Update CI-related stuff to new versions.

This updates our generated requirements.txt files and the various tools
we use in pre-commit to the latest versions. There is no runtime change;
this only affects what we use in testing and static analysis.

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
   # Start with the basic pre-commit hooks
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,8 +13,8 @@ repos:
 
   # Then others in alphabetical order:
 
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.265
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.291
     hooks:
       - id: ruff
 
@@ -23,19 +23,19 @@ repos:
     # the entire dependency list here we only install `attrs`. It will catch
     # a useful subset of errors but does not replace a full mypy run
     # (either locally or in CI).
-    rev: v1.0.0
+    rev: v1.5.1
     hooks:
       - id: mypy
         additional_dependencies: [attrs]
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1
+    rev: v3.0.3
     hooks:
       - id: prettier
         # For now we let this act on all files; if need be we can restrict it
         # with `types_or` in the future.
 
   - repo: https://github.com/psf/black
-    rev: "22.12.0"
+    rev: "23.9.1"
     hooks:
       - id: black

python-spec/requirements-py3.10.txt

@@ -1,16 +1,16 @@
-anndata==0.9.1
+anndata==0.9.2
 attrs==23.1.0
-h5py==3.8.0
-llvmlite==0.40.0
-natsort==8.3.1
-numba==0.57.0
-numpy==1.24.3
+h5py==3.9.0
+llvmlite==0.41.0
+natsort==8.4.0
+numba==0.58.0
+numpy==1.25.2
 packaging==23.1
-pandas==2.0.1
-pyarrow==12.0.0
+pandas==2.1.1
+pyarrow==13.0.0
 python-dateutil==2.8.2
-pytz==2023.3
-scipy==1.10.1
+pytz==2023.3.post1
+scipy==1.11.3
 six==1.16.0
-typing_extensions==4.5.0
+typing_extensions==4.8.0
 tzdata==2023.3

python-spec/requirements-py3.7-lint.txt

@@ -2,34 +2,34 @@ anndata==0.8.0
 attrs==23.1.0
 black==23.3.0
 cfgv==3.3.1
-click==8.1.3
-distlib==0.3.6
-filelock==3.12.0
+click==8.1.7
+distlib==0.3.7
+filelock==3.12.2
 h5py==3.8.0
 identify==2.5.24
-importlib-metadata==6.6.0
+importlib-metadata==6.7.0
 isort==5.11.5
 llvmlite==0.39.1
-mypy==1.2.0
+mypy==1.4.1
 mypy-extensions==1.0.0
-natsort==8.3.1
-nodeenv==1.7.0
+natsort==8.4.0
+nodeenv==1.8.0
 numba==0.56.4
 numpy==1.21.6
 packaging==23.1
 pandas==1.3.5
-pathspec==0.11.1
-platformdirs==3.5.0
+pathspec==0.11.2
+platformdirs==3.10.0
 pre-commit==2.21.0
-pyarrow==12.0.0
+pyarrow==12.0.1
 python-dateutil==2.8.2
-pytz==2023.3
-PyYAML==6.0
-ruff==0.0.265
+pytz==2023.3.post1
+PyYAML==6.0.1
+ruff==0.0.291
 scipy==1.7.3
 six==1.16.0
 tomli==2.0.1
-typed-ast==1.5.4
-typing_extensions==4.5.0
-virtualenv==20.23.0
+typed-ast==1.5.5
+typing_extensions==4.7.1
+virtualenv==20.24.5
 zipp==3.15.0

python-spec/requirements-py3.7.txt

@@ -1,17 +1,17 @@
 anndata==0.8.0
 attrs==23.1.0
 h5py==3.8.0
-importlib-metadata==6.6.0
+importlib-metadata==6.7.0
 llvmlite==0.39.1
-natsort==8.3.1
+natsort==8.4.0
 numba==0.56.4
 numpy==1.21.6
 packaging==23.1
 pandas==1.3.5
-pyarrow==12.0.0
+pyarrow==12.0.1
 python-dateutil==2.8.2
-pytz==2023.3
+pytz==2023.3.post1
 scipy==1.7.3
 six==1.16.0
-typing_extensions==4.5.0
+typing_extensions==4.7.1
 zipp==3.15.0

python-spec/requirements-py3.8.txt

@@ -1,18 +1,18 @@
-anndata==0.9.1
+anndata==0.9.2
 attrs==23.1.0
-h5py==3.8.0
-importlib-metadata==6.6.0
-llvmlite==0.40.0
-natsort==8.3.1
-numba==0.57.0
-numpy==1.24.3
+h5py==3.9.0
+importlib-metadata==6.8.0
+llvmlite==0.41.0
+natsort==8.4.0
+numba==0.58.0
+numpy==1.24.4
 packaging==23.1
-pandas==2.0.1
-pyarrow==12.0.0
+pandas==2.0.3
+pyarrow==13.0.0
 python-dateutil==2.8.2
-pytz==2023.3
+pytz==2023.3.post1
 scipy==1.10.1
 six==1.16.0
-typing_extensions==4.5.0
+typing_extensions==4.8.0
 tzdata==2023.3
-zipp==3.15.0
+zipp==3.17.0

python-spec/requirements-py3.9.txt

@@ -1,21 +1,20 @@
-anndata==0.9.1
+anndata==0.9.2
 attrs==23.1.0
-botocore==1.29.80
 docutils==0.16
-h5py==3.8.0
+h5py==3.9.0
 jmespath==1.0.1
-llvmlite==0.40.0
-natsort==8.3.1
-numba==0.57.0
-numpy==1.24.3
+llvmlite==0.41.0
+natsort==8.4.0
+numba==0.58.0
+numpy==1.25.2
 packaging==23.1
-pandas==2.0.1
-pyarrow==12.0.0
+pandas==2.1.1
+pyarrow==13.0.0
 python-dateutil==2.8.2
-pytz==2023.3
+pytz==2023.3.post1
 rsa==4.7.2
 s3transfer==0.6.0
-scipy==1.10.1
+scipy==1.11.3
 six==1.16.0
-typing_extensions==4.5.0
+typing_extensions==4.8.0
 tzdata==2023.3

python-spec/src/somacore/collection.py

@@ -14,7 +14,7 @@
 """Any implementation of a Collection."""
 
 
-class BaseCollection(
+class BaseCollection(  # type: ignore[misc]  # __eq__ false positive
     base.SOMAObject, MutableMapping[str, _Elem], metaclass=abc.ABCMeta
 ):
     """A generic string-keyed collection of :class:`base.SOMAObject`s.

python-spec/src/somacore/ephemeral/collections.py

@@ -103,7 +103,9 @@ def __len__(self) -> int:
         return len(self._entries)
 
 
-class Collection(BaseCollection[_Elem], collection.Collection):
+class Collection(  # type: ignore[misc]  # __eq__ false positive
+    BaseCollection[_Elem], collection.Collection
+):
     """An in-memory Collection imposing no semantics on the contents."""
 
     __slots__ = ()
@@ -119,13 +121,15 @@ class Collection(BaseCollection[_Elem], collection.Collection):
 """The loosest possible constraint of the abstract Measurement type."""
 
 
-class Measurement(BaseCollection[base.SOMAObject], _BasicAbstractMeasurement):
+class Measurement(  # type: ignore[misc]  # __eq__ false positive
+    BaseCollection[base.SOMAObject], _BasicAbstractMeasurement
+):
     """An in-memory Collection with Measurement semantics."""
 
     __slots__ = ()
 
 
-class Experiment(
+class Experiment(  # type: ignore[misc]  # __eq__ false positive
     BaseCollection[base.SOMAObject],
     experiment.Experiment[
         data.DataFrame,