MAINT: update pip constraints and pre-commit (#284)

* DX: highlight `.constraints/py*.txt` as pip requirements
* DX: implement `.envrc` for `direnv`
* DX: modernise VS Code extension list
* DX: switch to Python 3.12 as developer version
* FIX: downgrade to NumPy v1
* FIX: install `numpy~=1.22.4`
* FIX: install NumPy v1
* FIX: make notebooks non-executable
* Kick CI
* MAINT: address Ruff issues
* MAINT: implement Ruff autofixes
* MAINT: implement Ruff unsafe autofixes
* MAINT: remove redundant notebook cell metadata

.constraints/py3.10.txt

@@ -1,22 +1,21 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml -o .constraints/py3.10.txt --all-extras --no-annotate --python-version=3.10 --no-emit-package setuptools
 accessible-pygments==0.0.5
-alabaster==0.7.16
-anyio==4.3.0
+alabaster==1.0.0
+anyio==4.4.0
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
 asttokens==2.4.1
 async-lru==2.0.4
-attrs==23.2.0
+attrs==24.2.0
 babel==2.15.0
 beautifulsoup4==4.12.3
-black==24.4.2
 bleach==6.1.0
-cachetools==5.3.3
+cachetools==5.4.0
 cattrs==23.2.3
-certifi==2024.2.2
-cffi==1.16.0
+certifi==2024.7.4
+cffi==1.17.0
 cfgv==3.4.0
 chardet==5.2.0
 charset-normalizer==3.3.2
@@ -25,17 +24,17 @@ colorama==0.4.6
 comm==0.2.2
 contourpy==1.2.1
 cycler==0.12.1
-debugpy==1.8.1
+debugpy==1.8.5
 decorator==5.1.1
 defusedxml==0.7.1
 distlib==0.3.8
 docstring-to-markdown==0.15
 docutils==0.21.2
-exceptiongroup==1.2.1
+exceptiongroup==1.2.2
 executing==2.0.1
-fastjsonschema==2.19.1
-filelock==3.14.0
-fonttools==4.51.0
+fastjsonschema==2.20.0
+filelock==3.15.4
+fonttools==4.53.1
 fqdn==1.5.1
 gitdb==4.0.11
 gitpython==3.1.43
@@ -44,23 +43,22 @@ greenlet==3.0.3
 h11==0.14.0
 httpcore==1.0.5
 httpx==0.27.0
-identify==2.5.36
+identify==2.6.0
 idna==3.7
 imagesize==1.4.1
-importlib-metadata==7.1.0
+importlib-metadata==8.2.0
 iniconfig==2.0.0
-ipykernel==6.29.4
+ipykernel==6.29.5
 ipympl==0.9.4
-ipython==8.24.0
+ipython==8.26.0
 ipython-genutils==0.2.0
-ipywidgets==8.1.2
+ipywidgets==8.1.3
 isoduration==20.11.0
-isort==5.13.2
 jedi==0.19.1
 jinja2==3.1.4
 json5==0.9.25
-jsonpointer==2.4
-jsonschema==4.22.0
+jsonpointer==3.0.0
+jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 jupyter==1.0.0
 jupyter-cache==1.0.0
@@ -69,17 +67,17 @@ jupyter-console==6.6.3
 jupyter-core==5.7.2
 jupyter-events==0.10.0
 jupyter-lsp==2.2.5
-jupyter-server==2.14.0
+jupyter-server==2.14.2
 jupyter-server-mathjax==0.2.6
 jupyter-server-terminals==0.5.3
-jupyterlab==4.2.1
-jupyterlab-code-formatter==2.2.1
+jupyterlab==4.2.4
+jupyterlab-code-formatter==3.0.1
 jupyterlab-git==0.50.1
 jupyterlab-lsp==5.1.0
 jupyterlab-myst==2.4.2
 jupyterlab-pygments==0.3.0
-jupyterlab-server==2.27.2
-jupyterlab-widgets==3.0.10
+jupyterlab-server==2.27.3
+jupyterlab-widgets==3.0.11
 kiwisolver==1.4.5
 latexcodec==3.0.0
 lsprotocol==2023.0.1
@@ -91,111 +89,109 @@ mdit-py-plugins==0.4.1
 mdurl==0.1.2
 mistune==3.0.2
 mpl-interactions==0.24.1
-mypy-extensions==1.0.0
-myst-nb==1.1.0
-myst-parser==3.0.1
+myst-nb==1.1.1
+myst-parser==4.0.0
 nbclient==0.6.8
 nbconvert==7.16.4
 nbdime==4.0.1
 nbformat==5.10.4
-nbmake==1.5.3
+nbmake==1.5.4
 nest-asyncio==1.6.0
-nodeenv==1.8.0
-notebook==7.2.0
+nodeenv==1.9.1
+notebook==7.2.1
 notebook-shim==0.2.4
 numpy==1.26.4
 overrides==7.7.0
-packaging==24.0
+packaging==24.1
 pandocfilters==1.5.1
 parso==0.8.4
-pathspec==0.12.1
 pexpect==4.9.0
-pillow==10.3.0
+pillow==10.4.0
 platformdirs==4.2.2
 pluggy==1.5.0
-pre-commit==3.7.1
+pre-commit==3.8.0
 prometheus-client==0.20.0
-prompt-toolkit==3.0.43
-psutil==5.9.8
+prompt-toolkit==3.0.47
+psutil==6.0.0
 ptyprocess==0.7.0
-pure-eval==0.2.2
+pure-eval==0.2.3
 pybtex==0.24.0
 pybtex-docutils==1.0.3
 pycparser==2.22
-pydata-sphinx-theme==0.15.2
+pydata-sphinx-theme==0.15.4
 pygments==2.18.0
 pyparsing==3.1.2
-pyproject-api==1.6.1
-pytest==8.2.1
+pyproject-api==1.7.1
+pytest==8.3.2
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
 python-lsp-jsonrpc==1.1.2
-python-lsp-ruff==2.2.1
+python-lsp-ruff==2.2.2
 python-lsp-server==1.11.0
 pytoolconfig==1.3.1
-pyyaml==6.0.1
-pyzmq==26.0.3
+pyyaml==6.0.2
+pyzmq==26.1.0
 qtconsole==5.5.2
 qtpy==2.4.1
 referencing==0.35.1
-requests==2.32.2
+requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
 rope==1.13.0
-rpds-py==0.18.1
-ruff==0.4.5
+rpds-py==0.20.0
+ruff==0.5.6
 send2trash==1.8.3
 six==1.16.0
 smmap==5.0.1
 sniffio==1.3.1
 snowballstemmer==2.2.0
 soupsieve==2.5
-sphinx==7.3.7
+sphinx==8.0.2
 sphinx-api-relink==0.0.9
 sphinx-autobuild==2024.4.16
-sphinx-book-theme==1.1.2
-sphinx-codeautolink==0.15.1
+sphinx-book-theme==1.1.3
+sphinx-codeautolink==0.15.2
 sphinx-comments==0.0.3
 sphinx-copybutton==0.5.2
-sphinx-design==0.6.0
+sphinx-design==0.6.1
 sphinx-hep-pdgref==0.2.0
 sphinx-pybtex-etal-style==0.0.2
 sphinx-remove-toctrees==1.0.0.post1
 sphinx-thebe==0.3.1
 sphinx-togglebutton==0.3.2
-sphinxcontrib-applehelp==1.0.8
+sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-bibtex==2.6.2
-sphinxcontrib-devhelp==1.0.6
-sphinxcontrib-htmlhelp==2.0.5
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.7
-sphinxcontrib-serializinghtml==1.1.10
-sqlalchemy==2.0.30
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+sqlalchemy==2.0.32
 stack-data==0.6.3
-starlette==0.37.2
+starlette==0.38.2
 tabulate==0.9.0
 terminado==0.18.1
 tinycss2==1.3.0
 tomli==2.0.1
-tornado==6.4
-tox==4.15.0
+tornado==6.4.1
+tox==4.17.0
 traitlets==5.14.3
 types-python-dateutil==2.9.0.20240316
-typing-extensions==4.11.0
+typing-extensions==4.12.2
 ujson==5.10.0
 uri-template==1.3.0
-urllib3==2.2.1
-uvicorn==0.29.0
-virtualenv==20.26.2
-watchfiles==0.21.0
+urllib3==2.2.2
+uvicorn==0.30.5
+virtualenv==20.26.3
+watchfiles==0.23.0
 wcwidth==0.2.13
-webcolors==1.13
+webcolors==24.6.0
 webencodings==0.5.1
 websocket-client==1.8.0
 websockets==12.0
-wheel==0.43.0
-widgetsnbextension==4.0.10
-zipp==3.18.2
+wheel==0.44.0
+widgetsnbextension==4.0.11
+zipp==3.19.2
 
 # The following packages were excluded from the output:
 # setuptools