From bf90b4aa681f9722387c45a4fd1f89b622ae8530 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:24 +0200 Subject: [PATCH 01/33] MAINT: autoupdate pip constraints --- .constraints/py3.10.txt | 116 ++++++++++++++++++++-------------------- .constraints/py3.11.txt | 114 +++++++++++++++++++-------------------- .constraints/py3.12.txt | 114 +++++++++++++++++++-------------------- .constraints/py3.9.txt | 116 ++++++++++++++++++++-------------------- 4 files changed, 230 insertions(+), 230 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 1a53c2f..956b31e 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -2,58 +2,58 @@ # 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==4.4.0 +anyio==4.6.0 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==2.15.0 +babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 -cachetools==5.4.0 -cattrs==23.2.3 -certifi==2024.7.4 -cffi==1.17.0 +cachetools==5.5.0 +cattrs==24.1.2 +certifi==2024.8.30 +cffi==1.17.1 cfgv==3.4.0 chardet==5.2.0 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 colorama==0.4.6 comm==0.2.2 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.19 exceptiongroup==1.2.2 -executing==2.0.1 +executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.15.4 +filelock==3.16.1 flake8==7.1.1 -fonttools==4.53.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 -greenlet==3.0.3 +greenlet==3.1.1 h11==0.14.0 -httpcore==1.0.5 -httpx==0.27.0 -identify==2.6.0 -idna==3.7 +httpcore==1.0.6 +httpx==0.27.2 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.2.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.26.0 +ipython==8.28.0 ipython-genutils==0.2.0 -ipywidgets==8.1.3 +ipywidgets==8.1.5 isoduration==20.11.0 isort==5.13.2 jedi==0.19.1 @@ -61,45 +61,45 @@ jinja2==3.1.4 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 +jsonschema-specifications==2024.10.1 jupyter-cache==1.0.0 -jupyter-client==8.6.2 +jupyter-client==8.6.3 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==4.2.4 -jupyterlab-code-formatter==3.0.1 +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==3.0.11 -kiwisolver==1.4.5 +jupyterlab-widgets==3.0.13 +kiwisolver==1.4.7 lsprotocol==2023.0.1 markdown-it-py==2.2.0 -markupsafe==2.1.5 -matplotlib==3.9.1.post1 +markupsafe==3.0.1 +matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 mdit-py-plugins==0.3.5 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==1.0.0 nbclient==0.6.8 nbconvert==7.16.4 -nbdime==4.0.1 +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 -numpy==2.0.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 @@ -107,11 +107,11 @@ parso==0.8.4 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.2.2 +platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 +pre-commit==4.0.1 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -120,32 +120,32 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pyflakes==3.2.0 pygments==2.18.0 -pyparsing==3.1.2 -pyproject-api==1.7.1 -pytest==8.3.2 +pyparsing==3.1.4 +pyproject-api==1.8.0 +pytest==8.3.3 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==1.11.0 +python-lsp-server==1.12.0 pytoolconfig==1.3.1 pyyaml==6.0.2 -pyzmq==26.1.0 +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==0.5.6 +ruff==0.6.9 send2trash==1.8.3 six==1.16.0 smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 -soupsieve==2.5 +soupsieve==2.6 sphinx==5.3.0 -sphinx-autobuild==2024.4.16 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 @@ -158,32 +158,32 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.32 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.2 +starlette==0.39.2 tabulate==0.9.0 terminado==0.18.1 tinycss2==1.3.0 -tomli==2.0.1 +tomli==2.0.2 tornado==6.4.1 -tox==4.17.0 +tox==4.21.2 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240316 +types-python-dateutil==2.9.0.20241003 typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.5 -virtualenv==20.26.3 -watchfiles==0.23.0 +urllib3==2.2.3 +uvicorn==0.31.1 +virtualenv==20.26.6 +watchfiles==0.24.0 wcwidth==0.2.13 -webcolors==24.6.0 +webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -websockets==12.0 +websockets==13.1 wheel==0.44.0 -widgetsnbextension==4.0.11 -zipp==3.19.2 +widgetsnbextension==4.0.13 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt index c2b6ef2..57e50f3 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -2,57 +2,57 @@ # 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==0.7.16 -anyio==4.4.0 +anyio==4.6.0 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==2.15.0 +babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 -cachetools==5.4.0 -cattrs==23.2.3 -certifi==2024.7.4 -cffi==1.17.0 +cachetools==5.5.0 +cattrs==24.1.2 +certifi==2024.8.30 +cffi==1.17.1 cfgv==3.4.0 chardet==5.2.0 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 colorama==0.4.6 comm==0.2.2 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.19 -executing==2.0.1 +executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.15.4 +filelock==3.16.1 flake8==7.1.1 -fonttools==4.53.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 -greenlet==3.0.3 +greenlet==3.1.1 h11==0.14.0 -httpcore==1.0.5 -httpx==0.27.0 -identify==2.6.0 -idna==3.7 +httpcore==1.0.6 +httpx==0.27.2 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.2.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.26.0 +ipython==8.28.0 ipython-genutils==0.2.0 -ipywidgets==8.1.3 +ipywidgets==8.1.5 isoduration==20.11.0 isort==5.13.2 jedi==0.19.1 @@ -60,45 +60,45 @@ jinja2==3.1.4 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 +jsonschema-specifications==2024.10.1 jupyter-cache==1.0.0 -jupyter-client==8.6.2 +jupyter-client==8.6.3 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==4.2.4 -jupyterlab-code-formatter==3.0.1 +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==3.0.11 -kiwisolver==1.4.5 +jupyterlab-widgets==3.0.13 +kiwisolver==1.4.7 lsprotocol==2023.0.1 markdown-it-py==2.2.0 -markupsafe==2.1.5 -matplotlib==3.9.1.post1 +markupsafe==3.0.1 +matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 mdit-py-plugins==0.3.5 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==1.0.0 nbclient==0.6.8 nbconvert==7.16.4 -nbdime==4.0.1 +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 -numpy==2.0.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 @@ -106,11 +106,11 @@ parso==0.8.4 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.2.2 +platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 +pre-commit==4.0.1 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -119,32 +119,32 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pyflakes==3.2.0 pygments==2.18.0 -pyparsing==3.1.2 -pyproject-api==1.7.1 -pytest==8.3.2 +pyparsing==3.1.4 +pyproject-api==1.8.0 +pytest==8.3.3 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==1.11.0 +python-lsp-server==1.12.0 pytoolconfig==1.3.1 pyyaml==6.0.2 -pyzmq==26.1.0 +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==0.5.6 +ruff==0.6.9 send2trash==1.8.3 six==1.16.0 smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 -soupsieve==2.5 +soupsieve==2.6 sphinx==5.3.0 -sphinx-autobuild==2024.4.16 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 @@ -157,31 +157,31 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.32 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.2 +starlette==0.39.2 tabulate==0.9.0 terminado==0.18.1 tinycss2==1.3.0 tornado==6.4.1 -tox==4.17.0 +tox==4.21.2 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240316 +types-python-dateutil==2.9.0.20241003 typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.5 -virtualenv==20.26.3 -watchfiles==0.23.0 +urllib3==2.2.3 +uvicorn==0.31.1 +virtualenv==20.26.6 +watchfiles==0.24.0 wcwidth==0.2.13 -webcolors==24.6.0 +webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -websockets==12.0 +websockets==13.1 wheel==0.44.0 -widgetsnbextension==4.0.11 -zipp==3.19.2 +widgetsnbextension==4.0.13 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt index eceae14..dbece0f 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -2,57 +2,57 @@ # 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==0.7.16 -anyio==4.4.0 +anyio==4.6.0 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==2.15.0 +babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 -cachetools==5.4.0 -cattrs==23.2.3 -certifi==2024.7.4 -cffi==1.17.0 +cachetools==5.5.0 +cattrs==24.1.2 +certifi==2024.8.30 +cffi==1.17.1 cfgv==3.4.0 chardet==5.2.0 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 colorama==0.4.6 comm==0.2.2 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.19 -executing==2.0.1 +executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.15.4 +filelock==3.16.1 flake8==7.1.1 -fonttools==4.53.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 -greenlet==3.0.3 +greenlet==3.1.1 h11==0.14.0 -httpcore==1.0.5 -httpx==0.27.0 -identify==2.6.0 -idna==3.7 +httpcore==1.0.6 +httpx==0.27.2 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.2.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.26.0 +ipython==8.28.0 ipython-genutils==0.2.0 -ipywidgets==8.1.3 +ipywidgets==8.1.5 isoduration==20.11.0 isort==5.13.2 jedi==0.19.1 @@ -60,45 +60,45 @@ jinja2==3.1.4 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 +jsonschema-specifications==2024.10.1 jupyter-cache==1.0.0 -jupyter-client==8.6.2 +jupyter-client==8.6.3 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==4.2.4 -jupyterlab-code-formatter==3.0.1 +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==3.0.11 -kiwisolver==1.4.5 +jupyterlab-widgets==3.0.13 +kiwisolver==1.4.7 lsprotocol==2023.0.1 markdown-it-py==2.2.0 -markupsafe==2.1.5 -matplotlib==3.9.1.post1 +markupsafe==3.0.1 +matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 mdit-py-plugins==0.3.5 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==1.0.0 nbclient==0.6.8 nbconvert==7.16.4 -nbdime==4.0.1 +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 -numpy==2.0.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 @@ -106,11 +106,11 @@ parso==0.8.4 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.2.2 +platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 +pre-commit==4.0.1 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -119,32 +119,32 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pyflakes==3.2.0 pygments==2.18.0 -pyparsing==3.1.2 -pyproject-api==1.7.1 -pytest==8.3.2 +pyparsing==3.1.4 +pyproject-api==1.8.0 +pytest==8.3.3 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==1.11.0 +python-lsp-server==1.12.0 pytoolconfig==1.3.1 pyyaml==6.0.2 -pyzmq==26.1.0 +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==0.5.6 +ruff==0.6.9 send2trash==1.8.3 six==1.16.0 smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 -soupsieve==2.5 +soupsieve==2.6 sphinx==5.3.0 -sphinx-autobuild==2024.4.16 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 @@ -157,31 +157,31 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.32 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.2 +starlette==0.39.2 tabulate==0.9.0 terminado==0.18.1 tinycss2==1.3.0 tornado==6.4.1 -tox==4.17.0 +tox==4.21.2 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240316 +types-python-dateutil==2.9.0.20241003 typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.5 -virtualenv==20.26.3 -watchfiles==0.23.0 +urllib3==2.2.3 +uvicorn==0.31.1 +virtualenv==20.26.6 +watchfiles==0.24.0 wcwidth==0.2.13 -webcolors==24.6.0 +webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -websockets==12.0 +websockets==13.1 wheel==0.44.0 -widgetsnbextension==4.0.11 -zipp==3.19.2 +widgetsnbextension==4.0.13 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index 28a846b..01b990c 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -2,59 +2,59 @@ # 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 +anyio==4.6.0 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==2.15.0 +babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 -cachetools==5.4.0 -cattrs==23.2.3 -certifi==2024.7.4 -cffi==1.17.0 +cachetools==5.5.0 +cattrs==24.1.2 +certifi==2024.8.30 +cffi==1.17.1 cfgv==3.4.0 chardet==5.2.0 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 colorama==0.4.6 comm==0.2.2 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.19 exceptiongroup==1.2.2 -executing==2.0.1 +executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.15.4 +filelock==3.16.1 flake8==7.1.1 -fonttools==4.53.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 -greenlet==3.0.3 +greenlet==3.1.1 h11==0.14.0 -httpcore==1.0.5 -httpx==0.27.0 -identify==2.6.0 -idna==3.7 +httpcore==1.0.6 +httpx==0.27.2 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.2.0 -importlib-resources==6.4.0 +importlib-metadata==8.5.0 +importlib-resources==6.4.5 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 ipython==8.18.1 ipython-genutils==0.2.0 -ipywidgets==8.1.3 +ipywidgets==8.1.5 isoduration==20.11.0 isort==5.13.2 jedi==0.19.1 @@ -62,45 +62,45 @@ jinja2==3.1.4 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.23.0 -jsonschema-specifications==2023.12.1 +jsonschema-specifications==2024.10.1 jupyter-cache==1.0.0 -jupyter-client==8.6.2 +jupyter-client==8.6.3 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==4.2.4 -jupyterlab-code-formatter==3.0.1 +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==3.0.11 -kiwisolver==1.4.5 +jupyterlab-widgets==3.0.13 +kiwisolver==1.4.7 lsprotocol==2023.0.1 markdown-it-py==2.2.0 -markupsafe==2.1.5 -matplotlib==3.9.1.post1 +markupsafe==3.0.1 +matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 mdit-py-plugins==0.3.5 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==1.0.0 nbclient==0.6.8 nbconvert==7.16.4 -nbdime==4.0.1 +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 -numpy==2.0.1 +numpy==2.0.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 @@ -108,11 +108,11 @@ parso==0.8.4 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.2.2 +platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==3.8.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 +pre-commit==4.0.1 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -121,32 +121,32 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pyflakes==3.2.0 pygments==2.18.0 -pyparsing==3.1.2 -pyproject-api==1.7.1 -pytest==8.3.2 +pyparsing==3.1.4 +pyproject-api==1.8.0 +pytest==8.3.3 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==1.11.0 +python-lsp-server==1.12.0 pytoolconfig==1.3.1 pyyaml==6.0.2 -pyzmq==26.1.0 +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==0.5.6 +ruff==0.6.9 send2trash==1.8.3 six==1.16.0 smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 -soupsieve==2.5 +soupsieve==2.6 sphinx==5.3.0 -sphinx-autobuild==2024.4.16 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 @@ -159,32 +159,32 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.32 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.2 +starlette==0.39.2 tabulate==0.9.0 terminado==0.18.1 tinycss2==1.3.0 -tomli==2.0.1 +tomli==2.0.2 tornado==6.4.1 -tox==4.17.0 +tox==4.21.2 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240316 +types-python-dateutil==2.9.0.20241003 typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 -urllib3==2.2.2 -uvicorn==0.30.5 -virtualenv==20.26.3 -watchfiles==0.23.0 +urllib3==2.2.3 +uvicorn==0.31.1 +virtualenv==20.26.6 +watchfiles==0.24.0 wcwidth==0.2.13 -webcolors==24.6.0 +webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -websockets==12.0 +websockets==13.1 wheel==0.44.0 -widgetsnbextension==4.0.11 -zipp==3.19.2 +widgetsnbextension==4.0.13 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools From 1253727cdf1cb3c6be951102d2ca1a52f473868c Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:25 +0200 Subject: [PATCH 02/33] DX: autoupdate developer configuration --- .envrc | 11 +++++++- .gitattributes | 1 + .gitignore | 1 + .pre-commit-config.yaml | 49 ++++++++++++++++------------------ .vscode/settings.json | 3 ++- docs/lecture24_utilities.ipynb | 5 ---- environment.yml | 2 -- pyproject.toml | 21 ++++++++++++++- 8 files changed, 57 insertions(+), 36 deletions(-) create mode 100644 .gitattributes diff --git a/.envrc b/.envrc index cce3aa5..e1d415a 100644 --- a/.envrc +++ b/.envrc @@ -1 +1,10 @@ -layout anaconda +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 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..18f6c7e --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index fd936a0..12dda3f 100644 --- a/.gitignore +++ b/.gitignore @@ -31,6 +31,7 @@ prof/ # Virtual environments *venv/ +.pixi/ .tox/ pyvenv*/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 06a4471..e6ea4eb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,9 +1,6 @@ ci: autoupdate_commit_msg: "MAINT: update pip constraints and pre-commit" autoupdate_schedule: quarterly - skip: - - prettier - - taplo repos: - repo: meta @@ -11,11 +8,28 @@ repos: - id: check-hooks-apply - id: check-useless-excludes + - repo: https://github.com/ComPWA/policy + rev: 0.4.1 + hooks: + - id: check-dev-files + args: + - --dev-python-version=3.12 + - --no-github-actions + - --no-prettierrc + - --no-python + - --no-ruff + - --no-version-branches + - --pin-requirements=quarterly + - --repo-name=strong2020-salamanca + - id: colab-toc-visible + - id: remove-empty-tags + - repo: https://github.com/kynan/nbstripout rev: 0.7.1 hooks: - id: nbstripout args: + - --drop-empty-cells - --extra-keys - | cell.attachments @@ -38,23 +52,6 @@ repos: metadata.varInspector metadata.vscode - - repo: https://github.com/ComPWA/policy - rev: 0.3.18 - hooks: - - id: check-dev-files - args: - - --dev-python-version=3.12 - - --no-github-actions - - --no-gitpod - - --no-prettierrc - - --no-python - - --no-ruff - - --no-version-branches - - --pin-requirements=quarterly - - --repo-name=strong2020-salamanca - - id: colab-toc-visible - - id: remove-empty-tags - - repo: https://github.com/nbQA-dev/nbQA rev: 1.8.7 hooks: @@ -74,15 +71,15 @@ repos: - id: mixed-line-ending - id: trailing-whitespace - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v4.0.0-alpha.8 + - repo: https://github.com/ComPWA/prettier-pre-commit + rev: v3.3.3 hooks: - id: prettier - - repo: https://github.com/ComPWA/mirrors-taplo - rev: v0.8.1 + - repo: https://github.com/ComPWA/taplo-pre-commit + rev: v0.9.3 hooks: - - id: taplo + - id: taplo-format - repo: https://github.com/pappasam/toml-sort rev: v0.23.1 @@ -99,7 +96,7 @@ repos: types_or: [jupyter] - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: 2.7.3 + rev: 3.0.3 hooks: - id: editorconfig-checker name: editorconfig diff --git a/.vscode/settings.json b/.vscode/settings.json index e6b1ef9..673362d 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -27,7 +27,8 @@ "diffEditor.experimental.showMoves": true, "editor.formatOnSave": true, "files.associations": { - "**/.constraints/py*.txt": "pip-requirements" + "**/.constraints/py*.txt": "pip-requirements", + "**/pixi.lock": "yaml" }, "github-actions.workflows.pinned.workflows": [".github/workflows/ci.yml"], "gitlens.telemetry.enabled": false, diff --git a/docs/lecture24_utilities.ipynb b/docs/lecture24_utilities.ipynb index c5df6de..1bd40e6 100644 --- a/docs/lecture24_utilities.ipynb +++ b/docs/lecture24_utilities.ipynb @@ -75,11 +75,6 @@ " )\n", " return histo" ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] } ], "metadata": { diff --git a/environment.yml b/environment.yml index a8fc4de..31ee388 100644 --- a/environment.yml +++ b/environment.yml @@ -4,5 +4,3 @@ dependencies: - pip - pip: - -c .constraints/py3.12.txt -e .[dev] -variables: - PRETTIER_LEGACY_CLI: "1" diff --git a/pyproject.toml b/pyproject.toml index ab04d5d..5da426b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,6 +70,26 @@ sty = [ ] test = ["nbmake"] +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["linux-64"] + +[tool.pixi.activation.env] +PRETTIER_LEGACY_CLI = "1" + +[tool.pixi.dependencies] +python = "3.12.*" + +[tool.pixi.environments] +default = {features = [ + "dev", + "doc", + "format", + "jupyter", + "sty", + "test", +]} + [tool.tomlsort] all = false ignore_case = true @@ -80,7 +100,6 @@ sort_first = [ "tool.setuptools", "tool.setuptools_scm", ] -sort_table_keys = true spaces_indent_inline_array = 4 trailing_comma_inline_array = true From cce7df9c35f2e2d3defbd9ba111ab86e847072c4 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:25 +0200 Subject: [PATCH 03/33] MAINT: remove version restriction from Sphinx --- .constraints/py3.10.txt | 14 +++++++------- .constraints/py3.11.txt | 14 +++++++------- .constraints/py3.12.txt | 14 +++++++------- .constraints/py3.9.txt | 12 ++++++------ pyproject.toml | 2 +- 5 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 956b31e..42f1581 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -1,7 +1,7 @@ # 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 +alabaster==1.0.0 anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 @@ -30,7 +30,7 @@ decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 docstring-to-markdown==0.15 -docutils==0.19 +docutils==0.21.2 exceptiongroup==1.2.2 executing==2.1.0 fastjsonschema==2.20.0 @@ -80,17 +80,17 @@ jupyterlab-server==2.27.3 jupyterlab-widgets==3.0.13 kiwisolver==1.4.7 lsprotocol==2023.0.1 -markdown-it-py==2.2.0 +markdown-it-py==3.0.0 markupsafe==3.0.1 matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 -mdit-py-plugins==0.3.5 +mdit-py-plugins==0.4.2 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 myst-nb==1.1.2 -myst-parser==1.0.0 +myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 nbdime==4.0.2 @@ -144,12 +144,12 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==5.3.0 +sphinx==8.1.0 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 -sphinx-design==0.6.0 +sphinx-design==0.6.1 sphinx-exercise==0.4.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt index 57e50f3..80bfb2c 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -1,7 +1,7 @@ # 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==0.7.16 +alabaster==1.0.0 anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 @@ -30,7 +30,7 @@ decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 docstring-to-markdown==0.15 -docutils==0.19 +docutils==0.21.2 executing==2.1.0 fastjsonschema==2.20.0 filelock==3.16.1 @@ -79,17 +79,17 @@ jupyterlab-server==2.27.3 jupyterlab-widgets==3.0.13 kiwisolver==1.4.7 lsprotocol==2023.0.1 -markdown-it-py==2.2.0 +markdown-it-py==3.0.0 markupsafe==3.0.1 matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 -mdit-py-plugins==0.3.5 +mdit-py-plugins==0.4.2 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 myst-nb==1.1.2 -myst-parser==1.0.0 +myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 nbdime==4.0.2 @@ -143,12 +143,12 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==5.3.0 +sphinx==8.1.0 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 -sphinx-design==0.6.0 +sphinx-design==0.6.1 sphinx-exercise==0.4.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt index dbece0f..16ad224 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -1,7 +1,7 @@ # 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==0.7.16 +alabaster==1.0.0 anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 @@ -30,7 +30,7 @@ decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 docstring-to-markdown==0.15 -docutils==0.19 +docutils==0.21.2 executing==2.1.0 fastjsonschema==2.20.0 filelock==3.16.1 @@ -79,17 +79,17 @@ jupyterlab-server==2.27.3 jupyterlab-widgets==3.0.13 kiwisolver==1.4.7 lsprotocol==2023.0.1 -markdown-it-py==2.2.0 +markdown-it-py==3.0.0 markupsafe==3.0.1 matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 -mdit-py-plugins==0.3.5 +mdit-py-plugins==0.4.2 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 myst-nb==1.1.2 -myst-parser==1.0.0 +myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 nbdime==4.0.2 @@ -143,12 +143,12 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==5.3.0 +sphinx==8.1.0 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 -sphinx-design==0.6.0 +sphinx-design==0.6.1 sphinx-exercise==0.4.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index 01b990c..a698da2 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -30,7 +30,7 @@ decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 docstring-to-markdown==0.15 -docutils==0.19 +docutils==0.21.2 exceptiongroup==1.2.2 executing==2.1.0 fastjsonschema==2.20.0 @@ -81,17 +81,17 @@ jupyterlab-server==2.27.3 jupyterlab-widgets==3.0.13 kiwisolver==1.4.7 lsprotocol==2023.0.1 -markdown-it-py==2.2.0 +markdown-it-py==3.0.0 markupsafe==3.0.1 matplotlib==3.9.2 matplotlib-inline==0.1.7 mccabe==0.7.0 -mdit-py-plugins==0.3.5 +mdit-py-plugins==0.4.2 mdurl==0.1.2 mistune==3.0.2 mypy-extensions==1.0.0 myst-nb==1.1.2 -myst-parser==1.0.0 +myst-parser==3.0.1 nbclient==0.6.8 nbconvert==7.16.4 nbdime==4.0.2 @@ -145,12 +145,12 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==5.3.0 +sphinx==7.4.7 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-comments==0.0.3 sphinx-copybutton==0.5.2 -sphinx-design==0.6.0 +sphinx-design==0.6.1 sphinx-exercise==0.4.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 diff --git a/pyproject.toml b/pyproject.toml index 5da426b..1fc89f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,13 +41,13 @@ dev = [ doc = [ "ipympl", "myst-nb", + "sphinx", "sphinx-book-theme", "sphinx-comments", "sphinx-copybutton", "sphinx-design", "sphinx-exercise", "sphinx-togglebutton", - "sphinx<6", # https://github.com/ComPWA/strong2020-salamanca/issues/29 ] format = [ "black", From a987f14fe9a1ead5cfa708454c20e6d29682bb77 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:25 +0200 Subject: [PATCH 04/33] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .pre-commit-config.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e6ea4eb..fc041a7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,6 +2,8 @@ ci: autoupdate_commit_msg: "MAINT: update pip constraints and pre-commit" autoupdate_schedule: quarterly + skip: [] + repos: - repo: meta hooks: From 741832f279a3f34e794ce79c7e50a23fcaf4d05e Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:26 +0200 Subject: [PATCH 05/33] DX: modernize dev environment with `uv` --- .constraints/.gitignore | 1 - .constraints/py3.10.txt | 189 -- .constraints/py3.11.txt | 187 -- .constraints/py3.12.txt | 187 -- .constraints/py3.9.txt | 190 -- .editorconfig | 3 + .envrc | 12 +- .flake8 | 11 - .gitattributes | 1 - .github/release-drafter.yml | 37 + .github/workflows/cd.yml | 12 + .github/workflows/ci.yml | 14 +- .github/workflows/clean-caches.yml | 2 +- .github/workflows/pr-linting.yml | 23 +- .github/workflows/release-drafter.yml | 16 + .github/workflows/requirements.yml | 1 - .gitignore | 3 - .pre-commit-config.yaml | 37 +- .python-version | 1 + .vscode/extensions.json | 9 +- .vscode/settings.json | 17 +- CONTRIBUTING.md | 26 + README.md | 38 +- docs/index.md | 1 + environment.yml | 6 - pyproject.toml | 298 ++- uv.lock | 3393 +++++++++++++++++++++++++ 27 files changed, 3702 insertions(+), 1013 deletions(-) delete mode 100644 .constraints/.gitignore delete mode 100644 .constraints/py3.10.txt delete mode 100644 .constraints/py3.11.txt delete mode 100644 .constraints/py3.12.txt delete mode 100644 .constraints/py3.9.txt delete mode 100644 .flake8 delete mode 100644 .gitattributes create mode 100644 .github/release-drafter.yml create mode 100644 .github/workflows/cd.yml create mode 100644 .github/workflows/release-drafter.yml create mode 100644 .python-version create mode 100644 CONTRIBUTING.md delete mode 100644 environment.yml create mode 100644 uv.lock diff --git a/.constraints/.gitignore b/.constraints/.gitignore deleted file mode 100644 index 36a07ad..0000000 --- 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 42f1581..0000000 --- a/.constraints/py3.10.txt +++ /dev/null @@ -1,189 +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==4.6.0 -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 -black==24.10.0 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.2 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.4.0 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.3.0 -cycler==0.12.1 -debugpy==1.8.7 -decorator==5.1.1 -defusedxml==0.7.1 -distlib==0.3.9 -docstring-to-markdown==0.15 -docutils==0.21.2 -exceptiongroup==1.2.2 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -flake8==7.1.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -greenlet==3.1.1 -h11==0.14.0 -httpcore==1.0.6 -httpx==0.27.2 -identify==2.6.1 -idna==3.10 -imagesize==1.4.1 -importlib-metadata==8.5.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipympl==0.9.4 -ipython==8.28.0 -ipython-genutils==0.2.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -isort==5.13.2 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2024.10.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.3 -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 -kiwisolver==1.4.7 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.9.2 -matplotlib-inline==0.1.7 -mccabe==0.7.0 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy-extensions==1.0.0 -myst-nb==1.1.2 -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 -numpy==2.1.2 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -pathspec==0.12.1 -pexpect==4.9.0 -pillow==10.4.0 -platformdirs==4.3.6 -pluggy==1.5.0 -pre-commit==4.0.1 -prometheus-client==0.21.0 -prompt-toolkit==3.0.48 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pycodestyle==2.12.1 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pyflakes==3.2.0 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -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==0.6.9 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.1.0 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-exercise==0.4.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -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==2.0.35 -stack-data==0.6.3 -starlette==0.39.2 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.2 -tornado==6.4.1 -tox==4.21.2 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20241003 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.3 -uvicorn==0.31.1 -virtualenv==20.26.6 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.2 - -# 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 80bfb2c..0000000 --- a/.constraints/py3.11.txt +++ /dev/null @@ -1,187 +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==4.6.0 -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 -black==24.10.0 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.2 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.4.0 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.3.0 -cycler==0.12.1 -debugpy==1.8.7 -decorator==5.1.1 -defusedxml==0.7.1 -distlib==0.3.9 -docstring-to-markdown==0.15 -docutils==0.21.2 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -flake8==7.1.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -greenlet==3.1.1 -h11==0.14.0 -httpcore==1.0.6 -httpx==0.27.2 -identify==2.6.1 -idna==3.10 -imagesize==1.4.1 -importlib-metadata==8.5.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipympl==0.9.4 -ipython==8.28.0 -ipython-genutils==0.2.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -isort==5.13.2 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2024.10.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.3 -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 -kiwisolver==1.4.7 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.9.2 -matplotlib-inline==0.1.7 -mccabe==0.7.0 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy-extensions==1.0.0 -myst-nb==1.1.2 -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 -numpy==2.1.2 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -pathspec==0.12.1 -pexpect==4.9.0 -pillow==10.4.0 -platformdirs==4.3.6 -pluggy==1.5.0 -pre-commit==4.0.1 -prometheus-client==0.21.0 -prompt-toolkit==3.0.48 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pycodestyle==2.12.1 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pyflakes==3.2.0 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -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==0.6.9 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.1.0 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-exercise==0.4.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -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==2.0.35 -stack-data==0.6.3 -starlette==0.39.2 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tornado==6.4.1 -tox==4.21.2 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20241003 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.3 -uvicorn==0.31.1 -virtualenv==20.26.6 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.2 - -# 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 16ad224..0000000 --- a/.constraints/py3.12.txt +++ /dev/null @@ -1,187 +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==4.6.0 -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 -black==24.10.0 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.2 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.4.0 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.3.0 -cycler==0.12.1 -debugpy==1.8.7 -decorator==5.1.1 -defusedxml==0.7.1 -distlib==0.3.9 -docstring-to-markdown==0.15 -docutils==0.21.2 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -flake8==7.1.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -greenlet==3.1.1 -h11==0.14.0 -httpcore==1.0.6 -httpx==0.27.2 -identify==2.6.1 -idna==3.10 -imagesize==1.4.1 -importlib-metadata==8.5.0 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipympl==0.9.4 -ipython==8.28.0 -ipython-genutils==0.2.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -isort==5.13.2 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2024.10.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.3 -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 -kiwisolver==1.4.7 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.9.2 -matplotlib-inline==0.1.7 -mccabe==0.7.0 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy-extensions==1.0.0 -myst-nb==1.1.2 -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 -numpy==2.1.2 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -pathspec==0.12.1 -pexpect==4.9.0 -pillow==10.4.0 -platformdirs==4.3.6 -pluggy==1.5.0 -pre-commit==4.0.1 -prometheus-client==0.21.0 -prompt-toolkit==3.0.48 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pycodestyle==2.12.1 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pyflakes==3.2.0 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -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==0.6.9 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==8.1.0 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-exercise==0.4.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -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==2.0.35 -stack-data==0.6.3 -starlette==0.39.2 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tornado==6.4.1 -tox==4.21.2 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20241003 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.3 -uvicorn==0.31.1 -virtualenv==20.26.6 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.2 - -# 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 a698da2..0000000 --- a/.constraints/py3.9.txt +++ /dev/null @@ -1,190 +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==4.6.0 -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 -black==24.10.0 -bleach==6.1.0 -cachetools==5.5.0 -cattrs==24.1.2 -certifi==2024.8.30 -cffi==1.17.1 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.4.0 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.3.0 -cycler==0.12.1 -debugpy==1.8.7 -decorator==5.1.1 -defusedxml==0.7.1 -distlib==0.3.9 -docstring-to-markdown==0.15 -docutils==0.21.2 -exceptiongroup==1.2.2 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -flake8==7.1.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -greenlet==3.1.1 -h11==0.14.0 -httpcore==1.0.6 -httpx==0.27.2 -identify==2.6.1 -idna==3.10 -imagesize==1.4.1 -importlib-metadata==8.5.0 -importlib-resources==6.4.5 -iniconfig==2.0.0 -ipykernel==6.29.5 -ipympl==0.9.4 -ipython==8.18.1 -ipython-genutils==0.2.0 -ipywidgets==8.1.5 -isoduration==20.11.0 -isort==5.13.2 -jedi==0.19.1 -jinja2==3.1.4 -json5==0.9.25 -jsonpointer==3.0.0 -jsonschema==4.23.0 -jsonschema-specifications==2024.10.1 -jupyter-cache==1.0.0 -jupyter-client==8.6.3 -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 -kiwisolver==1.4.7 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.9.2 -matplotlib-inline==0.1.7 -mccabe==0.7.0 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mypy-extensions==1.0.0 -myst-nb==1.1.2 -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 -numpy==2.0.2 -overrides==7.7.0 -packaging==24.1 -pandocfilters==1.5.1 -parso==0.8.4 -pathspec==0.12.1 -pexpect==4.9.0 -pillow==10.4.0 -platformdirs==4.3.6 -pluggy==1.5.0 -pre-commit==4.0.1 -prometheus-client==0.21.0 -prompt-toolkit==3.0.48 -psutil==6.0.0 -ptyprocess==0.7.0 -pure-eval==0.2.3 -pycodestyle==2.12.1 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pyflakes==3.2.0 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -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==0.6.9 -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-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-exercise==0.4.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -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==2.0.35 -stack-data==0.6.3 -starlette==0.39.2 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.2 -tornado==6.4.1 -tox==4.21.2 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20241003 -typing-extensions==4.12.2 -ujson==5.10.0 -uri-template==1.3.0 -urllib3==2.2.3 -uvicorn==0.31.1 -virtualenv==20.26.6 -watchfiles==0.24.0 -wcwidth==0.2.13 -webcolors==24.8.0 -webencodings==0.5.1 -websocket-client==1.8.0 -websockets==13.1 -wheel==0.44.0 -widgetsnbextension==4.0.13 -zipp==3.20.2 - -# The following packages were excluded from the output: -# setuptools diff --git a/.editorconfig b/.editorconfig index 3146498..107937d 100644 --- a/.editorconfig +++ b/.editorconfig @@ -12,3 +12,6 @@ indent_size = unset [*.{py,toml}] indent_size = 4 + +[uv.lock] +indent_size = 4 diff --git a/.envrc b/.envrc index e1d415a..41fd2ca 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/.flake8 b/.flake8 deleted file mode 100644 index f36b2dd..0000000 --- a/.flake8 +++ /dev/null @@ -1,11 +0,0 @@ -[flake8] -extend-ignore = - E1, - E2, - E3, - E402, - E501, - E722, - E731, - E741, - F404, diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 18f6c7e..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml new file mode 100644 index 0000000..c521caf --- /dev/null +++ b/.github/release-drafter.yml @@ -0,0 +1,37 @@ +name-template: '"STRONG2020 HaSP School" $NEXT_PATCH_VERSION' +tag-template: $NEXT_PATCH_VERSION + +references: + - main + - epic/* + +categories: + - title: ✨ New features + label: ✨ Feature + - title: ⚠️ Enhancements and optimizations + label: ⚙️ Enhancement + - title: ⚠️ API changes + label: ⚠️ Interface + - title: ⚠️ Changes that may affect behavior + label: ❗ Behavior + - title: 🐛 Bug fixes + label: 🐛 Bug + - title: 📝 Documentation + label: 📝 Docs + - title: 🔨 Maintenance + label: 🔨 Maintenance + - title: 🖱️ Developer Experience + label: 🖱️ DX + +change-template: "- $TITLE (#$NUMBER)" + +replacers: + - search: /([A-Z]+!?:\s*)(.*)/g + replace: $2 + +sort-direction: ascending + +template: | + $CHANGES + + _The full changelog as commits can be found [here](https://github.com/ComPWA/strong2020-salamanca/compare/$PREVIOUS_TAG...$NEXT_PATCH_VERSION)._ diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml new file mode 100644 index 0000000..56f0c9c --- /dev/null +++ b/.github/workflows/cd.yml @@ -0,0 +1,12 @@ +name: CD + +on: + release: + types: + - prereleased + - released + +jobs: + milestone: + if: startsWith(github.ref, 'refs/tags') + uses: ComPWA/actions/.github/workflows/close-milestone.yml@v1 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4f243e6..2708cfa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,7 +2,11 @@ name: CI concurrency: group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true + cancel-in-progress: |- + ${{ github.ref != format('refs/heads/{0}', github.event.repository.default_branch) }} + +env: + PYTHONHASHSEED: "0" on: push: @@ -23,6 +27,14 @@ on: type: string jobs: + doc: + uses: ComPWA/actions/.github/workflows/ci-docs.yml@v1 + permissions: + pages: write + id-token: write + with: + gh-pages: true + specific-pip-packages: ${{ inputs.specific-pip-packages }} style: if: inputs.specific-pip-packages == '' secrets: diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index a66c407..939e136 100644 --- a/.github/workflows/clean-caches.yml +++ b/.github/workflows/clean-caches.yml @@ -14,7 +14,7 @@ on: jobs: cleanup: name: Remove caches - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: ComPWA/actions/clean-caches@v1 with: diff --git a/.github/workflows/pr-linting.yml b/.github/workflows/pr-linting.yml index cd3bb74..0fab841 100644 --- a/.github/workflows/pr-linting.yml +++ b/.github/workflows/pr-linting.yml @@ -10,24 +10,5 @@ on: - unlabeled jobs: - check-labels: - name: Check labels - runs-on: ubuntu-22.04 - steps: - - uses: docker://agilepathway/pull-request-label-checker:latest # cspell:ignore agilepathway - with: - any_of: >- - 🐛 Bug,✨ Feature,⚙️ Enhancement,⚠️ Interface,❗ Behavior,📝 Docs,🔨 Maintenance,🖱️ DX - none_of: Epic,💫 Good first issue - repo_token: ${{ secrets.GITHUB_TOKEN }} - - check-title: - name: Check title - runs-on: ubuntu-22.04 - steps: - - uses: actions/checkout@v4 - - run: npm install @compwa/commitlint-config - - name: Create commitlint config - run: | - echo "module.exports = {extends: ['@compwa/commitlint-config']}" > commitlint.config.js - - uses: JulienKode/pull-request-name-linter-action@v0.5.0 # cspell:ignore kode + lint-pr: + uses: ComPWA/actions/.github/workflows/pr-linting.yml@v1 diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml new file mode 100644 index 0000000..32c6579 --- /dev/null +++ b/.github/workflows/release-drafter.yml @@ -0,0 +1,16 @@ +name: Release Drafter + +on: + push: + branches: + - main + - epic/* + workflow_dispatch: + +jobs: + update_release_draft: + runs-on: ubuntu-24.04 + steps: + - uses: release-drafter/release-drafter@v6 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/requirements.yml b/.github/workflows/requirements.yml index af94bd3..75a6c15 100644 --- a/.github/workflows/requirements.yml +++ b/.github/workflows/requirements.yml @@ -11,7 +11,6 @@ on: - main - epic/* paths: - - .constraints/py3.*.txt - .pre-commit-config.yaml schedule: - cron: "0 3 7 */3 *" diff --git a/.gitignore b/.gitignore index 12dda3f..8498af0 100644 --- a/.gitignore +++ b/.gitignore @@ -15,7 +15,6 @@ version.py # Temporary files *.pyc -*condaenv.* .coverage .coverage.* .ipynb_checkpoints/ @@ -31,7 +30,6 @@ prof/ # Virtual environments *venv/ -.pixi/ .tox/ pyvenv*/ @@ -44,4 +42,3 @@ pyvenv*/ !.github/*/*.yml !.pre-commit-config.yaml !.vscode/*.json -!environment.yml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fc041a7..4e6eaf2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ ci: - autoupdate_commit_msg: "MAINT: update pip constraints and pre-commit" + autoupdate_commit_msg: "MAINT: update lock files" autoupdate_schedule: quarterly skip: [] @@ -10,19 +10,17 @@ repos: - id: check-hooks-apply - id: check-useless-excludes - - repo: https://github.com/ComPWA/policy - rev: 0.4.1 + - repo: /data/local/redeboer/work/ComPWA/policy + rev: 565f235682bdafe8ea5c0d7e88220c95a919a26f hooks: - id: check-dev-files args: - - --dev-python-version=3.12 - - --no-github-actions - --no-prettierrc - - --no-python - - --no-ruff + - --no-pypi - --no-version-branches - --pin-requirements=quarterly - --repo-name=strong2020-salamanca + - --repo-title="STRONG2020 HaSP School" - id: colab-toc-visible - id: remove-empty-tags @@ -54,13 +52,14 @@ repos: metadata.varInspector metadata.vscode - - repo: https://github.com/nbQA-dev/nbQA - rev: 1.8.7 + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.6.9 hooks: - - id: nbqa-flake8 - - id: nbqa-isort - - id: nbqa-pyupgrade - args: [--py39-plus] + - id: ruff + args: [--fix] + types_or: [python, pyi, jupyter] + - id: ruff-format + types_or: [python, pyi, jupyter] - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.6.0 @@ -90,13 +89,6 @@ repos: args: - --in-place - - repo: https://github.com/psf/black-pre-commit-mirror - rev: 24.8.0 - hooks: - - id: black-jupyter - args: [--line-length=85] - types_or: [jupyter] - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python rev: 3.0.3 hooks: @@ -107,3 +99,8 @@ repos: (?x)^( .*\.py )$ + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.4.20 + hooks: + - id: uv-lock diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 221ac5d..bee1df6 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,5 +1,6 @@ { "recommendations": [ + "charliermarsh.ruff", "eamodio.gitlens", "editorconfig.editorconfig", "esbenp.prettier-vscode", @@ -7,14 +8,12 @@ "github.vscode-github-actions", "github.vscode-pull-request-github", "mhutchie.git-graph", - "ms-python.black-formatter", - "ms-python.isort", "ms-python.python", "ms-toolsai.jupyter", "ms-toolsai.vscode-jupyter-cell-tags", "ms-toolsai.vscode-jupyter-slideshow", "ms-vscode.live-server", - "Soulcode.vscode-unwanted-extensions", + "soulcode.vscode-unwanted-extensions", "stkb.rewrap", "tamasfe.even-better-toml", "yzhang.markdown-all-in-one" @@ -23,7 +22,11 @@ "bungcip.better-toml", "davidanson.vscode-markdownlint", "garaioag.garaio-vscode-unwanted-recommendations", + "ms-python.black-formatter", + "ms-python.flake8", + "ms-python.isort", "ms-python.mypy-type-checker", + "ms-python.pylint", "travisillig.vscode-json-stable-stringify", "tyriar.sort-lines" ] diff --git a/.vscode/settings.json b/.vscode/settings.json index 673362d..ed59e12 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -17,30 +17,31 @@ "editor.codeActionsOnSave": { "source.organizeImports": "explicit" }, - "editor.defaultFormatter": "ms-python.black-formatter", + "editor.defaultFormatter": "charliermarsh.ruff", "editor.rulers": [88] }, "[yaml]": { "editor.defaultFormatter": "esbenp.prettier-vscode" }, - "black-formatter.importStrategy": "useBundled", "diffEditor.experimental.showMoves": true, "editor.formatOnSave": true, - "files.associations": { - "**/.constraints/py*.txt": "pip-requirements", - "**/pixi.lock": "yaml" - }, "github-actions.workflows.pinned.workflows": [".github/workflows/ci.yml"], "gitlens.telemetry.enabled": false, - "isort.args": ["--profile", "black"], "livePreview.defaultPreviewPath": "docs/_build/html", "multiDiffEditor.experimental.enabled": true, + "notebook.codeActionsOnSave": { + "notebook.source.organizeImports": "explicit" + }, + "notebook.formatOnSave.enabled": true, "notebook.gotoSymbols.showAllSymbols": true, "python.terminal.activateEnvironment": false, "redhat.telemetry.enabled": false, "rewrap.wrappingColumn": 88, + "ruff.enable": true, + "ruff.importStrategy": "fromEnvironment", + "ruff.organizeImports": true, "search.exclude": { - "**/.constraints/py*.txt": true + "**/uv.lock": true }, "telemetry.telemetryLevel": "off" } diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..068ab1a --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,26 @@ +# How to contribute? + +[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://github.dev/ComPWA/strong2020-salamanca) + +> [!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/strong2020-salamanca +cd strong2020-salamanca +``` + +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 047afba..b31cd06 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,10 @@ # STRONG2020 HaSP School +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier) [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/strong2020-salamanca/blob/main) [![GitHub Pages](https://github.com/ComPWA/strong2020-salamanca/actions/workflows/docs.yml/badge.svg)](https://github.com/ComPWA/strong2020-salamanca/actions/workflows/docs.yml) This (unofficial) repository contains the exercises for the [STRONG2020 HaSP School](https://indico.ific.uv.es/event/6803) which was organised in Salamanca in 2023. Many of the files hosted in this repository originate from the [lecture material](https://indico.ific.uv.es/event/6803/timetable). -## Installation - -1. Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html) - -2. Create and activate the virtual environment: - - ```shell - conda env create - conda activate strong2020-salamanca - ``` - -3. Run notebooks in [Jupyter Lab](https://jupyter.org): - - ```shell - jupyter lab - ``` - -## Documentation - -The website [compwa.github.io/strong2020-salamanca](https://compwa.github.io/strong2020-salamanca) is automatically generated from the notebooks in this repository using [Sphinx](https://www.sphinx-doc.org) and [MyST-NB](https://myst-nb.rtfd.io). You can also run the notebooks and build the documentation locally as follows: - -```shell -tox -e docnb -``` - -Alternatively, you can run the notebooks without building the documentation with - -```shell -tox -e nb -``` - -or build the documentation without running the notebooks with - -```shell -tox -e doc -``` +See [`CONTRIBUTING.md`](CONTRIBUTING.md) for information on how to contribute to this repository. diff --git a/docs/index.md b/docs/index.md index 11a3094..3f9baa7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,5 @@ :::{include} ../README.md +:end-before: See [`CONTRIBUTING.md` ::: ## Table of contents diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 31ee388..0000000 --- a/environment.yml +++ /dev/null @@ -1,6 +0,0 @@ -name: strong2020-salamanca -dependencies: - - python==3.12.* - - pip - - pip: - - -c .constraints/py3.12.txt -e .[dev] diff --git a/pyproject.toml b/pyproject.toml index 1fc89f4..e58bf6b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,20 +10,6 @@ authors = [ {name = "Common Partial Wave Analysis", email = "compwa-admin@ep1.rub.de"}, {name = "STRONG2020"}, ] -classifiers = [ - "Development Status :: 4 - Beta", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python", - "Topic :: Scientific/Engineering :: Physics", - "Topic :: Scientific/Engineering", -] description = "Jupyter notebooks for the STRONG2020 school in Salamanca, 2023" dynamic = ["version"] name = "strong2020-salamanca" @@ -49,46 +35,97 @@ doc = [ "sphinx-exercise", "sphinx-togglebutton", ] -format = [ - "black", - "isort", -] jupyter = [ - "isort", "jupyterlab", - "jupyterlab-code-formatter", + "jupyterlab-code-formatter >=3.0.0", "jupyterlab-git", "jupyterlab-lsp", "jupyterlab-myst", "python-lsp-ruff", - "python-lsp-server[flake8,rope]", + "python-lsp-server[rope]", "python-lsp-server[rope]", ] sty = [ - "pre-commit", + "pre-commit-uv", + "ruff", "strong2020-salamanca[format]", ] test = ["nbmake"] -[tool.pixi.project] -channels = ["conda-forge"] -platforms = ["linux-64"] +[tool.ruff] +extend-include = ["*.ipynb"] +preview = true +show-fixes = true + +[tool.ruff.format] +docstring-code-format = true +line-ending = "lf" + +[tool.ruff.lint] +ignore = [ + "ANN401", + "COM812", + "CPY001", + "D101", + "D102", + "D103", + "D105", + "D107", + "D203", + "D213", + "D407", + "D416", + "DOC", + "E501", + "FURB101", + "FURB103", + "FURB140", + "G004", + "ISC001", + "PLW1514", + "PT001", + "PTH", + "SIM108", +] +select = ["ALL"] +task-tags = ["cspell"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = ["display"] + +[tool.ruff.lint.flake8-comprehensions] +allow-dict-calls-with-keyword-arguments = true -[tool.pixi.activation.env] -PRETTIER_LEGACY_CLI = "1" +[tool.ruff.lint.isort] +split-on-trailing-comma = false -[tool.pixi.dependencies] -python = "3.12.*" +[tool.ruff.lint.per-file-ignores] +"*.ipynb" = [ + "ANN", + "B018", + "C90", + "D", + "E303", + "E703", + "N806", + "N816", + "PLR09", + "PLR2004", + "PLW0602", + "PLW0603", + "S101", + "T20", + "TCH00", +] +"docs/*" = [ + "INP001", + "S101", + "S113", +] +"docs/conf.py" = ["D100"] -[tool.pixi.environments] -default = {features = [ - "dev", - "doc", - "format", - "jupyter", - "sty", - "test", -]} +[tool.ruff.lint.pydocstyle] +convention = "google" [tool.tomlsort] all = false @@ -105,103 +142,90 @@ trailing_comma_inline_array = true [tool.tox] legacy_tox_ini = """ - [tox] - envlist = - doc, - sty, - skip_install = True - skip_missing_interpreters = True - skipsdist = True - - [testenv:doc] - allowlist_externals = - sphinx-build - commands = - sphinx-build \ - --keep-going \ - -TW \ - -b html \ - docs/ docs/_build/html - description 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setenv = - EXECUTE_NB = yes - FORCE_COLOR = yes - - [testenv:docnb-force] - allowlist_externals = - sphinx-build - commands = - sphinx-build -nW --keep-going -b html docs/ docs/_build/html - description = - Execute ALL Jupyter notebooks and build documentation with Sphinx - passenv = * - setenv = - FORCE_COLOR = yes - FORCE_EXECUTE_NB = yes - - [testenv:nb] - allowlist_externals = - pytest - commands = - pytest --nbmake {posargs:docs} - description = - Run all notebooks with pytest - passenv = * - setenv = - - [testenv:sty] - allowlist_externals = - pre-commit - commands = - pre-commit run {posargs} -a - description = - Perform all linting, formatting, and spelling checks +[tox] +envlist = + docnb-force, + linkcheck, + sty, +skip_install = True +skip_missing_interpreters = True +skipsdist = True + +[testenv] +passenv = * +setenv = + PYTHONHASHSEED = 0 + +[testenv:doc] +allowlist_externals = + sphinx-build +commands = + sphinx-build \ + --builder=html \ + --fail-on-warning \ + 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docs/lecture12d-phasespace.ipynb | 2 +- docs/lecture12e-longitudinal.ipynb | 2 +- docs/lecture17.ipynb | 2 +- docs/lecture18.ipynb | 2 +- docs/lecture24.ipynb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/lecture02.ipynb b/docs/lecture02.ipynb index 54518c1..b5db661 100644 --- a/docs/lecture02.ipynb +++ b/docs/lecture02.ipynb @@ -27,7 +27,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy particle" + "!uv pip install -q gdown matplotlib numpy particle" ] }, { diff --git a/docs/lecture06-gammap.ipynb b/docs/lecture06-gammap.ipynb index f2d6636..100d587 100644 --- a/docs/lecture06-gammap.ipynb +++ b/docs/lecture06-gammap.ipynb @@ -31,7 +31,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas pylorentz scipy" + "!uv pip install -q gdown matplotlib numpy pandas pylorentz scipy" ] }, { diff --git a/docs/lecture06-nbarp.ipynb b/docs/lecture06-nbarp.ipynb index dfacc6e..bb24d40 100644 --- a/docs/lecture06-nbarp.ipynb +++ b/docs/lecture06-nbarp.ipynb @@ -31,7 +31,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas scipy" + "!uv pip install -q gdown matplotlib numpy pandas scipy" ] }, { diff --git a/docs/lecture09.ipynb b/docs/lecture09.ipynb index f5df3ab..b5aae56 100644 --- a/docs/lecture09.ipynb +++ b/docs/lecture09.ipynb @@ -17,7 +17,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown lmfit matplotlib numpy scipy" + "!uv pip install -q gdown lmfit matplotlib numpy scipy" ] }, { diff --git a/docs/lecture12a-gammap-solution.ipynb b/docs/lecture12a-gammap-solution.ipynb index 0db677b..37d899e 100755 --- a/docs/lecture12a-gammap-solution.ipynb +++ b/docs/lecture12a-gammap-solution.ipynb @@ -31,7 +31,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas pylorentz scipy" + "!uv pip install -q gdown matplotlib numpy pandas pylorentz scipy" ] }, { diff --git a/docs/lecture12b-kinematics.ipynb b/docs/lecture12b-kinematics.ipynb index f77b1f4..cf38ccd 100644 --- a/docs/lecture12b-kinematics.ipynb +++ b/docs/lecture12b-kinematics.ipynb @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas pylorentz scipy" + "!uv pip install -q gdown matplotlib numpy pandas pylorentz scipy" ] }, { diff --git a/docs/lecture12c-angles.ipynb b/docs/lecture12c-angles.ipynb index 9dd483f..0a23421 100644 --- a/docs/lecture12c-angles.ipynb +++ b/docs/lecture12c-angles.ipynb @@ -19,7 +19,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas pylorentz" + "!uv pip install -q gdown matplotlib numpy pandas pylorentz" ] }, { diff --git a/docs/lecture12d-phasespace.ipynb b/docs/lecture12d-phasespace.ipynb index aaaee3b..c5f52a4 100644 --- a/docs/lecture12d-phasespace.ipynb +++ b/docs/lecture12d-phasespace.ipynb @@ -31,7 +31,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy phasespace pylorentz tf-keras" + "!uv pip install -q gdown matplotlib numpy phasespace pylorentz tf-keras" ] }, { diff --git a/docs/lecture12e-longitudinal.ipynb b/docs/lecture12e-longitudinal.ipynb index 798d39d..18f9195 100644 --- a/docs/lecture12e-longitudinal.ipynb +++ b/docs/lecture12e-longitudinal.ipynb @@ -25,7 +25,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy pandas pylorentz" + "!uv pip install -q gdown matplotlib numpy pandas pylorentz" ] }, { diff --git a/docs/lecture17.ipynb b/docs/lecture17.ipynb index c2c02a6..d0a56c7 100755 --- a/docs/lecture17.ipynb +++ b/docs/lecture17.ipynb @@ -17,7 +17,7 @@ }, "outputs": [], "source": [ - "%pip install -q \"ampform>=0.14.8\" plotly sympy" + "!uv pip install -q \"ampform>=0.14.8\" plotly sympy" ] }, { diff --git a/docs/lecture18.ipynb b/docs/lecture18.ipynb index 0ffba78..d1c5642 100755 --- a/docs/lecture18.ipynb +++ b/docs/lecture18.ipynb @@ -24,7 +24,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown matplotlib numpy" + "!uv pip install -q gdown matplotlib numpy" ] }, { diff --git a/docs/lecture24.ipynb b/docs/lecture24.ipynb index 6140868..a437831 100644 --- a/docs/lecture24.ipynb +++ b/docs/lecture24.ipynb @@ -17,7 +17,7 @@ }, "outputs": [], "source": [ - "%pip install -q gdown iminuit import-ipynb sweights\n", + "!uv pip install -q gdown iminuit import-ipynb sweights\n", "from IPython.display import display" ] }, From a3fad40aff51784e81c50a6df0c9b3a86a96bac6 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:27 +0200 Subject: [PATCH 08/33] MAINT: implement Ruff fixes and suggestions --- docs/conf.py | 14 +---- docs/lecture02.ipynb | 12 ++-- docs/lecture06-gammap.ipynb | 55 +++++------------ docs/lecture06-nbarp.ipynb | 28 +++------ docs/lecture09.ipynb | 45 +++++--------- docs/lecture12a-gammap-solution.ipynb | 63 +++++-------------- docs/lecture12b-kinematics.ipynb | 37 ++++------- docs/lecture12c-angles.ipynb | 2 +- docs/lecture12d-phasespace.ipynb | 2 +- docs/lecture12e-longitudinal.ipynb | 2 +- docs/lecture17.ipynb | 37 +++++------ docs/lecture18.ipynb | 2 +- docs/lecture24.ipynb | 39 ++++++------ docs/lecture24_utilities.ipynb | 19 +++--- pyproject.toml | 25 ++++++++ uv.lock | 89 +++++++++++++++++++-------- 16 files changed, 205 insertions(+), 266 deletions(-) mode change 100755 => 100644 docs/lecture12a-gammap-solution.ipynb mode change 100755 => 100644 docs/lecture17.ipynb mode change 100755 => 100644 docs/lecture18.ipynb diff --git a/docs/conf.py b/docs/conf.py index 5c32f1c..4363722 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,14 +1,4 @@ -import os - - -def get_execution_mode() -> str: - if "FORCE_EXECUTE_NB" in os.environ: - print("\033[93;1mWill run ALL Jupyter notebooks!\033[0m") - return "force" - if "EXECUTE_NB" in os.environ: - return "cache" - return "off" - +from sphinx_api_relink.helpers import get_execution_mode REPO_NAME = "strong2020-salamanca" BRANCH = "main" @@ -20,7 +10,7 @@ def get_execution_mode() -> str: } copybutton_prompt_is_regexp = True copybutton_prompt_text = r">>> |\.\.\. " # doctest -copyright = "2023" +copyright = "2023" # noqa: A001 exclude_patterns = [ "_build", "lecture24_utilities.ipynb", diff --git a/docs/lecture02.ipynb b/docs/lecture02.ipynb index b5db661..b65d97a 100644 --- a/docs/lecture02.ipynb +++ b/docs/lecture02.ipynb @@ -157,13 +157,11 @@ " mass: float, delta: float = 0.001, charge: float | None = None\n", ") -> list[Particle]:\n", " def identify(p) -> bool:\n", - " if p.pdgid in {21}:\n", - " return\n", + " if p.pdgid == 21:\n", + " return None\n", " if charge is not None and p.charge != charge:\n", " return False\n", - " if (mass - delta) < 1e-3 * p.mass < (mass + delta):\n", - " return True\n", - " return False\n", + " return mass - delta < 0.001 * p.mass < mass + delta\n", "\n", " return Particle.findall(identify)\n", "\n", @@ -307,7 +305,7 @@ "metadata": {}, "outputs": [], "source": [ - "m12_mean = m12[(s12 < 3) & (2.5 < s23) & (s23 < 10)].mean()\n", + "m12_mean = m12[(s12 < 3) & (s23 > 2.5) & (s23 < 10)].mean()\n", "m12_mean**2" ] }, @@ -558,7 +556,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture06-gammap.ipynb b/docs/lecture06-gammap.ipynb index 100d587..c87e8e8 100644 --- a/docs/lecture06-gammap.ipynb +++ b/docs/lecture06-gammap.ipynb @@ -623,8 +623,7 @@ "low_edge = 0.015\n", "up_edge = 0.035\n", "hist, bin_edges = np.histogram(missingMomentum.p, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -661,9 +660,7 @@ "fig = plt.figure()\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", "# this plots the curve only\n", - "plt.plot(\n", - " x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\"\n", - ")\n", + "plt.plot(x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\")\n", "plt.legend()\n", "\n", "# plot the experimental point of the portion of spectrum to be fitted\n", @@ -671,10 +668,6 @@ "\n", "# Normalise the histogram values\n", "weights = np.ones_like(y_hist) / y_hist.size\n", - "# plt.hist(x_hist, weights=weights)\n", - "# plt.hist(x_hist)\n", - "# plt.hist(hist)\n", - "\n", "\n", "# setting the label,title and grid of the plot\n", "plt.xlabel(\"Data: Random variable\")\n", @@ -712,8 +705,7 @@ " iup = ii\n", "\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "histfull = histfull.astype(float) / histfull.sum()\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -743,8 +735,7 @@ "low_edge = -0.001\n", "up_edge = 0.0\n", "hist, bin_edges = np.histogram(missingMomentum.m2, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -775,9 +766,7 @@ "fig = plt.figure()\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", "# this plots the curve only\n", - "plt.plot(\n", - " x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\"\n", - ")\n", + "plt.plot(x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\")\n", "plt.legend()\n", "\n", "# plot the experimental point of the portion of spectrum to be fitted\n", @@ -812,8 +801,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull.astype(float) / histfull.sum()\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -849,8 +837,7 @@ "low_edge = -0.0007\n", "up_edge = 0.0001\n", "hist, bin_edges = np.histogram(missingMomentum.m2, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -860,8 +847,6 @@ "y_hist = hist\n", "mean = sum(x_hist * y_hist) / sum(y_hist)\n", "sigma = sum(y_hist * (x_hist - mean) ** 2) / sum(y_hist)\n", - "# mean = mean1Fit\n", - "# sigma = sigma1Fit\n", "P1 = 0.0\n", "P2 = 0.0\n", "P3 = 0.0\n", @@ -900,13 +885,8 @@ "\n", "param_optimised_gauss = []\n", "param_optimised_bck = []\n", - "param_optimised_gauss.append(param_optimised[0])\n", - "param_optimised_gauss.append(param_optimised[1])\n", - "param_optimised_gauss.append(param_optimised[2])\n", - "param_optimised_bck.append(param_optimised[3])\n", - "param_optimised_bck.append(param_optimised[4])\n", - "param_optimised_bck.append(param_optimised[5])\n", - "param_optimised_bck.append(param_optimised[6])\n", + "param_optimised_gauss.extend(param_optimised[0:3])\n", + "param_optimised_bck.extend(param_optimised[3:7])\n", "\n", "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(7, 4))\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", @@ -937,8 +917,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull.astype(float) / histfull.sum()\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -980,11 +959,8 @@ "# normalize the histogram to 1\n", "low_edge = 0.8\n", "up_edge = 1.0\n", - "hist, bin_edges = np.histogram(\n", - " missingMomentumDipion.m2, 100, range=(low_edge, up_edge)\n", - ")\n", - "integral_hist = np.sum(hist)\n", - "hist = hist / integral_hist\n", + "hist, bin_edges = np.histogram(missingMomentumDipion.m2, 100, range=(low_edge, up_edge))\n", + "hist = hist.astype(float) / np.sum(hist)\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -994,8 +970,6 @@ "y_hist = hist\n", "mean = sum(x_hist * y_hist) / sum(y_hist)\n", "sigma = sum(y_hist * (x_hist - mean) ** 2) / sum(y_hist)\n", - "# mean = mean1Fit\n", - "# sigma = sigma1Fit\n", "P1 = 0.0\n", "P2 = 0.0\n", "P3 = 0.0\n", @@ -1071,8 +1045,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull.astype(float) / histfull.sum()\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -1105,7 +1078,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture06-nbarp.ipynb b/docs/lecture06-nbarp.ipynb index bb24d40..7f50cee 100644 --- a/docs/lecture06-nbarp.ipynb +++ b/docs/lecture06-nbarp.ipynb @@ -371,7 +371,6 @@ "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(7, 4))\n", "ax[0].hist2d(invariant_massSquared13, invariant_massSquared12, bins=100, cmap=\"jet\")\n", "ax[0].hist2d(invariant_massSquared23, invariant_massSquared12, bins=100, cmap=\"jet\")\n", - "# ax[0].colorbar()\n", "ax[0].set_xlabel(R\"i.m.$^2(\\pi^+_{(1,2)}\\pi^-_{3}$) [GeV$^2$]\")\n", "ax[0].set_ylabel(R\"i.m.$^2(\\pi^+\\pi^+$) [GeV$^2$]\")\n", "ax[1].hist2d(invariant_massSquared13, invariant_massSquared23, bins=100, cmap=\"jet\")\n", @@ -455,21 +454,12 @@ "outputs": [], "source": [ "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(7, 4))\n", - "ax[0].hist2d(\n", - " invariant_massSquared13mc, invariant_massSquared12mc, bins=100, cmap=\"jet\"\n", - ")\n", - "ax[0].hist2d(\n", - " invariant_massSquared23mc, invariant_massSquared12mc, bins=100, cmap=\"jet\"\n", - ")\n", - "# ax[0].colorbar()\n", + "ax[0].hist2d(invariant_massSquared13mc, invariant_massSquared12mc, bins=100, cmap=\"jet\")\n", + "ax[0].hist2d(invariant_massSquared23mc, invariant_massSquared12mc, bins=100, cmap=\"jet\")\n", "ax[0].set_xlabel(R\"i.m.$^2(\\pi^+_{(1,2)}\\pi^-_{3}$) [GeV$^2$]\")\n", "ax[0].set_ylabel(R\"i.m.$^2(\\pi^+\\pi^+$) [GeV$^2$]\")\n", - "ax[1].hist2d(\n", - " invariant_massSquared13mc, invariant_massSquared23mc, bins=100, cmap=\"jet\"\n", - ")\n", - "ax[1].hist2d(\n", - " invariant_massSquared23mc, invariant_massSquared13mc, bins=100, cmap=\"jet\"\n", - ")\n", + "ax[1].hist2d(invariant_massSquared13mc, invariant_massSquared23mc, bins=100, cmap=\"jet\")\n", + "ax[1].hist2d(invariant_massSquared23mc, invariant_massSquared13mc, bins=100, cmap=\"jet\")\n", "ax[1].set_xlabel(R\"i.m.$^2(\\pi^+_1\\pi^-$) [GeV$^2$]\")\n", "ax[1].set_ylabel(R\"i.m.$^2(\\pi^+_2\\pi^-$) [GeV$^2$]\")\n", "plt.show()" @@ -622,13 +612,13 @@ "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(9, 4))\n", "h0 = ax[0].hist2d(xmc, ymc, bins=100, cmap=\"rainbow\")\n", "fig.colorbar(h0[3], ax=ax[0])\n", - "ax[0].set_xlabel(\"$x_{mc}$\")\n", - "ax[0].set_ylabel(\"$y_{mc}$\")\n", + "ax[0].set_xlabel(\"$x_{mc}$\") # noqa: RUF027\n", + "ax[0].set_ylabel(\"$y_{mc}$\") # noqa: RUF027\n", "ax[0].set_title(R\"$\\pi^-_3$ vs $\\pi^+_1\\pi^+_2$ kin. energies DP\")\n", "h1 = ax[1].hist2d(x2entriesmc, y2entriesmc, bins=100, cmap=\"rainbow\")\n", "fig.colorbar(h1[3], ax=ax[1])\n", - "ax[1].set_xlabel(\"$x_{mc}$\")\n", - "ax[1].set_ylabel(\"$y_{mc}$\")\n", + "ax[1].set_xlabel(\"$x_{mc}$\") # noqa: RUF027\n", + "ax[1].set_ylabel(\"$y_{mc}$\") # noqa: RUF027\n", "ax[1].set_title(R\"$\\pi^+_{1,2}$ vs $\\pi^+_{2,1}\\pi^-_3$ kin. energies DP\")\n", "plt.show()" ] @@ -653,7 +643,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture09.ipynb b/docs/lecture09.ipynb index b5aae56..83a4cdf 100644 --- a/docs/lecture09.ipynb +++ b/docs/lecture09.ipynb @@ -40,11 +40,11 @@ "import matplotlib.pyplot as plt\n", "import numpy as np\n", "import scipy.optimize as opt\n", - "import scipy.stats as stats\n", "from lmfit import Model\n", "from lmfit.models import ExpressionModel\n", "from matplotlib.colors import BoundaryNorm\n", "from matplotlib.ticker import MaxNLocator\n", + "from scipy import stats\n", "from scipy.stats import chi2, norm" ] }, @@ -1473,7 +1473,7 @@ "source": [ "fig, ax = plt.subplots(figsize=(5, 3.75))\n", "fig.subplots_adjust(bottom=0.12)\n", - "for k, ls in zip(k_values, linestyles):\n", + "for k, ls in zip(k_values, linestyles, strict=True):\n", " dist = chi2(k)\n", " res = plt.plot(x, dist.pdf(x), ls=ls, c=\"black\", label=f\"$k={k}$\")\n", "plt.xlim(0, 10)\n", @@ -1556,16 +1556,6 @@ "Covariance is a measure of the relationship between two random variables. The metric evaluates how much – to what extent – the variables change together (but not the strength of the relationship)." ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# Select a random seed so we can all generate the same sample\n", - "np.random.seed(123)" - ] - }, { "cell_type": "code", "execution_count": null, @@ -1582,9 +1572,10 @@ "\n", "# Generate some synthetic data from the model.\n", "N = 50\n", - "x = np.sort(10 * np.random.rand(N))\n", + "rng = np.random.default_rng()\n", + "x = np.sort(10 * rng.standard_normal(N))\n", "y = m_true * x + c_true\n", - "y += np.random.randn(N)\n", + "y += rng.standard_normal(N)\n", "plt.errorbar(x, y, fmt=\".k\", capsize=0)\n", "starting_values = np.linspace(0, 10, num=500)\n", "plt.xlim(0, 10)\n", @@ -1941,11 +1932,11 @@ " return np.sin(a * x)\n", "\n", "\n", - "np.random.seed(123)\n", + "rng = np.random.default_rng(seed=123)\n", "n_points = 50\n", "x = np.linspace(0, 20, num=n_points)\n", - "y = (np.sin(x / 3) + np.random.normal(np.sin(x / 3), 0.2)) / 2\n", - "y_error = np.random.normal(0.1, 0.02, size=n_points)" + "y = (np.sin(x / 3) + rng.normal(np.sin(x / 3), 0.2)) / 2\n", + "y_error = rng.normal(0.1, 0.02, size=n_points)" ] }, { @@ -2126,7 +2117,6 @@ "outputs": [], "source": [ "residual = y - result.best_fit\n", - "# plt.plot(x, residual, 'bo', label='Residuals')\n", "fig, ax = plt.subplots()\n", "ax.stem(x, residual, markerfmt=\" \")\n", "plt.xlabel(\"x\")\n", @@ -2148,7 +2138,6 @@ "outputs": [], "source": [ "residualUnc = (y - result.best_fit) / y_error\n", - "# plt.plot(x, residual, 'bo', label='Residuals')\n", "fig, ax = plt.subplots()\n", "ax.stem(x, residualUnc, markerfmt=\" \")\n", "plt.xlabel(\"x\")\n", @@ -2199,9 +2188,7 @@ " else:\n", " errcounts.append(10)\n", "# Why do we do the above, i.e. setting zero values with large uncertainties?\n", - "xvals = []\n", - "for i in range(len(xbins) - 1):\n", - " xvals.append((xbins[i] + xbins[i + 1]) / 2)\n", + "xvals = [(xbins[i] + xbins[i + 1]) / 2 for i in range(len(xbins) - 1)]\n", "plt.errorbar(xvals, counts, errcounts, ls=\"\", marker=\".\")\n", "plt.xlabel(\"residual\")\n", "plt.ylabel(\"counts\")\n", @@ -2241,11 +2228,10 @@ "metadata": {}, "outputs": [], "source": [ - "np.random.seed(32)\n", - "\n", + "rng = np.random.default_rng(seed=32)\n", "sample_size = 20\n", "x = np.linspace(1, 10, num=sample_size)\n", - "y = np.vectorize(lambda z: np.random.poisson(13 * np.exp(-z / 3)))(x)\n", + "y = np.vectorize(lambda z: rng.poisson(13 * np.exp(-z / 3)))(x)\n", "y" ] }, @@ -2268,7 +2254,6 @@ "source": [ "# We generate noisy data on integer values of x to mimick the idea of bins and low-statistics...\n", "plt.errorbar(data_x, data_y, data_y_err, ls=\"\", marker=\".\")\n", - "# plt.plot(x,y,'o',label=\"data\")\n", "plt.xlabel(\"t\")\n", "plt.ylabel(\"counts\")\n", "plt.show()" @@ -2340,7 +2325,7 @@ "def chi2(a, b):\n", " return sum(\n", " ((y - func(x, a, b)) ** 2) / (ey**2)\n", - " for x, y, ey in zip(data_x, data_y, data_y_err)\n", + " for x, y, ey in zip(data_x, data_y, data_y_err, strict=True)\n", " )" ] }, @@ -2416,7 +2401,7 @@ " a, b = param\n", " return sum(\n", " 2 * (func(x, a, b) - y * np.log(func(x, a, b)))\n", - " for x, y in zip(data_x, data_y)\n", + " for x, y in zip(data_x, data_y, strict=True)\n", " )" ] }, @@ -2961,7 +2946,7 @@ " quiet=True,\n", ")\n", "with open(output_path) as f:\n", - " values = [float(line) for line in f.readlines()]" + " values = [float(line) for line in f]" ] }, { @@ -3179,7 +3164,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.13" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture12a-gammap-solution.ipynb b/docs/lecture12a-gammap-solution.ipynb old mode 100755 new mode 100644 index 37d899e..c57c649 --- a/docs/lecture12a-gammap-solution.ipynb +++ b/docs/lecture12a-gammap-solution.ipynb @@ -310,9 +310,7 @@ "source": [ "# @title Solution\n", "plt.hist(invariant_mass_13, bins=200, color=\"tomato\", range=(1.0, 2.0))\n", - "plt.hist(\n", - " invariant_mass_23, bins=200, color=\"darkmagenta\", alpha=0.4, range=(1.0, 2.0)\n", - ")\n", + "plt.hist(invariant_mass_23, bins=200, color=\"darkmagenta\", alpha=0.4, range=(1.0, 2.0))\n", "plt.xlabel(\"Invariant mass [GeV]\")\n", "plt.ylabel(\"Entries/(5 MeV)\")\n", "plt.show()" @@ -511,9 +509,7 @@ "ax[0].set_ylabel(\"Entries/(12 MeV)\")\n", "ax[0].set_title(\"($\\\\pi^+\\\\pi^-$) i.m. \\n\")\n", "# plot the histogram pi+p\n", - "ax[1].hist(\n", - " np.sqrt(inv_mass_squared_13_mc), color=\"tomato\", bins=100, range=(1.0, 2.0)\n", - ")\n", + "ax[1].hist(np.sqrt(inv_mass_squared_13_mc), color=\"tomato\", bins=100, range=(1.0, 2.0))\n", "ax[1].set_xlabel(R\"($\\pi^+p$) Invariant mass [GeV]\")\n", "ax[1].set_ylabel(\"Entries/(10 MeV)\")\n", "ax[1].set_title(\"($\\\\pi^+p$) i.m. \\n\")\n", @@ -748,8 +744,7 @@ "low_edge = 0.015\n", "up_edge = 0.035\n", "hist, bin_edges = np.histogram(missingMomentum.p, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -786,9 +781,7 @@ "fig = plt.figure()\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", "# this plots the curve only\n", - "plt.plot(\n", - " x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\"\n", - ")\n", + "plt.plot(x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\")\n", "plt.legend()\n", "\n", "# plot the experimental point of the portion of spectrum to be fitted\n", @@ -796,10 +789,6 @@ "\n", "# Normalise the histogram values\n", "weights = np.ones_like(y_hist) / y_hist.size\n", - "# plt.hist(x_hist, weights=weights)\n", - "# plt.hist(x_hist)\n", - "# plt.hist(hist)\n", - "\n", "\n", "# setting the label,title and grid of the plot\n", "plt.xlabel(\"Data: Random variable\")\n", @@ -837,8 +826,7 @@ " iup = ii\n", "\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull / histfull.sum().astype(float)\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -868,8 +856,7 @@ "low_edge = -0.001\n", "up_edge = 0.0\n", "hist, bin_edges = np.histogram(missingMomentum.m2, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -900,9 +887,7 @@ "fig = plt.figure()\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", "# this plots the curve only\n", - "plt.plot(\n", - " x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\"\n", - ")\n", + "plt.plot(x_hist_2, gaus(x_hist_2, *param_optimised), color=\"red\", label=\"Gaussian fit\")\n", "plt.legend()\n", "\n", "# plot the experimental point of the portion of spectrum to be fitted\n", @@ -937,8 +922,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull / histfull.sum().astype(float)\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -974,8 +958,7 @@ "low_edge = -0.0007\n", "up_edge = 0.0001\n", "hist, bin_edges = np.histogram(missingMomentum.m2, 100, range=(low_edge, up_edge))\n", - "integral_hist = sum(hist)\n", - "hist = hist / integral_hist\n", + "hist = hist.astype(float) / hist.sum()\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -985,8 +968,6 @@ "y_hist = hist\n", "mean = sum(x_hist * y_hist) / sum(y_hist)\n", "sigma = sum(y_hist * (x_hist - mean) ** 2) / sum(y_hist)\n", - "# mean = mean1Fit\n", - "# sigma = sigma1Fit\n", "P1 = 0.0\n", "P2 = 0.0\n", "P3 = 0.0\n", @@ -1025,13 +1006,8 @@ "\n", "param_optimised_gauss = []\n", "param_optimised_bck = []\n", - "param_optimised_gauss.append(param_optimised[0])\n", - "param_optimised_gauss.append(param_optimised[1])\n", - "param_optimised_gauss.append(param_optimised[2])\n", - "param_optimised_bck.append(param_optimised[3])\n", - "param_optimised_bck.append(param_optimised[4])\n", - "param_optimised_bck.append(param_optimised[5])\n", - "param_optimised_bck.append(param_optimised[6])\n", + "param_optimised_gauss.extend(param_optimised[0:3])\n", + "param_optimised_bck.extend(param_optimised[3:7])\n", "\n", "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(7, 4))\n", "x_hist_2 = np.linspace(np.min(x_hist), np.max(x_hist), 100)\n", @@ -1062,8 +1038,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull / histfull.sum().astype(float)\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -1105,11 +1080,8 @@ "# normalize the histogram to 1\n", "low_edge = 0.8\n", "up_edge = 1.0\n", - "hist, bin_edges = np.histogram(\n", - " missingMomentumDipion.m2, 100, range=(low_edge, up_edge)\n", - ")\n", - "integral_hist = np.sum(hist)\n", - "hist = hist / integral_hist\n", + "hist, bin_edges = np.histogram(missingMomentumDipion.m2, 100, range=(low_edge, up_edge))\n", + "hist = hist.astype(float) / np.sum(hist)\n", "\n", "n = hist.size\n", "x_hist = np.zeros((n), dtype=float)\n", @@ -1119,8 +1091,6 @@ "y_hist = hist\n", "mean = sum(x_hist * y_hist) / sum(y_hist)\n", "sigma = sum(y_hist * (x_hist - mean) ** 2) / sum(y_hist)\n", - "# mean = mean1Fit\n", - "# sigma = sigma1Fit\n", "P1 = 0.0\n", "P2 = 0.0\n", "P3 = 0.0\n", @@ -1196,8 +1166,7 @@ "for ii in range(n):\n", " xf_hist[ii] = (bin_edgesf[ii + 1] + bin_edgesf[ii]) / 2\n", "\n", - "integralFull = sum(histfull)\n", - "histfull = histfull / integralFull\n", + "integralFull = histfull / histfull.sum().astype(float)\n", "yf_hist = histfull\n", "histfull = histfull * np.max(y_hist) / np.max(yf_hist)\n", "yf_hist = histfull\n", @@ -1230,7 +1199,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture12b-kinematics.ipynb b/docs/lecture12b-kinematics.ipynb index cf38ccd..e786a06 100644 --- a/docs/lecture12b-kinematics.ipynb +++ b/docs/lecture12b-kinematics.ipynb @@ -185,21 +185,13 @@ "outputs": [], "source": [ "fig, ax = plt.subplots(1, 2, tight_layout=True, figsize=(9, 4))\n", - "h0 = ax[0].hist2d(\n", - " invariantMassSquared13, invariantMassSquared12, bins=100, cmap=\"jet\"\n", - ")\n", - "h0 = ax[0].hist2d(\n", - " invariantMassSquared23, invariantMassSquared12, bins=100, cmap=\"jet\"\n", - ")\n", + "h0 = ax[0].hist2d(invariantMassSquared13, invariantMassSquared12, bins=100, cmap=\"jet\")\n", + "h0 = ax[0].hist2d(invariantMassSquared23, invariantMassSquared12, bins=100, cmap=\"jet\")\n", "fig.colorbar(h0[3], ax=ax[0])\n", "ax[0].set_xlabel(R\"i.m.$^2(\\pi^+_{(1,2)}\\pi^-_{3}$) [GeV$^2$]\")\n", "ax[0].set_ylabel(R\"i.m.$^2(\\pi^+\\pi^+$) [GeV$^2$]\")\n", - "h1 = ax[1].hist2d(\n", - " invariantMassSquared13, invariantMassSquared23, bins=100, cmap=\"jet\"\n", - ")\n", - "h1 = ax[1].hist2d(\n", - " invariantMassSquared23, invariantMassSquared13, bins=100, cmap=\"jet\"\n", - ")\n", + "h1 = ax[1].hist2d(invariantMassSquared13, invariantMassSquared23, bins=100, cmap=\"jet\")\n", + "h1 = ax[1].hist2d(invariantMassSquared23, invariantMassSquared13, bins=100, cmap=\"jet\")\n", "fig.colorbar(h1[3], ax=ax[1])\n", "ax[1].set_xlabel(R\"i.m.$^2(\\pi^+_1\\pi^-$) [GeV$^2$]\")\n", "ax[1].set_ylabel(R\"i.m.$^2(\\pi^+_2\\pi^-$) [GeV$^2$]\")\n", @@ -370,15 +362,11 @@ "source": [ "fig, ax = plt.subplots(2, 2, tight_layout=True, figsize=(9, 4))\n", "ax[0, 0].hist(u_lab_1, bins=100, color=\"HotPink\")\n", - "ax[0, 0].set_xlabel(\n", - " R\"u = $(p_{nbar} - p_{\\pi^+_2})^2$ lab RF [$(\\mathrm{GeV}/c^2)^2$]\"\n", - ")\n", + "ax[0, 0].set_xlabel(R\"u = $(p_{nbar} - p_{\\pi^+_2})^2$ lab RF [$(\\mathrm{GeV}/c^2)^2$]\")\n", "ax[0, 1].hist(u_lab_2, bins=100, color=\"DeepPink\")\n", "ax[0, 1].set_xlabel(R\"u = $(p_p - p_D)^2$ lab RF [$(\\mathrm{GeV}/c^2)^2$]\")\n", "ax[1, 0].hist(u_cm_1, bins=100, color=\"Fuchsia\")\n", - "ax[1, 0].set_xlabel(\n", - " R\"u = $(p_{nbar} - p_{\\pi^+_2})^2$ CM RF [$(\\mathrm{GeV}/c^2)^2$]\"\n", - ")\n", + "ax[1, 0].set_xlabel(R\"u = $(p_{nbar} - p_{\\pi^+_2})^2$ CM RF [$(\\mathrm{GeV}/c^2)^2$]\")\n", "ax[1, 1].hist(u_cm_2, bins=100, color=\"DarkMagenta\")\n", "ax[1, 1].set_xlabel(R\"u = $(p_p - p_D)^2$ CM RF [$(\\mathrm{GeV}/c^2)^2$]\")\n", "plt.show()" @@ -472,9 +460,10 @@ "ax[1].set_xlabel(R\"$\\mathrm{E}_{tot}(2\\pi^+\\pi^-)$ [GeV]\")\n", "ax[1].set_ylabel(R\"$\\mathrm{p}_{tot}(2\\pi^+\\pi^-)$ [GeV/c]\")\n", "# missing mass recoiling against the neutral dipion (2 entries/event)\n", - "all_missing_dipion = np.concatenate(\n", - " [recoiling_missing_mass1.m2, recoiling_missing_mass2.m2]\n", - ")\n", + "all_missing_dipion = np.concatenate([\n", + " recoiling_missing_mass1.m2,\n", + " recoiling_missing_mass2.m2,\n", + "])\n", "missingHisto = ax[2].hist(all_missing_dipion, bins=100, color=\"darkorange\")\n", "ax[2].set_xlabel(R\"m.m. recoiling against $(\\pi^+\\pi^-)$ [$(\\mathrm{GeV}/c^2)^2$]\")\n", "ax[2].xaxis.get_label().set_fontsize(8)\n", @@ -515,7 +504,7 @@ "\n", "# add a 'best fit' line\n", "y = norm.pdf(bins, mu, sigma)\n", - "l = plt.plot(bins, y, \"r--\", linewidth=2)\n", + "plt.plot(bins, y, \"r--\", linewidth=2)\n", "print(\"The missing mass in GeV/c^2 is: \", np.sqrt(mu))" ] }, @@ -535,7 +524,7 @@ "plt.xlabel(\"missing mass recoiling against the neutral dipion\")\n", "plt.ylabel(\"counts\")\n", "plt.title(Rf\"$\\mu={mu:.3f},\\ \\sigma={sigma:.3f}$\")\n", - "plt.grid(True)\n", + "plt.grid(True) # noqa: FBT003\n", "plt.hist(\n", " all_missing_dipion, 100, density=True, facecolor=\"orange\", histtype=\"barstacked\"\n", ")\n", @@ -562,7 +551,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture12c-angles.ipynb b/docs/lecture12c-angles.ipynb index 0a23421..958d5c0 100644 --- a/docs/lecture12c-angles.ipynb +++ b/docs/lecture12c-angles.ipynb @@ -366,7 +366,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture12d-phasespace.ipynb b/docs/lecture12d-phasespace.ipynb index c5f52a4..2fa2262 100644 --- a/docs/lecture12d-phasespace.ipynb +++ b/docs/lecture12d-phasespace.ipynb @@ -558,7 +558,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.14" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture12e-longitudinal.ipynb b/docs/lecture12e-longitudinal.ipynb index 18f9195..72bf4ce 100644 --- a/docs/lecture12e-longitudinal.ipynb +++ b/docs/lecture12e-longitudinal.ipynb @@ -245,7 +245,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture17.ipynb b/docs/lecture17.ipynb old mode 100755 new mode 100644 index d0a56c7..e855f0b --- a/docs/lecture17.ipynb +++ b/docs/lecture17.ipynb @@ -36,10 +36,9 @@ }, "outputs": [], "source": [ - "from __future__ import annotations\n", - "\n", "import warnings\n", - "from typing import Any, Callable\n", + "from collections.abc import Callable\n", + "from typing import Any\n", "\n", "import numpy as np\n", "import plotly.graph_objects as go\n", @@ -110,11 +109,12 @@ " Z = X + Y * 1j\n", " T = [f(Z) for f in funcs]\n", " if mask is not None:\n", - " the_mask = np.full(Z.shape, False)\n", + " the_mask = np.full(Z.shape, fill_value=False)\n", " for t in T:\n", " the_mask |= mask(Z, t)\n", " if np.all(the_mask):\n", - " raise ValueError(\"All points were masked away\")\n", + " msg = \"All points were masked away\"\n", + " raise ValueError(msg)\n", " X[the_mask] = np.nan\n", " Y[the_mask] = np.nan\n", " Z[the_mask] = np.nan\n", @@ -163,7 +163,7 @@ " else:\n", " x_res, y_res = resolution, resolution\n", " box_min, box_max = boundaries\n", - " if isinstance(box_max, (float, int)):\n", + " if isinstance(box_max, float | int):\n", " pos, r_max = box_min, box_max\n", " R, Θ = np.meshgrid(\n", " np.linspace(0, r_max, num=x_res),\n", @@ -183,13 +183,13 @@ "\n", "\n", "def cut_t(\n", - " cutoff: float | tuple[float, float]\n", + " cutoff: float | tuple[float, float],\n", ") -> Callable[[np.ndarray, np.ndarray], bool]:\n", " if isinstance(cutoff, tuple):\n", " re_cut, im_cut = cutoff\n", " else:\n", " re_cut, im_cut = cutoff, cutoff\n", - " return lambda z, t: (np.abs(t.real) > re_cut) | (np.abs(t.imag) > im_cut)" + " return lambda _, t: (np.abs(t.real) > re_cut) | (np.abs(t.imag) > im_cut)" ] }, { @@ -349,7 +349,7 @@ "plot_riemann_surfaces(\n", " funcs=[sp.lambdify(z, SignedSqrt(z).doit())],\n", " func_unicode=\"⁺√z\",\n", - " mask=lambda z, t: (np.abs(z.imag) < 1e-5) & (z.real > 0),\n", + " mask=lambda z, _: (np.abs(z.imag) < 1e-5) & (z.real > 0),\n", " resolution=(30, 301),\n", ")" ] @@ -481,7 +481,7 @@ " boundaries=(240 - 40j, 320 + 40j),\n", " colorize=False,\n", " resolution=(50, 401),\n", - " mask=lambda z, t: np.abs(z.imag) == 0,\n", + " mask=lambda z, _: np.abs(z.imag) == 0,\n", ")" ] }, @@ -526,7 +526,7 @@ " return f\"S_{{{number}}}({s})\"\n", "\n", " def evaluate(self) -> sp.Expr:\n", - " s, m, Mρ, GV, fπ, g0, sign = self.args\n", + " s, m, *_ = self.args\n", " return 1 - 2 * sp.I * Sigma(s, m) / (16 * sp.pi) * T(*self.args)\n", "\n", "\n", @@ -643,10 +643,7 @@ "outputs": [], "source": [ "T_exprs = [\n", - " T(s, m, Mρ, GV, fπ, g0, sign)\n", - " .doit()\n", - " .xreplace(substitutions)\n", - " .xreplace(substitutions)\n", + " T(s, m, Mρ, GV, fπ, g0, sign).doit().xreplace(substitutions).xreplace(substitutions)\n", " for sign in [-1, +1]\n", "]\n", "T_funcs = [sp.lambdify(s, expr) for expr in T_exprs]" @@ -683,9 +680,7 @@ " surfacecolor=t.imag,\n", ")\n", "Sn = go.Surface(x=X, y=Yn, z=Tn.real, **sty(Tn), name=\"Unphysical\")\n", - "Sp = go.Surface(\n", - " x=X, y=Yp, z=Tp.real, **sty(Tp), name=\"Physical\", colorbar_title=\"Re T\"\n", - ")\n", + "Sp = go.Surface(x=X, y=Yp, z=Tp.real, **sty(Tp), name=\"Physical\", colorbar_title=\"Re T\")\n", "y = Yp[0]\n", "z = x + y * 1j\n", "line = go.Scatter3d(\n", @@ -727,9 +722,7 @@ " surfacecolor=t.real,\n", ")\n", "Sn = go.Surface(x=X, y=Yn, z=Tn.imag, **sty(Tn), name=\"Unphysical\")\n", - "Sp = go.Surface(\n", - " x=X, y=Yp, z=Tp.imag, **sty(Tp), name=\"Physical\", colorbar_title=\"Im T\"\n", - ")\n", + "Sp = go.Surface(x=X, y=Yp, z=Tp.imag, **sty(Tp), name=\"Physical\", colorbar_title=\"Im T\")\n", "y = Yp[0]\n", "z = x + y * 1j\n", "line = go.Scatter3d(\n", @@ -770,7 +763,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.13" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture18.ipynb b/docs/lecture18.ipynb old mode 100755 new mode 100644 index d1c5642..cff258c --- a/docs/lecture18.ipynb +++ b/docs/lecture18.ipynb @@ -590,7 +590,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture24.ipynb b/docs/lecture24.ipynb index a437831..077801d 100644 --- a/docs/lecture24.ipynb +++ b/docs/lecture24.ipynb @@ -117,8 +117,7 @@ "import import_ipynb # noqa: F401\n", "import lecture24_utilities as s2020\n", "\n", - "s2020.about()\n", - "#!more /content/lecture24_utilities.ipynb" + "s2020.about()" ] }, { @@ -244,9 +243,7 @@ "# call utility function histSqrtErrorBars to raw histograms with error bars\n", "mass_hist = s2020.histSqrtErrorBars(mass, massbins, \"all\")\n", "sig_mass_hist = s2020.histSqrtErrorBars(mass[np.abs(state) == 1], massbins, \"signal\")\n", - "bg_mass_hist = s2020.histSqrtErrorBars(\n", - " mass[np.abs(state) == 2], massbins, \"background\"\n", - ")\n", + "bg_mass_hist = s2020.histSqrtErrorBars(mass[np.abs(state) == 2], massbins, \"background\")\n", "plt.legend(loc=\"upper right\")\n", "plt.show()" ] @@ -902,8 +899,7 @@ "para_bg_mass_hist = s2020.histSqrtErrorBars(mass[state == 2], massbins, \"background\")\n", "plt.plot(\n", " massbins,\n", - " BgMassNExt(massbins, bg_c1, bg_c2, bg_c3, bg_c4, bg_c5, Nminuit)[1]\n", - " / massbins.size,\n", + " BgMassNExt(massbins, bg_c1, bg_c2, bg_c3, bg_c4, bg_c5, Nminuit)[1] / massbins.size,\n", " \"r-\",\n", " label=\"best fit\",\n", ")\n", @@ -956,7 +952,7 @@ "metadata": {}, "outputs": [], "source": [ - "def CombinedMassNExt(xmass, smean, swidth, bc0, bc1, bc2, bc3, bc4, Ys, Yb):\n", + "def CombinedMassNExt(xmass, smean, swidth, bc0, bc1, bc2, bc3, bc4, Ys, Yb): # noqa: ARG001\n", " return (\n", " (Ys + Yb),\n", " Ys * SignalMassPDF(xmass, smean, swidth)\n", @@ -1102,7 +1098,7 @@ "jp-MarkdownHeadingCollapsed": true }, "source": [ - "## sPlots" + "## Plots" ] }, { @@ -1569,9 +1565,9 @@ "bt_sigmas = []\n", "\n", "# loop over Nboot samples\n", - "for bt in range(Nboot):\n", - " # use random choice to do sampling with replacements\n", - " phi_bt = np.random.choice(sig_pos_phi, Nsamp)\n", + "for _ in range(Nboot):\n", + " rng = np.random.default_rng()\n", + " phi_bt = rng.choice(sig_pos_phi, Nsamp)\n", "\n", " # and do the fit for this bootstrap sample\n", " btmi = Minuit(UnbinnedNLL(phi_bt, PhotonAsymmetryPDF), Sigma=-0.5)\n", @@ -1675,8 +1671,9 @@ "# so we instead choose to sample the array indices\n", "all_indices = np.arange(Nk)\n", "\n", - "for bt in range(Nboot):\n", - " indices_bt = np.random.choice(all_indices, Nsamp)\n", + "for _ in range(Nboot):\n", + " rng = np.random.default_rng()\n", + " indices_bt = rng.choice(all_indices, Nsamp)\n", " wgts_bt = sweighter.get_weight(0, pos_mass[indices_bt])\n", " # now need to create nll\n", " btnll = lambda Sigma: PhotonAsymWeightedNLL(Sigma, pos_phi[indices_bt], wgts_bt)\n", @@ -1793,9 +1790,7 @@ }, { "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true - }, + "metadata": {}, "source": [ "### Toy Acceptance Model" ] @@ -1822,7 +1817,8 @@ " condarr = data array with which to test the acceptance (does not have to be same as darr)\n", " acc_func = takes a data array and returns a probability of being accepted for each entry\n", " \"\"\"\n", - " rands = np.random.uniform(0, 1, condarr.size)\n", + " rng = np.random.default_rng()\n", + " rands = rng.uniform(0, 1, condarr.size)\n", " mask = rands[:] < acc_func(condarr)\n", " return darr[mask]\n", "\n", @@ -2037,8 +2033,9 @@ " bt_sigmas = []\n", "\n", " # bootstrap loop : sample, fit, store\n", - " for bt in range(Nboot):\n", - " phi_bt = np.random.choice(all_data, Nsamp)\n", + " for _ in range(Nboot):\n", + " rng = np.random.default_rng()\n", + " phi_bt = rng.choice(all_data, Nsamp)\n", " btmi = Minuit(nll(phi_bt), Sigma=0)\n", " btmi.migrad()\n", " bt_sigmas.append(btmi.values[0])\n", @@ -2134,7 +2131,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.13" + "version": "3.12.6" } }, "nbformat": 4, diff --git a/docs/lecture24_utilities.ipynb b/docs/lecture24_utilities.ipynb index 1bd40e6..dec1c22 100644 --- a/docs/lecture24_utilities.ipynb +++ b/docs/lecture24_utilities.ipynb @@ -37,11 +37,10 @@ "outputs": [], "source": [ "def histSqrtErrorBars(data, xbins, lab):\n", - " binvals, edges = np.histogram(data, bins=xbins)\n", + " binvals, _ = np.histogram(data, bins=xbins)\n", " errs = np.sqrt(binvals)\n", " bincenters = (xbins[1:] + xbins[:-1]) / 2\n", - " histo = plt.errorbar(bincenters, binvals, errs, linewidth=1, fmt=\".\", label=lab)\n", - " return histo" + " return plt.errorbar(bincenters, binvals, errs, linewidth=1, fmt=\".\", label=lab)" ] }, { @@ -58,22 +57,18 @@ "outputs": [], "source": [ "def histWeightsSqrtErrorBars(data, wgts, xbins, lab):\n", - " binvals, edges = np.histogram(data, weights=wgts, bins=xbins)\n", + " binvals, _ = np.histogram(data, weights=wgts, bins=xbins)\n", " errs = np.sqrt(binvals)\n", " bincenters = (xbins[1:] + xbins[:-1]) / 2\n", - " histo = plt.errorbar(bincenters, binvals, errs, linewidth=1, fmt=\".\", label=lab)\n", - " return histo\n", + " return plt.errorbar(bincenters, binvals, errs, linewidth=1, fmt=\".\", label=lab)\n", "\n", "\n", "def histWeightedErrorBars(data, wgts, xbins, lab, offset=0):\n", - " sumweights, edges = np.histogram(data, weights=wgts, bins=xbins)\n", - " sumweight_sqrd, edges = np.histogram(data, weights=wgts * wgts, bins=xbins)\n", + " sumweights, _ = np.histogram(data, weights=wgts, bins=xbins)\n", + " sumweight_sqrd, _ = np.histogram(data, weights=wgts * wgts, bins=xbins)\n", " errs = np.sqrt(sumweight_sqrd)\n", " bincenters = (xbins[1:] + xbins[:-1]) / 2 + offset\n", - " histo = plt.errorbar(\n", - " bincenters, sumweights, errs, linewidth=1, fmt=\".\", label=lab\n", - " )\n", - " return histo" + " return plt.errorbar(bincenters, sumweights, errs, linewidth=1, fmt=\".\", label=lab)" ] } ], diff --git a/pyproject.toml b/pyproject.toml index ef895a3..704e96b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,7 @@ doc = [ "ipympl", "myst-nb", "sphinx", + "sphinx-api-relink", "sphinx-book-theme", "sphinx-comments", "sphinx-copybutton", @@ -62,6 +63,7 @@ docstring-code-format = true line-ending = "lf" [tool.ruff.lint] +allowed-confusables = ["–"] ignore = [ "ANN401", "COM812", @@ -96,6 +98,9 @@ builtins-ignorelist = ["display"] [tool.ruff.lint.flake8-comprehensions] allow-dict-calls-with-keyword-arguments = true +[tool.ruff.lint.flake8-self] +ignore-names = ["_print"] + [tool.ruff.lint.isort] 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}, { name = "sphinx", marker = "extra == 'doc'" }, + { name = "sphinx-api-relink", marker = "extra == 'doc'" }, { name = "sphinx-autobuild", marker = "extra == 'dev'" }, { name = "sphinx-book-theme", marker = "extra == 'doc'" }, { name = "sphinx-comments", marker = "extra == 'doc'" }, From 80e1567c39bd5ef08b2ee21de2f56e4d4bb6cad4 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 21:40:27 +0200 Subject: [PATCH 09/33] MAINT: update lock files and dev environment --- .binder/postBuild | 11 ++ .binder/runtime.txt | 1 + .github/release-drafter.yml | 37 ---- .github/workflows/cd.yml | 12 -- .github/workflows/ci.yml | 4 +- .github/workflows/clean-caches.yml | 2 +- .../workflows/{requirements.yml => lock.yml} | 7 +- .github/workflows/pr-linting.yml | 2 +- .github/workflows/release-drafter.yml | 16 -- .gitignore | 1 + .pre-commit-config.yaml | 13 +- README.md | 1 + uv.lock | 174 ++++++++++-------- 13 files changed, 123 insertions(+), 158 deletions(-) create mode 100755 .binder/postBuild create mode 100644 .binder/runtime.txt delete mode 100644 .github/release-drafter.yml delete mode 100644 .github/workflows/cd.yml rename .github/workflows/{requirements.yml => lock.yml} (80%) delete mode 100644 .github/workflows/release-drafter.yml diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100755 index 0000000..48d530c --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,11 @@ +#!/bin/bash +set -ex +curl -LsSf https://astral.sh/uv/install.sh | sh +source $HOME/.cargo/env +uv export \ + --extra jupyter \ + > 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 0000000..d2aca3a --- /dev/null +++ b/.binder/runtime.txt @@ -0,0 +1 @@ +python-3.12 diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml deleted file mode 100644 index c521caf..0000000 --- a/.github/release-drafter.yml +++ /dev/null @@ -1,37 +0,0 @@ -name-template: '"STRONG2020 HaSP School" $NEXT_PATCH_VERSION' -tag-template: $NEXT_PATCH_VERSION - -references: - - main - - epic/* - -categories: - - title: ✨ New features - label: ✨ Feature - - title: ⚠️ Enhancements and optimizations - label: ⚙️ Enhancement - - title: ⚠️ API changes - label: ⚠️ Interface - - title: ⚠️ Changes that may affect behavior - label: ❗ Behavior - - title: 🐛 Bug fixes - label: 🐛 Bug - - title: 📝 Documentation - label: 📝 Docs - - title: 🔨 Maintenance - label: 🔨 Maintenance - - title: 🖱️ Developer Experience - label: 🖱️ DX - -change-template: "- $TITLE (#$NUMBER)" - -replacers: - - search: /([A-Z]+!?:\s*)(.*)/g - replace: $2 - -sort-direction: ascending - -template: | - $CHANGES - - _The full changelog as commits can be found [here](https://github.com/ComPWA/strong2020-salamanca/compare/$PREVIOUS_TAG...$NEXT_PATCH_VERSION)._ diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml deleted file mode 100644 index 56f0c9c..0000000 --- a/.github/workflows/cd.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: CD - -on: - release: - types: - - prereleased - - released - -jobs: - milestone: - if: startsWith(github.ref, 'refs/tags') - uses: ComPWA/actions/.github/workflows/close-milestone.yml@v1 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2708cfa..1920091 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ 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 @@ -39,4 +39,4 @@ 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 diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index 939e136..7986e0c 100644 --- a/.github/workflows/clean-caches.yml +++ b/.github/workflows/clean-caches.yml @@ -16,7 +16,7 @@ jobs: name: Remove caches 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 80% rename from .github/workflows/requirements.yml rename to .github/workflows/lock.yml index 75a6c15..67157b3 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 }} @@ -12,12 +12,13 @@ on: - epic/* paths: - .pre-commit-config.yaml + - uv.lock schedule: - cron: "0 3 7 */3 *" 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 0fab841..44dc9e4 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 deleted file mode 100644 index 32c6579..0000000 --- a/.github/workflows/release-drafter.yml +++ /dev/null @@ -1,16 +0,0 @@ -name: Release Drafter - -on: - push: - branches: - - main - - epic/* - workflow_dispatch: - -jobs: - update_release_draft: - runs-on: ubuntu-24.04 - steps: - - uses: release-drafter/release-drafter@v6 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 8498af0..08491a1 100644 --- a/.gitignore +++ b/.gitignore @@ -38,6 +38,7 @@ pyvenv*/ **.code-workspace # Exceptions 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rev: 0.4.26 + rev: 0.4.27 hooks: - id: uv-lock diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 068ab1a..d54a646 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -19,8 +19,26 @@ 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**: +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 install `pre-commit` with `uv`: + +```shell +uv tool install pre-commit --with pre-commit-uv --force-reinstall +``` + +and [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**: ```shell pre-commit install --install-hooks ``` + +In addition, it may be handy to install `tox`: + +```shell +uv tool install tox --with tox-uv +``` + +If the repository provides a Tox configuration under [`pyproject.toml`](./pyproject.toml), you can see which jobs it defines with: + +```shell +tox list +``` diff --git a/uv.lock b/uv.lock index 2ee5c64..fe925f1 100644 --- a/uv.lock +++ b/uv.lock @@ -609,7 +609,7 @@ wheels = [ [[package]] name = "ipython" -version = "8.28.0" +version = "8.29.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "colorama", marker = "sys_platform == 'win32'" }, @@ -622,9 +622,9 @@ dependencies = [ { name = "stack-data" }, { name = "traitlets" }, ] -sdist = { url = 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From 17b9ec34d7f96cecea23dbe986ca3c6a5197b431 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:15 +0100 Subject: [PATCH 17/33] FIX: remove `format` extras --- pyproject.toml | 5 +---- uv.lock | 1 - 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 192c6bf..1d921b8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,10 +45,7 @@ jupyter = [ "python-lsp-server[rope]", "python-lsp-server[rope]", ] -sty = [ - "ruff", - "strong2020-salamanca[format]", -] +sty = ["ruff"] test = ["nbmake"] [tool.ruff] diff --git a/uv.lock b/uv.lock index fe925f1..9482140 100644 --- a/uv.lock +++ b/uv.lock @@ -2265,7 +2265,6 @@ requires-dist = [ { name = "sphinx-exercise", marker = "extra == 'doc'" }, { name = "sphinx-togglebutton", marker = "extra == 'doc'" }, { name = "strong2020-salamanca", extras = ["doc"], marker = "extra == 'dev'" }, - { name = "strong2020-salamanca", extras = ["format"], marker = "extra == 'sty'" }, { name = "strong2020-salamanca", extras = ["jupyter"], marker = "extra == 'dev'" }, { name = "strong2020-salamanca", extras = ["sty"], marker = "extra == 'dev'" }, { name = "strong2020-salamanca", extras = ["test"], marker = "extra == 'dev'" }, From 31aab13b76e1acc047a9af4817744df16299d5e7 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:15 +0100 Subject: [PATCH 18/33] MAINT: remove duplicate `python-lsp-server` --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1d921b8..254c09d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,6 @@ jupyter = [ "jupyterlab-myst", "python-lsp-ruff", "python-lsp-server[rope]", - "python-lsp-server[rope]", ] sty = ["ruff"] test = ["nbmake"] From 45422309b3cb1957ad6d3a269787334dbc62ef5b Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:15 +0100 Subject: [PATCH 19/33] FIX: remove developer dependencies from extras --- .binder/postBuild | 4 ++- .github/workflows/ci.yml | 2 +- .pre-commit-config.yaml | 2 +- CONTRIBUTING.md | 2 +- pyproject.toml | 13 ++++--- uv.lock | 75 ++++++++++++++++++++++++---------------- 6 files changed, 58 insertions(+), 40 deletions(-) diff --git a/.binder/postBuild b/.binder/postBuild index 48d530c..00acf5d 100755 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -3,9 +3,11 @@ set -ex curl -LsSf https://astral.sh/uv/install.sh | sh source $HOME/.cargo/env uv export \ - --extra jupyter \ + --group jupyter \ + --no-dev \ > requirements.txt uv pip install \ --requirement requirements.txt \ --system +rm requirements.txt uv cache clean diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 65614d9..7ddd7cc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ on: jobs: doc: - uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2 + uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2.1 permissions: pages: write id-token: write diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8a9327a..4d2ddd6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.5.3 + rev: 0.5.5 hooks: - id: check-dev-files args: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d54a646..abb4785 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -15,7 +15,7 @@ cd strong2020-salamanca 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 +uv sync --all-extras source .venv/bin/activate ``` diff --git a/pyproject.toml b/pyproject.toml index 254c09d..b570e5e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,13 +15,13 @@ dynamic = ["version"] name = "strong2020-salamanca" requires-python = ">=3.12" -[project.optional-dependencies] +[dependency-groups] dev = [ + "ruff", "sphinx-autobuild", - "strong2020-salamanca[doc]", - "strong2020-salamanca[jupyter]", - "strong2020-salamanca[sty]", - "strong2020-salamanca[test]", + {include-group = "doc"}, + {include-group = "jupyter"}, + {include-group = "test"}, ] doc = [ "ipympl", @@ -37,14 +37,13 @@ doc = [ ] jupyter = [ "jupyterlab", - "jupyterlab-code-formatter >=3.0.0", + "jupyterlab-code-formatter", "jupyterlab-git", "jupyterlab-lsp", "jupyterlab-myst", "python-lsp-ruff", "python-lsp-server[rope]", ] -sty = ["ruff"] test = ["nbmake"] [tool.ruff] diff --git a/uv.lock b/uv.lock index 9482140..6437cf3 100644 --- a/uv.lock +++ b/uv.lock @@ -2191,7 +2191,7 @@ name = "strong2020-salamanca" version = "0.0.0" source = { editable = "." } -[package.optional-dependencies] +[package.dependency-groups] dev = [ { name = "ipympl" }, { name = "jupyterlab" }, @@ -2235,40 +2235,57 @@ jupyter = [ { name = "python-lsp-ruff" }, { name = "python-lsp-server", extra = ["rope"] }, ] -sty = [ - { name = "ruff" }, -] test = [ { name = "nbmake" }, ] [package.metadata] -requires-dist = [ - { name = "ipympl", marker = "extra == 'doc'" }, - { name = "jupyterlab", marker = "extra == 'jupyter'" }, - { name = "jupyterlab-code-formatter", marker = "extra == 'jupyter'", specifier = ">=3.0.0" }, - { name = "jupyterlab-git", marker = "extra == 'jupyter'" }, - { name = "jupyterlab-lsp", marker = "extra == 'jupyter'" }, - { name = "jupyterlab-myst", marker = "extra == 'jupyter'" }, - { name = "myst-nb", marker = "extra == 'doc'" }, - { name = "nbmake", marker = "extra == 'test'" }, - { name = "python-lsp-ruff", marker = "extra == 'jupyter'" }, - { name = "python-lsp-server", extras = ["rope"], marker = "extra == 'jupyter'" }, - { name = "ruff", marker = "extra == 'sty'" }, - { name = "sphinx", marker = "extra == 'doc'" }, - { name = "sphinx-api-relink", marker = "extra == 'doc'" }, - { name = "sphinx-autobuild", marker = "extra == 'dev'" }, - { name = "sphinx-book-theme", marker = "extra == 'doc'" }, - { name = "sphinx-comments", marker = "extra == 'doc'" }, - { name = "sphinx-copybutton", marker = "extra == 'doc'" }, - { name = "sphinx-design", marker = "extra == 'doc'" }, - { name = "sphinx-exercise", marker = "extra == 'doc'" }, - { name = "sphinx-togglebutton", marker = "extra == 'doc'" }, - { name = "strong2020-salamanca", extras = ["doc"], marker = "extra == 'dev'" }, - { name = "strong2020-salamanca", extras = ["jupyter"], marker = "extra == 'dev'" }, - { name = "strong2020-salamanca", extras = ["sty"], marker = "extra == 'dev'" }, - { name = "strong2020-salamanca", extras = ["test"], marker = "extra == 'dev'" }, + +[package.metadata.dependency-groups] +dev = [ + { name = "ipympl" }, + { name = "jupyterlab" }, + { name = "jupyterlab-code-formatter" }, + { name = "jupyterlab-git" }, + { name = "jupyterlab-lsp" }, + { name = "jupyterlab-myst" }, + { name = "myst-nb" }, + { name = "nbmake" }, + { name = "python-lsp-ruff" }, + { name = "python-lsp-server", extras = ["rope"] }, + { name = "ruff" }, + { name = "sphinx" }, + { name = "sphinx-api-relink" }, + { name = "sphinx-autobuild" }, + { name = "sphinx-book-theme" }, + { name = "sphinx-comments" }, + { name = "sphinx-copybutton" }, + { name = "sphinx-design" }, + { name = "sphinx-exercise" }, + { name = "sphinx-togglebutton" }, +] +doc = [ + { name = "ipympl" }, + { name = "myst-nb" }, + { name = "sphinx" }, + { name = "sphinx-api-relink" }, + { name = "sphinx-book-theme" }, + { name = "sphinx-comments" }, + { name = "sphinx-copybutton" }, + { name = "sphinx-design" }, + { name = "sphinx-exercise" }, + { name = "sphinx-togglebutton" }, +] +jupyter = [ + { name = "jupyterlab" }, + { name = "jupyterlab-code-formatter" }, + { name = "jupyterlab-git" }, + { name = "jupyterlab-lsp" }, + { name = "jupyterlab-myst" }, + { name = "python-lsp-ruff" }, + { name = "python-lsp-server", extras = ["rope"] }, ] +test = [{ name = "nbmake" }] [[package]] name = "tabulate" From ed611a52da13febd59d153605bd0309d1593b291 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:15 +0100 Subject: [PATCH 20/33] FIX: set `passenv` in jobs that have a different `base` --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index b570e5e..5e3f227 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -185,6 +185,7 @@ commands = --show-traceback \ docs/ docs/_build/html description = Build documentation as website +passenv = * setenv = PYTHONWARNINGS = @@ -212,6 +213,7 @@ commands = --watch=docs \ docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages +passenv = * setenv = PYTHONWARNINGS = From 4e2b1bffbed882b363a34f3c88713688ee919924 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:16 +0100 Subject: [PATCH 21/33] DX: install `pyproject-local-kernel` in `notebooks` group --- .binder/postBuild | 1 + pyproject.toml | 8 +++++++- uv.lock | 29 ++++++++++++++++++++++++++++- 3 files changed, 36 insertions(+), 2 deletions(-) diff --git a/.binder/postBuild b/.binder/postBuild index 00acf5d..06472a5 100755 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -4,6 +4,7 @@ curl -LsSf https://astral.sh/uv/install.sh | sh source $HOME/.cargo/env uv export \ --group jupyter \ + --group notebooks \ --no-dev \ > requirements.txt uv pip install \ diff --git a/pyproject.toml b/pyproject.toml index 5e3f227..9f4ab55 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,7 @@ doc = [ "sphinx-design", "sphinx-exercise", "sphinx-togglebutton", + {include-group = "notebooks"}, ] jupyter = [ "jupyterlab", @@ -43,8 +44,13 @@ jupyter = [ "jupyterlab-myst", "python-lsp-ruff", "python-lsp-server[rope]", + {include-group = "notebooks"}, +] +notebooks = ["pyproject-local-kernel"] +test = [ + "nbmake", + {include-group = "notebooks"}, ] -test = ["nbmake"] [tool.ruff] extend-include = ["*.ipynb"] diff --git a/uv.lock b/uv.lock index 6437cf3..fd29ba6 100644 --- a/uv.lock +++ b/uv.lock @@ -1565,6 +1565,19 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/be/ec/2eb3cd785efd67806c46c13a17339708ddc346cbb684eade7a6e6f79536a/pyparsing-3.2.0-py3-none-any.whl", hash = "sha256:93d9577b88da0bbea8cc8334ee8b918ed014968fd2ec383e868fb8afb1ccef84", size = 106921 }, ] +[[package]] +name = "pyproject-local-kernel" +version = "0.12.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "jupyter-client" }, + { name = "traitlets" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/40/fb/94358922dd72d940b1a10e6cdcb11b97d9f39f9212717b8cce32f7f00a15/pyproject_local_kernel-0.12.1.tar.gz", hash = "sha256:a983a370a4c8b29acfbcc4ccda22d13215c97f24e2b51d980830fa7d5d37fcc5", size = 331109 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/a7/17/f2b6d2c93896d19bfe53bea78a23bf65e5b8f36890dd2dc4d9fc56d49e60/pyproject_local_kernel-0.12.1-py3-none-any.whl", hash = "sha256:ed788fa70864c4635ff65a4414739cc247a7908a9d9b3543e705514d1b98dce2", size = 19236 }, +] + [[package]] name = "pytest" version = "8.3.3" @@ -2201,6 +2214,7 @@ dev = [ { name = "jupyterlab-myst" }, { name = "myst-nb" }, { name = "nbmake" }, + { name = "pyproject-local-kernel" }, { name = "python-lsp-ruff" }, { name = "python-lsp-server", extra = ["rope"] }, { name = "ruff" }, @@ -2217,6 +2231,7 @@ dev = [ doc = [ { name = "ipympl" }, { name = "myst-nb" }, + { name = "pyproject-local-kernel" }, { name = "sphinx" }, { name = "sphinx-api-relink" }, { name = "sphinx-book-theme" }, @@ -2232,11 +2247,16 @@ jupyter = [ { name = "jupyterlab-git" }, { name = "jupyterlab-lsp" }, { name = "jupyterlab-myst" }, + { name = "pyproject-local-kernel" }, { name = "python-lsp-ruff" }, { name = "python-lsp-server", extra = ["rope"] }, ] +notebooks = [ + { name = "pyproject-local-kernel" }, +] test = [ { name = "nbmake" }, + { name = "pyproject-local-kernel" }, ] [package.metadata] @@ -2251,6 +2271,7 @@ dev = [ { name = "jupyterlab-myst" }, { name = "myst-nb" }, { name = "nbmake" }, + { name = "pyproject-local-kernel" }, { name = "python-lsp-ruff" }, { name = "python-lsp-server", extras = ["rope"] }, { name = "ruff" }, @@ -2267,6 +2288,7 @@ dev = [ doc = [ { name = "ipympl" }, { name = "myst-nb" }, + { name = "pyproject-local-kernel" }, { name = "sphinx" }, { name = "sphinx-api-relink" }, { name = "sphinx-book-theme" }, @@ -2282,10 +2304,15 @@ jupyter = [ { name = "jupyterlab-git" }, { name = "jupyterlab-lsp" }, { name = "jupyterlab-myst" }, + { name = "pyproject-local-kernel" }, { name = "python-lsp-ruff" }, { name = "python-lsp-server", extras = ["rope"] }, ] -test = [{ name = "nbmake" }] +notebooks = [{ name = "pyproject-local-kernel" }] +test = [ + { name = "nbmake" }, + { name = "pyproject-local-kernel" }, +] [[package]] name = "tabulate" From 025aa5a539f84f71e145f9ff61e0de7069edaf0a Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:16 +0100 Subject: [PATCH 22/33] DX: add `pytest` configuration for `nbmake` --- pyproject.toml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9f4ab55..d447cf9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,6 +52,22 @@ test = [ {include-group = "notebooks"}, ] +[tool.pytest.ini_options] +addopts = [ + "--color=yes", + "--durations=0", + "--nbmake", + "--nbmake-timeout=1200", +] +filterwarnings = [ + "error", +] +norecursedirs = [ + ".ipynb_checkpoints", + ".virtual_documents", + "_build", +] + [tool.ruff] extend-include = ["*.ipynb"] preview = true @@ -245,7 +261,7 @@ description = Check external links in the documentation (requires internet conne allowlist_externals = pytest commands = - pytest --nbmake {posargs:docs} + pytest {posargs:docs} description = Run all notebooks with pytest [testenv:sty] From 584e097d2d73dc5fea64e710d5690bd805a263c6 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:02:17 +0100 Subject: [PATCH 23/33] DX!: pin dependencies per notebook --- docs/conf.py | 7 +- docs/index.md | 2 +- .../index.ipynb} | 22 +- docs/lecture02/pyproject.toml | 31 + docs/lecture02/uv.lock | 380 +++++++++ .../index.ipynb} | 21 +- docs/lecture06-gammap/pyproject.toml | 34 + docs/lecture06-gammap/uv.lock | 410 ++++++++++ .../index.ipynb} | 19 +- docs/lecture06-nbarp/pyproject.toml | 25 + docs/lecture06-nbarp/uv.lock | 378 +++++++++ .../index.ipynb} | 19 +- docs/lecture09/pyproject.toml | 34 + docs/lecture09/uv.lock | 403 ++++++++++ .../index.ipynb} | 21 +- .../lecture12a-gammap-solution/pyproject.toml | 34 + docs/lecture12a-gammap-solution/uv.lock | 410 ++++++++++ .../index.ipynb} | 19 +- docs/lecture12b-kinematics/pyproject.toml | 28 + docs/lecture12b-kinematics/uv.lock | 410 ++++++++++ .../index.ipynb} | 19 +- docs/lecture12c-angles/pyproject.toml | 26 + docs/lecture12c-angles/uv.lock | 389 +++++++++ .../index.ipynb} | 19 +- docs/lecture12d-phasespace/pyproject.toml | 27 + docs/lecture12d-phasespace/uv.lock | 735 ++++++++++++++++++ .../index.ipynb} | 19 +- docs/lecture12e-longitudinal/pyproject.toml | 25 + docs/lecture12e-longitudinal/uv.lock | 389 +++++++++ .../index.ipynb} | 19 +- docs/lecture17/pyproject.toml | 46 ++ docs/lecture17/uv.lock | 336 ++++++++ docs/{ => lecture18}/.gitignore | 0 .../index.ipynb} | 19 +- docs/{ => lecture18}/lecture18.cpp | 0 docs/lecture18/pyproject.toml | 24 + docs/lecture18/uv.lock | 337 ++++++++ .../index.ipynb} | 26 +- docs/lecture24/pyproject.toml | 47 ++ .../utilities.ipynb} | 2 +- docs/lecture24/uv.lock | 703 +++++++++++++++++ pyproject.toml | 9 - 42 files changed, 5709 insertions(+), 214 deletions(-) rename docs/{lecture02.ipynb => lecture02/index.ipynb} (97%) create mode 100644 docs/lecture02/pyproject.toml create mode 100644 docs/lecture02/uv.lock rename docs/{lecture06-gammap.ipynb => lecture06-gammap/index.ipynb} (98%) create mode 100644 docs/lecture06-gammap/pyproject.toml create mode 100644 docs/lecture06-gammap/uv.lock rename docs/{lecture06-nbarp.ipynb => lecture06-nbarp/index.ipynb} (98%) create mode 100644 docs/lecture06-nbarp/pyproject.toml create mode 100644 docs/lecture06-nbarp/uv.lock rename docs/{lecture09.ipynb => lecture09/index.ipynb} (99%) create mode 100644 docs/lecture09/pyproject.toml create mode 100644 docs/lecture09/uv.lock rename docs/{lecture12a-gammap-solution.ipynb => lecture12a-gammap-solution/index.ipynb} (98%) create mode 100644 docs/lecture12a-gammap-solution/pyproject.toml create mode 100644 docs/lecture12a-gammap-solution/uv.lock rename docs/{lecture12b-kinematics.ipynb => lecture12b-kinematics/index.ipynb} (98%) create mode 100644 docs/lecture12b-kinematics/pyproject.toml create mode 100644 docs/lecture12b-kinematics/uv.lock rename docs/{lecture12c-angles.ipynb => lecture12c-angles/index.ipynb} (97%) create mode 100644 docs/lecture12c-angles/pyproject.toml create mode 100644 docs/lecture12c-angles/uv.lock rename docs/{lecture12d-phasespace.ipynb => lecture12d-phasespace/index.ipynb} (97%) create mode 100644 docs/lecture12d-phasespace/pyproject.toml create mode 100644 docs/lecture12d-phasespace/uv.lock rename docs/{lecture12e-longitudinal.ipynb => lecture12e-longitudinal/index.ipynb} (95%) create mode 100644 docs/lecture12e-longitudinal/pyproject.toml create mode 100644 docs/lecture12e-longitudinal/uv.lock rename docs/{lecture17.ipynb => lecture17/index.ipynb} (98%) create mode 100644 docs/lecture17/pyproject.toml create mode 100644 docs/lecture17/uv.lock rename docs/{ => lecture18}/.gitignore (100%) rename docs/{lecture18.ipynb => lecture18/index.ipynb} (98%) rename docs/{ => lecture18}/lecture18.cpp (100%) create mode 100644 docs/lecture18/pyproject.toml create mode 100644 docs/lecture18/uv.lock rename docs/{lecture24.ipynb => lecture24/index.ipynb} (99%) create mode 100644 docs/lecture24/pyproject.toml rename docs/{lecture24_utilities.ipynb => lecture24/utilities.ipynb} (98%) create mode 100644 docs/lecture24/uv.lock diff --git a/docs/conf.py b/docs/conf.py index 951dfcd..002fee7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,7 +13,10 @@ copyright = "2023" # noqa: A001 exclude_patterns = [ "_build", - "lecture24_utilities.ipynb", + "**/.ipynb_checkpoints/", + "**/.venv/*", + "**/.virtual_documents/", + "lecture24/utilities.ipynb", ] extensions = [ "myst_nb", @@ -95,7 +98,7 @@ nb_execution_excludepatterns = [ "**.ipynb_checkpoints", ".virtual_documents/*", - "lecture24_utilities.ipynb", + "lecture24/utilities.ipynb", ] nb_execution_mode = get_execution_mode() nb_execution_show_tb = True diff --git a/docs/index.md b/docs/index.md index 3f9baa7..8b3f3de 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,5 +7,5 @@ ```{toctree} :glob: :maxdepth: 2 -lecture* +lecture*/index ``` diff --git a/docs/lecture02.ipynb b/docs/lecture02/index.ipynb similarity index 97% rename from docs/lecture02.ipynb rename to docs/lecture02/index.ipynb index b65d97a..cd94a6f 100644 --- a/docs/lecture02.ipynb +++ b/docs/lecture02/index.ipynb @@ -14,22 +14,6 @@ "[Lecture 2](https://indico.ific.uv.es/event/6803/contributions/21220) by Vincent Mathieu contains a few data files containing four-momenta data samples. Our goal in this notebook is to identify which reaction was used to generate these data samples." ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q gdown matplotlib numpy particle" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -542,9 +526,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -556,7 +540,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture02/pyproject.toml b/docs/lecture02/pyproject.toml new file mode 100644 index 0000000..202d301 --- /dev/null +++ b/docs/lecture02/pyproject.toml @@ -0,0 +1,31 @@ +[project] +dependencies = [ + "gdown", + "matplotlib", + "numpy", + "particle", +] +name = "lecture" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +allowed-confusables = ["–"] +ignore = [ + "ANN001", + "COM812", + "CPY001", + "D", + "ISC001", + "PLR2004", + "T201", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = ["display"] + +[tool.uv.workspace] diff --git a/docs/lecture02/uv.lock b/docs/lecture02/uv.lock new file mode 100644 index 0000000..f5be61d --- /dev/null +++ b/docs/lecture02/uv.lock @@ -0,0 +1,380 @@ +version = 1 +requires-python = ">=3.12.0, <3.13" + +[[package]] +name = "attrs" +version = "24.2.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/fc/0f/aafca9af9315aee06a89ffde799a10a582fe8de76c563ee80bbcdc08b3fb/attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346", size = 792678 } 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look to the missing mass distribution (final - initial\n", - "state). Let's start from the real data using the pylorentz package to build 4-vectors (first, work out the [`lecture12b-kinematics.ipynb`](./lecture12b-kinematics.ipynb) notebook)." + "state). Let's start from the real data using the pylorentz package to build 4-vectors (first, work out the [`lecture12b-kinematics/index.ipynb`](../lecture12b-kinematics/index.ipynb) notebook)." ] }, { @@ -1064,9 +1051,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -1078,7 +1065,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture06-gammap/pyproject.toml b/docs/lecture06-gammap/pyproject.toml new file mode 100644 index 0000000..14a97e7 --- /dev/null +++ b/docs/lecture06-gammap/pyproject.toml @@ -0,0 +1,34 @@ +[project] +dependencies = [ + "gdown", + "matplotlib", + "numpy", + "pandas", + "pylorentz", + "scipy", +] +name = "lecture" +requires-python = "~=3.12.0" +version = 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docs/lecture09/index.ipynb index 83a4cdf..126dd50 100644 --- a/docs/lecture09.ipynb +++ b/docs/lecture09/index.ipynb @@ -7,19 +7,6 @@ "# Lecture 9 – Estimators" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q gdown lmfit matplotlib numpy scipy" - ] - }, { "cell_type": "code", "execution_count": null, @@ -3150,9 +3137,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -3164,7 +3151,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture09/pyproject.toml b/docs/lecture09/pyproject.toml new file mode 100644 index 0000000..afb3650 --- /dev/null +++ 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Missing mass distributions\n", "\n", "Now, let's take a look to the missing mass distribution (final - initial\n", - "state). Let's start from the real data using the pylorentz package to build 4-vectors (first, work out the [`lecture12b-kinematics.ipynb`](./lecture12b-kinematics.ipynb) notebook)." + "state). Let's start from the real data using the pylorentz package to build 4-vectors (first, work out the [`lecture12b-kinematics/index.ipynb`](../lecture12b-kinematics/index.ipynb) notebook)." ] }, { @@ -1185,9 +1172,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -1199,7 +1186,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture12a-gammap-solution/pyproject.toml b/docs/lecture12a-gammap-solution/pyproject.toml new file mode 100644 index 0000000..14a97e7 --- /dev/null +++ b/docs/lecture12a-gammap-solution/pyproject.toml @@ -0,0 +1,34 @@ +[project] +dependencies = [ + "gdown", + "matplotlib", + "numpy", + "pandas", + "pylorentz", + "scipy", +] +name = "lecture" +requires-python 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index 97% rename from docs/lecture12d-phasespace.ipynb rename to docs/lecture12d-phasespace/index.ipynb index 2fa2262..0b6e0a6 100644 --- a/docs/lecture12d-phasespace.ipynb +++ b/docs/lecture12d-phasespace/index.ipynb @@ -21,19 +21,6 @@ "Prepare the notebook by importing [`numpy`](https://numpy.org), [`matplotlib.pyplot`](https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html), and [`pylorentz`](https://github.com/PyLorentz/PyLorentz) and download the data file (CSV format) from Google Drive." ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q gdown matplotlib numpy phasespace pylorentz tf-keras" - ] - }, { "cell_type": "code", "execution_count": null, @@ -544,9 +531,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" 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pylorentz" - ] - }, { "cell_type": "code", "execution_count": null, @@ -231,9 +218,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -245,7 +232,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture12e-longitudinal/pyproject.toml b/docs/lecture12e-longitudinal/pyproject.toml new file mode 100644 index 0000000..b86002b --- /dev/null +++ b/docs/lecture12e-longitudinal/pyproject.toml @@ -0,0 +1,25 @@ +[project] +dependencies = [ + "gdown", + "matplotlib", + "numpy", + "pandas", + "pylorentz", +] +name = "lecture" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "COM812", + "CPY001", + "D", + "ISC001", +] +select = 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docs/lecture17.ipynb rename to docs/lecture17/index.ipynb index e855f0b..8de4ad7 100644 --- a/docs/lecture17.ipynb +++ b/docs/lecture17/index.ipynb @@ -7,19 +7,6 @@ "# Lecture 17 – Collision theory" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q \"ampform>=0.14.8\" plotly sympy" - ] - }, { "cell_type": "code", "execution_count": null, @@ -749,9 +736,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -763,7 +750,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture17/pyproject.toml b/docs/lecture17/pyproject.toml new file mode 100644 index 0000000..39ed9b2 --- 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rename to docs/lecture18/.gitignore diff --git a/docs/lecture18.ipynb b/docs/lecture18/index.ipynb similarity index 98% rename from docs/lecture18.ipynb rename to docs/lecture18/index.ipynb index cff258c..3ee831a 100644 --- a/docs/lecture18.ipynb +++ b/docs/lecture18/index.ipynb @@ -14,19 +14,6 @@ "**Polarization observables extraction examples: RGK data on KΛ electroproduction data and MC.**" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q gdown matplotlib numpy" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -576,9 +563,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -590,7 +577,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - 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Likelihood" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "!uv pip install -q gdown iminuit import-ipynb sweights\n", - "from IPython.display import display" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -89,7 +75,7 @@ "source": [ "\n", "\n", - "Load some helper functions from another notebook `lecture24_utilities.ipynb` by running the following cell." + "Load some helper functions from another notebook `utilities.ipynb` by running the following cell." ] }, { @@ -109,13 +95,13 @@ "\n", "import gdown\n", "\n", - "sfile = \"lecture24_utilities.ipynb\"\n", + "sfile = \"utilities.ipynb\"\n", "if not os.path.exists(sfile):\n", " url = \"https://drive.google.com/uc?id=1E899ebABgwcgfA7d-tXRud4dB7aGWIje\"\n", " gdown.download(url, sfile, quiet=False)\n", "\n", "import import_ipynb # noqa: F401\n", - "import lecture24_utilities as s2020\n", + "import utilities as s2020\n", "\n", "s2020.about()" ] @@ -2117,9 +2103,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { @@ -2131,7 +2117,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.6" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/docs/lecture24/pyproject.toml b/docs/lecture24/pyproject.toml new file mode 100644 index 0000000..1e1fbee --- /dev/null +++ b/docs/lecture24/pyproject.toml @@ -0,0 +1,47 @@ +[project] +dependencies = [ + "gdown", + "iminuit", + "import-ipynb", + "matplotlib", + "numpy", + "sweights", +] +name = "lecture" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN001", + "ANN201", + "B023", + "BLE001", + "COM812", + "CPY001", + "D", + "DOC201", + "E402", + "E501", + "E731", + 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split-on-trailing-comma = false @@ -126,11 +122,9 @@ split-on-trailing-comma = false "C90", "D", "E303", - "E402", "E703", "N806", "N816", - "PLC2401", "PLR09", "PLR2004", "PLW0602", @@ -164,9 +158,6 @@ split-on-trailing-comma = false [tool.ruff.lint.pydocstyle] convention = "google" -[tool.ruff.lint.pylint] -allow-dunder-method-names = ["_latex_repr_"] - [tool.tomlsort] all = false ignore_case = true From c323556680415b29ca3642283e345604b62ac8f1 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:08:20 +0100 Subject: [PATCH 24/33] MAINT: update lock files --- .pre-commit-config.yaml | 2 +- uv.lock | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4d2ddd6..7f1419f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -97,6 +97,6 @@ repos: )$ - repo: https://github.com/astral-sh/uv-pre-commit - rev: 0.4.27 + rev: 0.4.28 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insertions(+), 2 deletions(-) diff --git a/uv.lock b/uv.lock index 4c0073d..fa8e383 100644 --- a/uv.lock +++ b/uv.lock @@ -2204,7 +2204,7 @@ name = "strong2020-salamanca" version = "0.0.0" source = { editable = "." } -[package.dependency-groups] +[package.dev-dependencies] dev = [ { name = "ipympl" }, { name = "jupyterlab" }, @@ -2261,7 +2261,7 @@ test = [ [package.metadata] -[package.metadata.dependency-groups] +[package.metadata.requires-dev] dev = [ { name = "ipympl" }, { name = "jupyterlab" }, From feb6ab234e760b70a1dede2a67b651fdc7c1ef87 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 29 Oct 2024 13:26:53 +0100 Subject: [PATCH 26/33] MAINT: remove outdated `docs` workflow --- .github/workflows/docs.yml | 59 -------------------------------------- 1 file changed, 59 deletions(-) delete mode 100644 .github/workflows/docs.yml diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index 95989e7..0000000 --- a/.github/workflows/docs.yml +++ /dev/null @@ -1,59 +0,0 @@ -name: Documentation - -on: - push: - pull_request: - branches: - - main - workflow_dispatch: - -jobs: - doc: - if: github.event_name == 'push' && (github.repository != 'ComPWA/strong2020-salamanca' || github.ref_name == 'main') || github.event_name == 'pull_request' - name: Execute and build - runs-on: ubuntu-22.04 - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 - with: - python-version: "3.10" - - run: pip install -e .[doc] tox -c .constraints/py3.10.txt - - name: Fetch Jupyter cache - uses: actions/cache@v3 - with: - key: jupyter-cache-${{ hashFiles('docs/**.ipynb') }} - restore-keys: | - jupyter-cache-${{ hashFiles('docs/**.ipynb') }} - jupyter-cache - path: | - ./docs/_build/.jupyter_cache - - name: Fetch downloaded data - uses: actions/cache@v3 - with: - key: data-${{ hashFiles('docs/**.ipynb') }} - restore-keys: | - data-${{ hashFiles('docs/**.ipynb') }} - data - path: | - 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"https://indico.ific.uv.es/event/6803", +] myst_enable_extensions = [ "amsmath", "colon_fence", From 60c841b15970c5c074341c9f98e2f908cfde21cd Mon Sep 17 00:00:00 2001 From: GitHub Date: Tue, 29 Oct 2024 15:48:08 +0000 Subject: [PATCH 32/33] MAINT: update lock files --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index d70cda1..a98805f 100644 --- a/uv.lock +++ b/uv.lock @@ -918,7 +918,7 @@ wheels = [ [[package]] name = "jupyterlab-git" -version = "0.50.1" +version = "0.50.2" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "jupyter-server" }, @@ -928,9 +928,9 @@ dependencies = [ { name = "pexpect" }, { name = "traitlets" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/79/aa/b2cc8a1edd51464c036956404d9d16b12dbf0e5bfbbdca18d25e00f0f3b0/jupyterlab_git-0.50.1.tar.gz", hash = "sha256:bf4f06a3fbc2b2ab84ea5d52326aa0e0b8ccf4e9a3357fa318a119560e1c6a4d", size = 15248048 } +sdist = { url = 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ReactionAmplitudeExamples.jl https://github.com/mmikhasenko/ReactionAmplitudeExamples.jl/issues/11 --- docs/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/conf.py b/docs/conf.py index ec6d3b0..a81466a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -89,6 +89,7 @@ linkcheck_anchors = False linkcheck_ignore = [ "https://indico.ific.uv.es/event/6803", + "https://mmikhasenko.github.io/ReactionAmplitudeExamples.jl", ] myst_enable_extensions = [ "amsmath",