From c743249505a3b7ae885a16642d84a0ecc6cc7f76 Mon Sep 17 00:00:00 2001 From: Remco de Boer Date: Mon, 21 Feb 2022 10:21:36 +0100 Subject: [PATCH] ci: update pip constraints and pre-commit config (#153) * docs: import IPython.display.display() in notebooks * fix: remove leading zero from week number in cron job Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: GitHub --- .constraints/py3.10.txt | 67 +++++++++++++------------ .constraints/py3.6.txt | 37 +++++++------- .constraints/py3.7.txt | 63 +++++++++++------------ .constraints/py3.8.txt | 67 +++++++++++++------------ .constraints/py3.9.txt | 67 +++++++++++++------------ .github/workflows/requirements-cron.yml | 12 +++-- .pre-commit-config.yaml | 14 +++--- docs/usage.ipynb | 20 ++++---- docs/usage/conservation.ipynb | 20 ++++---- docs/usage/custom-topology.ipynb | 20 ++++---- docs/usage/ls-coupling.ipynb | 20 ++++---- docs/usage/particle.ipynb | 20 ++++---- docs/usage/reaction.ipynb | 20 ++++---- docs/usage/visualize.ipynb | 20 ++++---- 14 files changed, 245 insertions(+), 222 deletions(-) diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt index 820e0b39..84da83c4 100644 --- a/.constraints/py3.10.txt +++ b/.constraints/py3.10.txt @@ -20,20 +20,20 @@ bleach==4.1.0 certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1 -charset-normalizer==2.0.11 -click==8.0.3 +charset-normalizer==2.0.12 +click==8.0.4 colorama==0.4.4 -coverage==6.3 +coverage==6.3.2 debugpy==1.5.1 decorator==5.1.1 defusedxml==0.7.1 deprecated==1.2.13 distlib==0.3.4 docutils==0.16 -entrypoints==0.3 +entrypoints==0.4 execnet==1.9.0 executing==0.8.2 -filelock==3.4.2 +filelock==3.6.0 flake8==4.0.1 flake8-blind-except==0.2.0 flake8-bugbear==22.1.11 @@ -46,17 +46,17 @@ flake8-rst-docstrings==0.2.5 flake8-type-ignore==0.1.0.post2 ; python_version >= "3.8.0" flake8-use-fstring==1.3 gitdb==4.0.9 -gitpython==3.1.26 +gitpython==3.1.27 gprof2dot==2021.2.21 graphviz==0.19.1 greenlet==1.1.2 hepunits==2.2.0 -identify==2.4.7 +identify==2.4.10 idna==3.3 imagesize==1.3.0 -importlib-metadata==4.10.1 +importlib-metadata==4.11.1 iniconfig==1.1.1 -ipykernel==6.7.0 +ipykernel==6.9.1 ipython==8.0.1 ipython-genutils==0.2.0 ipywidgets==7.6.5 @@ -69,11 +69,11 @@ jupyter==1.0.0 jupyter-cache==0.4.3 jupyter-client==7.1.2 jupyter-console==6.4.0 -jupyter-core==4.9.1 -jupyter-server==1.13.4 -jupyter-server-mathjax==0.2.3 +jupyter-core==4.9.2 +jupyter-server==1.13.5 +jupyter-server-mathjax==0.2.4 jupyter-sphinx==0.3.2 -jupyterlab==3.2.8 +jupyterlab==3.2.9 jupyterlab-code-formatter==1.4.10 jupyterlab-markup==1.0.1 jupyterlab-myst==0.1.6 ; python_version >= "3.7.0" @@ -84,18 +84,18 @@ latexcodec==2.0.1 lazy-object-proxy==1.7.1 livereload==2.6.3 markdown-it-py==1.1.0 -markupsafe==2.0.1 +markupsafe==2.1.0 matplotlib-inline==0.1.3 mccabe==0.6.1 mdit-py-plugins==0.2.8 mistune==0.8.4 mypy==0.931 mypy-extensions==0.4.3 -myst-nb==0.13.1 +myst-nb==0.13.2 myst-parser==0.15.2 nbclassic==0.3.5 -nbclient==0.5.10 -nbconvert==6.4.1 +nbclient==0.5.11 +nbconvert==6.4.2 nbdime==3.1.1 nbformat==5.1.3 nbmake==1.2 @@ -111,12 +111,12 @@ pep517==0.12.0 pep8-naming==0.12.1 pexpect==4.8.0 pickleshare==0.7.5 -pip-tools==6.4.0 -platformdirs==2.4.1 +pip-tools==6.5.1 +platformdirs==2.5.1 pluggy==1.0.0 pre-commit==2.17.0 prometheus-client==0.13.1 -prompt-toolkit==3.0.26 +prompt-toolkit==3.0.28 ptyprocess==0.7.0 pure-eval==0.2.2 py==1.11.0 @@ -144,7 +144,7 @@ pytz==2021.3 pyyaml==6.0 pyzmq==22.3.0 qtconsole==5.2.2 -qtpy==2.0.0 +qtpy==2.0.1 requests==2.27.1 restructuredtext-lint==1.3.2 send2trash==1.8.0 @@ -157,10 +157,11 @@ sphinx==4.4.0 sphinx-autobuild==2021.3.14 sphinx-book-theme==0.2.0 sphinx-codeautolink==0.10.0 -sphinx-copybutton==0.4.0 +sphinx-comments==0.0.3 +sphinx-copybutton==0.5.0 sphinx-panels==0.6.0 -sphinx-thebe==0.0.10 -sphinx-togglebutton==0.2.3 +sphinx-thebe==0.1.1 +sphinx-togglebutton==0.3.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.4.1 sphinxcontrib-devhelp==1.0.2 @@ -169,26 +170,26 @@ sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sphobjinv==2.2 +sphobjinv==2.2.1 sqlalchemy==1.4.31 -stack-data==0.1.4 +stack-data==0.2.0 terminado==0.13.1 testpath==0.5.0 toml==0.10.2 -tomli==2.0.0 +tomli==2.0.1 tornado==6.1 tox==3.24.5 tqdm==4.62.3 traitlets==5.1.1 -types-docutils==0.17.4 +types-docutils==0.17.6 types-pkg-resources==0.1.3 types-pyyaml==6.0.4 -types-requests==2.27.8 -types-setuptools==57.4.8 -types-urllib3==1.26.8 -typing-extensions==4.0.1 +types-requests==2.27.10 +types-setuptools==57.4.9 +types-urllib3==1.26.9 +typing-extensions==4.1.1 urllib3==1.26.8 -virtualenv==20.13.0 +virtualenv==20.13.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.3 diff --git a/.constraints/py3.6.txt b/.constraints/py3.6.txt index cd5b5f31..1154c352 100644 --- a/.constraints/py3.6.txt +++ b/.constraints/py3.6.txt @@ -20,8 +20,8 @@ bleach==4.1.0 certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1 -charset-normalizer==2.0.11 -click==8.0.3 +charset-normalizer==2.0.12 +click==8.0.4 colorama==0.4.4 contextvars==2.4 coverage==6.2 @@ -31,7 +31,7 @@ defusedxml==0.7.1 deprecated==1.2.13 distlib==0.3.4 docutils==0.16 -entrypoints==0.3 +entrypoints==0.4 execnet==1.9.0 filelock==3.4.1 flake8==4.0.1 @@ -70,11 +70,11 @@ jupyter==1.0.0 jupyter-cache==0.4.3 jupyter-client==7.1.2 jupyter-console==6.4.0 -jupyter-core==4.9.1 +jupyter-core==4.9.2 jupyter-server==1.13.1 jupyter-server-mathjax==0.2.3 jupyter-sphinx==0.3.2 -jupyterlab==3.2.8 +jupyterlab==3.2.9 jupyterlab-code-formatter==1.4.10 jupyterlab-pygments==0.1.2 jupyterlab-server==2.10.3 @@ -89,7 +89,7 @@ mdit-py-plugins==0.2.8 mistune==0.8.4 mypy==0.931 mypy-extensions==0.4.3 -myst-nb==0.13.1 +myst-nb==0.13.2 myst-parser==0.15.2 nbclassic==0.3.5 nbclient==0.5.9 @@ -114,7 +114,7 @@ platformdirs==2.4.0 pluggy==1.0.0 pre-commit==2.17.0 prometheus-client==0.13.1 -prompt-toolkit==3.0.26 +prompt-toolkit==3.0.28 ptyprocess==0.7.0 py==1.11.0 pybtex==0.24.0 @@ -141,7 +141,7 @@ pytz==2021.3 pyyaml==6.0 pyzmq==22.3.0 qtconsole==5.2.2 -qtpy==2.0.0 +qtpy==2.0.1 requests==2.27.1 restructuredtext-lint==1.3.2 send2trash==1.8.0 @@ -154,10 +154,11 @@ sphinx==4.3.2 ; python_version < "3.8.0" sphinx-autobuild==2021.3.14 sphinx-book-theme==0.2.0 sphinx-codeautolink==0.10.0 -sphinx-copybutton==0.4.0 +sphinx-comments==0.0.3 +sphinx-copybutton==0.5.0 sphinx-panels==0.6.0 -sphinx-thebe==0.0.10 -sphinx-togglebutton==0.2.3 +sphinx-thebe==0.1.1 +sphinx-togglebutton==0.3.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.4.1 sphinxcontrib-devhelp==1.0.2 @@ -166,7 +167,7 @@ sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sphobjinv==2.2 +sphobjinv==2.2.1 sqlalchemy==1.4.31 terminado==0.12.1 testpath==0.5.0 @@ -177,15 +178,15 @@ tox==3.24.5 tqdm==4.62.3 traitlets==4.3.3 typed-ast==1.5.2 -types-docutils==0.17.4 +types-docutils==0.17.6 types-pkg-resources==0.1.3 types-pyyaml==6.0.4 -types-requests==2.27.8 -types-setuptools==57.4.8 -types-urllib3==1.26.8 -typing-extensions==4.0.1 ; python_version < "3.8.0" +types-requests==2.27.10 +types-setuptools==57.4.9 +types-urllib3==1.26.9 +typing-extensions==4.1.1 ; python_version < "3.8.0" urllib3==1.26.8 -virtualenv==20.13.0 +virtualenv==20.13.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.3 diff --git a/.constraints/py3.7.txt b/.constraints/py3.7.txt index 19e6a3c3..2cc40cf7 100644 --- a/.constraints/py3.7.txt +++ b/.constraints/py3.7.txt @@ -19,19 +19,19 @@ bleach==4.1.0 certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1 -charset-normalizer==2.0.11 -click==8.0.3 +charset-normalizer==2.0.12 +click==8.0.4 colorama==0.4.4 -coverage==6.3 +coverage==6.3.2 debugpy==1.5.1 decorator==5.1.1 defusedxml==0.7.1 deprecated==1.2.13 distlib==0.3.4 docutils==0.16 -entrypoints==0.3 +entrypoints==0.4 execnet==1.9.0 -filelock==3.4.2 +filelock==3.6.0 flake8==4.0.1 flake8-blind-except==0.2.0 flake8-bugbear==22.1.11 @@ -43,18 +43,18 @@ flake8-pytest-style==1.6.0 flake8-rst-docstrings==0.2.5 flake8-use-fstring==1.3 gitdb==4.0.9 -gitpython==3.1.26 +gitpython==3.1.27 gprof2dot==2021.2.21 graphviz==0.19.1 greenlet==1.1.2 hepunits==2.2.0 -identify==2.4.7 +identify==2.4.10 idna==3.3 imagesize==1.3.0 importlib-metadata==4.2.0 importlib-resources==5.4.0 iniconfig==1.1.1 -ipykernel==6.7.0 +ipykernel==6.9.1 ipython==7.31.1 ipython-genutils==0.2.0 ipywidgets==7.6.5 @@ -67,11 +67,11 @@ jupyter==1.0.0 jupyter-cache==0.4.3 jupyter-client==7.1.2 jupyter-console==6.4.0 -jupyter-core==4.9.1 -jupyter-server==1.13.4 -jupyter-server-mathjax==0.2.3 +jupyter-core==4.9.2 +jupyter-server==1.13.5 +jupyter-server-mathjax==0.2.4 jupyter-sphinx==0.3.2 -jupyterlab==3.2.8 +jupyterlab==3.2.9 jupyterlab-code-formatter==1.4.10 jupyterlab-markup==1.0.1 jupyterlab-myst==0.1.6 ; python_version >= "3.7.0" @@ -82,18 +82,18 @@ latexcodec==2.0.1 lazy-object-proxy==1.7.1 livereload==2.6.3 markdown-it-py==1.1.0 -markupsafe==2.0.1 +markupsafe==2.1.0 matplotlib-inline==0.1.3 mccabe==0.6.1 mdit-py-plugins==0.2.8 mistune==0.8.4 mypy==0.931 mypy-extensions==0.4.3 -myst-nb==0.13.1 +myst-nb==0.13.2 myst-parser==0.15.2 nbclassic==0.3.5 -nbclient==0.5.10 -nbconvert==6.4.1 +nbclient==0.5.11 +nbconvert==6.4.2 nbdime==3.1.1 nbformat==5.1.3 nbmake==1.2 @@ -109,12 +109,12 @@ pep517==0.12.0 pep8-naming==0.12.1 pexpect==4.8.0 pickleshare==0.7.5 -pip-tools==6.4.0 -platformdirs==2.4.1 +pip-tools==6.5.1 +platformdirs==2.5.1 pluggy==1.0.0 pre-commit==2.17.0 prometheus-client==0.13.1 -prompt-toolkit==3.0.26 +prompt-toolkit==3.0.28 ptyprocess==0.7.0 py==1.11.0 pybtex==0.24.0 @@ -141,7 +141,7 @@ pytz==2021.3 pyyaml==6.0 pyzmq==22.3.0 qtconsole==5.2.2 -qtpy==2.0.0 +qtpy==2.0.1 requests==2.27.1 restructuredtext-lint==1.3.2 send2trash==1.8.0 @@ -154,10 +154,11 @@ sphinx==4.3.2 ; python_version < "3.8.0" sphinx-autobuild==2021.3.14 sphinx-book-theme==0.2.0 sphinx-codeautolink==0.10.0 -sphinx-copybutton==0.4.0 +sphinx-comments==0.0.3 +sphinx-copybutton==0.5.0 sphinx-panels==0.6.0 -sphinx-thebe==0.0.10 -sphinx-togglebutton==0.2.3 +sphinx-thebe==0.1.1 +sphinx-togglebutton==0.3.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.4.1 sphinxcontrib-devhelp==1.0.2 @@ -166,26 +167,26 @@ sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sphobjinv==2.2 +sphobjinv==2.2.1 sqlalchemy==1.4.31 terminado==0.13.1 testpath==0.5.0 toml==0.10.2 -tomli==2.0.0 +tomli==2.0.1 tornado==6.1 tox==3.24.5 tqdm==4.62.3 traitlets==5.1.1 typed-ast==1.5.2 -types-docutils==0.17.4 +types-docutils==0.17.6 types-pkg-resources==0.1.3 types-pyyaml==6.0.4 -types-requests==2.27.8 -types-setuptools==57.4.8 -types-urllib3==1.26.8 -typing-extensions==4.0.1 ; python_version < "3.8.0" +types-requests==2.27.10 +types-setuptools==57.4.9 +types-urllib3==1.26.9 +typing-extensions==4.1.1 ; python_version < "3.8.0" urllib3==1.26.8 -virtualenv==20.13.0 +virtualenv==20.13.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.3 diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt index 4103a357..32a3eb02 100644 --- a/.constraints/py3.8.txt +++ b/.constraints/py3.8.txt @@ -20,20 +20,20 @@ bleach==4.1.0 certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1 -charset-normalizer==2.0.11 -click==8.0.3 +charset-normalizer==2.0.12 +click==8.0.4 colorama==0.4.4 -coverage==6.3 +coverage==6.3.2 debugpy==1.5.1 decorator==5.1.1 defusedxml==0.7.1 deprecated==1.2.13 distlib==0.3.4 docutils==0.16 -entrypoints==0.3 +entrypoints==0.4 execnet==1.9.0 executing==0.8.2 -filelock==3.4.2 +filelock==3.6.0 flake8==4.0.1 flake8-blind-except==0.2.0 flake8-bugbear==22.1.11 @@ -46,18 +46,18 @@ flake8-rst-docstrings==0.2.5 flake8-type-ignore==0.1.0.post2 ; python_version >= "3.8.0" flake8-use-fstring==1.3 gitdb==4.0.9 -gitpython==3.1.26 +gitpython==3.1.27 gprof2dot==2021.2.21 graphviz==0.19.1 greenlet==1.1.2 hepunits==2.2.0 -identify==2.4.7 +identify==2.4.10 idna==3.3 imagesize==1.3.0 -importlib-metadata==4.10.1 +importlib-metadata==4.11.1 importlib-resources==5.4.0 iniconfig==1.1.1 -ipykernel==6.7.0 +ipykernel==6.9.1 ipython==8.0.1 ipython-genutils==0.2.0 ipywidgets==7.6.5 @@ -70,11 +70,11 @@ jupyter==1.0.0 jupyter-cache==0.4.3 jupyter-client==7.1.2 jupyter-console==6.4.0 -jupyter-core==4.9.1 -jupyter-server==1.13.4 -jupyter-server-mathjax==0.2.3 +jupyter-core==4.9.2 +jupyter-server==1.13.5 +jupyter-server-mathjax==0.2.4 jupyter-sphinx==0.3.2 -jupyterlab==3.2.8 +jupyterlab==3.2.9 jupyterlab-code-formatter==1.4.10 jupyterlab-markup==1.0.1 jupyterlab-myst==0.1.6 ; python_version >= "3.7.0" @@ -85,18 +85,18 @@ latexcodec==2.0.1 lazy-object-proxy==1.7.1 livereload==2.6.3 markdown-it-py==1.1.0 -markupsafe==2.0.1 +markupsafe==2.1.0 matplotlib-inline==0.1.3 mccabe==0.6.1 mdit-py-plugins==0.2.8 mistune==0.8.4 mypy==0.931 mypy-extensions==0.4.3 -myst-nb==0.13.1 +myst-nb==0.13.2 myst-parser==0.15.2 nbclassic==0.3.5 -nbclient==0.5.10 -nbconvert==6.4.1 +nbclient==0.5.11 +nbconvert==6.4.2 nbdime==3.1.1 nbformat==5.1.3 nbmake==1.2 @@ -112,12 +112,12 @@ pep517==0.12.0 pep8-naming==0.12.1 pexpect==4.8.0 pickleshare==0.7.5 -pip-tools==6.4.0 -platformdirs==2.4.1 +pip-tools==6.5.1 +platformdirs==2.5.1 pluggy==1.0.0 pre-commit==2.17.0 prometheus-client==0.13.1 -prompt-toolkit==3.0.26 +prompt-toolkit==3.0.28 ptyprocess==0.7.0 pure-eval==0.2.2 py==1.11.0 @@ -145,7 +145,7 @@ pytz==2021.3 pyyaml==6.0 pyzmq==22.3.0 qtconsole==5.2.2 -qtpy==2.0.0 +qtpy==2.0.1 requests==2.27.1 restructuredtext-lint==1.3.2 send2trash==1.8.0 @@ -158,10 +158,11 @@ sphinx==4.4.0 sphinx-autobuild==2021.3.14 sphinx-book-theme==0.2.0 sphinx-codeautolink==0.10.0 -sphinx-copybutton==0.4.0 +sphinx-comments==0.0.3 +sphinx-copybutton==0.5.0 sphinx-panels==0.6.0 -sphinx-thebe==0.0.10 -sphinx-togglebutton==0.2.3 +sphinx-thebe==0.1.1 +sphinx-togglebutton==0.3.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.4.1 sphinxcontrib-devhelp==1.0.2 @@ -170,26 +171,26 @@ sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sphobjinv==2.2 +sphobjinv==2.2.1 sqlalchemy==1.4.31 -stack-data==0.1.4 +stack-data==0.2.0 terminado==0.13.1 testpath==0.5.0 toml==0.10.2 -tomli==2.0.0 +tomli==2.0.1 tornado==6.1 tox==3.24.5 tqdm==4.62.3 traitlets==5.1.1 -types-docutils==0.17.4 +types-docutils==0.17.6 types-pkg-resources==0.1.3 types-pyyaml==6.0.4 -types-requests==2.27.8 -types-setuptools==57.4.8 -types-urllib3==1.26.8 -typing-extensions==4.0.1 +types-requests==2.27.10 +types-setuptools==57.4.9 +types-urllib3==1.26.9 +typing-extensions==4.1.1 urllib3==1.26.8 -virtualenv==20.13.0 +virtualenv==20.13.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.3 diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt index a3afea01..e211c900 100644 --- a/.constraints/py3.9.txt +++ b/.constraints/py3.9.txt @@ -20,20 +20,20 @@ bleach==4.1.0 certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1 -charset-normalizer==2.0.11 -click==8.0.3 +charset-normalizer==2.0.12 +click==8.0.4 colorama==0.4.4 -coverage==6.3 +coverage==6.3.2 debugpy==1.5.1 decorator==5.1.1 defusedxml==0.7.1 deprecated==1.2.13 distlib==0.3.4 docutils==0.16 -entrypoints==0.3 +entrypoints==0.4 execnet==1.9.0 executing==0.8.2 -filelock==3.4.2 +filelock==3.6.0 flake8==4.0.1 flake8-blind-except==0.2.0 flake8-bugbear==22.1.11 @@ -46,17 +46,17 @@ flake8-rst-docstrings==0.2.5 flake8-type-ignore==0.1.0.post2 ; python_version >= "3.8.0" flake8-use-fstring==1.3 gitdb==4.0.9 -gitpython==3.1.26 +gitpython==3.1.27 gprof2dot==2021.2.21 graphviz==0.19.1 greenlet==1.1.2 hepunits==2.2.0 -identify==2.4.7 +identify==2.4.10 idna==3.3 imagesize==1.3.0 -importlib-metadata==4.10.1 +importlib-metadata==4.11.1 iniconfig==1.1.1 -ipykernel==6.7.0 +ipykernel==6.9.1 ipython==8.0.1 ipython-genutils==0.2.0 ipywidgets==7.6.5 @@ -69,11 +69,11 @@ jupyter==1.0.0 jupyter-cache==0.4.3 jupyter-client==7.1.2 jupyter-console==6.4.0 -jupyter-core==4.9.1 -jupyter-server==1.13.4 -jupyter-server-mathjax==0.2.3 +jupyter-core==4.9.2 +jupyter-server==1.13.5 +jupyter-server-mathjax==0.2.4 jupyter-sphinx==0.3.2 -jupyterlab==3.2.8 +jupyterlab==3.2.9 jupyterlab-code-formatter==1.4.10 jupyterlab-markup==1.0.1 jupyterlab-myst==0.1.6 ; python_version >= "3.7.0" @@ -84,18 +84,18 @@ latexcodec==2.0.1 lazy-object-proxy==1.7.1 livereload==2.6.3 markdown-it-py==1.1.0 -markupsafe==2.0.1 +markupsafe==2.1.0 matplotlib-inline==0.1.3 mccabe==0.6.1 mdit-py-plugins==0.2.8 mistune==0.8.4 mypy==0.931 mypy-extensions==0.4.3 -myst-nb==0.13.1 +myst-nb==0.13.2 myst-parser==0.15.2 nbclassic==0.3.5 -nbclient==0.5.10 -nbconvert==6.4.1 +nbclient==0.5.11 +nbconvert==6.4.2 nbdime==3.1.1 nbformat==5.1.3 nbmake==1.2 @@ -111,12 +111,12 @@ pep517==0.12.0 pep8-naming==0.12.1 pexpect==4.8.0 pickleshare==0.7.5 -pip-tools==6.4.0 -platformdirs==2.4.1 +pip-tools==6.5.1 +platformdirs==2.5.1 pluggy==1.0.0 pre-commit==2.17.0 prometheus-client==0.13.1 -prompt-toolkit==3.0.26 +prompt-toolkit==3.0.28 ptyprocess==0.7.0 pure-eval==0.2.2 py==1.11.0 @@ -144,7 +144,7 @@ pytz==2021.3 pyyaml==6.0 pyzmq==22.3.0 qtconsole==5.2.2 -qtpy==2.0.0 +qtpy==2.0.1 requests==2.27.1 restructuredtext-lint==1.3.2 send2trash==1.8.0 @@ -157,10 +157,11 @@ sphinx==4.4.0 sphinx-autobuild==2021.3.14 sphinx-book-theme==0.2.0 sphinx-codeautolink==0.10.0 -sphinx-copybutton==0.4.0 +sphinx-comments==0.0.3 +sphinx-copybutton==0.5.0 sphinx-panels==0.6.0 -sphinx-thebe==0.0.10 -sphinx-togglebutton==0.2.3 +sphinx-thebe==0.1.1 +sphinx-togglebutton==0.3.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.4.1 sphinxcontrib-devhelp==1.0.2 @@ -169,26 +170,26 @@ sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sphobjinv==2.2 +sphobjinv==2.2.1 sqlalchemy==1.4.31 -stack-data==0.1.4 +stack-data==0.2.0 terminado==0.13.1 testpath==0.5.0 toml==0.10.2 -tomli==2.0.0 +tomli==2.0.1 tornado==6.1 tox==3.24.5 tqdm==4.62.3 traitlets==5.1.1 -types-docutils==0.17.4 +types-docutils==0.17.6 types-pkg-resources==0.1.3 types-pyyaml==6.0.4 -types-requests==2.27.8 -types-setuptools==57.4.8 -types-urllib3==1.26.8 -typing-extensions==4.0.1 +types-requests==2.27.10 +types-setuptools==57.4.9 +types-urllib3==1.26.9 +typing-extensions==4.1.1 urllib3==1.26.8 -virtualenv==20.13.0 +virtualenv==20.13.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.3 diff --git a/.github/workflows/requirements-cron.yml b/.github/workflows/requirements-cron.yml index 367d8dae..f0132229 100644 --- a/.github/workflows/requirements-cron.yml +++ b/.github/workflows/requirements-cron.yml @@ -12,10 +12,14 @@ jobs: steps: - name: Determine if week number is even run: | - WEEK_NUMBER=$(date +%U) - IS_EVEN_WEEK="$(($WEEK_NUMBER % 2 == 0))" - echo "This is week $WEEK_NUMBER. It even week: $IS_EVEN_WEEK" - echo ::set-output name=is-even-week::"$IS_EVEN_WEEK" + if [[ $GITHUB_EVENT_NAME == "workflow_dispatch" ]]; then + echo ::set-output name=is-even-week::"-1" + else + WEEK_NUMBER=$(date +"%-U") + IS_EVEN_WEEK="$(($WEEK_NUMBER % 2 == 0))" + echo "This is week $WEEK_NUMBER. Is even week: $IS_EVEN_WEEK" + echo ::set-output name=is-even-week::"$IS_EVEN_WEEK" + fi id: is-even-week outputs: is-even-week: ${{ steps.is-even-week.outputs.is-even-week }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c45fccd8..8221aec8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -41,18 +41,18 @@ repos: - id: trailing-whitespace - repo: https://github.com/ComPWA/repo-maintenance - rev: 0.0.102 + rev: 0.0.108 hooks: - id: check-dev-files args: - --pin-requirements - - id: fix-first-nbcell + - id: fix-nbformat-version + - id: format-setup-cfg + - id: set-nb-cells args: - --add-install-cell - --additional-packages=IPython - --extras-require=doc,viz - - id: fix-nbformat-version - - id: format-setup-cfg - repo: https://github.com/psf/black rev: 22.1.0 @@ -65,7 +65,7 @@ repos: - id: blacken-docs - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v5.8.1 + rev: v5.8.4 hooks: - id: cspell @@ -93,7 +93,7 @@ repos: - id: isort - repo: https://github.com/igorshubovych/markdownlint-cli - rev: v0.30.0 + rev: v0.31.1 hooks: - id: markdownlint @@ -145,7 +145,7 @@ repos: - id: pydocstyle - repo: https://github.com/ComPWA/mirrors-pyright - rev: v1.1.216 + rev: v1.1.222 hooks: - id: pyright diff --git a/docs/usage.ipynb b/docs/usage.ipynb index 76ba3732..24f846ba 100644 --- a/docs/usage.ipynb +++ b/docs/usage.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/conservation.ipynb b/docs/usage/conservation.ipynb index c61d84e0..6c6b64f7 100644 --- a/docs/usage/conservation.ipynb +++ b/docs/usage/conservation.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/custom-topology.ipynb b/docs/usage/custom-topology.ipynb index 022116eb..be98818a 100644 --- a/docs/usage/custom-topology.ipynb +++ b/docs/usage/custom-topology.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/ls-coupling.ipynb b/docs/usage/ls-coupling.ipynb index 59f009c9..3fe6773e 100644 --- a/docs/usage/ls-coupling.ipynb +++ b/docs/usage/ls-coupling.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/particle.ipynb b/docs/usage/particle.ipynb index 8e90b606..950b76dd 100644 --- a/docs/usage/particle.ipynb +++ b/docs/usage/particle.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/reaction.ipynb b/docs/usage/reaction.ipynb index 376e7576..10e6b62b 100644 --- a/docs/usage/reaction.ipynb +++ b/docs/usage/reaction.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, { diff --git a/docs/usage/visualize.ipynb b/docs/usage/visualize.ipynb index da19a400..eb663fb3 100644 --- a/docs/usage/visualize.ipynb +++ b/docs/usage/visualize.ipynb @@ -14,15 +14,14 @@ "slide_type": "skip" }, "tags": [ - "remove-cell" + "remove-cell", + "skip-execution" ] }, "outputs": [], "source": [ - "%config InlineBackend.figure_formats = ['svg']\n", - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" + "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", + "%pip install -q qrules[doc,viz] IPython" ] }, { @@ -39,14 +38,17 @@ "slide_type": "skip" }, "tags": [ - "remove-cell", - "skip-execution" + "remove-cell" ] }, "outputs": [], "source": [ - "# WARNING: advised to install a specific version, e.g. qrules==0.1.2\n", - "%pip install -q qrules[doc,viz] IPython" + "%config InlineBackend.figure_formats = ['svg']\n", + "import os\n", + "\n", + "from IPython.display import display # noqa: F401\n", + "\n", + "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, {