From ea00accd6ac4c22788c28c37a0df2d7f770c0ebd Mon Sep 17 00:00:00 2001 From: GitHub Date: Mon, 7 Oct 2024 03:20:02 +0000 Subject: [PATCH 01/44] MAINT: update pip constraints and pre-commit --- .constraints/py3.10.txt | 72 ++++++++++++++++++++--------------------- .constraints/py3.11.txt | 72 ++++++++++++++++++++--------------------- .constraints/py3.12.txt | 70 +++++++++++++++++++-------------------- .constraints/py3.7.txt | 12 +++---- .constraints/py3.8.txt | 58 ++++++++++++++++----------------- .constraints/py3.9.txt | 68 +++++++++++++++++++------------------- 6 files changed, 176 insertions(+), 176 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 29658e75..5ed9c79c 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -2,7 +2,7 @@ # uv pip compile pyproject.toml -o .constraints/py3.10.txt --all-extras --no-annotate --python-version=3.10 --no-emit-package setuptools accessible-pygments==0.0.5 alabaster==1.0.0 -anyio==4.4.0 +anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 @@ -14,7 +14,7 @@ beautifulsoup4==4.12.3 black==24.8.0 bleach==6.1.0 cachetools==5.5.0 -cattrs==24.1.0 +cattrs==24.1.2 certifi==2024.8.30 cffi==1.17.1 cfgv==3.4.0 @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.8 @@ -36,26 +36,26 @@ exceptiongroup==1.2.2 execnet==2.1.1 executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.16.0 -fonttools==4.53.1 +filelock==3.16.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2024.6.6 graphviz==0.20.3 -greenlet==3.1.0 +greenlet==3.1.1 h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 +hepunits==2.3.5 +httpcore==1.0.6 httpx==0.27.2 -identify==2.6.0 -idna==3.8 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.27.0 +ipython==8.28.0 ipython-genutils==0.2.0 ipywidgets==8.1.5 isoduration==20.11.0 @@ -66,7 +66,7 @@ jsonpointer==3.0.0 jsonschema==4.23.0 jsonschema-specifications==2023.12.1 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 @@ -95,7 +95,7 @@ mpl-interactions==0.24.2 mpmath==1.3.0 mypy==1.11.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 @@ -105,20 +105,20 @@ nbmake==1.5.4 nest-asyncio==1.6.0 nodeenv==1.9.1 notebook-shim==0.2.4 -numpy==2.1.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.0 +particle==0.25.1 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.3.2 +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==4.0.0 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -129,7 +129,7 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pygments==2.18.0 pyparsing==3.1.4 -pyproject-api==1.7.1 +pyproject-api==1.8.0 pytest==8.3.3 pytest-benchmark==4.0.0 pytest-cov==5.0.0 @@ -149,10 +149,10 @@ referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.8.1 +rich==13.9.2 rope==1.13.0 rpds-py==0.20.0 -ruff==0.6.4 +ruff==0.6.9 scipy==1.14.1 send2trash==1.8.3 six==1.16.0 @@ -162,7 +162,7 @@ snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.0.2 sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 sphinx-comments==0.0.3 @@ -173,40 +173,40 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.3.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.5 -sympy==1.13.2 +starlette==0.39.2 +sympy==1.13.3 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==4.18.1 +tox==4.21.2 tqdm==4.66.5 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 +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==0.30.6 -virtualenv==20.26.4 +urllib3==2.2.3 +uvicorn==0.31.0 +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==13.0.1 +websockets==13.1 wheel==0.44.0 widgetsnbextension==4.0.13 -zipp==3.20.1 +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 021623d6..e0353e87 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -2,7 +2,7 @@ # uv pip compile pyproject.toml -o .constraints/py3.11.txt --all-extras --no-annotate --python-version=3.11 --no-emit-package setuptools accessible-pygments==0.0.5 alabaster==1.0.0 -anyio==4.4.0 +anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 @@ -14,7 +14,7 @@ beautifulsoup4==4.12.3 black==24.8.0 bleach==6.1.0 cachetools==5.5.0 -cattrs==24.1.0 +cattrs==24.1.2 certifi==2024.8.30 cffi==1.17.1 cfgv==3.4.0 @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.8 @@ -35,26 +35,26 @@ docutils==0.21.2 execnet==2.1.1 executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.16.0 -fonttools==4.53.1 +filelock==3.16.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2024.6.6 graphviz==0.20.3 -greenlet==3.1.0 +greenlet==3.1.1 h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 +hepunits==2.3.5 +httpcore==1.0.6 httpx==0.27.2 -identify==2.6.0 -idna==3.8 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.27.0 +ipython==8.28.0 ipython-genutils==0.2.0 ipywidgets==8.1.5 isoduration==20.11.0 @@ -65,7 +65,7 @@ jsonpointer==3.0.0 jsonschema==4.23.0 jsonschema-specifications==2023.12.1 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 @@ -94,7 +94,7 @@ mpl-interactions==0.24.2 mpmath==1.3.0 mypy==1.11.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 @@ -104,20 +104,20 @@ nbmake==1.5.4 nest-asyncio==1.6.0 nodeenv==1.9.1 notebook-shim==0.2.4 -numpy==2.1.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.0 +particle==0.25.1 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.3.2 +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==4.0.0 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -128,7 +128,7 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pygments==2.18.0 pyparsing==3.1.4 -pyproject-api==1.7.1 +pyproject-api==1.8.0 pytest==8.3.3 pytest-benchmark==4.0.0 pytest-cov==5.0.0 @@ -148,10 +148,10 @@ referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.8.1 +rich==13.9.2 rope==1.13.0 rpds-py==0.20.0 -ruff==0.6.4 +ruff==0.6.9 scipy==1.14.1 send2trash==1.8.3 six==1.16.0 @@ -161,7 +161,7 @@ snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.0.2 sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 sphinx-comments==0.0.3 @@ -172,40 +172,40 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.3.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.5 -sympy==1.13.2 +starlette==0.39.2 +sympy==1.13.3 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==4.18.1 +tox==4.21.2 tqdm==4.66.5 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 +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==0.30.6 -virtualenv==20.26.4 +urllib3==2.2.3 +uvicorn==0.31.0 +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==13.0.1 +websockets==13.1 wheel==0.44.0 widgetsnbextension==4.0.13 -zipp==3.20.1 +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 5d2d5637..131d1e85 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -2,7 +2,7 @@ # uv pip compile pyproject.toml -o .constraints/py3.12.txt --all-extras --no-annotate --python-version=3.12 --no-emit-package setuptools accessible-pygments==0.0.5 alabaster==1.0.0 -anyio==4.4.0 +anyio==4.6.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 @@ -14,7 +14,7 @@ beautifulsoup4==4.12.3 black==24.8.0 bleach==6.1.0 cachetools==5.5.0 -cattrs==24.1.0 +cattrs==24.1.2 certifi==2024.8.30 cffi==1.17.1 cfgv==3.4.0 @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.8 @@ -35,26 +35,26 @@ docutils==0.21.2 execnet==2.1.1 executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.16.0 -fonttools==4.53.1 +filelock==3.16.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2024.6.6 graphviz==0.20.3 -greenlet==3.1.0 +greenlet==3.1.1 h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 +hepunits==2.3.5 +httpcore==1.0.6 httpx==0.27.2 -identify==2.6.0 -idna==3.8 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 iniconfig==2.0.0 ipykernel==6.29.5 ipympl==0.9.4 -ipython==8.27.0 +ipython==8.28.0 ipython-genutils==0.2.0 ipywidgets==8.1.5 isoduration==20.11.0 @@ -65,7 +65,7 @@ jsonpointer==3.0.0 jsonschema==4.23.0 jsonschema-specifications==2023.12.1 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 @@ -94,7 +94,7 @@ mpl-interactions==0.24.2 mpmath==1.3.0 mypy==1.11.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==4.0.0 nbclient==0.6.8 nbconvert==7.16.4 @@ -104,20 +104,20 @@ nbmake==1.5.4 nest-asyncio==1.6.0 nodeenv==1.9.1 notebook-shim==0.2.4 -numpy==2.1.1 +numpy==2.1.2 overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.0 +particle==0.25.1 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.3.2 +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==4.0.0 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -128,7 +128,7 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pygments==2.18.0 pyparsing==3.1.4 -pyproject-api==1.7.1 +pyproject-api==1.8.0 pytest==8.3.3 pytest-benchmark==4.0.0 pytest-cov==5.0.0 @@ -148,10 +148,10 @@ referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.8.1 +rich==13.9.2 rope==1.13.0 rpds-py==0.20.0 -ruff==0.6.4 +ruff==0.6.9 scipy==1.14.1 send2trash==1.8.3 six==1.16.0 @@ -161,7 +161,7 @@ snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.0.2 sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 sphinx-comments==0.0.3 @@ -172,39 +172,39 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.3.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.5 -sympy==1.13.2 +starlette==0.39.2 +sympy==1.13.3 tabulate==0.9.0 terminado==0.18.1 tinycss2==1.3.0 tornado==6.4.1 -tox==4.18.1 +tox==4.21.2 tqdm==4.66.5 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 +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==0.30.6 -virtualenv==20.26.4 +urllib3==2.2.3 +uvicorn==0.31.0 +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==13.0.1 +websockets==13.1 wheel==0.44.0 widgetsnbextension==4.0.13 -zipp==3.20.1 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools diff --git a/.constraints/py3.7.txt b/.constraints/py3.7.txt index ce9abc77..9b567897 100644 --- a/.constraints/py3.7.txt +++ b/.constraints/py3.7.txt @@ -44,10 +44,10 @@ gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2022.7.29 graphviz==0.20.1 -greenlet==3.1.0 +greenlet==3.1.1 hepunits==2.3.3 identify==2.5.24 -idna==3.8 +idna==3.10 imagesize==1.4.1 importlib-metadata==6.7.0 importlib-resources==5.12.0 @@ -122,7 +122,7 @@ platformdirs==4.0.0 pluggy==1.2.0 pre-commit==2.21.0 prometheus-client==0.17.1 -prompt-toolkit==3.0.47 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 py-cpuinfo==9.0.0 @@ -147,7 +147,7 @@ python-lsp-jsonrpc==1.0.0 python-lsp-ruff==1.6.0 python-lsp-server==1.7.4 pytoolconfig==1.3.0 -pytz==2024.1 +pytz==2024.2 pyyaml==6.0.1 pyzmq==26.2.0 qrules==0.10.2 @@ -178,7 +178,7 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.2.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==1.0.2 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 @@ -199,7 +199,7 @@ typing-extensions==4.7.1 ujson==5.7.0 uri-template==1.3.0 urllib3==2.0.7 -virtualenv==20.26.4 +virtualenv==20.26.6 wcwidth==0.2.13 webcolors==1.13 webencodings==0.5.1 diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt index 800cface..344433c2 100644 --- a/.constraints/py3.8.txt +++ b/.constraints/py3.8.txt @@ -2,7 +2,7 @@ # uv pip compile pyproject.toml -o .constraints/py3.8.txt --all-extras --no-annotate --python-version=3.8 --no-emit-package setuptools accessible-pygments==0.0.4 alabaster==0.7.13 -anyio==4.4.0 +anyio==4.5.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 @@ -15,7 +15,7 @@ beautifulsoup4==4.12.3 black==24.8.0 bleach==6.1.0 cachetools==5.5.0 -cattrs==24.1.0 +cattrs==24.1.2 certifi==2024.8.30 cffi==1.17.1 cfgv==3.4.0 @@ -27,7 +27,7 @@ comm==0.2.2 contourpy==1.1.1 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.8 @@ -37,22 +37,22 @@ exceptiongroup==1.2.2 execnet==2.1.1 executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.16.0 -fonttools==4.53.1 +filelock==3.16.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2024.6.6 graphviz==0.20.3 -greenlet==3.1.0 +greenlet==3.1.1 h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 +hepunits==2.3.5 +httpcore==1.0.6 httpx==0.27.2 -identify==2.6.0 -idna==3.8 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 importlib-resources==6.4.5 iniconfig==2.0.0 ipykernel==6.29.5 @@ -68,7 +68,7 @@ jsonpointer==3.0.0 jsonschema==4.23.0 jsonschema-specifications==2023.12.1 jupyter-cache==0.6.1 -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 @@ -113,17 +113,17 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.0 +particle==0.25.1 pathspec==0.12.1 pexpect==4.9.0 pickleshare==0.7.5 pillow==10.4.0 pkgutil-resolve-name==1.3.10 -platformdirs==4.3.2 +platformdirs==4.3.6 pluggy==1.5.0 pre-commit==3.5.0 -prometheus-client==0.20.0 -prompt-toolkit==3.0.47 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -134,7 +134,7 @@ pycparser==2.22 pydata-sphinx-theme==0.14.4 pygments==2.18.0 pyparsing==3.1.4 -pyproject-api==1.7.1 +pyproject-api==1.8.0 pytest==8.3.3 pytest-benchmark==4.0.0 pytest-cov==5.0.0 @@ -147,7 +147,7 @@ python-lsp-jsonrpc==1.1.2 python-lsp-ruff==2.2.2 python-lsp-server==1.12.0 pytoolconfig==1.3.1 -pytz==2024.1 +pytz==2024.2 pyyaml==6.0.2 pyzmq==26.2.0 qrules==0.10.2 @@ -155,10 +155,10 @@ referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.8.1 +rich==13.9.2 rope==1.13.0 rpds-py==0.20.0 -ruff==0.6.4 +ruff==0.6.9 scipy==1.10.1 send2trash==1.8.3 six==1.16.0 @@ -179,36 +179,36 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.3.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sqlalchemy==2.0.34 +sqlalchemy==2.0.35 stack-data==0.6.3 -sympy==1.13.2 +sympy==1.13.3 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==4.18.1 +tox==4.21.2 tqdm==4.66.5 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 +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 -virtualenv==20.26.4 +urllib3==2.2.3 +virtualenv==20.26.6 wcwidth==0.2.13 webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 wheel==0.44.0 widgetsnbextension==4.0.13 -zipp==3.20.1 +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 35a1147b..ce16b9ad 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -2,7 +2,7 @@ # 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 @@ -14,7 +14,7 @@ beautifulsoup4==4.12.3 black==24.8.0 bleach==6.1.0 cachetools==5.5.0 -cattrs==24.1.0 +cattrs==24.1.2 certifi==2024.8.30 cffi==1.17.1 cfgv==3.4.0 @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.5 +debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.8 @@ -36,22 +36,22 @@ exceptiongroup==1.2.2 execnet==2.1.1 executing==2.1.0 fastjsonschema==2.20.0 -filelock==3.16.0 -fonttools==4.53.1 +filelock==3.16.1 +fonttools==4.54.1 fqdn==1.5.1 gitdb==4.0.11 gitpython==3.1.43 gprof2dot==2024.6.6 graphviz==0.20.3 -greenlet==3.1.0 +greenlet==3.1.1 h11==0.14.0 -hepunits==2.3.4 -httpcore==1.0.5 +hepunits==2.3.5 +httpcore==1.0.6 httpx==0.27.2 -identify==2.6.0 -idna==3.8 +identify==2.6.1 +idna==3.10 imagesize==1.4.1 -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 importlib-resources==6.4.5 iniconfig==2.0.0 ipykernel==6.29.5 @@ -67,7 +67,7 @@ jsonpointer==3.0.0 jsonschema==4.23.0 jsonschema-specifications==2023.12.1 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 @@ -96,7 +96,7 @@ mpl-interactions==0.24.2 mpmath==1.3.0 mypy==1.11.2 mypy-extensions==1.0.0 -myst-nb==1.1.1 +myst-nb==1.1.2 myst-parser==3.0.1 nbclient==0.6.8 nbconvert==7.16.4 @@ -111,15 +111,15 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.0 +particle==0.25.1 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 -platformdirs==4.3.2 +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==4.0.0 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 psutil==6.0.0 ptyprocess==0.7.0 pure-eval==0.2.3 @@ -130,7 +130,7 @@ pycparser==2.22 pydata-sphinx-theme==0.15.4 pygments==2.18.0 pyparsing==3.1.4 -pyproject-api==1.7.1 +pyproject-api==1.8.0 pytest==8.3.3 pytest-benchmark==4.0.0 pytest-cov==5.0.0 @@ -150,10 +150,10 @@ referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.8.1 +rich==13.9.2 rope==1.13.0 rpds-py==0.20.0 -ruff==0.6.4 +ruff==0.6.9 scipy==1.13.1 send2trash==1.8.3 six==1.16.0 @@ -163,7 +163,7 @@ snowballstemmer==2.2.0 soupsieve==2.6 sphinx==7.4.7 sphinx-api-relink==0.0.9 -sphinx-autobuild==2024.9.3 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 sphinx-comments==0.0.3 @@ -174,40 +174,40 @@ sphinx-pybtex-etal-style==0.0.2 sphinx-thebe==0.3.1 sphinx-togglebutton==0.3.2 sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.3 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sqlalchemy==2.0.34 +sqlalchemy==2.0.35 stack-data==0.6.3 -starlette==0.38.5 -sympy==1.13.2 +starlette==0.39.2 +sympy==1.13.3 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==4.18.1 +tox==4.21.2 tqdm==4.66.5 traitlets==5.14.3 -types-python-dateutil==2.9.0.20240906 +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==0.30.6 -virtualenv==20.26.4 +urllib3==2.2.3 +uvicorn==0.31.0 +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==13.0.1 +websockets==13.1 wheel==0.44.0 widgetsnbextension==4.0.13 -zipp==3.20.1 +zipp==3.20.2 # The following packages were excluded from the output: # setuptools From 7e1adfe93e90e401bca13eb482e798e8af37e799 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:58:19 +0200 Subject: [PATCH 02/44] MAINT: share `passenv` through base environment --- tox.ini | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/tox.ini b/tox.ini index 481dffb7..b92dd7c2 100644 --- a/tox.ini +++ b/tox.ini @@ -14,6 +14,7 @@ commands = pytest {posargs} description = Run all unit tests +passenv = * setenv = PYTHONHASHSEED = 0 @@ -53,7 +54,6 @@ commands = docs/ docs/_build/html description = Build documentation and API through Sphinx -passenv = * setenv = FORCE_COLOR = yes PYTHONHASHSEED = 0 @@ -87,7 +87,6 @@ commands = docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages -passenv = * setenv = FORCE_COLOR = yes PYTHONHASHSEED = 0 @@ -103,7 +102,6 @@ commands = docs/ docs/_build/html description = Build documentation through Sphinx WITH output of Jupyter notebooks -passenv = * setenv = EXECUTE_NB = yes FORCE_COLOR = yes @@ -138,7 +136,6 @@ commands = docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages -passenv = * setenv = EXECUTE_NB = yes FORCE_COLOR = yes @@ -155,7 +152,6 @@ commands = docs/ docs/_build/html description = Execute ALL Jupyter notebooks and build documentation with Sphinx -passenv = * setenv = FORCE_COLOR = yes FORCE_EXECUTE_NB = yes @@ -180,7 +176,6 @@ commands = docs/ docs/_build/linkcheck description = Check external links in the documentation (requires internet connection) -passenv = * setenv = FORCE_COLOR = yes @@ -191,7 +186,6 @@ commands = pytest --nbmake {posargs:docs} description = Run all notebooks with pytest -passenv = * setenv = PYTHONHASHSEED = 0 @@ -207,7 +201,6 @@ deps = pydeps description = Visualize module dependencies -passenv = * [testenv:sty] allowlist_externals = From b2c12f2da55e89322d2a5285d2d6711311650357 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:58:34 +0200 Subject: [PATCH 03/44] MAINT: move `description` on one line --- tox.ini | 39 +++++++++++++-------------------------- 1 file changed, 13 insertions(+), 26 deletions(-) diff --git a/tox.ini b/tox.ini index b92dd7c2..1e288060 100644 --- a/tox.ini +++ b/tox.ini @@ -12,8 +12,7 @@ allowlist_externals = pytest commands = pytest {posargs} -description = - Run all unit tests +description = Run all unit tests passenv = * setenv = PYTHONHASHSEED = 0 @@ -26,8 +25,7 @@ commands = --durations=0 \ --benchmark-autosave \ -k benchmark -description = - Run benchmark tests and visualize in histogram +description = Run benchmark tests and visualize in histogram [testenv:cov] allowlist_externals = @@ -38,8 +36,7 @@ commands = --cov-report=html \ --cov-report=xml \ --cov=ampform -description = - Compute test coverage +description = Compute test coverage setenv = PYTHONHASHSEED = 0 @@ -52,8 +49,7 @@ commands = --keep-going \ --show-traceback --fail-on-warning \ docs/ docs/_build/html -description = - Build documentation and API through Sphinx +description = Build documentation and API through Sphinx setenv = FORCE_COLOR = yes PYTHONHASHSEED = 0 @@ -85,8 +81,7 @@ commands = --watch docs \ --watch src \ docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages +description = Set up a server to directly preview changes to the HTML pages setenv = FORCE_COLOR = yes PYTHONHASHSEED = 0 @@ -100,8 +95,7 @@ commands = --keep-going \ --show-traceback --fail-on-warning \ docs/ docs/_build/html -description = - Build documentation through Sphinx WITH output of Jupyter notebooks +description = Build documentation through Sphinx WITH output of Jupyter notebooks setenv = EXECUTE_NB = yes FORCE_COLOR = yes @@ -134,8 +128,7 @@ commands = --watch docs \ --watch src \ docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages +description = Set up a server to directly preview changes to the HTML pages setenv = EXECUTE_NB = yes FORCE_COLOR = yes @@ -150,8 +143,7 @@ commands = --builder html \ -nW \ docs/ docs/_build/html -description = - Execute ALL Jupyter notebooks and build documentation with Sphinx +description = Execute ALL Jupyter notebooks and build documentation with Sphinx setenv = FORCE_COLOR = yes FORCE_EXECUTE_NB = yes @@ -163,8 +155,7 @@ allowlist_externals = changedir = docs/_build commands = jcache {posargs:notebook list} -description = - Inspect Jupyter cache +description = Inspect Jupyter cache [testenv:linkcheck] allowlist_externals = @@ -174,8 +165,7 @@ commands = --builder linkcheck \ --show-traceback \ docs/ docs/_build/linkcheck -description = - Check external links in the documentation (requires internet connection) +description = Check external links in the documentation (requires internet connection) setenv = FORCE_COLOR = yes @@ -184,8 +174,7 @@ allowlist_externals = pytest commands = pytest --nbmake {posargs:docs} -description = - Run all notebooks with pytest +description = Run all notebooks with pytest setenv = PYTHONHASHSEED = 0 @@ -199,15 +188,13 @@ commands = --noshow deps = pydeps -description = - Visualize module dependencies +description = Visualize module dependencies [testenv:sty] allowlist_externals = pre-commit commands = pre-commit run {posargs} -a -description = - Perform all linting, formatting, and spelling checks +description = Perform all linting, formatting, and spelling checks setenv = SKIP = pyright From bf731c2bf493505aab2ff07f7b7861cc1616e3bf Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:59:04 +0200 Subject: [PATCH 04/44] MAINT: remove `FORCE_COLOR` from `tox` --- tox.ini | 7 ------- 1 file changed, 7 deletions(-) diff --git a/tox.ini b/tox.ini index 1e288060..37f2b9d6 100644 --- a/tox.ini +++ b/tox.ini @@ -51,7 +51,6 @@ commands = docs/ docs/_build/html description = Build documentation and API through Sphinx setenv = - FORCE_COLOR = yes PYTHONHASHSEED = 0 [testenv:doclive] @@ -83,7 +82,6 @@ commands = docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages setenv = - FORCE_COLOR = yes PYTHONHASHSEED = 0 [testenv:docnb] @@ -98,7 +96,6 @@ commands = description = Build documentation through Sphinx WITH output of Jupyter notebooks setenv = EXECUTE_NB = yes - FORCE_COLOR = yes PYTHONHASHSEED = 0 [testenv:docnblive] @@ -131,7 +128,6 @@ commands = description = Set up a server to directly preview changes to the HTML pages setenv = EXECUTE_NB = yes - FORCE_COLOR = yes PYTHONHASHSEED = 0 [testenv:docnb-force] @@ -145,7 +141,6 @@ commands = docs/ docs/_build/html description = Execute ALL Jupyter notebooks and build documentation with Sphinx setenv = - FORCE_COLOR = yes FORCE_EXECUTE_NB = yes PYTHONHASHSEED = 0 @@ -166,8 +161,6 @@ commands = --show-traceback \ docs/ docs/_build/linkcheck description = Check external links in the documentation (requires internet connection) -setenv = - FORCE_COLOR = yes [testenv:nb] allowlist_externals = From 30f7f0ca0f78a16340490710e6121ce82b1bd015 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:08:38 +0200 Subject: [PATCH 05/44] DX: remove `pydeps` support --- pyproject.toml | 9 --------- tox.ini | 12 ------------ 2 files changed, 21 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ea651f9f..69b37727 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -302,15 +302,6 @@ env = {FORCE_COLOR = "yes"} [tool.pixi.feature.dev.tasks.nb] cmd = "pytest --nbmake docs" -[tool.pixi.feature.dev.tasks.pydeps] -cmd = """ -pydeps ampform \ - -o module_structure.svg \ - --exclude *._* \ - --max-bacon=1 \ - --noshow -""" - [tool.pixi.feature.dev.tasks.sty] cmd = "pre-commit run -a" env = {SKIP = "pyright"} diff --git a/tox.ini b/tox.ini index 37f2b9d6..ebc37304 100644 --- a/tox.ini +++ b/tox.ini @@ -171,18 +171,6 @@ description = Run all notebooks with pytest setenv = PYTHONHASHSEED = 0 -[testenv:pydeps] -changedir = src -commands = - pydeps ampform \ - -o module_structure.svg \ - --exclude *._* \ - --max-bacon=1 \ - --noshow -deps = - pydeps -description = Visualize module dependencies - [testenv:sty] allowlist_externals = pre-commit From f4d64292b204888879f08bba59ebd282829699f7 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:09:13 +0200 Subject: [PATCH 06/44] DX: remove `jcache` job --- tox.ini | 8 -------- 1 file changed, 8 deletions(-) diff --git a/tox.ini b/tox.ini index ebc37304..4b493ef7 100644 --- a/tox.ini +++ b/tox.ini @@ -144,14 +144,6 @@ setenv = FORCE_EXECUTE_NB = yes PYTHONHASHSEED = 0 -[testenv:jcache] -allowlist_externals = - jcache -changedir = docs/_build -commands = - jcache {posargs:notebook list} -description = Inspect Jupyter cache - [testenv:linkcheck] allowlist_externals = sphinx-build From e66ea7f3e71e332b477c039701a6a402c5965e7e Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:10:23 +0200 Subject: [PATCH 07/44] MAINT: simplify `tox.ini` with `base` --- tox.ini | 70 +++++++++------------------------------------------------ 1 file changed, 10 insertions(+), 60 deletions(-) diff --git a/tox.ini b/tox.ini index 4b493ef7..1210e48e 100644 --- a/tox.ini +++ b/tox.ini @@ -37,8 +37,6 @@ commands = --cov-report=xml \ --cov=ampform description = Compute test coverage -setenv = - PYTHONHASHSEED = 0 [testenv:doc] allowlist_externals = @@ -50,8 +48,6 @@ commands = --show-traceback --fail-on-warning \ docs/ docs/_build/html description = Build documentation and API through Sphinx -setenv = - PYTHONHASHSEED = 0 [testenv:doclive] allowlist_externals = @@ -81,68 +77,24 @@ commands = --watch src \ docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages -setenv = - PYTHONHASHSEED = 0 [testenv:docnb] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder html \ - --keep-going \ - --show-traceback --fail-on-warning \ - docs/ docs/_build/html -description = Build documentation through Sphinx WITH output of Jupyter notebooks -setenv = - EXECUTE_NB = yes - PYTHONHASHSEED = 0 - -[testenv:docnblive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --builder html \ - --open-browser \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*\.gitignore \ - --re-ignore .*\.tmp \ - --re-ignore docs/_build/.* \ - --re-ignore docs/_images/.* \ - --re-ignore docs/.*\.csv \ - --re-ignore docs/.*\.gif \ - --re-ignore docs/.*\.gv \ - --re-ignore docs/.*\.inv \ - --re-ignore docs/.*\.json \ - --re-ignore docs/.*\.pickle \ - --re-ignore docs/.*\.png \ - --re-ignore docs/.*\.svg \ - --re-ignore docs/.*\.yaml \ - --re-ignore docs/.*\.yml \ - --re-ignore docs/api/.* \ - --watch docs \ - --watch src \ - docs/ docs/_build/html -description = Set up a server to directly preview changes to the HTML pages +base = doc setenv = + {[testenv:doc]}setenv EXECUTE_NB = yes - PYTHONHASHSEED = 0 [testenv:docnb-force] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --keep-going \ - --builder html \ - -nW \ - docs/ docs/_build/html -description = Execute ALL Jupyter notebooks and build documentation with Sphinx +base = doc setenv = + {[testenv:doc]}setenv FORCE_EXECUTE_NB = yes - PYTHONHASHSEED = 0 + +[testenv:docnblive] +base = doclive +setenv = + {[testenv:doclive]}setenv + EXECUTE_NB = yes [testenv:linkcheck] allowlist_externals = @@ -160,8 +112,6 @@ allowlist_externals = commands = pytest --nbmake {posargs:docs} description = Run all notebooks with pytest -setenv = - PYTHONHASHSEED = 0 [testenv:sty] allowlist_externals = From 5e0602e5a186f35bdaf61e0169a1c33dbf7aa56e Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:15:37 +0200 Subject: [PATCH 08/44] MAINT: write CLI flags with `=` sign and quotation marks --- tox.ini | 49 +++++++++++++++++++++++++------------------------ 1 file changed, 25 insertions(+), 24 deletions(-) diff --git a/tox.ini b/tox.ini index 1210e48e..5ea87b06 100644 --- a/tox.ini +++ b/tox.ini @@ -43,9 +43,10 @@ allowlist_externals = sphinx-build commands = sphinx-build \ - --builder html \ + --builder=html \ + --fail-on-warning \ --keep-going \ - --show-traceback --fail-on-warning \ + --show-traceback \ docs/ docs/_build/html description = Build documentation and API through Sphinx @@ -54,27 +55,27 @@ allowlist_externals = sphinx-autobuild commands = sphinx-autobuild \ - --builder html \ + --builder=html \ --open-browser \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*\.gitignore \ - --re-ignore .*\.tmp \ - --re-ignore docs/_build/.* \ - --re-ignore docs/_images/.* \ - --re-ignore docs/.*\.csv \ - --re-ignore docs/.*\.gif \ - --re-ignore docs/.*\.gv \ - --re-ignore docs/.*\.inv \ - --re-ignore docs/.*\.json \ - --re-ignore docs/.*\.pickle \ - --re-ignore docs/.*\.png \ - --re-ignore docs/.*\.svg \ - --re-ignore docs/.*\.yaml \ - --re-ignore docs/.*\.yml \ - --re-ignore docs/api/.* \ - --watch docs \ - --watch src \ + --re-ignore='.*/__pycache__/.*' \ + --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*\.gitignore' \ + --re-ignore='.*\.tmp' \ + --re-ignore='docs/_build/.*' \ + --re-ignore='docs/_images/.*' \ + --re-ignore='docs/.*\.csv' \ + --re-ignore='docs/.*\.gif' \ + --re-ignore='docs/.*\.gv' \ + --re-ignore='docs/.*\.inv' \ + --re-ignore='docs/.*\.json' \ + --re-ignore='docs/.*\.pickle' \ + --re-ignore='docs/.*\.png' \ + --re-ignore='docs/.*\.svg' \ + --re-ignore='docs/.*\.yaml' \ + --re-ignore='docs/.*\.yml' \ + --re-ignore='docs/api/.*' \ + --watch=docs \ + --watch=src \ docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages @@ -101,7 +102,7 @@ allowlist_externals = sphinx-build commands = sphinx-build \ - --builder linkcheck \ + --builder=linkcheck \ --show-traceback \ docs/ docs/_build/linkcheck description = Check external links in the documentation (requires internet connection) @@ -117,7 +118,7 @@ description = Run all notebooks with pytest allowlist_externals = pre-commit commands = - pre-commit run {posargs} -a + pre-commit run {posargs} --all-files description = Perform all linting, formatting, and spelling checks setenv = SKIP = pyright From 1dd70c6fc15921255949faf8aa49e6d107891f7d Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:17:18 +0200 Subject: [PATCH 09/44] MAINT: use `--ignore` instead of `--re-ignore` where possible --- tox.ini | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/tox.ini b/tox.ini index 5ea87b06..d9da4b63 100644 --- a/tox.ini +++ b/tox.ini @@ -56,24 +56,23 @@ allowlist_externals = commands = sphinx-autobuild \ --builder=html \ + --ignore=docs/_build/ \ + --ignore=docs/_images/ \ + --ignore=docs/api/ \ --open-browser \ --re-ignore='.*/__pycache__/.*' \ --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*\.csv' \ + --re-ignore='.*\.gif' \ --re-ignore='.*\.gitignore' \ + --re-ignore='.*\.gv' \ + --re-ignore='.*\.inv' \ + --re-ignore='.*\.json' \ + --re-ignore='.*\.pickle' \ + --re-ignore='.*\.png' \ + --re-ignore='.*\.svg' \ --re-ignore='.*\.tmp' \ - --re-ignore='docs/_build/.*' \ - --re-ignore='docs/_images/.*' \ - --re-ignore='docs/.*\.csv' \ - --re-ignore='docs/.*\.gif' \ - --re-ignore='docs/.*\.gv' \ - --re-ignore='docs/.*\.inv' \ - --re-ignore='docs/.*\.json' \ - --re-ignore='docs/.*\.pickle' \ - --re-ignore='docs/.*\.png' \ - --re-ignore='docs/.*\.svg' \ - --re-ignore='docs/.*\.yaml' \ - --re-ignore='docs/.*\.yml' \ - --re-ignore='docs/api/.*' \ + --re-ignore='.*\.ya?ml' \ --watch=docs \ --watch=src \ docs/ docs/_build/html From 607e5fda8364ae902945f3954dd2b9d689b532a6 Mon Sep 17 00:00:00 2001 From: GitHub Date: Thu, 10 Oct 2024 15:26:53 +0000 Subject: [PATCH 10/44] MAINT: update pip constraints and pre-commit --- .constraints/py3.10.txt | 18 +++++++++--------- .constraints/py3.11.txt | 18 +++++++++--------- .constraints/py3.12.txt | 18 +++++++++--------- .constraints/py3.7.txt | 4 ++-- .constraints/py3.8.txt | 6 +++--- .constraints/py3.9.txt | 18 +++++++++--------- 6 files changed, 41 insertions(+), 41 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 5ed9c79c..79df1c93 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -11,7 +11,7 @@ async-lru==2.0.4 attrs==24.2.0 babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 cachetools==5.5.0 cattrs==24.1.2 @@ -19,17 +19,17 @@ 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==1.3.0 -coverage==7.6.1 +coverage==7.6.2 cycler==0.12.1 debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.21.2 exceptiongroup==1.2.2 @@ -64,7 +64,7 @@ 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==8.6.3 jupyter-core==5.7.2 @@ -85,7 +85,7 @@ kiwisolver==1.4.7 latexcodec==3.0.0 lsprotocol==2023.0.1 markdown-it-py==3.0.0 -markupsafe==2.1.5 +markupsafe==3.0.1 matplotlib==3.8.4 matplotlib-inline==0.1.7 mdit-py-plugins==0.4.2 @@ -110,13 +110,13 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.1 +particle==0.25.2 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==4.0.0 +pre-commit==4.0.1 prometheus-client==0.21.0 prompt-toolkit==3.0.48 psutil==6.0.0 @@ -196,7 +196,7 @@ typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 urllib3==2.2.3 -uvicorn==0.31.0 +uvicorn==0.31.1 virtualenv==20.26.6 watchfiles==0.24.0 wcwidth==0.2.13 diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt index e0353e87..8bd8edd0 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -11,7 +11,7 @@ async-lru==2.0.4 attrs==24.2.0 babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 cachetools==5.5.0 cattrs==24.1.2 @@ -19,17 +19,17 @@ 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==1.3.0 -coverage==7.6.1 +coverage==7.6.2 cycler==0.12.1 debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.21.2 execnet==2.1.1 @@ -63,7 +63,7 @@ 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==8.6.3 jupyter-core==5.7.2 @@ -84,7 +84,7 @@ kiwisolver==1.4.7 latexcodec==3.0.0 lsprotocol==2023.0.1 markdown-it-py==3.0.0 -markupsafe==2.1.5 +markupsafe==3.0.1 matplotlib==3.8.4 matplotlib-inline==0.1.7 mdit-py-plugins==0.4.2 @@ -109,13 +109,13 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.1 +particle==0.25.2 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==4.0.0 +pre-commit==4.0.1 prometheus-client==0.21.0 prompt-toolkit==3.0.48 psutil==6.0.0 @@ -195,7 +195,7 @@ typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 urllib3==2.2.3 -uvicorn==0.31.0 +uvicorn==0.31.1 virtualenv==20.26.6 watchfiles==0.24.0 wcwidth==0.2.13 diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt index 131d1e85..38fe0d81 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -11,7 +11,7 @@ async-lru==2.0.4 attrs==24.2.0 babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 cachetools==5.5.0 cattrs==24.1.2 @@ -19,17 +19,17 @@ 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==1.3.0 -coverage==7.6.1 +coverage==7.6.2 cycler==0.12.1 debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.21.2 execnet==2.1.1 @@ -63,7 +63,7 @@ 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==8.6.3 jupyter-core==5.7.2 @@ -84,7 +84,7 @@ kiwisolver==1.4.7 latexcodec==3.0.0 lsprotocol==2023.0.1 markdown-it-py==3.0.0 -markupsafe==2.1.5 +markupsafe==3.0.1 matplotlib==3.8.4 matplotlib-inline==0.1.7 mdit-py-plugins==0.4.2 @@ -109,13 +109,13 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.1 +particle==0.25.2 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==4.0.0 +pre-commit==4.0.1 prometheus-client==0.21.0 prompt-toolkit==3.0.48 psutil==6.0.0 @@ -194,7 +194,7 @@ typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 urllib3==2.2.3 -uvicorn==0.31.0 +uvicorn==0.31.1 virtualenv==20.26.6 watchfiles==0.24.0 wcwidth==0.2.13 diff --git a/.constraints/py3.7.txt b/.constraints/py3.7.txt index 9b567897..aa3092e0 100644 --- a/.constraints/py3.7.txt +++ b/.constraints/py3.7.txt @@ -21,7 +21,7 @@ certifi==2024.8.30 cffi==1.15.1 cfgv==3.3.1 chardet==5.2.0 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 colorama==0.4.6 comm==0.1.4 @@ -30,7 +30,7 @@ cycler==0.11.0 debugpy==1.7.0 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.17.1 entrypoints==0.4 diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt index 344433c2..c957438b 100644 --- a/.constraints/py3.8.txt +++ b/.constraints/py3.8.txt @@ -20,7 +20,7 @@ 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 @@ -30,7 +30,7 @@ cycler==0.12.1 debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.17.1 exceptiongroup==1.2.2 @@ -113,7 +113,7 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.1 +particle==0.25.2 pathspec==0.12.1 pexpect==4.9.0 pickleshare==0.7.5 diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index ce16b9ad..f9c41c34 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -11,7 +11,7 @@ async-lru==2.0.4 attrs==24.2.0 babel==2.16.0 beautifulsoup4==4.12.3 -black==24.8.0 +black==24.10.0 bleach==6.1.0 cachetools==5.5.0 cattrs==24.1.2 @@ -19,17 +19,17 @@ 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==1.3.0 -coverage==7.6.1 +coverage==7.6.2 cycler==0.12.1 debugpy==1.8.6 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 +distlib==0.3.9 docstring-to-markdown==0.15 docutils==0.21.2 exceptiongroup==1.2.2 @@ -65,7 +65,7 @@ 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==8.6.3 jupyter-core==5.7.2 @@ -86,7 +86,7 @@ kiwisolver==1.4.7 latexcodec==3.0.0 lsprotocol==2023.0.1 markdown-it-py==3.0.0 -markupsafe==2.1.5 +markupsafe==3.0.1 matplotlib==3.8.4 matplotlib-inline==0.1.7 mdit-py-plugins==0.4.2 @@ -111,13 +111,13 @@ overrides==7.7.0 packaging==24.1 pandocfilters==1.5.1 parso==0.8.4 -particle==0.25.1 +particle==0.25.2 pathspec==0.12.1 pexpect==4.9.0 pillow==10.4.0 platformdirs==4.3.6 pluggy==1.5.0 -pre-commit==4.0.0 +pre-commit==4.0.1 prometheus-client==0.21.0 prompt-toolkit==3.0.48 psutil==6.0.0 @@ -197,7 +197,7 @@ typing-extensions==4.12.2 ujson==5.10.0 uri-template==1.3.0 urllib3==2.2.3 -uvicorn==0.31.0 +uvicorn==0.31.1 virtualenv==20.26.6 watchfiles==0.24.0 wcwidth==0.2.13 From c384a63be8b2d11f9ad51511fd845a6de95b7e2f Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 4 Oct 2024 16:49:47 +0200 Subject: [PATCH 11/44] FIX: update links to ComPWA TRs --- docs/_extend_docstrings.py | 2 +- docs/conf.py | 1 + docs/usage/dynamics/analytic-continuation.ipynb | 2 +- docs/usage/dynamics/k-matrix.ipynb | 4 ++-- docs/usage/helicity/spin-alignment.ipynb | 4 ++-- docs/usage/kinematics.ipynb | 4 ++-- src/ampform/dynamics/form_factor.py | 4 ++-- src/ampform/dynamics/kmatrix.py | 4 ++-- src/ampform/helicity/__init__.py | 2 +- src/ampform/sympy/deprecated.py | 2 +- src/ampform/sympy/math.py | 2 +- src/symplot/__init__.py | 2 +- 12 files changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/_extend_docstrings.py b/docs/_extend_docstrings.py index 7d44e164..59608a53 100644 --- a/docs/_extend_docstrings.py +++ b/docs/_extend_docstrings.py @@ -515,7 +515,7 @@ def extend_chew_mandelstam_s_wave() -> None: with :math:`q^2(s)` defined as :eq:`BreakupMomentumSquared`. - .. seealso:: :doc:`compwa:report/003` + .. seealso:: :doc:`compwa-report:003` """, ) diff --git a/docs/conf.py b/docs/conf.py index 974c4dc1..e63a0e91 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -266,6 +266,7 @@ def _get_dataclasses(module): "IPython": (f"https://ipython.readthedocs.io/en/{pin('IPython')}", None), "attrs": (f"https://www.attrs.org/en/{pin('attrs')}", None), "compwa": ("https://compwa.github.io", None), + "compwa-report": ("https://compwa.github.io/report", None), "graphviz": ("https://graphviz.readthedocs.io/en/stable", None), "ipywidgets": (f"https://ipywidgets.readthedocs.io/en/{pin('ipywidgets')}", None), "matplotlib": (f"https://matplotlib.org/{pin('matplotlib')}", None), diff --git a/docs/usage/dynamics/analytic-continuation.ipynb b/docs/usage/dynamics/analytic-continuation.ipynb index e67f6752..21144482 100644 --- a/docs/usage/dynamics/analytic-continuation.ipynb +++ b/docs/usage/dynamics/analytic-continuation.ipynb @@ -63,7 +63,7 @@ "source": [ ":::{note}\n", "\n", - "Improvements to analytic continuation in AmpForm are currently being developed in {doc}`compwa:report/003` and {doc}`compwa:report/004`.\n", + "Improvements to analytic continuation in AmpForm are currently being developed in {doc}`compwa-report:003` and {doc}`compwa-report:004`.\n", "\n", ":::" ] diff --git a/docs/usage/dynamics/k-matrix.ipynb b/docs/usage/dynamics/k-matrix.ipynb index e0368a90..7997d649 100644 --- a/docs/usage/dynamics/k-matrix.ipynb +++ b/docs/usage/dynamics/k-matrix.ipynb @@ -74,7 +74,7 @@ "\n", ":::{note}\n", "\n", - "The $\\boldsymbol{K}$-matrix approach was originally worked worked out in {doc}`compwa:report/005`, {doc}`compwa:report/009`, and {doc}`compwa:report/010`. Those reports contained a few mistakes, which have been addressed here.\n", + "The $\\boldsymbol{K}$-matrix approach was originally worked worked out in {doc}`compwa-report:005`, {doc}`compwa-report:009`, and {doc}`compwa-report:010`. Those reports contained a few mistakes, which have been addressed here.\n", "\n", ":::\n", "\n", @@ -331,7 +331,7 @@ "\\end{eqnarray}\n", "$$ (K-hat-and-T-hat)\n", "\n", - "[^rho-dagger]: An unpublished primer on the $\\boldsymbol{K}$-matrix by Chung {cite}`chungPrimerKmatrixFormalism1995` uses a conjugate transpose of $\\boldsymbol{\\rho}$, e.g. $\\boldsymbol{T} = \\sqrt{\\boldsymbol{\\rho^\\dagger}} \\; \\boldsymbol{\\hat{T}} \\sqrt{\\boldsymbol{\\rho}}$. This should not matter above threshold, where the phase space factor is real, but could have effects below threshold. This is where things become tricky: on the one hand, we need to ensure that $\\boldsymbol{K}$ remains real (unitarity) and on the other, we need to take keep track of which imaginary square root we choose (**Riemann sheet**). The latter is often called the requirement of **analyticity**. This is currently being explored in {doc}`compwa:report/003` and {doc}`compwa:report/004`.\n", + "[^rho-dagger]: An unpublished primer on the $\\boldsymbol{K}$-matrix by Chung {cite}`chungPrimerKmatrixFormalism1995` uses a conjugate transpose of $\\boldsymbol{\\rho}$, e.g. $\\boldsymbol{T} = \\sqrt{\\boldsymbol{\\rho^\\dagger}} \\; \\boldsymbol{\\hat{T}} \\sqrt{\\boldsymbol{\\rho}}$. This should not matter above threshold, where the phase space factor is real, but could have effects below threshold. This is where things become tricky: on the one hand, we need to ensure that $\\boldsymbol{K}$ remains real (unitarity) and on the other, we need to take keep track of which imaginary square root we choose (**Riemann sheet**). The latter is often called the requirement of **analyticity**. This is currently being explored in {doc}`compwa-report:003` and {doc}`compwa-report:004`.\n", "\n", "With these definitions, we can deduce that:\n", "\n", diff --git a/docs/usage/helicity/spin-alignment.ipynb b/docs/usage/helicity/spin-alignment.ipynb index 8308998c..efd137f4 100644 --- a/docs/usage/helicity/spin-alignment.ipynb +++ b/docs/usage/helicity/spin-alignment.ipynb @@ -93,7 +93,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "As described in {doc}`compwa:report/015`, the {doc}`'standard' helicity formalism ` is not suited for state transitions that have different decay topologies. For this reason, the {class}`.HelicityAmplitudeBuilder` can insert a number of Wigner-$D$ functions into the amplitude model to 'align' the final state spins of underlying {class}`~qrules.topology.Topology` instances in the full decay.\n", + "As described in {doc}`compwa-report:015`, the {doc}`'standard' helicity formalism ` is not suited for state transitions that have different decay topologies. For this reason, the {class}`.HelicityAmplitudeBuilder` can insert a number of Wigner-$D$ functions into the amplitude model to 'align' the final state spins of underlying {class}`~qrules.topology.Topology` instances in the full decay.\n", "\n", "Imagine we have the following the decay:" ] @@ -388,7 +388,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "For more information about these angles, see {ref}`compwa:report/015:Compute Wigner rotation angles` in {doc}`TR-015 `." + "For more information about these angles, see {ref}`compwa-report:015:Compute Wigner rotation angles` in {doc}`TR-015 `." ] } ], diff --git a/docs/usage/kinematics.ipynb b/docs/usage/kinematics.ipynb index 37d4f08d..96f7dacc 100644 --- a/docs/usage/kinematics.ipynb +++ b/docs/usage/kinematics.ipynb @@ -260,7 +260,7 @@ "metadata": {}, "source": [ ":::{margin}\n", - "This notebook originates from {doc}`compwa:report/017`.\n", + "This notebook originates from {doc}`compwa-report:017`.\n", ":::\n", "\n", "Kinematics for a three-body decay $0 \\to 123$ can be fully described by two **Mandelstam variables** $\\sigma_1, \\sigma_2$, because the third variable $\\sigma_3$ can be expressed in terms $\\sigma_1, \\sigma_2$, the mass $m_0$ of the initial state, and the masses $m_1, m_2, m_3$ of the final state. As can be seen, the roles of $\\sigma_1, \\sigma_2, \\sigma_3$ are interchangeable.\n", @@ -384,7 +384,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "See {doc}`compwa:report/017` for an interactive visualization of the phase space region and an analytic expression for the phase space boundary." + "See {doc}`compwa-report:017` for an interactive visualization of the phase space region and an analytic expression for the phase space boundary." ] } ], diff --git a/src/ampform/dynamics/form_factor.py b/src/ampform/dynamics/form_factor.py index e1c6b733..0ab30547 100644 --- a/src/ampform/dynamics/form_factor.py +++ b/src/ampform/dynamics/form_factor.py @@ -52,7 +52,7 @@ class BlattWeisskopfSquared(sp.Expr): :pdg-review:`2021; Resonances; p.9`. We normalize the form factor such that :math:`B_L^2(1)=1` and that :math:`B_L^2` is unitless no matter what :math:`z` is. - .. seealso:: :ref:`usage/dynamics:Form factor`, :doc:`TR-029`, + .. seealso:: :ref:`usage/dynamics:Form factor`, :doc:`TR-029`, and :cite:`chungFormulasAngularMomentumBarrier2015`. With this, the implementation becomes @@ -94,7 +94,7 @@ def _formulate_blatt_weisskopf(ell, z) -> sp.Expr: class SphericalHankel1(sp.Expr): r"""Spherical Hankel function of the first kind for real-valued :math:`z`. - See :cite:`VonHippel:1972fg`, Equation (A12), and :doc:`TR-029` + See :cite:`VonHippel:1972fg`, Equation (A12), and :doc:`TR-029` for more info. `This page `_ explains the difference with the *general* Hankel function of the first kind, diff --git a/src/ampform/dynamics/kmatrix.py b/src/ampform/dynamics/kmatrix.py index 47bf7dd2..d73512c0 100644 --- a/src/ampform/dynamics/kmatrix.py +++ b/src/ampform/dynamics/kmatrix.py @@ -2,8 +2,8 @@ .. seealso:: :doc:`/usage/dynamics/k-matrix`. -This module is an implementation of :doc:`compwa:report/005`, -:doc:`compwa:report/009`, and :doc:`compwa:report/010`. It works with classes to +This module is an implementation of :doc:`compwa-report:005`, +:doc:`compwa-report:009`, and :doc:`compwa-report:010`. It works with classes to keep the code organized and to enable caching of the matrix multiplications, but this might change once these dynamics are implemented into the amplitude builder. """ diff --git a/src/ampform/helicity/__init__.py b/src/ampform/helicity/__init__.py index e1df7257..61d69871 100644 --- a/src/ampform/helicity/__init__.py +++ b/src/ampform/helicity/__init__.py @@ -128,7 +128,7 @@ class HelicityModel: helicity combination. These amplitudes are indicated with as `sp.Indexed ` instances and this attribute provides the definitions for each of these. See also - :ref:`TR-014 `. + :ref:`TR-014 `. """ parameter_defaults: ParameterValues = field(converter=_to_parameter_values) """A mapping of suggested parameter values. diff --git a/src/ampform/sympy/deprecated.py b/src/ampform/sympy/deprecated.py index f7093155..eb83d173 100644 --- a/src/ampform/sympy/deprecated.py +++ b/src/ampform/sympy/deprecated.py @@ -31,7 +31,7 @@ class UnevaluatedExpression(sp.Expr): 1. condense the LaTeX representation of an expression tree by providing a custom :meth:`_latex` method. 2. overwrite its printer methods (see `.NumPyPrintable` and e.g. - :doc:`compwa:report/001`). + :doc:`compwa-report:001`). The `UnevaluatedExpression` base class makes implementations of its derived classes more secure by enforcing the developer to provide implementations for these methods, diff --git a/src/ampform/sympy/math.py b/src/ampform/sympy/math.py index b7370c08..8f6f1d66 100644 --- a/src/ampform/sympy/math.py +++ b/src/ampform/sympy/math.py @@ -26,7 +26,7 @@ class ComplexSqrt(NumPyPrintable): A special version :func:`~sympy.functions.elementary.miscellaneous.sqrt` that renders nicely as LaTeX and and can be used as a handle for lambdify printers. See - :doc:`compwa:report/000`, :doc:`compwa:report/001`, and + :doc:`compwa-report:000`, :doc:`compwa-report:001`, and :doc:`sympy:modules/printing` for how to implement a custom :func:`~sympy.utilities.lambdify.lambdify` printer. """ diff --git a/src/symplot/__init__.py b/src/symplot/__init__.py index 6b504a2d..5d7a811b 100644 --- a/src/symplot/__init__.py +++ b/src/symplot/__init__.py @@ -390,7 +390,7 @@ def rename_symbols( def substitute_indexed_symbols(expression: sp.Expr) -> sp.Expr: """Substitute `~sympy.tensor.indexed.IndexedBase` with symbols. - See :doc:`compwa:report/008` for more info. + See :doc:`compwa-report:008` for more info. """ return expression.xreplace({ s: _indexed_to_symbol(s) From 6057cc325ec9100ec582dfb9aeb335f0d4560e8a Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 20:36:36 +0200 Subject: [PATCH 12/44] DX: disable Sphinx warnings in `linkcheck` job --- tox.ini | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/tox.ini b/tox.ini index d9da4b63..e476fc6f 100644 --- a/tox.ini +++ b/tox.ini @@ -49,6 +49,8 @@ commands = --show-traceback \ docs/ docs/_build/html description = Build documentation and API through Sphinx +setenv = + PYTHONWARNINGS = [testenv:doclive] allowlist_externals = @@ -77,23 +79,25 @@ commands = --watch=src \ docs/ docs/_build/html description = Set up a server to directly preview changes to the HTML pages +setenv = + {[testenv:doc]setenv} [testenv:docnb] base = doc setenv = - {[testenv:doc]}setenv + {[testenv:doc]setenv} EXECUTE_NB = yes [testenv:docnb-force] base = doc setenv = - {[testenv:doc]}setenv + {[testenv:doc]setenv} FORCE_EXECUTE_NB = yes [testenv:docnblive] base = doclive setenv = - {[testenv:doclive]}setenv + {[testenv:doclive]setenv} EXECUTE_NB = yes [testenv:linkcheck] @@ -105,6 +109,8 @@ commands = --show-traceback \ docs/ docs/_build/linkcheck description = Check external links in the documentation (requires internet connection) +setenv = + {[testenv:doclive]setenv} [testenv:nb] allowlist_externals = From 797872dc626af7687b95b0cc2bf37012fca372b8 Mon Sep 17 00:00:00 2001 From: GitHub Date: Thu, 10 Oct 2024 18:37:42 +0000 Subject: [PATCH 13/44] MAINT: update pip constraints and pre-commit --- .constraints/py3.10.txt | 4 ++-- .constraints/py3.11.txt | 4 ++-- .constraints/py3.12.txt | 4 ++-- .constraints/py3.8.txt | 2 +- .constraints/py3.9.txt | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 79df1c93..c4acfa7d 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.2 cycler==0.12.1 -debugpy==1.8.6 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 @@ -160,7 +160,7 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==8.0.2 +sphinx==8.1.0 sphinx-api-relink==0.0.9 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt index 8bd8edd0..a507e2ad 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.2 cycler==0.12.1 -debugpy==1.8.6 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 @@ -159,7 +159,7 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==8.0.2 +sphinx==8.1.0 sphinx-api-relink==0.0.9 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt index 38fe0d81..8aa7de35 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.2 cycler==0.12.1 -debugpy==1.8.6 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 @@ -159,7 +159,7 @@ smmap==5.0.1 sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 -sphinx==8.0.2 +sphinx==8.1.0 sphinx-api-relink==0.0.9 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt index c957438b..bca29b05 100644 --- a/.constraints/py3.8.txt +++ b/.constraints/py3.8.txt @@ -27,7 +27,7 @@ comm==0.2.2 contourpy==1.1.1 coverage==7.6.1 cycler==0.12.1 -debugpy==1.8.6 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index f9c41c34..f677e1fa 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -26,7 +26,7 @@ comm==0.2.2 contourpy==1.3.0 coverage==7.6.2 cycler==0.12.1 -debugpy==1.8.6 +debugpy==1.8.7 decorator==5.1.1 defusedxml==0.7.1 distlib==0.3.9 From 9719708f2134595cd901ae94b3f9a95d8d8221c4 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Thu, 10 Oct 2024 21:19:07 +0200 Subject: [PATCH 14/44] FIX: start `sphinx-autobuild` on random available port --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index e476fc6f..67208ec0 100644 --- a/tox.ini +++ b/tox.ini @@ -62,6 +62,7 @@ commands = --ignore=docs/_images/ \ --ignore=docs/api/ \ --open-browser \ + --port=0 \ --re-ignore='.*/__pycache__/.*' \ --re-ignore='.*/.ipynb_checkpoints/.*' \ --re-ignore='.*\.csv' \ From d2909cc5c1833f7018aea2635368b64670aaa8e1 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:48:49 +0200 Subject: [PATCH 15/44] DX: run `cov`, `docnb-force`, `linkcheck`, and `sty` in `tox` --- tox.ini | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tox.ini b/tox.ini index 67208ec0..adb9b551 100644 --- a/tox.ini +++ b/tox.ini @@ -1,7 +1,8 @@ [tox] envlist = - py, - doc, + cov, + docnb-force, + linkcheck, sty, skip_install = True skip_missing_interpreters = True From 7a42c1ea48e86604e5d49c1071a61fd929bb6c9a Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:50:30 +0200 Subject: [PATCH 16/44] DOC: improve Tox job descriptions --- tox.ini | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tox.ini b/tox.ini index adb9b551..6883179d 100644 --- a/tox.ini +++ b/tox.ini @@ -86,18 +86,21 @@ setenv = [testenv:docnb] base = doc +description = {[testenv:doc]description} with cached notebook execution setenv = {[testenv:doc]setenv} EXECUTE_NB = yes [testenv:docnb-force] base = doc +description = {[testenv:doc]description} with notebook execution (no cache) setenv = {[testenv:doc]setenv} FORCE_EXECUTE_NB = yes [testenv:docnblive] base = doclive +description = {[testenv:doclive]description} with cached notebook execution setenv = {[testenv:doclive]setenv} EXECUTE_NB = yes From 4fd44ae64948d1254245c1ec5abd0b71df338d2c Mon Sep 17 00:00:00 2001 From: GitHub Date: Fri, 11 Oct 2024 09:51:37 +0000 Subject: [PATCH 17/44] MAINT: update pip constraints and pre-commit --- .constraints/py3.10.txt | 2 +- .constraints/py3.11.txt | 2 +- .constraints/py3.12.txt | 2 +- .constraints/py3.9.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index c4acfa7d..4dcdd947 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -161,7 +161,7 @@ sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.1.0 -sphinx-api-relink==0.0.9 +sphinx-api-relink==0.0.10 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt index a507e2ad..67565b0a 100644 --- a/.constraints/py3.11.txt +++ b/.constraints/py3.11.txt @@ -160,7 +160,7 @@ sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.1.0 -sphinx-api-relink==0.0.9 +sphinx-api-relink==0.0.10 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 diff --git a/.constraints/py3.12.txt b/.constraints/py3.12.txt index 8aa7de35..c48cbfc5 100644 --- a/.constraints/py3.12.txt +++ b/.constraints/py3.12.txt @@ -160,7 +160,7 @@ sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 sphinx==8.1.0 -sphinx-api-relink==0.0.9 +sphinx-api-relink==0.0.10 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index f677e1fa..6d3a4cd7 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -162,7 +162,7 @@ sniffio==1.3.1 snowballstemmer==2.2.0 soupsieve==2.6 sphinx==7.4.7 -sphinx-api-relink==0.0.9 +sphinx-api-relink==0.0.10 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-codeautolink==0.15.2 From 99b85c49e6744e16162517e05772875195c13b11 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:55:27 +0200 Subject: [PATCH 18/44] MAINT: ignore links to PRD --- docs/conf.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index e63a0e91..b84a475e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -283,11 +283,12 @@ def _get_dataclasses(module): linkcheck_anchors = False linkcheck_ignore = [ "http://www.curtismeyer.com", - "https://doi.org/10.1002/andp.19955070504", # 403 for onlinelibrary.wiley.com - "https://doi.org/10.1093/ptep/ptaa104", - "https://doi.org/10.1155/2020/6674595", # 403 for hindawi.com + "https://doi.org/10.1002", # 403 for onlinelibrary.wiley.com + "https://doi.org/10.1103", # 403 for Phys Rev D + "https://doi.org/10.1155", # 403 for hindawi.com "https://home.fnal.gov/~kutschke/Angdist/angdist.ps", "https://hss-opus.ub.ruhr-uni-bochum.de", + "https://journals.aps.org/prd", # 403 for Phys Rev D "https://physique.cuso.ch", "https://suchung.web.cern.ch", "https://www.bookfinder.com", From 56764ee36a501fe451ab90e459cdb4d7b9e3fe96 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 11 Oct 2024 12:18:43 +0200 Subject: [PATCH 19/44] DOC: group doc jobs for `tox list` --- tox.ini | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/tox.ini b/tox.ini index 6883179d..2208b3f0 100644 --- a/tox.ini +++ b/tox.ini @@ -53,6 +53,20 @@ description = Build documentation and API through Sphinx setenv = PYTHONWARNINGS = +[testenv:docnb] +base = doc +description = {[testenv:doc]description} with cached notebook execution +setenv = + {[testenv:doc]setenv} + EXECUTE_NB = yes + +[testenv:docnb-force] +base = doc +description = {[testenv:doc]description} with notebook execution (no cache) +setenv = + {[testenv:doc]setenv} + FORCE_EXECUTE_NB = yes + [testenv:doclive] allowlist_externals = sphinx-autobuild @@ -84,20 +98,6 @@ description = Set up a server to directly preview changes to the HTML pages setenv = {[testenv:doc]setenv} -[testenv:docnb] -base = doc -description = {[testenv:doc]description} with cached notebook execution -setenv = - {[testenv:doc]setenv} - EXECUTE_NB = yes - -[testenv:docnb-force] -base = doc -description = {[testenv:doc]description} with notebook execution (no cache) -setenv = - {[testenv:doc]setenv} - FORCE_EXECUTE_NB = yes - [testenv:docnblive] base = doclive description = {[testenv:doclive]description} with cached notebook execution From 02b542d867b253960bcf816079510610add186ad Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 11 Oct 2024 13:50:19 +0200 Subject: [PATCH 20/44] DX: add `.virtual_documents` to `--re-ignore` --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index 2208b3f0..83191636 100644 --- a/tox.ini +++ b/tox.ini @@ -80,6 +80,7 @@ commands = --port=0 \ --re-ignore='.*/__pycache__/.*' \ --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*/.virtual_documents/.*' \ --re-ignore='.*\.csv' \ --re-ignore='.*\.gif' \ --re-ignore='.*\.gitignore' \ From 247e6754b7f72e569cf2a67faad5800bd8736a82 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 15 Oct 2024 09:36:21 +0200 Subject: [PATCH 21/44] DX: migrate to `uv` environment --- .constraints/.gitignore | 1 - .constraints/py3.10.txt | 212 -- .constraints/py3.11.txt | 211 -- .constraints/py3.12.txt | 210 -- .constraints/py3.9.txt | 213 -- .cspell.json | 3 - .editorconfig | 3 + .envrc | 12 +- .gitattributes | 1 - .github/workflows/cd.yml | 2 +- .github/workflows/clean-caches.yml | 2 +- .github/workflows/release-drafter.yml | 2 +- .github/workflows/requirements.yml | 1 - .gitignore | 3 - .pre-commit-config.yaml | 22 +- .python-version | 1 + .readthedocs.yml | 5 +- .vscode/settings.json | 9 +- CONTRIBUTING.md | 25 +- README.md | 1 + docs/install.md | 65 +- environment.yml | 12 - pyproject.toml | 262 +- tox.ini | 135 - uv.lock | 4008 +++++++++++++++++++++++++ 25 files changed, 4205 insertions(+), 1216 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 .gitattributes create mode 100644 .python-version delete mode 100644 environment.yml delete mode 100644 tox.ini create mode 100644 uv.lock diff --git a/.constraints/.gitignore b/.constraints/.gitignore deleted file mode 100644 index 36a07ad0..00000000 --- a/.constraints/.gitignore +++ /dev/null @@ -1 +0,0 @@ -!py3.*.txt diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt deleted file mode 100644 index 4dcdd947..00000000 --- a/.constraints/py3.10.txt +++ /dev/null @@ -1,212 +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 -coverage==7.6.2 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.1 -h11==0.14.0 -hepunits==2.3.5 -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 -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 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.8.4 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mpl-interactions==0.24.2 -mpmath==1.3.0 -mypy==1.11.2 -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 -particle==0.25.2 -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 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -pytest-benchmark==4.0.0 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -qrules==0.10.2 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rich==13.9.2 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.9 -scipy==1.14.1 -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-api-relink==0.0.10 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.3 -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 -sympy==1.13.3 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.2 -tornado==6.4.1 -tox==4.21.2 -tqdm==4.66.5 -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 67565b0a..00000000 --- a/.constraints/py3.11.txt +++ /dev/null @@ -1,211 +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 -coverage==7.6.2 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.1 -h11==0.14.0 -hepunits==2.3.5 -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 -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 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.8.4 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mpl-interactions==0.24.2 -mpmath==1.3.0 -mypy==1.11.2 -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 -particle==0.25.2 -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 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -pytest-benchmark==4.0.0 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -qrules==0.10.2 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rich==13.9.2 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.9 -scipy==1.14.1 -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-api-relink==0.0.10 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.3 -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 -sympy==1.13.3 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.2 -tornado==6.4.1 -tox==4.21.2 -tqdm==4.66.5 -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 c48cbfc5..00000000 --- a/.constraints/py3.12.txt +++ /dev/null @@ -1,210 +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 -coverage==7.6.2 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.1 -h11==0.14.0 -hepunits==2.3.5 -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 -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 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.8.4 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mpl-interactions==0.24.2 -mpmath==1.3.0 -mypy==1.11.2 -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 -particle==0.25.2 -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 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -pytest-benchmark==4.0.0 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -qrules==0.10.2 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rich==13.9.2 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.9 -scipy==1.14.1 -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-api-relink==0.0.10 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.3 -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 -sympy==1.13.3 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tornado==6.4.1 -tox==4.21.2 -tqdm==4.66.5 -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 6d3a4cd7..00000000 --- a/.constraints/py3.9.txt +++ /dev/null @@ -1,213 +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 -coverage==7.6.2 -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 -execnet==2.1.1 -executing==2.1.0 -fastjsonschema==2.20.0 -filelock==3.16.1 -fonttools==4.54.1 -fqdn==1.5.1 -gitdb==4.0.11 -gitpython==3.1.43 -gprof2dot==2024.6.6 -graphviz==0.20.3 -greenlet==3.1.1 -h11==0.14.0 -hepunits==2.3.5 -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 -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 -latexcodec==3.0.0 -lsprotocol==2023.0.1 -markdown-it-py==3.0.0 -markupsafe==3.0.1 -matplotlib==3.8.4 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -mistune==3.0.2 -mpl-interactions==0.24.2 -mpmath==1.3.0 -mypy==1.11.2 -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 -particle==0.25.2 -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 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pybtex-docutils==1.0.3 -pycparser==2.22 -pydata-sphinx-theme==0.15.4 -pygments==2.18.0 -pyparsing==3.1.4 -pyproject-api==1.8.0 -pytest==8.3.3 -pytest-benchmark==4.0.0 -pytest-cov==5.0.0 -pytest-profiling==1.7.0 -pytest-xdist==3.6.1 -python-constraint2==2.0.0b5 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -python-lsp-jsonrpc==1.1.2 -python-lsp-ruff==2.2.2 -python-lsp-server==1.12.0 -pytoolconfig==1.3.1 -pyyaml==6.0.2 -pyzmq==26.2.0 -qrules==0.10.2 -referencing==0.35.1 -requests==2.32.3 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rich==13.9.2 -rope==1.13.0 -rpds-py==0.20.0 -ruff==0.6.9 -scipy==1.13.1 -send2trash==1.8.3 -six==1.16.0 -smmap==5.0.1 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.6 -sphinx==7.4.7 -sphinx-api-relink==0.0.10 -sphinx-autobuild==2024.10.3 -sphinx-book-theme==1.1.3 -sphinx-codeautolink==0.15.2 -sphinx-comments==0.0.3 -sphinx-copybutton==0.5.2 -sphinx-design==0.6.1 -sphinx-hep-pdgref==0.2.0 -sphinx-pybtex-etal-style==0.0.2 -sphinx-thebe==0.3.1 -sphinx-togglebutton==0.3.2 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-bibtex==2.6.3 -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 -sympy==1.13.3 -tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.3.0 -tomli==2.0.2 -tornado==6.4.1 -tox==4.21.2 -tqdm==4.66.5 -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/.cspell.json b/.cspell.json index 75779f22..d5505979 100644 --- a/.cspell.json +++ b/.cspell.json @@ -23,10 +23,8 @@ "**/*.bib", "**/.cspell.json", "*.ico", - ".constraints/*.txt", ".editorconfig", ".envrc", - ".gitattributes", ".gitignore", ".pre-commit-config.yaml", ".prettierignore", @@ -36,7 +34,6 @@ "codecov.yml", "docs/conf.py", "pyproject.toml", - "tox.ini", "typings" ], "ignoreWords": [ diff --git a/.editorconfig b/.editorconfig index 88befe69..9e92189a 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,3 +18,6 @@ indent_size = unset [setup.cfg] indent_size = 4 + +[uv.lock] +indent_size = 4 diff --git a/.envrc b/.envrc index e1d415a5..41fd2cab 100644 --- a/.envrc +++ b/.envrc @@ -1,10 +1,2 @@ -if [ -e .venv ]; then - source .venv/bin/activate -elif [ -e venv ]; then - source venv/bin/activate -elif [ -e .pixi ]; then - watch_file pixi.lock - eval "$(pixi shell-hook)" -else - layout anaconda -fi +uv sync --all-extras --quiet +source .venv/bin/activate diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 18f6c7e9..00000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 54ae3bc8..2f66c9ab 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -22,7 +22,7 @@ jobs: - package-name permissions: id-token: write - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: ComPWA/actions/build-pypi-distribution@v1 - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index a66c407b..939e1361 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/release-drafter.yml b/.github/workflows/release-drafter.yml index 52340935..32c6579c 100644 --- a/.github/workflows/release-drafter.yml +++ b/.github/workflows/release-drafter.yml @@ -9,7 +9,7 @@ on: jobs: update_release_draft: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: release-drafter/release-drafter@v6 env: diff --git a/.github/workflows/requirements.yml b/.github/workflows/requirements.yml index 6716e974..e1639791 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 */1 *" diff --git a/.gitignore b/.gitignore index c54ff596..0849c1fd 100644 --- a/.gitignore +++ b/.gitignore @@ -21,7 +21,6 @@ version.py # Temporary files *.pyc -*condaenv.* .coverage .coverage.* .ipynb_checkpoints/ @@ -36,7 +35,6 @@ prof/ # Virtual environments *venv/ -.pixi/ .tox/ pyvenv*/ @@ -53,5 +51,4 @@ pyvenv*/ !.vscode/*.json !.zenodo.json !codecov.yml -!environment.yml !pyrightconfig.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6de6e2a9..c72f8001 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,10 +1,11 @@ ci: - autoupdate_commit_msg: "MAINT: update pip constraints and pre-commit" + autoupdate_commit_msg: "MAINT: update lock files" autoupdate_schedule: quarterly # already done by requirements-cron.yml skip: - check-jsonschema - mypy - pyright + - uv-lock repos: - repo: meta @@ -13,7 +14,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.4.0 + rev: 0.5.0rc0 hooks: - id: check-dev-files args: @@ -61,7 +62,7 @@ repos: metadata.vscode - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.6.9 hooks: - id: ruff args: [--fix] @@ -70,7 +71,7 @@ repos: types_or: [python, pyi, jupyter] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: check-ast - id: check-case-conflict @@ -115,7 +116,7 @@ repos: - --in-place - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.2 + rev: 0.29.4 hooks: - id: check-jsonschema name: Check CITATION.cff @@ -128,7 +129,7 @@ repos: pass_filenames: false - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v8.13.3 + rev: v8.15.1 hooks: - id: cspell @@ -153,7 +154,12 @@ repos: types: - python - - repo: https://github.com/ComPWA/mirrors-pyright - rev: v1.1.379 + - repo: https://github.com/ComPWA/pyright-pre-commit + rev: v1.1.384 hooks: - id: pyright + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.4.21 + hooks: + - id: uv-lock diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..2c073331 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/.readthedocs.yml b/.readthedocs.yml index 0d8c6c56..ed305ab4 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,7 +1,7 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: python: "3.11" apt_packages: @@ -9,8 +9,7 @@ build: jobs: post_install: - python -m pip install 'uv>=0.2.0' - - python -m uv pip install -c .constraints/py3.11.txt -e .[doc] - + - python -m uv sync --extra=doc formats: - htmlzip diff --git a/.vscode/settings.json b/.vscode/settings.json index 5a1269b0..b3fff235 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -29,17 +29,13 @@ "[yaml]": { "editor.defaultFormatter": "esbenp.prettier-vscode" }, + "cSpell.enabled": true, "coverage-gutters.coverageFileNames": ["coverage.xml"], "coverage-gutters.coverageReportFileName": "**/htmlcov/index.html", "coverage-gutters.showGutterCoverage": false, "coverage-gutters.showLineCoverage": true, - "cSpell.enabled": true, "diffEditor.experimental.showMoves": true, "editor.formatOnSave": true, - "files.associations": { - "**/.constraints/py*.txt": "pip-requirements", - "**/pixi.lock": "yaml" - }, "files.watcherExclude": { "**/*_cache/**": true, "**/.eggs/**": true, @@ -67,7 +63,6 @@ "notebook.gotoSymbols.showAllSymbols": true, "python.analysis.autoImportCompletions": false, "python.analysis.inlayHints.pytestParameters": true, - "python.analysis.typeCheckingMode": "strict", "python.terminal.activateEnvironment": false, "python.testing.pytestArgs": ["--color=no", "--no-cov"], "python.testing.pytestEnabled": true, @@ -80,7 +75,7 @@ "search.exclude": { "**/benchmarks/**/__init__.py": true, "**/tests/**/__init__.py": true, - ".constraints/*.txt": true, + "**/uv.lock": true, "typings/**": true }, "telemetry.telemetryLevel": "off", diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 324a59dd..d1f7d694 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,5 +1,26 @@ # How to contribute? -[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/ampform) +[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://github.dev/ComPWA/ampform) -This package is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to [compwa.github.io/develop](https://compwa.github.io/develop)! +> [!TIP] +> This package is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to **[compwa.github.io/develop](https://compwa.github.io/develop)**! + +To contribute to the project, you need to install the package in a virtual environment. This can be done best with [`uv`](https://docs.astral.sh/uv) (see installation instructions [here](https://docs.astral.sh/uv/getting-started/installation)). For this, you first need to get the source code with [Git](https://git-scm.com): + +```shell +git clone https://github.com/ComPWA/ampform +cd ampform +``` + +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 03b11596..f8922668 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,7 @@ [![Spelling checked](https://img.shields.io/badge/cspell-checked-brightgreen.svg)](https://github.com/streetsidesoftware/cspell/tree/master/packages/cspell) [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) AmpForm is a Python library of spin formalisms and dynamics with which you can automatically formulate symbolic amplitude models for Partial Wave Analysis. The diff --git a/docs/install.md b/docs/install.md index f5434a54..47d1e8e7 100644 --- a/docs/install.md +++ b/docs/install.md @@ -9,7 +9,6 @@ The fastest way of installing this package is through PyPI or Conda: ::::{tab-set} - :::{tab-item} PyPI ```shell @@ -17,7 +16,6 @@ python3 -m pip install ampform ``` ::: - :::{tab-item} Conda ```shell @@ -25,7 +23,6 @@ conda install -c conda-forge ampform ``` ::: - :::: This installs the [latest release](https://github.com/ComPWA/ampform/releases) that you @@ -46,64 +43,10 @@ can be installed as follows: python3 -m pip install git+https://github.com/ComPWA/ampform@main ``` -## Editable installation - -It is highly recommend to use the more dynamic -{ref}`'editable installation' `. This allows -you to: - -- exactly {ref}`pin all dependencies ` - to a specific version, so that your work is **reproducible**. -- edit the source code of the framework and - {doc}`help improving it `. - -For this, you first need to get the source code with [Git](https://git-scm.com): - -```shell -git clone https://github.com/ComPWA/ampform.git -cd ampform -``` - -Next, you install the project in editable mode with either -[Conda](https://docs.conda.io) or [`pip`](https://pypi.org/project/pip). It's -recommended to use Conda, because this also pins the version of Python. - -::::{tab-set} - -:::{tab-item} Conda - -```shell -conda env create -``` - -This installs the project in a Conda environment following the definitions in -[`environment.yml`](https://github.com/ComPWA/ampform/blob/main/environment.yml). - -::: - -:::{tab-item} PyPI - -1. **[Recommended]** Create a virtual environment with - [`venv`](https://docs.python.org/3/library/venv.html) (see - {ref}`here `). - -2. Install the project as an - {ref}`'editable installation' ` with - {ref}`additional packages ` for the - developer and all dependencies pinned through - [constraints files](https://pip.pypa.io/en/stable/user_guide/#constraints-files): - - ```shell - python3 -m pip install -c .constraints/py3.x.txt -e .[dev] - ``` +## Developer installation +:::{include} ../CONTRIBUTING.md +:start-after: **[compwa.github.io/develop](https://compwa.github.io/develop)**! ::: -:::: - -See {ref}`compwa:develop:Updating` for how to update the dependencies when new -commits come in. - -That's all! Have a look at {doc}`/usage` to try out the package. You can also have a -look at {doc}`compwa:develop` for tips on how to work with this 'editable' developer -setup! +That's all! Have a look at {doc}`/usage` to try out the package. You can also have a look at {doc}`compwa:develop` for tips on how to work with this 'editable' developer setup! diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 0e013abc..00000000 --- a/environment.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: ampform -channels: - - defaults -dependencies: - - python==3.11.* - - pip - - graphviz - - pip: - - -c .constraints/py3.11.txt -e .[dev] -variables: - PYDEVD_DISABLE_FILE_VALIDATION: 1 - PYTHONHASHSEED: 0 diff --git a/pyproject.toml b/pyproject.toml index 7590077d..0d542fda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,7 +95,7 @@ scipy = ["scipy"] sty = [ "ampform[types]", "mypy >=0.730", - "pre-commit >=1.4.0", + "pre-commit-uv", "ruff", ] test = [ @@ -143,7 +143,7 @@ where = ["src"] [tool.setuptools_scm] local_scheme = "no-local-version" -version_scheme = "post-release" +version_scheme = "only-version" write_to = "src/ampform/version.py" [tool.coverage.run] @@ -189,124 +189,6 @@ module = ["benchmarks.*", "tests.*"] ignore_errors = true module = ["typings.*"] -[tool.pixi.project] -channels = ["conda-forge"] -platforms = ["linux-64"] - -[tool.pixi.activation.env] -PRETTIER_LEGACY_CLI = "1" -PYDEVD_DISABLE_FILE_VALIDATION = "1" -PYTHONHASHSEED = "0" - -[tool.pixi.dependencies] -graphviz = "*" -python = "3.11.*" - -[tool.pixi.environments] -default = {features = [ - "all", - "dev", - "doc", - "jupyter", - "scipy", - "sty", - "test", - "types", - "viz", -]} - -[tool.pixi.feature.dev.tasks.bench] -cmd = """ -pytest benchmarks \ - --durations=0 \ - --benchmark-autosave \ - -k benchmark -""" - -[tool.pixi.feature.dev.tasks.ci] -depends_on = ["cov", "docnb", "linkcheck", "sty"] - -[tool.pixi.feature.dev.tasks.cov] -cmd = """ -pytest src tests \ - --cov-fail-under=75 \ - --cov-report=html \ - --cov-report=xml \ - --cov=ampform -""" - -[tool.pixi.feature.dev.tasks.doc] -cmd = """ -sphinx-build \ - --builder html \ - --keep-going \ - --show-traceback --fail-on-warning \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.doclive] -cmd = """ -sphinx-autobuild \ - --builder html \ - --open-browser \ - --re-ignore '.*/__pycache__/.*' \ - --re-ignore '.*/.ipynb_checkpoints/.*' \ - --re-ignore '.*\\.gitignore' \ - --re-ignore '.*\\.tmp' \ - --re-ignore 'docs/_build/.*' \ - --re-ignore 'docs/_images/.*' \ - --re-ignore 'docs/.*\\.csv' \ - --re-ignore 'docs/.*\\.gif' \ - --re-ignore 'docs/.*\\.gv' \ - --re-ignore 'docs/.*\\.inv' \ - --re-ignore 'docs/.*\\.json' \ - --re-ignore 'docs/.*\\.pickle' \ - --re-ignore 'docs/.*\\.png' \ - --re-ignore 'docs/.*\\.svg' \ - --re-ignore 'docs/.*\\.yaml' \ - --re-ignore 'docs/.*\\.yml' \ - --re-ignore 'docs/api/.*' \ - --watch docs \ - --watch src \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.docnb] -cmd = "pixi run doc" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.docnb-force] -cmd = "pixi run doc" -env = {FORCE_COLOR = "yes", FORCE_EXECUTE_NB = "yes"} - -[tool.pixi.feature.dev.tasks.docnblive] -cmd = "pixi run doclive" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.linkcheck] -cmd = """ -sphinx-build \ - --builder linkcheck \ - --show-traceback \ - docs/ docs/_build/linkcheck -""" -env = {FORCE_COLOR = "yes"} - -[tool.pixi.feature.dev.tasks.nb] -cmd = "pytest --nbmake docs" - -[tool.pixi.feature.dev.tasks.sty] -cmd = "pre-commit run -a" -env = {SKIP = "pyright"} - -[tool.pixi.feature.dev.tasks.tests] -cmd = "pytest" - -[tool.pixi.pypi-dependencies] -ampform = {path = ".", editable = true} - [tool.pyright] exclude = [ "**/.git", @@ -314,6 +196,7 @@ exclude = [ "**/.mypy_cache", "**/.pytest_cache", "**/.tox", + "**/.venv/", "**/__pycache__", "**/_build", "**/typings", @@ -548,3 +431,142 @@ sort_first = [ ] spaces_indent_inline_array = 4 trailing_comma_inline_array = true + +[tool.tox] +legacy_tox_ini = """ +[tox] +envlist = + cov, + docnb-force, + linkcheck, + sty, +skip_install = True +skip_missing_interpreters = True +skipsdist = True + +[testenv] +allowlist_externals = + pytest +commands = + pytest {posargs} +description = Run all unit tests +passenv = * +setenv = + PYTHONHASHSEED = 0 + +[testenv:bench] +allowlist_externals = + pytest +commands = + pytest {posargs:benchmarks} \ + --durations=0 \ + --benchmark-autosave \ + -k benchmark +description = Run benchmark tests and visualize in histogram + +[testenv:cov] +allowlist_externals = + pytest +commands = + pytest {posargs:src tests} \ + --cov-fail-under=75 \ + --cov-report=html \ + --cov-report=xml \ + --cov=ampform +description = Compute test coverage + +[testenv:doc] +allowlist_externals = + sphinx-build +commands = + sphinx-build \ + --builder=html \ + --fail-on-warning \ + --keep-going \ + --show-traceback \ + docs/ docs/_build/html +description = Build documentation and API through Sphinx +setenv = + PYTHONWARNINGS = + +[testenv:docnb] +base = doc +description = {[testenv:doc]description} with cached notebook execution +setenv = + {[testenv:doc]setenv} + EXECUTE_NB = yes + +[testenv:docnb-force] +base = doc +description = {[testenv:doc]description} with notebook execution (no cache) +setenv = + {[testenv:doc]setenv} + FORCE_EXECUTE_NB = yes + +[testenv:doclive] +allowlist_externals = + sphinx-autobuild +commands = + sphinx-autobuild \ + --builder=html \ + --ignore=docs/_build/ \ + --ignore=docs/_images/ \ + --ignore=docs/api/ \ + --open-browser \ + --port=0 \ + --re-ignore='.*/__pycache__/.*' \ + --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*/.virtual_documents/.*' \ + --re-ignore='.*\\.csv' \ + --re-ignore='.*\\.gif' \ + --re-ignore='.*\\.gitignore' \ + --re-ignore='.*\\.gv' \ + --re-ignore='.*\\.inv' \ + --re-ignore='.*\\.json' \ + --re-ignore='.*\\.pickle' \ + --re-ignore='.*\\.png' \ + --re-ignore='.*\\.svg' \ + --re-ignore='.*\\.tmp' \ + --re-ignore='.*\\.ya?ml' \ + --watch=docs \ + --watch=src \ + docs/ docs/_build/html +description = Set up a server to directly preview changes to the HTML pages +setenv = + {[testenv:doc]setenv} + +[testenv:docnblive] +base = doclive +description = {[testenv:doclive]description} with cached notebook execution +setenv = + {[testenv:doclive]setenv} + EXECUTE_NB = yes + +[testenv:linkcheck] +allowlist_externals = + sphinx-build +commands = + sphinx-build \ + --builder=linkcheck \ + --show-traceback \ + docs/ docs/_build/linkcheck +description = Check external links in the documentation (requires internet connection) +setenv = + {[testenv:doclive]setenv} + +[testenv:nb] +allowlist_externals = + pytest +commands = + pytest --nbmake {posargs:docs} +description = Run all notebooks with pytest + +[testenv:sty] +allowlist_externals = + pre-commit +commands = + pre-commit run {posargs} --all-files +description = Perform all linting, formatting, and spelling checks +setenv = + SKIP = pyright +""" diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 83191636..00000000 --- a/tox.ini +++ /dev/null @@ -1,135 +0,0 @@ -[tox] -envlist = - cov, - docnb-force, - linkcheck, - sty, -skip_install = True -skip_missing_interpreters = True -skipsdist = True - -[testenv] -allowlist_externals = - pytest -commands = - pytest {posargs} -description = Run all unit tests -passenv = * -setenv = - PYTHONHASHSEED = 0 - -[testenv:bench] -allowlist_externals = - pytest -commands = - pytest {posargs:benchmarks} \ - --durations=0 \ - --benchmark-autosave \ - -k benchmark -description = Run benchmark tests and visualize in histogram - -[testenv:cov] -allowlist_externals = - pytest -commands = - pytest {posargs:src tests} \ - --cov-fail-under=75 \ - --cov-report=html \ - --cov-report=xml \ - --cov=ampform -description = Compute test coverage - -[testenv:doc] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder=html \ - --fail-on-warning \ - --keep-going \ - --show-traceback \ - docs/ docs/_build/html -description = Build documentation and API through Sphinx -setenv = - PYTHONWARNINGS = - -[testenv:docnb] -base = doc -description = {[testenv:doc]description} with cached notebook execution -setenv = - {[testenv:doc]setenv} - EXECUTE_NB = yes - -[testenv:docnb-force] -base = doc -description = {[testenv:doc]description} with notebook execution (no cache) -setenv = - {[testenv:doc]setenv} - FORCE_EXECUTE_NB = yes - -[testenv:doclive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --builder=html \ - --ignore=docs/_build/ \ - --ignore=docs/_images/ \ - --ignore=docs/api/ \ - --open-browser \ - --port=0 \ - --re-ignore='.*/__pycache__/.*' \ - --re-ignore='.*/.ipynb_checkpoints/.*' \ - --re-ignore='.*/.virtual_documents/.*' \ - --re-ignore='.*\.csv' \ - --re-ignore='.*\.gif' \ - --re-ignore='.*\.gitignore' \ - --re-ignore='.*\.gv' \ - --re-ignore='.*\.inv' \ - --re-ignore='.*\.json' \ - --re-ignore='.*\.pickle' \ - --re-ignore='.*\.png' \ - --re-ignore='.*\.svg' \ - --re-ignore='.*\.tmp' \ - --re-ignore='.*\.ya?ml' \ - --watch=docs \ - --watch=src \ - docs/ docs/_build/html -description = Set up a server to directly preview changes to the HTML pages -setenv = - {[testenv:doc]setenv} - -[testenv:docnblive] -base = doclive -description = {[testenv:doclive]description} with cached notebook execution -setenv = - {[testenv:doclive]setenv} - EXECUTE_NB = yes - -[testenv:linkcheck] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder=linkcheck \ - --show-traceback \ - docs/ docs/_build/linkcheck -description = Check external links in the documentation (requires internet connection) -setenv = - {[testenv:doclive]setenv} - -[testenv:nb] -allowlist_externals = - pytest -commands = - pytest --nbmake {posargs:docs} -description = Run all notebooks with pytest - -[testenv:sty] -allowlist_externals = - pre-commit -commands = - pre-commit run {posargs} --all-files -description = Perform all linting, formatting, and spelling checks -setenv = - SKIP = pyright diff 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tox -e doc + mkdir -p $READTHEDOCS_OUTPUT + mv docs/_build/html $READTHEDOCS_OUTPUT From f48e749bdb6e92e45801d8834b610afb17c86af5 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Tue, 15 Oct 2024 16:32:22 +0200 Subject: [PATCH 23/44] MAINT: update ComPWA/policy and apply changes --- .github/workflows/cd.yml | 8 ++++---- .github/workflows/ci.yml | 6 +++--- .github/workflows/clean-caches.yml | 2 +- .github/workflows/pr-linting.yml | 2 +- .github/workflows/requirements.yml | 2 +- .pre-commit-config.yaml | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 2f66c9ab..cf34984b 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -9,9 +9,9 @@ on: jobs: milestone: if: startsWith(github.ref, 'refs/tags') - uses: ComPWA/actions/.github/workflows/close-milestone.yml@v1 + uses: ComPWA/actions/.github/workflows/close-milestone.yml@v2 package-name: - uses: 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"ampform", extras = ["notebooks"], marker = "extra == 'doc'" }, { name = "ampform", extras = ["scipy"], marker = "extra == 'all'" }, { name = "ampform", extras = ["scipy"], marker = "extra == 'test'" }, { name = "ampform", extras = ["sty"], marker = "extra == 'dev'" }, @@ -162,9 +170,8 @@ requires-dist = [ { name = "ampform", extras = ["types"], marker = "extra == 'sty'" }, { name = "ampform", extras = ["viz"], marker = "extra == 'all'" }, { name = "attrs", specifier = ">=20.1.0" }, - { name = "black", marker = "extra == 'doc'" }, { name = "graphviz", marker = "extra == 'viz'" }, - { name = "ipympl", marker = "extra == 'doc'" }, + { name = "ipympl", marker = "extra == 'notebooks'" }, { name = "ipython", marker = "extra == 'types'" }, { name = "ipywidgets", marker = "extra == 'test'" }, { name = "ipywidgets", marker = "extra == 'types'" }, @@ -173,13 +180,13 @@ requires-dist = [ { name = "jupyterlab-git", marker = "extra == 'jupyter'" }, { name = "jupyterlab-lsp", marker = "extra == 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notebooks \ + > requirements.txt +uv pip install \ + --requirement requirements.txt \ + --system +uv cache clean diff --git a/.github/workflows/lock.yml b/.github/workflows/lock.yml index ac2c035b..e6a5c10a 100644 --- a/.github/workflows/lock.yml +++ b/.github/workflows/lock.yml @@ -12,6 +12,7 @@ on: - epic/* paths: - .pre-commit-config.yaml + - uv.lock schedule: - cron: "0 3 7 */1 *" workflow_dispatch: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9c6c1bbc..6819ba7f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.5.0rc5 + rev: 0.5.0rc6 hooks: - id: check-dev-files args: From d6b9d129fe2b9adc22734573264aa02ae194ec7e Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Wed, 16 Oct 2024 15:28:36 +0200 Subject: [PATCH 32/44] DX: switch to Lab interface on Binder --- README.md | 2 +- docs/conf.py | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f8922668..69ca8b46 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Conda package](https://anaconda.org/conda-forge/ampform/badges/version.svg)](https://anaconda.org/conda-forge/ampform) [![Supported Python versions](https://img.shields.io/pypi/pyversions/ampform)](https://pypi.org/project/ampform) -[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/ampform/stable?filepath=docs/usage) +[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/ampform/stable?urlpath=lab) [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/ampform/blob/stable) [![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/ampform) diff --git a/docs/conf.py b/docs/conf.py index 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b/pyproject.toml @@ -573,3 +573,8 @@ description = Perform all linting, formatting, and spelling checks setenv = SKIP = pyright """ + +[tool.uv] +constraint-dependencies = [ + "pytest-profiling!=1.8.0", +] diff --git a/uv.lock b/uv.lock index 6d780d7b..44aeb7a4 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,9 @@ version = 1 requires-python = ">=3.9" +[manifest] +constraints = [{ name = "pytest-profiling", specifier = "!=1.8.0" }] + [[package]] name = "accessible-pygments" version = "0.0.5" @@ -2582,16 +2585,16 @@ wheels = [ [[package]] name = "pytest-profiling" -version = "1.8.0" +version = "1.7.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "gprof2dot" }, { name = "pytest" }, { name = "six" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/5e/3f/e84badafc1a95b82d021c3615efb535bbd6015ea4dbd748ecb56b86e0739/pytest-profiling-1.8.0.tar.gz", hash = "sha256:4c3a7ee88bcd9a3723c01b4e885ea9da6d070d62110d800e51ddd7f35ea82cf7", size = 33491 } +sdist = 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workflows to `ubuntu-24.04` --- .github/workflows/benchmark.yml | 2 +- .github/workflows/ci-qrules-v0.9.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index aa8353b6..92ed10c3 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -20,7 +20,7 @@ on: jobs: benchmark: name: Performance regression - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - uses: ComPWA/actions/pip-install@v1 diff --git a/.github/workflows/ci-qrules-v0.9.yml b/.github/workflows/ci-qrules-v0.9.yml index b416eba2..ac92a94a 100644 --- a/.github/workflows/ci-qrules-v0.9.yml +++ b/.github/workflows/ci-qrules-v0.9.yml @@ -23,7 +23,7 @@ on: jobs: pytest: name: Run unit tests - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - uses: ComPWA/actions/pip-install@v1 From f3720c161ccfd481abdb113f5276b176a08c8d88 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 18 Oct 2024 11:19:27 +0200 Subject: [PATCH 39/44] FIX: run additiona `pytest` worfklows with setup-uv --- .cspell.json | 1 + .github/workflows/benchmark.yml | 31 ++++++++++++++++++++-------- .github/workflows/ci-qrules-v0.9.yml | 18 +++++++++------- 3 files changed, 34 insertions(+), 16 deletions(-) diff --git a/.cspell.json b/.cspell.json index d5505979..51795b79 100644 --- a/.cspell.json +++ b/.cspell.json @@ -150,6 +150,7 @@ "nowrap", "nrows", "nsimplify", + "numprocesses", "numpycode", "pandoc", "pbar", diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 92ed10c3..6b69d6ee 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -23,18 +23,31 @@ jobs: runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - - uses: ComPWA/actions/pip-install@v1 + - uses: actions/setup-python@v5 with: - editable: "yes" - extras: test,all - python-version: "3.9" - specific-packages: ${{ inputs.specific-pip-packages }} + python-version: "3.12" + - uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + - id: with + if: inputs.specific-pip-packages + name: Determine additional packages to install + run: | + additional_packages='' + for package in ${{ inputs.specific-pip-packages }}; do + additional_packages="$additional_packages --with $package" + done + echo "packages=$additional_packages" | tee -a $GITHUB_OUTPUT - name: Run pytest-benchmark run: | - pytest \ - -k benchmark \ - --benchmark-json output.json \ - --durations=0 + uv run \ + --extra all \ + --extra test \ + ${{ steps.with.outputs.packages }} \ + pytest \ + -k benchmark \ + --benchmark-json output.json \ + --durations=0 working-directory: benchmarks - name: Store result if: github.event_name == 'push' diff --git a/.github/workflows/ci-qrules-v0.9.yml b/.github/workflows/ci-qrules-v0.9.yml index ac92a94a..31d4bc39 100644 --- a/.github/workflows/ci-qrules-v0.9.yml +++ b/.github/workflows/ci-qrules-v0.9.yml @@ -26,11 +26,15 @@ jobs: runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - - uses: ComPWA/actions/pip-install@v1 + - uses: actions/setup-python@v5 with: - additional-packages: tox - editable: "yes" - extras: test - python-version: "3.9" - specific-packages: qrules==0.9.* - - run: pytest -n auto + python-version: "3.12" + - uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + - name: Run pytest with QRules v0.9 + run: | + uv run \ + --extra test \ + --with qrules~=0.9.0 \ + pytest --numprocesses auto From 89becd486d21b313311e29dbe52ac602399e9ba4 Mon Sep 17 00:00:00 2001 From: GitHub Date: Fri, 18 Oct 2024 12:39:44 +0000 Subject: [PATCH 40/44] MAINT: update lock files --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 433b74b8..64c91df6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.5.0rc10 + rev: 0.5.0 hooks: - id: check-dev-files args: From 210cbe38d99441b2954b682b8f5df59609f7d8cf Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 12:41:04 +0000 Subject: [PATCH 41/44] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .readthedocs.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index e596ba8b..8d4743d6 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -11,10 +11,7 @@ build: pixi global install graphviz uv - |- export UV_LINK_MODE=copy - uv run \ - --extra doc \ - --locked \ - --with tox \ + uv run --extra doc --locked --with tox \ tox -e doc mkdir -p $READTHEDOCS_OUTPUT mv docs/_build/html $READTHEDOCS_OUTPUT From 96ba8f795a718fada2b8d0ab6989fb6a30c0a9c8 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 18 Oct 2024 14:47:39 +0200 Subject: [PATCH 42/44] MAINT: remove redundant comment --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 64c91df6..f5fd446c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ ci: autoupdate_commit_msg: "MAINT: update lock files" - autoupdate_schedule: quarterly # already done by requirements-cron.yml + autoupdate_schedule: quarterly skip: - check-jsonschema - mypy From 24b01258afdc6501f5feb638f10119c2ede78acc Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 18 Oct 2024 14:48:02 +0200 Subject: [PATCH 43/44] MAINT: remove redundant EditorConfig setting --- .editorconfig | 3 --- 1 file changed, 3 deletions(-) diff --git a/.editorconfig b/.editorconfig index 9e92189a..674376ff 100644 --- a/.editorconfig +++ b/.editorconfig @@ -16,8 +16,5 @@ indent_size = 4 [LICENSE] indent_size = unset -[setup.cfg] -indent_size = 4 - [uv.lock] indent_size = 4 From 4510b2898ab629197ee4f64d5ecf7ef0612442d3 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 18 Oct 2024 14:58:09 +0200 Subject: [PATCH 44/44] DOC: update Binder links --- docs/conf.py | 2 +- docs/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 4138b79a..7df083fb 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -232,7 +232,7 @@ def _get_dataclasses(module): }, { "name": "Launch on Binder", - "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?filepath=docs", + "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?urlpath=lab", "icon": "https://mybinder.readthedocs.io/en/latest/_static/favicon.png", "type": "url", }, diff --git a/docs/index.md b/docs/index.md index e9854668..742c19dc 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,7 +7,7 @@ [![10.5281/zenodo.5526648](https://zenodo.org/badge/doi/10.5281/zenodo.5526648.svg)](https://doi.org/10.5281/zenodo.5526648) [![Supported Python versions](https://img.shields.io/pypi/pyversions/ampform)](https://pypi.org/project/ampform) {{ '[![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/ampform/blob/{})'.format(branch) }} -{{ '[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/ampform/{}?filepath=docs/usage)'.format(branch) }} +{{ '[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/ampform/{}?urlpath=lab)'.format(branch) }} :::{margin}