diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index b5a7bcc..d6760c1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -17,7 +17,7 @@ jobs: python-version: "3.12" - name: Install dependencies - run: pip install -r requirements.txt + run: pip install -r requirements_CI.txt - name: Build Docs run: make -C docs diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 9d13e33..e2d96dd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -23,7 +23,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install -r requirements.txt + python -m pip install -r requirements_CI.txt - name: Tests for reference implementation run: | cd reference_implementation diff --git a/requirements.txt b/requirements.txt index f57417b..e8a6814 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,449 +1,12 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile -p 3.12 requirements_old.txt -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==0.7.16 - # via sphinx -anyio==4.6.2.post1 - # via jupyter-server -argon2-cffi==23.1.0 - # via jupyter-server -argon2-cffi-bindings==21.2.0 - # via argon2-cffi -arrow==1.3.0 - # via isoduration -asttokens==2.4.1 - # via stack-data -attrs==24.2.0 - # via - # demes - # hypothesis - # jsonschema - # jupyter-cache - # referencing -babel==2.16.0 - # via - # pydata-sphinx-theme - # sphinx -beautifulsoup4==4.12.3 - # via - # nbconvert - # pydata-sphinx-theme -bleach==6.2.0 - # via nbconvert -certifi==2024.8.30 - # via requests -cffi==1.17.1 - # via argon2-cffi-bindings -charset-normalizer==3.4.0 - # via requests -click==8.1.7 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -comm==0.2.2 - # via ipykernel -contourpy==1.3.1 - # via matplotlib -coverage==7.6.7 - # via pytest-cov -cycler==0.12.1 - # via matplotlib -debugpy==1.8.8 - # via ipykernel -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -demes==0.2.3 - # via - # -r requirements_old.txt - # demesdraw -demesdraw==0.4.0 - # via -r requirements_old.txt -docutils==0.20.1 - # via - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # sphinx - # sphinx-rtd-theme - # sphinx-togglebutton - # sphinxcontrib-bibtex -executing==2.1.0 - # via stack-data -fastjsonschema==2.20.0 - # via nbformat -fonttools==4.55.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -greenlet==3.1.1 - # via sqlalchemy -hypothesis==6.119.3 - # via hypothesis-jsonschema -hypothesis-jsonschema==0.23.1 - # via -r requirements_old.txt -idna==3.10 - # via - # anyio - # jsonschema - # requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.5.0 - # via - # jupyter-cache - # myst-nb -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via myst-nb -ipython==8.29.0 - # via - # ipykernel - # myst-nb -isoduration==20.11.0 - # via jsonschema -jedi==0.19.2 - # via ipython -jinja2==3.1.4 - # via - # -r requirements_old.txt - # jupyter-book - # jupyter-server - # myst-parser - # nbconvert - # sphinx -jsonpointer==3.0.0 - # via jsonschema -jsonschema==4.23.0 - # via - # -r requirements_old.txt - # hypothesis-jsonschema - # jupyter-book - # jupyter-events - # nbformat -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-book==1.0.3 - # via -r requirements_old.txt -jupyter-cache==1.0.1 - # via myst-nb -jupyter-client==8.6.3 - # via - # ipykernel - # jupyter-server - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat -jupyter-events==0.10.0 - # via jupyter-server -jupyter-server==2.14.2 - # via -r requirements_old.txt -jupyter-server-terminals==0.5.3 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.4.7 - # via matplotlib -latexcodec==3.0.0 - # via pybtex -linkify-it-py==2.0.3 - # via jupyter-book -markdown-it-py==3.0.0 - # via - # mdit-py-plugins - # myst-parser -markupsafe==3.0.2 - # via - # jinja2 - # nbconvert -matplotlib==3.9.2 - # via demesdraw -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mdit-py-plugins==0.4.2 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -mistune==3.0.2 - # via nbconvert -myst-nb==1.1.2 - # via jupyter-book -myst-parser==2.0.0 - # via - # jupyter-book - # myst-nb -nbclient==0.10.0 - # via - # jupyter-cache - # myst-nb - # nbconvert -nbconvert==7.16.4 - # via jupyter-server -nbformat==5.10.4 - # via - # jupyter-cache - # jupyter-server - # myst-nb - # nbclient - # nbconvert -nest-asyncio==1.6.0 - # via ipykernel -numpy==2.1.3 - # via - # contourpy - # demesdraw - # matplotlib - # scipy -overrides==7.7.0 - # via jupyter-server -packaging==24.2 - # via - # ipykernel - # jupyter-server - # matplotlib - # nbconvert - # pytest - # sphinx - # sphinx-jupyterbook-latex -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==11.0.0 - # via matplotlib -platformdirs==4.3.6 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prometheus-client==0.21.0 - # via jupyter-server -prompt-toolkit==3.0.48 - # via ipython -psutil==6.1.0 - # via ipykernel -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pybtex==0.24.0 - # via - # pybtex-docutils - # sphinxcontrib-bibtex -pybtex-docutils==1.0.3 - # via sphinxcontrib-bibtex -pycparser==2.22 - # via cffi -pydata-sphinx-theme==0.16.0 - # via sphinx-book-theme -pygments==2.18.0 - # via - # accessible-pygments - # ipython - # nbconvert - # pydata-sphinx-theme - # sphinx -pyparsing==3.2.0 - # via matplotlib -pytest==8.3.3 - # via - # -r requirements_old.txt - # pytest-cov -pytest-cov==6.0.0 - # via -r requirements_old.txt -python-dateutil==2.9.0.post0 - # via - # arrow - # jupyter-client - # matplotlib -python-json-logger==2.0.7 - # via jupyter-events -pyyaml==6.0.2 - # via - # jupyter-book - # jupyter-cache - # jupyter-events - # myst-nb - # myst-parser - # pybtex - # sphinx-external-toc -pyzmq==26.2.0 - # via - # ipykernel - # jupyter-client - # jupyter-server -referencing==0.35.1 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -requests==2.32.3 - # via sphinx -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rpds-py==0.21.0 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.6 - # via - # -r requirements_old.txt - # demes -ruamel-yaml-clib==0.2.12 - # via ruamel-yaml -scipy==1.14.1 - # via demesdraw -send2trash==1.8.3 - # via jupyter-server -setuptools==75.5.0 - # via - # sphinx-togglebutton - # sphinxcontrib-bibtex -six==1.16.0 - # via - # asttokens - # pybtex - # python-dateutil - # rfc3339-validator -sniffio==1.3.1 - # via anyio -snowballstemmer==2.2.0 - # via sphinx -sortedcontainers==2.4.0 - # via hypothesis -soupsieve==2.6 - # via beautifulsoup4 -sphinx==7.4.7 - # via - # -r requirements_old.txt - # jupyter-book - # myst-nb - # myst-parser - # pydata-sphinx-theme - # sphinx-book-theme - # sphinx-comments - # sphinx-copybutton - # sphinx-design - # sphinx-external-toc - # sphinx-jupyterbook-latex - # sphinx-multitoc-numbering - # sphinx-rtd-theme - # sphinx-thebe - # sphinx-togglebutton - # sphinxcontrib-bibtex - # sphinxcontrib-jquery -sphinx-book-theme==1.1.3 - # via jupyter-book -sphinx-comments==0.0.3 - # via jupyter-book -sphinx-copybutton==0.5.2 - # via jupyter-book -sphinx-design==0.6.1 - # via jupyter-book -sphinx-external-toc==1.0.1 - # via jupyter-book -sphinx-jupyterbook-latex==1.0.0 - # via jupyter-book -sphinx-multitoc-numbering==0.1.3 - # via jupyter-book -sphinx-rtd-theme==3.0.2 - # via -r requirements_old.txt -sphinx-thebe==0.3.1 - # via jupyter-book -sphinx-togglebutton==0.3.2 - # via jupyter-book -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-bibtex==2.6.3 - # via jupyter-book -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jquery==4.1 - # via sphinx-rtd-theme -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -sqlalchemy==2.0.36 - # via jupyter-cache -stack-data==0.6.3 - # via ipython -tabulate==0.9.0 - # via jupyter-cache -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals -tinycss2==1.4.0 - # via nbconvert -tornado==6.4.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # terminado -traitlets==5.14.3 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat -types-python-dateutil==2.9.0.20241003 - # via arrow -typing-extensions==4.12.2 - # via - # myst-nb - # pydata-sphinx-theme - # sqlalchemy -uc-micro-py==1.0.3 - # via linkify-it-py -uri-template==1.3.0 - # via jsonschema -urllib3==2.2.3 - # via requests -wcwidth==0.2.13 - # via prompt-toolkit -webcolors==24.11.1 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.8.0 - # via jupyter-server -wheel==0.45.0 - # via sphinx-togglebutton -zipp==3.21.0 - # via importlib-metadata +jinja2 +jupyter-book +sphinx +sphinx_rtd_theme +pytest +pytest-cov +jsonschema +ruamel.yaml +demes +demesdraw +hypothesis-jsonschema +jupyter-server diff --git a/requirements_CI.txt b/requirements_CI.txt new file mode 100644 index 0000000..f57417b --- /dev/null +++ b/requirements_CI.txt @@ -0,0 +1,449 @@ +# This file was autogenerated by uv via the following command: +# uv pip compile -p 3.12 requirements_old.txt +accessible-pygments==0.0.5 + # via pydata-sphinx-theme +alabaster==0.7.16 + # via sphinx +anyio==4.6.2.post1 + # via jupyter-server +argon2-cffi==23.1.0 + # via jupyter-server +argon2-cffi-bindings==21.2.0 + # via argon2-cffi +arrow==1.3.0 + # via isoduration +asttokens==2.4.1 + # via stack-data +attrs==24.2.0 + # via + # demes + # hypothesis + # jsonschema + # jupyter-cache + # referencing +babel==2.16.0 + # via + # pydata-sphinx-theme + # sphinx +beautifulsoup4==4.12.3 + # via + # nbconvert + # pydata-sphinx-theme +bleach==6.2.0 + # via nbconvert +certifi==2024.8.30 + # via requests +cffi==1.17.1 + # via argon2-cffi-bindings +charset-normalizer==3.4.0 + # via requests +click==8.1.7 + # via + # jupyter-book + # jupyter-cache + # sphinx-external-toc +comm==0.2.2 + # via ipykernel +contourpy==1.3.1 + # via matplotlib +coverage==7.6.7 + # via pytest-cov +cycler==0.12.1 + # via matplotlib +debugpy==1.8.8 + # via ipykernel +decorator==5.1.1 + # via ipython +defusedxml==0.7.1 + # via nbconvert +demes==0.2.3 + # via + # -r requirements_old.txt + # demesdraw +demesdraw==0.4.0 + # via -r requirements_old.txt +docutils==0.20.1 + # via + # myst-parser + # pybtex-docutils + # pydata-sphinx-theme + # sphinx + # sphinx-rtd-theme + # sphinx-togglebutton + # sphinxcontrib-bibtex +executing==2.1.0 + # via stack-data +fastjsonschema==2.20.0 + # via nbformat +fonttools==4.55.0 + # via matplotlib +fqdn==1.5.1 + # via jsonschema +greenlet==3.1.1 + # via sqlalchemy +hypothesis==6.119.3 + # via hypothesis-jsonschema +hypothesis-jsonschema==0.23.1 + # via -r requirements_old.txt +idna==3.10 + # via + # anyio + # jsonschema + # requests +imagesize==1.4.1 + # via sphinx +importlib-metadata==8.5.0 + # via + # jupyter-cache + # myst-nb +iniconfig==2.0.0 + # via pytest +ipykernel==6.29.5 + # via myst-nb +ipython==8.29.0 + # via + # ipykernel + # myst-nb +isoduration==20.11.0 + # via jsonschema +jedi==0.19.2 + # via ipython +jinja2==3.1.4 + # via + # -r requirements_old.txt + # jupyter-book + # jupyter-server + # myst-parser + # nbconvert + # sphinx +jsonpointer==3.0.0 + # via jsonschema +jsonschema==4.23.0 + # via + # -r requirements_old.txt + # hypothesis-jsonschema + # jupyter-book + # jupyter-events + # nbformat +jsonschema-specifications==2024.10.1 + # via jsonschema +jupyter-book==1.0.3 + # via -r requirements_old.txt +jupyter-cache==1.0.1 + # via myst-nb +jupyter-client==8.6.3 + # via + # ipykernel + # jupyter-server + # nbclient +jupyter-core==5.7.2 + # via + # ipykernel + # jupyter-client + # jupyter-server + # nbclient + # nbconvert + # nbformat +jupyter-events==0.10.0 + # via jupyter-server +jupyter-server==2.14.2 + # via -r requirements_old.txt +jupyter-server-terminals==0.5.3 + # via jupyter-server +jupyterlab-pygments==0.3.0 + # via nbconvert +kiwisolver==1.4.7 + # via matplotlib +latexcodec==3.0.0 + # via pybtex +linkify-it-py==2.0.3 + # via jupyter-book +markdown-it-py==3.0.0 + # via + # mdit-py-plugins + # myst-parser +markupsafe==3.0.2 + # via + # jinja2 + # nbconvert +matplotlib==3.9.2 + # via demesdraw +matplotlib-inline==0.1.7 + # via + # ipykernel + # ipython +mdit-py-plugins==0.4.2 + # via myst-parser +mdurl==0.1.2 + # via markdown-it-py +mistune==3.0.2 + # via nbconvert +myst-nb==1.1.2 + # via jupyter-book +myst-parser==2.0.0 + # via + # jupyter-book + # myst-nb +nbclient==0.10.0 + # via + # jupyter-cache + # myst-nb + # nbconvert +nbconvert==7.16.4 + # via jupyter-server +nbformat==5.10.4 + # via + # jupyter-cache + # jupyter-server + # myst-nb + # nbclient + # nbconvert +nest-asyncio==1.6.0 + # via ipykernel +numpy==2.1.3 + # via + # contourpy + # demesdraw + # matplotlib + # scipy +overrides==7.7.0 + # via jupyter-server +packaging==24.2 + # via + # ipykernel + # jupyter-server + # matplotlib + # nbconvert + # pytest + # sphinx + # sphinx-jupyterbook-latex +pandocfilters==1.5.1 + # via nbconvert +parso==0.8.4 + # via jedi +pexpect==4.9.0 + # via ipython +pillow==11.0.0 + # via matplotlib +platformdirs==4.3.6 + # via jupyter-core +pluggy==1.5.0 + # via pytest +prometheus-client==0.21.0 + # via jupyter-server +prompt-toolkit==3.0.48 + # via ipython +psutil==6.1.0 + # via ipykernel +ptyprocess==0.7.0 + # via + # pexpect + # terminado +pure-eval==0.2.3 + # via stack-data +pybtex==0.24.0 + # via + # pybtex-docutils + # sphinxcontrib-bibtex +pybtex-docutils==1.0.3 + # via sphinxcontrib-bibtex +pycparser==2.22 + # via cffi +pydata-sphinx-theme==0.16.0 + # via sphinx-book-theme +pygments==2.18.0 + # via + # accessible-pygments + # ipython + # nbconvert + # pydata-sphinx-theme + # sphinx +pyparsing==3.2.0 + # via matplotlib +pytest==8.3.3 + # via + # -r requirements_old.txt + # pytest-cov +pytest-cov==6.0.0 + # via -r requirements_old.txt +python-dateutil==2.9.0.post0 + # via + # arrow + # jupyter-client + # matplotlib +python-json-logger==2.0.7 + # via jupyter-events +pyyaml==6.0.2 + # via + # jupyter-book + # jupyter-cache + # jupyter-events + # myst-nb + # myst-parser + # pybtex + # sphinx-external-toc +pyzmq==26.2.0 + # via + # ipykernel + # jupyter-client + # jupyter-server +referencing==0.35.1 + # via + # jsonschema + # jsonschema-specifications + # jupyter-events +requests==2.32.3 + # via sphinx +rfc3339-validator==0.1.4 + # via + # jsonschema + # jupyter-events +rfc3986-validator==0.1.1 + # via + # jsonschema + # jupyter-events +rpds-py==0.21.0 + # via + # jsonschema + # referencing +ruamel-yaml==0.18.6 + # via + # -r requirements_old.txt + # demes +ruamel-yaml-clib==0.2.12 + # via ruamel-yaml +scipy==1.14.1 + # via demesdraw +send2trash==1.8.3 + # via jupyter-server +setuptools==75.5.0 + # via + # sphinx-togglebutton + # sphinxcontrib-bibtex +six==1.16.0 + # via + # asttokens + # pybtex + # python-dateutil + # rfc3339-validator +sniffio==1.3.1 + # via anyio +snowballstemmer==2.2.0 + # via sphinx +sortedcontainers==2.4.0 + # via hypothesis +soupsieve==2.6 + # via beautifulsoup4 +sphinx==7.4.7 + # via + # -r requirements_old.txt + # jupyter-book + # myst-nb + # myst-parser + # pydata-sphinx-theme + # sphinx-book-theme + # sphinx-comments + # sphinx-copybutton + # sphinx-design + # sphinx-external-toc + # sphinx-jupyterbook-latex + # sphinx-multitoc-numbering + # sphinx-rtd-theme + # sphinx-thebe + # sphinx-togglebutton + # sphinxcontrib-bibtex + # sphinxcontrib-jquery +sphinx-book-theme==1.1.3 + # via jupyter-book +sphinx-comments==0.0.3 + # via jupyter-book +sphinx-copybutton==0.5.2 + # via jupyter-book +sphinx-design==0.6.1 + # via jupyter-book +sphinx-external-toc==1.0.1 + # via jupyter-book +sphinx-jupyterbook-latex==1.0.0 + # via jupyter-book +sphinx-multitoc-numbering==0.1.3 + # via jupyter-book +sphinx-rtd-theme==3.0.2 + # via -r requirements_old.txt +sphinx-thebe==0.3.1 + # via jupyter-book +sphinx-togglebutton==0.3.2 + # via jupyter-book +sphinxcontrib-applehelp==2.0.0 + # via sphinx +sphinxcontrib-bibtex==2.6.3 + # via jupyter-book +sphinxcontrib-devhelp==2.0.0 + # via sphinx +sphinxcontrib-htmlhelp==2.1.0 + # via sphinx +sphinxcontrib-jquery==4.1 + # via sphinx-rtd-theme +sphinxcontrib-jsmath==1.0.1 + # via sphinx +sphinxcontrib-qthelp==2.0.0 + # via sphinx +sphinxcontrib-serializinghtml==2.0.0 + # via sphinx +sqlalchemy==2.0.36 + # via jupyter-cache +stack-data==0.6.3 + # via ipython +tabulate==0.9.0 + # via jupyter-cache +terminado==0.18.1 + # via + # jupyter-server + # jupyter-server-terminals +tinycss2==1.4.0 + # via nbconvert +tornado==6.4.1 + # via + # ipykernel + # jupyter-client + # jupyter-server + # terminado +traitlets==5.14.3 + # via + # comm + # ipykernel + # ipython + # jupyter-client + # jupyter-core + # jupyter-events + # jupyter-server + # matplotlib-inline + # nbclient + # nbconvert + # nbformat +types-python-dateutil==2.9.0.20241003 + # via arrow +typing-extensions==4.12.2 + # via + # myst-nb + # pydata-sphinx-theme + # sqlalchemy +uc-micro-py==1.0.3 + # via linkify-it-py +uri-template==1.3.0 + # via jsonschema +urllib3==2.2.3 + # via requests +wcwidth==0.2.13 + # via prompt-toolkit +webcolors==24.11.1 + # via jsonschema +webencodings==0.5.1 + # via + # bleach + # tinycss2 +websocket-client==1.8.0 + # via jupyter-server +wheel==0.45.0 + # via sphinx-togglebutton +zipp==3.21.0 + # via importlib-metadata diff --git a/requirements_old.txt b/requirements_old.txt deleted file mode 100644 index e83d6cc..0000000 --- a/requirements_old.txt +++ /dev/null @@ -1,13 +0,0 @@ -jinja2==3.0.3 -jupyter-book==0.13.1 -sphinx==4.5.0 -sphinx_rtd_theme==1.0.0 -pytest==6.2.5 -pytest-cov==3.0.0 -jsonschema==3.2.0 -ruamel.yaml==0.17.17 -demes==0.2.2 -demesdraw==0.3.0 -hypothesis-jsonschema==0.20.1 -# See https://github.com/executablebooks/jupyter-book/issues/1902 -jupyter-server<2