5
     # via
     #   biopython
     #   pandas
 packaging==25.0
     # via pytest
-pandas==2.2.3
+pandas==2.3.3
     # via cladetime (pyproject.toml)
 pluggy==1.6.0
     # via pytest
-polars==1.28.1
+polars==1.36.1
     # via cladetime (pyproject.toml)
-pyarrow==20.0.0
+pyarrow==22.0.0
     # via
     #   cladetime (pyproject.toml)
     #   biobear
 pyasn1==0.6.1
     # via rsa
-pycparser==2.22
+pycparser==2.23
     # via cffi
-pygments==2.19.1
+pygments==2.19.2
     # via rich
-pytest==8.3.5
+pytest==9.0.2
     # via
     #   cladetime (pyproject.toml)
     #   pytest-mock
-pytest-mock==3.14.0
+pytest-mock==3.15.1
     # via cladetime (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
@@ -106,50 +106,50 @@ python-dateutil==2.9.0.post0
     #   pandas
 pytz==2025.2
     # via pandas
-pyyaml==6.0.2
+pyyaml==6.0.3
     # via
     #   awscli
     #   responses
-requests==2.32.3
+requests==2.32.5
     # via
     #   cladetime (pyproject.toml)
     #   docker
     #   moto
     #   responses
-responses==0.25.7
+responses==0.25.8
     # via moto
-rich==14.0.0
+rich==14.2.0
     # via cladetime (pyproject.toml)
-rsa==4.7.2
+rsa==4.9.1
     # via awscli
-ruff==0.11.10
+ruff==0.14.9
     # via cladetime (pyproject.toml)
-s3transfer==0.12.0
+s3transfer==0.16.0
     # via
     #   awscli
     #   boto3
 six==1.17.0
     # via python-dateutil
-structlog==25.3.0
+structlog==25.5.0
     # via cladetime (pyproject.toml)
 tqdm==4.67.1
     # via cladetime (pyproject.toml)
-types-awscrt==0.27.2
+types-awscrt==0.30.0
     # via botocore-stubs
 types-python-dateutil==2.9.0.20250516
     # via cladetime (pyproject.toml)
-types-requests==2.32.0.20250515
+types-requests==2.32.4.20250913
     # via cladetime (pyproject.toml)
-types-s3transfer==0.12.0
+types-s3transfer==0.16.0
     # via boto3-stubs
-typing-extensions==4.13.2
+typing-extensions==4.15.0
     # via
     #   boto3-stubs
     #   mypy
     #   mypy-boto3-s3
-tzdata==2025.2
+tzdata==2025.3
     # via pandas
-urllib3==2.4.0
+urllib3==2.6.2
     # via
     #   cladetime (pyproject.toml)
     #   botocore
@@ -159,9 +159,9 @@ urllib3==2.4.0
     #   types-requests
 us==3.2.0
     # via cladetime (pyproject.toml)
-werkzeug==3.1.3
+werkzeug==3.1.4
     # via moto
-xmltodict==0.14.2
+xmltodict==1.0.2
     # via moto
-zstandard==0.23.0
+zstandard==0.25.0
     # via cladetime (pyproject.toml)