MAINT: update pip constraints and pre-commit (#526)

* FIX: remove `PytestRemovedIn8Warning` ignore
* MAINT: address linting issues

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: GitHub <noreply@github.com>
Co-authored-by: Remco de Boer <29308176+redeboer@users.noreply.github.com>

.constraints/py3.10.txt

@@ -14,7 +14,7 @@ async-lru==2.0.4
 attrs==23.2.0
 babel==2.14.0
 beautifulsoup4==4.12.3
-black==24.2.0
+black==24.3.0
 bleach==6.1.0
 cachetools==5.3.3
 cattrs==23.2.3
@@ -26,9 +26,9 @@ charset-normalizer==3.3.2
 click==8.1.7
 cloudpickle==3.0.0
 colorama==0.4.6
-comm==0.2.1
-contourpy==1.2.0
-coverage==7.4.3
+comm==0.2.2
+contourpy==1.2.1
+coverage==7.4.4
 cycler==0.12.1
 debugpy==1.8.1
 decorator==5.1.1
@@ -38,155 +38,151 @@ dm-tree==0.1.8
 docstring-to-markdown==0.15
 docutils==0.20.1
 exceptiongroup==1.2.0
-execnet==2.0.2
+execnet==2.1.0
 executing==2.0.1
 fastjsonschema==2.19.1
-filelock==3.13.1
-flatbuffers==24.3.6
-fonttools==4.49.0
+filelock==3.13.3
+flatbuffers==24.3.25
+fonttools==4.51.0
 fqdn==1.5.1
 gast==0.5.4
 gitdb==4.0.11
-gitpython==3.1.42
-google-auth==2.28.1
-google-auth-oauthlib==1.2.0
+gitpython==3.1.43
 google-pasta==0.2.0
-graphviz==0.20.1
+graphviz==0.20.3
 greenlet==3.0.3
-grpcio==1.62.0
+grpcio==1.62.1
 h11==0.14.0
 h5py==3.10.0
 hepunits==2.3.3
-httpcore==1.0.4
+httpcore==1.0.5
 httpx==0.27.0
 identify==2.5.35
 idna==3.6
 imagesize==1.4.1
 iminuit==2.25.2
-importlib-metadata==7.0.2
+importlib-metadata==7.1.0
 iniconfig==2.0.0
-ipykernel==6.29.3
+ipykernel==6.29.4
 ipympl==0.9.3
-ipython==8.22.2
+ipython==8.23.0
 ipython-genutils==0.2.0
 ipywidgets==8.1.2
 isoduration==20.11.0
 isort==5.13.2
-jax==0.4.25
-jaxlib==0.4.25
+jax==0.4.26
+jaxlib==0.4.26
 jedi==0.19.1
 jinja2==3.1.3
-json5==0.9.22
+json5==0.9.24
 jsonpointer==2.4
 jsonschema==4.21.1
 jsonschema-specifications==2023.12.1
 jupyter==1.0.0
 jupyter-cache==1.0.0
-jupyter-client==8.6.0
+jupyter-client==8.6.1
 jupyter-console==6.6.3
-jupyter-core==5.7.1
-jupyter-events==0.9.0
+jupyter-core==5.7.2
+jupyter-events==0.10.0
 jupyter-lsp==2.2.4
 jupyter-server==2.13.0
 jupyter-server-mathjax==0.2.6
-jupyter-server-terminals==0.5.2
-jupyterlab==4.1.4
+jupyter-server-terminals==0.5.3
+jupyterlab==4.1.5
 jupyterlab-code-formatter==2.2.1
 jupyterlab-git==0.50.0
 jupyterlab-lsp==5.1.0
-jupyterlab-myst==2.3.1
+jupyterlab-myst==2.3.2
 jupyterlab-pygments==0.3.0
-jupyterlab-server==2.25.3
+jupyterlab-server==2.25.4
 jupyterlab-widgets==3.0.10
-keras==2.15.0
+keras==3.1.1
 kiwisolver==1.4.5
-libclang==16.0.6
+libclang==18.1.1
 livereload==2.6.3
 llvmlite==0.42.0
 lsprotocol==2023.0.1
-markdown==3.5.2
+markdown==3.6
 markdown-it-py==3.0.0
 markupsafe==2.1.5
-matplotlib==3.8.3
+matplotlib==3.8.4
 matplotlib-inline==0.1.6
 mdit-py-plugins==0.4.0
 mdurl==0.1.2
 mistune==3.0.2
-ml-dtypes==0.2.0
+ml-dtypes==0.3.2
 mpmath==1.3.0
-mypy==1.8.0
+mypy==1.9.0
 mypy-extensions==1.0.0
 myst-nb==1.0.0
 myst-parser==2.0.0
+namex==0.0.7
 nbclient==0.6.8
-nbconvert==7.16.2
+nbconvert==7.16.3
 nbdime==4.0.1
-nbformat==5.9.2
+nbformat==5.10.4
 nbmake==1.5.3
 nest-asyncio==1.6.0
 nodeenv==1.8.0
-notebook==7.1.1
+notebook==7.1.2
 notebook-shim==0.2.4
-numba==0.59.0
+numba==0.59.1
 numpy==1.26.4
-oauthlib==3.2.2
 opt-einsum==3.3.0
+optree==0.11.0
 overrides==7.7.0
-packaging==23.2
+packaging==24.0
 pandas==2.2.1
 pandocfilters==1.5.1
-parso==0.8.3
+parso==0.8.4
 particle==0.23.1
 pathspec==0.12.1
 pexpect==4.9.0
 phasespace==1.9.0
-pillow==10.2.0
+pillow==10.3.0
 platformdirs==4.2.0
 pluggy==1.4.0
-pre-commit==3.6.2
+pre-commit==3.7.0
 prometheus-client==0.20.0
 prompt-toolkit==3.0.43
 protobuf==4.25.3
 psutil==5.9.8
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0
-pyarrow==15.0.0
-pyasn1==0.5.1
-pyasn1-modules==0.3.0
-pycparser==2.21
+pyarrow==15.0.2
+pycparser==2.22
 pydata-sphinx-theme==0.15.2
 pygments==2.17.2
 pyparsing==3.1.2
 pyproject-api==1.6.1
-pytest==8.0.2
+pytest==8.1.1
 pytest-benchmark==4.0.0
-pytest-cov==4.1.0
-pytest-mock==3.12.0
+pytest-cov==5.0.0
+pytest-mock==3.14.0
 pytest-xdist==3.5.0
 python-constraint==1.3.1
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
 python-lsp-jsonrpc==1.1.2
 python-lsp-ruff==2.2.0
-python-lsp-server==1.10.0
+python-lsp-server==1.11.0
 pytoolconfig==1.3.1
 pytz==2024.1
 pyyaml==6.0.1
 pyzmq==25.1.2
 qrules==0.10.1
 qtconsole==5.5.1
 qtpy==2.4.1
-referencing==0.33.0
+referencing==0.34.0
 requests==2.31.0
-requests-oauthlib==1.3.1
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
-rope==1.12.0
+rich==13.7.1
+rope==1.13.0
 rpds-py==0.18.0
-rsa==4.9
-ruff==0.3.1
-scipy==1.12.0
+ruff==0.3.5
+scipy==1.13.0
 send2trash==1.8.2
 six==1.16.0
 smmap==5.0.1
@@ -210,31 +206,30 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.7
 sphinxcontrib-serializinghtml==1.1.10
 sphobjinv==2.3.1
-sqlalchemy==2.0.28
+sqlalchemy==2.0.29
 stack-data==0.6.3
 sympy==1.12
 tabulate==0.9.0
-tensorboard==2.15.2
+tensorboard==2.16.2
 tensorboard-data-server==0.7.2
-tensorflow==2.15.0
-tensorflow-estimator==2.15.0
+tensorflow==2.16.1
 tensorflow-io-gcs-filesystem==0.36.0
-tensorflow-probability==0.23.0
+tensorflow-probability==0.24.0
 termcolor==2.4.0
-terminado==0.18.0
+terminado==0.18.1
 tinycss2==1.2.1
 tomli==2.0.1
 tornado==6.4
-tox==4.14.1
+tox==4.14.2
 tqdm==4.66.2
-traitlets==5.14.1
-types-protobuf==4.24.0.20240302
-types-python-dateutil==2.8.19.20240106
-types-pyyaml==6.0.12.12
-types-requests==2.31.0.20240218
-types-tensorflow==2.15.0.20240303
+traitlets==5.14.2
+types-protobuf==4.24.0.20240311
+types-python-dateutil==2.9.0.20240316
+types-pyyaml==6.0.12.20240311
+types-requests==2.31.0.20240406
+types-tensorflow==2.15.0.20240314
 types-tqdm==4.66.0.20240106
-typing-extensions==4.10.0
+typing-extensions==4.11.0
 tzdata==2024.1
 ujson==5.9.0
 uri-template==1.3.0
@@ -244,11 +239,11 @@ wcwidth==0.2.13
 webcolors==1.13
 webencodings==0.5.1
 websocket-client==1.7.0
-werkzeug==3.0.1
-wheel==0.42.0
+werkzeug==3.0.2
+wheel==0.43.0
 widgetsnbextension==4.0.10
-wrapt==1.14.1
-zipp==3.17.0
+wrapt==1.16.0
+zipp==3.18.1
 
 # The following packages were excluded from the output:
 # setuptools