diff --git a/.binder/apt.txt b/.binder/apt.txt new file mode 100644 index 00000000..4d956093 --- /dev/null +++ b/.binder/apt.txt @@ -0,0 +1 @@ +graphviz diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100755 index 00000000..71195648 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,12 @@ +#!/bin/bash +set -ex +curl -LsSf https://astral.sh/uv/install.sh | sh +source $HOME/.cargo/env +uv export \ + --extra jupyter \ + --extra notebooks \ + > requirements.txt +uv pip install \ + --requirement requirements.txt \ + --system +uv cache clean diff --git a/.binder/runtime.txt b/.binder/runtime.txt new file mode 100644 index 00000000..8fdd9071 --- /dev/null +++ b/.binder/runtime.txt @@ -0,0 +1 @@ +python-3.9 diff --git a/.constraints/.gitignore b/.constraints/.gitignore deleted file mode 100644 index 36a07ad0..00000000 --- a/.constraints/.gitignore +++ /dev/null @@ -1 +0,0 @@ -!py3.*.txt diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt deleted file mode 100644 index 5491cc8a..00000000 --- a/.constraints/py3.10.txt +++ /dev/null @@ -1,196 +0,0 @@ -# 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==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==24.2.0 -babel==2.16.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.0 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -coverage==7.6.1 -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==1.2.2 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.0 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.0 -h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 -httpx==0.27.2 -identify==2.6.0 -idna==3.8 -imagesize==1.4.1 -importlib-metadata==8.4.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipython==8.27.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.2 -jupyter-core==5.7.2 -jupyter-events==0.10.0 -jupyter-lsp==2.2.5 -jupyter-server==2.14.2 -jupyter-server-mathjax==0.2.6 -jupyter-server-terminals==0.5.3 -jupyterlab==4.2.5 -jupyterlab-code-formatter==3.0.2 -jupyterlab-git==0.50.1 -jupyterlab-lsp==5.1.0 -jupyterlab-myst==2.4.2 -jupyterlab-pygments==0.3.0 -jupyterlab-server==2.27.3 -jupyterlab-widgets==3.0.13 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy==1.11.2 -mypy-extensions==1.0.0 -myst-nb==1.1.1 -myst-parser==4.0.0 -nbclient==0.6.8 -nbconvert==7.16.4 -nbdime==4.0.2 -nbformat==5.10.4 -nbmake==1.5.4 -nest-asyncio==1.6.0 -nodeenv==1.9.1 -notebook-shim==0.2.4 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -particle==0.25.0 -pexpect==4.9.0 -platformdirs==4.3.2 -pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pydot==1.4.2 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.7.1 -pytest==8.3.3 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.4 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.0.2 -sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 -sphinxcontrib-devhelp==2.0.0 -sphinxcontrib-htmlhelp==2.1.0 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==2.0.0 -sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 -stack-data==0.6.3 -starlette==0.38.5 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.1 -tornado==6.4.1 -tox==4.18.1 -tqdm==4.66.5 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 -types-pyyaml==6.0.12.20240808 -types-setuptools==74.1.0.20240907 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.6 -virtualenv==20.26.4 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.0.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.1 - -# The following packages were excluded from the output: -# setuptools diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt deleted file mode 100644 index 2452cbf5..00000000 --- a/.constraints/py3.11.txt +++ /dev/null @@ -1,195 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile pyproject.toml -o .constraints/py3.11.txt --all-extras --no-annotate --python-version=3.11 --no-emit-package setuptools -accessible-pygments==0.0.5 -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==24.2.0 -babel==2.16.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.0 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -coverage==7.6.1 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.0 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.0 -h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 -httpx==0.27.2 -identify==2.6.0 -idna==3.8 -imagesize==1.4.1 -importlib-metadata==8.4.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipython==8.27.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.2 -jupyter-core==5.7.2 -jupyter-events==0.10.0 -jupyter-lsp==2.2.5 -jupyter-server==2.14.2 -jupyter-server-mathjax==0.2.6 -jupyter-server-terminals==0.5.3 -jupyterlab==4.2.5 -jupyterlab-code-formatter==3.0.2 -jupyterlab-git==0.50.1 -jupyterlab-lsp==5.1.0 -jupyterlab-myst==2.4.2 -jupyterlab-pygments==0.3.0 -jupyterlab-server==2.27.3 -jupyterlab-widgets==3.0.13 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy==1.11.2 -mypy-extensions==1.0.0 -myst-nb==1.1.1 -myst-parser==4.0.0 -nbclient==0.6.8 -nbconvert==7.16.4 -nbdime==4.0.2 -nbformat==5.10.4 -nbmake==1.5.4 -nest-asyncio==1.6.0 -nodeenv==1.9.1 -notebook-shim==0.2.4 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -particle==0.25.0 -pexpect==4.9.0 -platformdirs==4.3.2 -pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pydot==1.4.2 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.7.1 -pytest==8.3.3 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.4 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.0.2 -sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 -sphinxcontrib-devhelp==2.0.0 -sphinxcontrib-htmlhelp==2.1.0 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==2.0.0 -sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 -stack-data==0.6.3 -starlette==0.38.5 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.1 -tornado==6.4.1 -tox==4.18.1 -tqdm==4.66.5 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 -types-pyyaml==6.0.12.20240808 -types-setuptools==74.1.0.20240907 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.6 -virtualenv==20.26.4 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.0.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.1 - -# The following packages were excluded from the output: -# setuptools diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt deleted file mode 100644 index 24badb1f..00000000 --- a/.constraints/py3.12.txt +++ /dev/null @@ -1,194 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile pyproject.toml -o .constraints/py3.12.txt --all-extras --no-annotate --python-version=3.12 --no-emit-package setuptools -accessible-pygments==0.0.5 -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==24.2.0 -babel==2.16.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.0 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -coverage==7.6.1 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.0 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.0 -h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 -httpx==0.27.2 -identify==2.6.0 -idna==3.8 -imagesize==1.4.1 -importlib-metadata==8.4.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipython==8.27.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.2 -jupyter-core==5.7.2 -jupyter-events==0.10.0 -jupyter-lsp==2.2.5 -jupyter-server==2.14.2 -jupyter-server-mathjax==0.2.6 -jupyter-server-terminals==0.5.3 -jupyterlab==4.2.5 -jupyterlab-code-formatter==3.0.2 -jupyterlab-git==0.50.1 -jupyterlab-lsp==5.1.0 -jupyterlab-myst==2.4.2 -jupyterlab-pygments==0.3.0 -jupyterlab-server==2.27.3 -jupyterlab-widgets==3.0.13 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy==1.11.2 -mypy-extensions==1.0.0 -myst-nb==1.1.1 -myst-parser==4.0.0 -nbclient==0.6.8 -nbconvert==7.16.4 -nbdime==4.0.2 -nbformat==5.10.4 -nbmake==1.5.4 -nest-asyncio==1.6.0 -nodeenv==1.9.1 -notebook-shim==0.2.4 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -particle==0.25.0 -pexpect==4.9.0 -platformdirs==4.3.2 -pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pydot==1.4.2 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.7.1 -pytest==8.3.3 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.4 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.0.2 -sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 -sphinxcontrib-devhelp==2.0.0 -sphinxcontrib-htmlhelp==2.1.0 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==2.0.0 -sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 -stack-data==0.6.3 -starlette==0.38.5 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tornado==6.4.1 -tox==4.18.1 -tqdm==4.66.5 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 -types-pyyaml==6.0.12.20240808 -types-setuptools==74.1.0.20240907 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.6 -virtualenv==20.26.4 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.0.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.1 - -# The following packages were excluded from the output: -# setuptools diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt deleted file mode 100644 index eee16a4e..00000000 --- a/.constraints/py3.9.txt +++ /dev/null @@ -1,196 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile pyproject.toml -o .constraints/py3.9.txt --all-extras --no-annotate --python-version=3.9 --no-emit-package setuptools -accessible-pygments==0.0.5 -alabaster==0.7.16 -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==24.2.0 -babel==2.16.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.0 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -coverage==7.6.1 -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==1.2.2 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.0 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.0 -h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 -httpx==0.27.2 -identify==2.6.0 -idna==3.8 -imagesize==1.4.1 -importlib-metadata==8.4.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipython==8.18.1 -ipywidgets==8.1.5 -isoduration==20.11.0 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.2 -jupyter-core==5.7.2 -jupyter-events==0.10.0 -jupyter-lsp==2.2.5 -jupyter-server==2.14.2 -jupyter-server-mathjax==0.2.6 -jupyter-server-terminals==0.5.3 -jupyterlab==4.2.5 -jupyterlab-code-formatter==3.0.2 -jupyterlab-git==0.50.1 -jupyterlab-lsp==5.1.0 -jupyterlab-myst==2.4.2 -jupyterlab-pygments==0.3.0 -jupyterlab-server==2.27.3 -jupyterlab-widgets==3.0.13 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy==1.11.2 -mypy-extensions==1.0.0 -myst-nb==1.1.1 -myst-parser==3.0.1 -nbclient==0.6.8 -nbconvert==7.16.4 -nbdime==4.0.2 -nbformat==5.10.4 -nbmake==1.5.4 -nest-asyncio==1.6.0 -nodeenv==1.9.1 -notebook-shim==0.2.4 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -particle==0.25.0 -pexpect==4.9.0 -platformdirs==4.3.2 -pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pydot==1.4.2 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.7.1 -pytest==8.3.3 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.4 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==7.4.7 -sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 -sphinxcontrib-devhelp==2.0.0 -sphinxcontrib-htmlhelp==2.1.0 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==2.0.0 -sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 -stack-data==0.6.3 -starlette==0.38.5 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.1 -tornado==6.4.1 -tox==4.18.1 -tqdm==4.66.5 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 -types-pyyaml==6.0.12.20240808 -types-setuptools==74.1.0.20240907 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.6 -virtualenv==20.26.4 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.0.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.1 - -# The following packages were excluded from the output: -# setuptools diff --git a/.cspell.json b/.cspell.json index 9aa9ea83..a0fad7f2 100644 --- a/.cspell.json +++ b/.cspell.json @@ -24,10 +24,8 @@ "**/.cspell.json", "*.ico", "*particle*.*ml", - ".constraints/*.txt", ".editorconfig", ".envrc", - ".gitattributes", ".gitignore", ".pre-commit-config.yaml", ".prettierignore", @@ -37,7 +35,6 @@ "codecov.yml", "docs/conf.py", "pyproject.toml", - "tox.ini", "typings" ], "ignoreWords": [ diff --git a/.editorconfig b/.editorconfig index 88befe69..674376ff 100644 --- a/.editorconfig +++ b/.editorconfig @@ -16,5 +16,5 @@ indent_size = 4 [LICENSE] indent_size = unset -[setup.cfg] +[uv.lock] indent_size = 4 diff --git a/.envrc b/.envrc index e1d415a5..41fd2cab 100644 --- a/.envrc +++ b/.envrc @@ -1,10 +1,2 @@ -if [ -e .venv ]; then - source .venv/bin/activate -elif [ -e venv ]; then - source venv/bin/activate -elif [ -e .pixi ]; then - watch_file pixi.lock - eval "$(pixi shell-hook)" -else - layout anaconda -fi +uv sync --all-extras --quiet +source .venv/bin/activate diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 18f6c7e9..00000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 54ae3bc8..cf34984b 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -9,9 +9,9 @@ on: jobs: milestone: if: startsWith(github.ref, 'refs/tags') - uses: ComPWA/actions/.github/workflows/close-milestone.yml@v1 + uses: ComPWA/actions/.github/workflows/close-milestone.yml@v2 package-name: - uses: ComPWA/actions/.github/workflows/get-pypi-name.yml@v1 + uses: ComPWA/actions/.github/workflows/get-pypi-name.yml@v2 pypi: environment: name: PyPI @@ -22,11 +22,11 @@ jobs: - package-name permissions: id-token: write - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - - uses: ComPWA/actions/build-pypi-distribution@v1 + - uses: ComPWA/actions/build-pypi-distribution@v2 - uses: pypa/gh-action-pypi-publish@release/v1 push: if: startsWith(github.ref, 'refs/tags') && !github.event.release.prerelease secrets: inherit - uses: ComPWA/actions/.github/workflows/push-to-version-branches.yml@v1 + uses: ComPWA/actions/.github/workflows/push-to-version-branches.yml@v2 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index baaf7849..0d2a1a22 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,15 +28,16 @@ on: jobs: doc: - uses: ComPWA/actions/.github/workflows/ci-docs.yml@v1 + uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2 permissions: pages: write id-token: write with: apt-packages: graphviz + python-version: "3.9" specific-pip-packages: ${{ inputs.specific-pip-packages }} pytest: - uses: ComPWA/actions/.github/workflows/pytest.yml@v1 + uses: ComPWA/actions/.github/workflows/pytest.yml@v2 with: coverage-target: qrules macos-python-version: "3.9" @@ -46,4 +47,6 @@ jobs: if: inputs.specific-pip-packages == '' secrets: token: ${{ secrets.PAT }} - uses: ComPWA/actions/.github/workflows/pre-commit.yml@v1 + uses: ComPWA/actions/.github/workflows/pre-commit.yml@v2 + with: + python-version: "3.9" diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index a66c407b..7986e0cf 100644 --- a/.github/workflows/clean-caches.yml +++ b/.github/workflows/clean-caches.yml @@ -14,9 +14,9 @@ on: jobs: cleanup: name: Remove caches - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - - uses: ComPWA/actions/clean-caches@v1 + - uses: ComPWA/actions/clean-caches@v2 with: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} ref: ${{ inputs.ref }} diff --git a/.github/workflows/requirements.yml b/.github/workflows/lock.yml similarity index 75% rename from .github/workflows/requirements.yml rename to .github/workflows/lock.yml index 6716e974..e6a5c10a 100644 --- a/.github/workflows/requirements.yml +++ b/.github/workflows/lock.yml @@ -1,4 +1,4 @@ -name: Requirements +name: Update concurrency: group: ${{ github.workflow }}-${{ github.ref }} @@ -11,14 +11,14 @@ on: - main - epic/* paths: - - .constraints/py3.*.txt - .pre-commit-config.yaml + - uv.lock schedule: - cron: "0 3 7 */1 *" workflow_dispatch: jobs: - requirements: - uses: ComPWA/actions/.github/workflows/requirements.yml@v1 + lock: + uses: ComPWA/actions/.github/workflows/lock.yml@v2 secrets: token: ${{ secrets.PAT }} diff --git a/.github/workflows/pr-linting.yml b/.github/workflows/pr-linting.yml index 0fab8410..44dc9e42 100644 --- a/.github/workflows/pr-linting.yml +++ b/.github/workflows/pr-linting.yml @@ -11,4 +11,4 @@ on: jobs: lint-pr: - uses: ComPWA/actions/.github/workflows/pr-linting.yml@v1 + uses: ComPWA/actions/.github/workflows/pr-linting.yml@v2 diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml index 52340935..32c6579c 100644 --- a/.github/workflows/release-drafter.yml +++ b/.github/workflows/release-drafter.yml @@ -9,7 +9,7 @@ on: jobs: update_release_draft: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: release-drafter/release-drafter@v6 env: diff --git a/.gitignore b/.gitignore index cd08a7f8..6f8b0e62 100644 --- a/.gitignore +++ b/.gitignore @@ -23,7 +23,6 @@ version.py *.pyc *.swp *.tmp -*condaenv.* .coverage .coverage.* .ipynb_checkpoints/ @@ -40,7 +39,6 @@ TAGS # Virtual environments *venv/ -.pixi/ .tox/ pyvenv*/ @@ -57,5 +55,4 @@ pyvenv*/ !.vscode/*.json !.zenodo.json !codecov.yml -!environment.yml !pyrightconfig.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8ac11a11..8785b953 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,10 +1,11 @@ ci: - autoupdate_commit_msg: "MAINT: update pip constraints and pre-commit" - autoupdate_schedule: quarterly # already done by requirements-cron.yml + autoupdate_commit_msg: "MAINT: update lock files" + autoupdate_schedule: quarterly skip: - check-jsonschema - mypy - pyright + - uv-lock repos: - repo: meta @@ -13,15 +14,15 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.4.0 + rev: 0.5.0 hooks: - id: check-dev-files args: + - --dev-python-version=3.9 - --doc-apt-packages=graphviz - - --no-prettierrc - - --pin-requirements=monthly - --repo-name=qrules - --repo-title=QRules + - --update-lock-files=monthly - id: colab-toc-visible - id: fix-nbformat-version - id: remove-empty-tags @@ -60,7 +61,7 @@ repos: metadata.vscode - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.7.0 hooks: - id: ruff args: [--fix] @@ -69,7 +70,7 @@ repos: types_or: [python, pyi, jupyter] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: check-ast - id: check-case-conflict @@ -109,7 +110,7 @@ repos: - --in-place - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.2 + rev: 0.29.4 hooks: - id: check-jsonschema name: Check CITATION.cff @@ -122,7 +123,7 @@ repos: pass_filenames: false - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v8.13.3 + rev: v8.15.1 hooks: - id: cspell @@ -147,7 +148,12 @@ repos: types: - python - - repo: https://github.com/ComPWA/mirrors-pyright - rev: v1.1.379 + - repo: https://github.com/ComPWA/pyright-pre-commit + rev: v1.1.385 hooks: - id: pyright + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.4.24 + hooks: + - id: uv-lock diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..bd28b9c5 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.9 diff --git a/.readthedocs.yml b/.readthedocs.yml index 1fa04aaf..98b51c8f 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,20 +1,17 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: python: "3.9" - apt_packages: - - graphviz - jobs: - post_install: - - python -m pip install 'uv>=0.2.0' - - python -m uv pip install -c .constraints/py3.9.txt -e .[doc] - -formats: - - htmlzip - -sphinx: - builder: html - configuration: docs/conf.py - fail_on_warning: true + commands: + - |- + export PIXI_HOME=$READTHEDOCS_VIRTUALENV_PATH + curl -fsSL https://pixi.sh/install.sh | bash + pixi global install graphviz uv + - |- + export UV_LINK_MODE=copy + uv run --extra doc --locked --with tox \ + tox -e doc + mkdir -p $READTHEDOCS_OUTPUT + mv docs/_build/html $READTHEDOCS_OUTPUT diff --git a/.vscode/settings.json b/.vscode/settings.json index f63375fb..a91a3d20 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -26,17 +26,13 @@ "[yaml]": { "editor.defaultFormatter": "esbenp.prettier-vscode" }, + "cSpell.enabled": true, "coverage-gutters.coverageFileNames": ["coverage.xml"], "coverage-gutters.coverageReportFileName": "**/htmlcov/index.html", "coverage-gutters.showGutterCoverage": false, "coverage-gutters.showLineCoverage": true, - "cSpell.enabled": true, "diffEditor.experimental.showMoves": true, "editor.formatOnSave": true, - "files.associations": { - "**/.constraints/py*.txt": "pip-requirements", - "**/pixi.lock": "yaml" - }, "files.watcherExclude": { "**/*_cache/**": true, "**/.eggs/**": true, @@ -67,7 +63,6 @@ "notebook.gotoSymbols.showAllSymbols": true, "python.analysis.autoImportCompletions": false, "python.analysis.inlayHints.pytestParameters": true, - "python.analysis.typeCheckingMode": "strict", "python.terminal.activateEnvironment": false, "python.testing.pytestArgs": ["--color=no", "--no-cov"], "python.testing.pytestEnabled": true, @@ -79,7 +74,7 @@ "ruff.organizeImports": true, "search.exclude": { "**/tests/**/__init__.py": true, - ".constraints/*.txt": true + "**/uv.lock": true }, "telemetry.telemetryLevel": "off", "yaml.schemas": { diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4d2abc42..2f5ab117 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,5 +1,26 @@ # How to contribute? -[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/qrules) +[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://github.dev/ComPWA/qrules) -This package is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to [compwa.github.io/develop](https://compwa.github.io/develop)! +> [!TIP] +> This package is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to **[compwa.github.io/develop](https://compwa.github.io/develop)**! + +To contribute to the project, you need to install the package in a virtual environment. This can be done best with [`uv`](https://docs.astral.sh/uv) (see installation instructions [here](https://docs.astral.sh/uv/getting-started/installation)). For this, you first need to get the source code with [Git](https://git-scm.com): + +```shell +git clone https://github.com/ComPWA/qrules +cd qrules +``` + +Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/#project-lockfile). + +```shell +uv sync +source .venv/bin/activate +``` + +Formatting and linting checks are automatically performed when committing changes. This is done with [pre-commit](https://pre-commit.com). To install the hooks in your local repository, run [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**: + +```shell +pre-commit install --install-hooks +``` diff --git a/README.md b/README.md index 29bccede..e36026d2 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Conda package](https://anaconda.org/conda-forge/qrules/badges/version.svg)](https://anaconda.org/conda-forge/qrules) [![Supported Python versions](https://img.shields.io/pypi/pyversions/qrules)](https://pypi.org/project/qrules) -[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/qrules/stable?filepath=docs/usage) +[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/qrules/stable?urlpath=lab) [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/qrules/blob/stable) [![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/qrules) @@ -20,6 +20,7 @@ [![Spelling checked](https://img.shields.io/badge/cspell-checked-brightgreen.svg)](https://github.com/streetsidesoftware/cspell/tree/master/packages/cspell) [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) QRules is a Python package for **validating and generating particle reactions** using quantum number conservation rules. The user only has to provide a certain set of diff --git a/docs/conf.py b/docs/conf.py index d395ae1e..890d61fd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -28,7 +28,9 @@ REPO_NAME = "qrules" REPO_TITLE = "Quantum number conservation rules" -BINDER_LINK = f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?filepath=docs/usage" +BINDER_LINK = ( + f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?urlpath=lab" +) add_module_names = False api_github_repo = f"{ORGANIZATION}/{REPO_NAME}" @@ -186,7 +188,7 @@ }, { "name": "Launch on Binder", - "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?filepath=docs", + "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?urlpath=lab/docs", "icon": "https://mybinder.readthedocs.io/en/latest/_static/favicon.png", "type": "url", }, @@ -219,7 +221,7 @@ } html_title = REPO_TITLE intersphinx_mapping = { - "ampform": ("https://ampform.readthedocs.io/en/stable", None), + "ampform": ("https://ampform.readthedocs.io/stable", None), "attrs": (f"https://www.attrs.org/en/{pin('attrs')}", None), "compwa": ("https://compwa.github.io", None), "constraint": ("https://python-constraint.github.io/python-constraint", None), diff --git a/docs/index.md b/docs/index.md index 40154494..db0511c9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,7 +7,7 @@ [![10.5281/zenodo.5526360](https://zenodo.org/badge/doi/10.5281/zenodo.5526360.svg)](https://doi.org/10.5281/zenodo.5526360) [![Supported Python versions](https://img.shields.io/pypi/pyversions/qrules)](https://pypi.org/project/qrules) {{ '[![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/qrules/blob/{})'.format(branch) }} -{{ '[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/qrules/{}?filepath=docs/usage)'.format(branch) }} +{{ '[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/qrules/{}?urlpath=lab)'.format(branch) }} :::{margin} diff --git a/docs/install.md b/docs/install.md index 41d991f8..b3d79e5d 100644 --- a/docs/install.md +++ b/docs/install.md @@ -9,7 +9,6 @@ The fastest way of installing this package is through PyPI or Conda: ::::{tab-set} - :::{tab-item} PyPI ```shell @@ -17,7 +16,6 @@ python3 -m pip install qrules ``` ::: - :::{tab-item} Conda ```shell @@ -25,7 +23,6 @@ conda install -c conda-forge qrules ``` ::: - :::: This installs the [latest release](https://github.com/ComPWA/qrules/releases) that you @@ -46,64 +43,10 @@ can be installed as follows: python3 -m pip install git+https://github.com/ComPWA/qrules@main ``` -## Editable installation - -It is highly recommend to use the more dynamic -{ref}`'editable installation' `. This allows -you to: - -- exactly {ref}`pin all dependencies ` - to a specific version, so that your work is **reproducible**. -- edit the source code of the framework and - {doc}`help improving it `. - -For this, you first need to get the source code with [Git](https://git-scm.com): - -```shell -git clone https://github.com/ComPWA/qrules.git -cd qrules -``` - -Next, you install the project in editable mode with either -[Conda](https://docs.conda.io) or [`pip`](https://pypi.org/project/pip). It's -recommended to use Conda, because this also pins the version of Python. - -::::{tab-set} - -:::{tab-item} Conda - -```shell -conda env create -``` - -This installs the project in a Conda environment following the definitions in -[`environment.yml`](https://github.com/ComPWA/qrules/blob/main/environment.yml). - -::: - -:::{tab-item} PyPI - -1. **[Recommended]** Create a virtual environment with - [`venv`](https://docs.python.org/3/library/venv.html) (see - {ref}`here `). - -2. Install the project as an - {ref}`'editable installation' ` with - {ref}`additional packages ` for the - developer and all dependencies pinned through - [constraints files](https://pip.pypa.io/en/stable/user_guide/#constraints-files): - - ```shell - python3 -m pip install -c .constraints/py3.x.txt -e .[dev] - ``` +## Developer installation +:::{include} ../CONTRIBUTING.md +:start-after: **[compwa.github.io/develop](https://compwa.github.io/develop)**! ::: -:::: - -See {ref}`compwa:develop:Updating` for how to update the dependencies when new -commits come in. - -That's all! Have a look at {doc}`/usage` to try out the package. You can also have a -look at {doc}`compwa:develop` for tips on how to work with this 'editable' developer -setup! +That's all! Have a look at {doc}`/usage` to try out the package. You can also have a look at {doc}`compwa:develop` for tips on how to work with this 'editable' developer setup! diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 28571326..00000000 --- a/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ -name: qrules -channels: - - defaults -dependencies: - - python==3.9.* - - pip - - graphviz - - pip: - - -c .constraints/py3.9.txt -e .[dev] diff --git a/pyproject.toml b/pyproject.toml index a2fe9749..1e4b5084 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ dependencies = [ "attrs >=20.1.0", # on_setattr and https://www.attrs.org/en/stable/api.html#next-gen "jsonschema", "particle", - "python-constraint2", + "python-constraint", "tqdm >=4.24.0", # autonotebook ] description = "Rule-based particle reaction problem solver on a quantum number level" @@ -59,13 +59,13 @@ dev = [ "qrules[sty]", "qrules[test]", "sphinx-autobuild", - "tox >=1.9", # for skip_install, use_develop + "tox", ] doc = [ - "Sphinx >=3", - "myst-nb", # nb_ configuration prefixes - "qrules[viz]", - "sphinx-api-relink >=0.0.4", + "myst-nb", + "qrules[notebooks]", + "sphinx", + "sphinx-api-relink", "sphinx-book-theme", "sphinx-codeautolink[ipython]", "sphinx-comments", @@ -87,9 +87,12 @@ jupyter = [ "python-lsp-ruff", "python-lsp-server[rope]", ] +notebooks = [ + "qrules[viz]", +] sty = [ - "mypy >=0.730", # attrs and error code support - "pre-commit >=1.4.0", + "mypy", + "pre-commit-uv", "qrules[types]", "ruff", ] @@ -106,7 +109,7 @@ types = [ "ipython", "pydot <2", # problem with pydot.graph_from_dot_data "pytest", - "sphinx-api-relink >=0.0.4", + "sphinx-api-relink", "types-PyYAML", "types-setuptools", ] @@ -141,7 +144,7 @@ where = ["src"] [tool.setuptools_scm] local_scheme = "no-local-version" -version_scheme = "post-release" +version_scheme = "only-version" write_to = "src/qrules/version.py" [tool.coverage.run] @@ -197,128 +200,6 @@ module = ["sphinx.*"] ignore_missing_imports = true module = ["tqdm.*"] -[tool.pixi.project] -channels = ["conda-forge"] -platforms = ["linux-64"] - -[tool.pixi.activation.env] -PRETTIER_LEGACY_CLI = "1" - -[tool.pixi.dependencies] -graphviz = "*" -python = "3.9.*" - -[tool.pixi.environments] -default = {features = [ - "all", - "dev", - "doc", - "jupyter", - "sty", - "test", - "types", - "viz", -]} - -[tool.pixi.feature.dev.tasks.ci] -depends_on = ["cov", "docnb", "linkcheck", "sty"] - -[tool.pixi.feature.dev.tasks.cov] -cmd = """ -pytest tests/unit \ - --cov-fail-under=90 \ - --cov-report=html \ - --cov-report=xml \ - --cov=qrules -""" - -[tool.pixi.feature.dev.tasks.doc] -cmd = """ -sphinx-build \ - --builder html \ - --keep-going \ - --show-traceback --fail-on-warning \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.doclive] -cmd = """ -sphinx-autobuild \ - --builder html \ - --open-browser \ - --re-ignore '.*/__pycache__/.*' \ - --re-ignore '.*/.ipynb_checkpoints/.*' \ - --re-ignore '.*\\.tmp' \ - --re-ignore 'docs/_build/.*' \ - --re-ignore 'docs/_images/.*' \ - --re-ignore 'docs/_static/logo\\..*' \ - --re-ignore 'docs/.*\\.csv' \ - --re-ignore 'docs/.*\\.gv' \ - --re-ignore 'docs/.*\\.inv' \ - --re-ignore 'docs/.*\\.json' \ - --re-ignore 'docs/.*\\.pickle' \ - --re-ignore 'docs/.*\\.yaml' \ - --re-ignore 'docs/.*\\.yml' \ - --re-ignore 'docs/api/.*' \ - --watch docs \ - --watch src \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.docnb] -cmd = "pixi run doc" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.docnb-force] -cmd = "pixi run doc" -env = {FORCE_COLOR = "yes", FORCE_EXECUTE_NB = "yes", PYTHONHASHSEED = "0"} - -[tool.pixi.feature.dev.tasks.docnblive] -cmd = "pixi run doclive" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "yes", PYTHONHASHSEED = "0"} - -[tool.pixi.feature.dev.tasks.linkcheck] -cmd = """ -sphinx-build \ - --builder linkcheck \ - --show-traceback \ - docs/ docs/_build/linkcheck -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.nb] -cmd = "pytest --nbmake docs" - -[tool.pixi.feature.dev.tasks.pydeps] -cmd = """ -pydeps qrules \ - -o ../module_structure.svg \ - --exclude *._* \ - --max-bacon=1 \ - --noshow -""" - -[tool.pixi.feature.dev.tasks.sty] -cmd = "pre-commit run -a" -env = {SKIP = "pyright"} - -[tool.pixi.feature.dev.tasks.test] -cmd = """ -pytest \ - --cov-fail-under=90 \ - --cov-report=html \ - --cov-report=xml \ - --cov=qrules -""" - -[tool.pixi.feature.dev.tasks.tests] -cmd = "pytest src tests/unit" - -[tool.pixi.pypi-dependencies] -qrules = {path = ".", editable = true} - [tool.pyright] exclude = [ "**/.git", @@ -326,6 +207,7 @@ exclude = [ "**/.mypy_cache", "**/.pytest_cache", "**/.tox", + "**/.venv/", "**/__pycache__", "**/_build", ] @@ -517,3 +399,135 @@ sort_first = [ ] spaces_indent_inline_array = 4 trailing_comma_inline_array = true + +[tool.tox] +legacy_tox_ini = """ +[tox] +envlist = + docnb-force, + linkcheck, + sty, + test, +skip_install = True +skip_missing_interpreters = True +skipsdist = True + +[testenv] +allowlist_externals = + pytest +commands = + pytest {posargs:src tests/unit} +description = Run all fast unit tests and doctests +passenv = * + +[testenv:cov] +allowlist_externals = + pytest +commands = + pytest {posargs:src tests/unit} \ + --cov-fail-under=85 \ + --cov-report=html \ + --cov-report=xml \ + --cov=qrules +description = Compute the test coverage of all unit tests + +[testenv:doc] +allowlist_externals = + sphinx-build +commands = + sphinx-build \ + --builder=html \ + --fail-on-warning \ + --keep-going \ + --show-traceback \ + docs/ docs/_build/html +description = Build documentation and API through Sphinx +setenv = + PYTHONWARNINGS = + +[testenv:doclive] +allowlist_externals = + sphinx-autobuild +commands = + sphinx-autobuild \ + --builder=html \ + --ignore=docs/_build/ \ + --ignore=docs/_images/ \ + --ignore=docs/_static/logo.* \ + --ignore=docs/api/ \ + --open-browser \ + --port=0 \ + --re-ignore='.*/__pycache__/.*' \ + --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*/.virtual_documents/.*' \ + --re-ignore='.*\\.csv' \ + --re-ignore='.*\\.gv' \ + --re-ignore='.*\\.inv' \ + --re-ignore='.*\\.json' \ + --re-ignore='.*\\.pickle' \ + --re-ignore='.*\\.tmp' \ + --re-ignore='.*\\.ya?ml' \ + --watch=docs \ + --watch=src \ + docs/ docs/_build/html +description = Set up a server to directly preview changes to the HTML pages + +[testenv:docnb] +base = doc +setenv = + EXECUTE_NB = yes + +[testenv:docnblive] +base = doclive +setenv = + EXECUTE_NB = yes + +[testenv:docnb-force] +base = doc +description = Execute Jupyter notebooks without cache and build documentation with Sphinx +setenv = + FORCE_EXECUTE_NB = yes + +[testenv:linkcheck] +allowlist_externals = + sphinx-build +base = doc +commands = + sphinx-build \ + --builder=linkcheck \ + --show-traceback \ + docs/ docs/_build/linkcheck +description = Check external links in the documentation (requires internet connection) + +[testenv:nb] +allowlist_externals = + pytest +commands = + pytest --nbmake {posargs:docs} +description = Run all notebooks with pytest + +[testenv:sty] +allowlist_externals = + pre-commit +commands = + pre-commit run --all-files {posargs} +description = Perform all linting, formatting, and spelling checks +setenv = + SKIP = pyright + +[testenv:test] +allowlist_externals = + pytest +commands = + pytest {posargs} \ + --cov-fail-under=85 \ + --cov-report=html \ + --cov-report=xml \ + --cov=qrules +description = Run ALL tests, including the slow channel tests, and compute coverage +""" + +[tool.uv] +constraint-dependencies = [ + "pytest-profiling!=1.8.0", +] diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 889faea2..00000000 --- a/tox.ini +++ /dev/null @@ -1,207 +0,0 @@ -[tox] -envlist = - py, - doc, - sty, -skip_install = True -skip_missing_interpreters = True -skipsdist = True - -[testenv] -allowlist_externals = - pytest -commands = - pytest src {posargs:tests/unit} -description = - Run all fast unit tests and doctests - -[testenv:cov] -allowlist_externals = - pytest -commands = - pytest {posargs:tests/unit} \ - --cov-fail-under=90 \ - --cov-report=html \ - --cov-report=xml \ - --cov=qrules -description = - Compute the test coverage of all unit tests - -[testenv:doc] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder html \ - --fail-on-warning \ - --keep-going \ - --show-traceback \ - docs/ docs/_build/html -description = - Build documentation and API through Sphinx -passenv = * -setenv = - FORCE_COLOR = yes - -[testenv:doclive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --builder html \ - --open-browser \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*\.tmp \ - --re-ignore docs/_build/.* \ - --re-ignore docs/_images/.* \ - --re-ignore docs/_static/logo\..* \ - --re-ignore docs/.*\.csv \ - --re-ignore docs/.*\.gv \ - --re-ignore docs/.*\.inv \ - --re-ignore docs/.*\.json \ - --re-ignore docs/.*\.pickle \ - --re-ignore docs/.*\.yaml \ - --re-ignore docs/.*\.yml \ - --re-ignore docs/api/.* \ - --watch docs \ - --watch src \ - docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages -passenv = * -setenv = - FORCE_COLOR = yes - -[testenv:docnb] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder html \ - --keep-going \ - --show-traceback --fail-on-warning \ - docs/ docs/_build/html -description = - Build documentation through Sphinx WITH output of Jupyter notebooks -passenv = * -setenv = - EXECUTE_NB = yes - FORCE_COLOR = yes - - -[testenv:docnblive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --builder html \ - --open-browser \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*\.tmp \ - --re-ignore docs/_build/.* \ - --re-ignore docs/_images/.* \ - --re-ignore docs/_static/logo\..* \ - --re-ignore docs/.*\.csv \ - --re-ignore docs/.*\.gv \ - --re-ignore docs/.*\.inv \ - --re-ignore docs/.*\.json \ - --re-ignore docs/.*\.pickle \ - --re-ignore docs/.*\.yaml \ - --re-ignore docs/.*\.yml \ - --re-ignore docs/api/.* \ - --watch docs \ - --watch src \ - docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages -passenv = * -setenv = - EXECUTE_NB = yes - FORCE_COLOR = yes - PYTHONHASHSEED = 0 - -[testenv:docnb-force] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder html \ - --fail-on-warning \ - --keep-going \ - docs/ docs/_build/html -description = - Execute ALL Jupyter notebooks and build documentation with Sphinx -passenv = * -setenv = - FORCE_COLOR = yes - FORCE_EXECUTE_NB = yes - PYTHONHASHSEED = 0 - -[testenv:jcache] -allowlist_externals = - jcache -changedir = docs/_build -commands = - jcache {posargs:notebook list} -description = - Inspect Jupyter cache - -[testenv:linkcheck] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder linkcheck \ - --show-traceback \ - docs/ docs/_build/linkcheck -description = - Check external links in the documentation (requires internet connection) -passenv = * -setenv = - FORCE_COLOR = yes - -[testenv:nb] -allowlist_externals = - pytest -commands = - pytest --nbmake {posargs:docs} -description = - Run all notebooks with pytest - -[testenv:pydeps] -changedir = src -commands = - pydeps qrules \ - -o ../module_structure.svg \ - --exclude *._* \ - --max-bacon=1 \ - --noshow -deps = - pydeps -description = - Visualize module dependencies -passenv = * - -[testenv:sty] -allowlist_externals = - pre-commit -commands = - pre-commit run {posargs} -a -description = - Perform all linting, formatting, and spelling checks -setenv = - SKIP = pyright - -[testenv:test] -allowlist_externals = - pytest -commands = - pytest {posargs} \ - --cov-fail-under=90 \ - --cov-report=html \ - --cov-report=xml \ 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