diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index 389b6c4d62..939742e158 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -26,11 +26,16 @@ jobs: uses: actions/checkout@v4 with: submodules: true + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v5 + with: + version: "latest" + python-version: ${{ matrix.python }} - name: Install black run: | - python -m pip install black=="24.10.0" + uv sync --only-group format - name: Validate code run: | - find . -name '*.py'|grep -v headers|grep -v demes-spec|xargs python -m black --check + find fwdpy11 tests tests_with_cpp examples -name '*.py' | grep -v headers | grep -v demes-spec | xargs python -m black --check diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index d0d6dfa2df..8a8cbc5e44 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -56,10 +56,6 @@ jobs: run: | sudo apt install --fix-missing -y libgsl-dev cmake - - name: Install Python dependencies - run: | - uv pip install -r requirements/CI_${{ matrix.python-version }}.txt - - name: rustc version run: | rustc --version @@ -68,9 +64,9 @@ jobs: run: | cbindgen --version - - name: Build module + - name: uv sync run: | - uv pip install -e . + uv sync -p ${{ matrix.python-version }} --locked --group build --group doc --no-dev - name: Build the docs working-directory: doc diff --git a/.github/workflows/macos_CI.yml b/.github/workflows/macos_CI.yml index da6f18d735..f49a114694 100644 --- a/.github/workflows/macos_CI.yml +++ b/.github/workflows/macos_CI.yml @@ -52,7 +52,11 @@ jobs: - name: Install Python dependencies run: | - uv pip install -r requirements/CI_${{ matrix.python }}.txt + # We need to build the C++ test suite, etc., so + # we don't let uv install the project (b/c the other + # stuff isn't built in that case) + uv sync -p ${{ matrix.python }} --no-install-project --frozen --group build + - name: Build extension module run: | cmake -S. -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON_UNIT_TESTS=ON -DDISABLE_LTO=ON diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml index cbd5ca1160..80054de36a 100644 --- a/.github/workflows/ubuntu.yml +++ b/.github/workflows/ubuntu.yml @@ -89,9 +89,12 @@ jobs: run: | python --version - - name: Install pip dependencies + - name: Install python dependencies run: | - uv pip install -r requirements/CI_${{ matrix.python }}.txt + # We need to build the C++ test suite, etc., so + # we don't let uv install the project (b/c the other + # stuff isn't built in that case) + uv sync -p ${{ matrix.python }} --no-install-project --frozen --group build # Need# ed so that we don't affect building any pip dependencies with these flags - name: Set CPPFLAGS for C++ builds diff --git a/doc/misc/developersguide.md b/doc/misc/developersguide.md index cc4a4c025f..3049f3b83d 100644 --- a/doc/misc/developersguide.md +++ b/doc/misc/developersguide.md @@ -36,8 +36,6 @@ The C++ test suite requires: :::{warning} `conda` users **must** install all of these dependencies using that system, including the compilers! See [here](https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html) for info about `conda` compilers for Linux and for macOS. - -The `requirements/` folder of the source code repository contains a list of minimal `conda` dependencies that we use for CI. ::: #### Python @@ -45,7 +43,7 @@ The `requirements/` folder of the source code repository contains a list of mini To reproduce the environments that we use for CI and deployment: ```sh -python3 -m pip install -r requirements/development.txt +uv sync --no-install-package --all-groups ``` ```{note} diff --git a/pyproject.toml b/pyproject.toml index a61e5dfe09..970016eccb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,8 @@ [build-system] # We need setup.cfg support, which setuptools indtroduced in 30.3.0. requires = [ - "scikit-build-core>=0.3.3", - "setuptools_scm>=8", + "scikit-build-core==0.11.1", + "setuptools_scm==7.1.0", "pybind11[global]==2.12.0", "numpy >= 2.0" ] @@ -31,6 +31,49 @@ dependencies = [ ] requires-python = ">=3.10, <3.14" +[dependency-groups] +# NOTE: we are doing a very odd hack here! +# uv does NOT currently support locking build dependencies +# so we add it as a dependency group and force it. +# The PROBLEM is that we have TWO places to modify +# things in the future. +build = [ + "scikit-build-core==0.11.1", + "setuptools_scm==7.1.0", + "pybind11[global]==2.12.0", + "numpy >= 2.0" +] +format = [ + "black==24.10.0" +] +lint = [ + "flake8", + "flake8-bugbear", +] +dev = [ +#below are for building package +#and running tests + "pytest", + "pytest-xdist", + "hypothesis==6.56.4", + "msprime ~= 1.3.0", + "build", + "twine", +] + +doc = [ + "jupyter-book~=0.15.1", + "pydata-sphinx-theme==0.13.1", + "matplotlib", + "msprime", + "pandas", +# pyarrow will be a requirement of pandas soon. +# right now, not having it raises a warning + "pyarrow", + "sphinx-issues", + "demesdraw~=0.4.0", +] + [project.scripts] fwdpy11 = "fwdpy11.__main__:main" @@ -69,3 +112,8 @@ before-all = "./deployment/linux_wheels/cibuildwheel.sh" archs = "x86_64" # skip = "pp* *musllinux*" +[tool.uv] +required-environments = [ + "sys_platform == 'darwin' and implementation_name == 'cpython'", + "sys_platform == 'linux' and implementation_name == 'cpython'", +] diff --git a/requirements/CI_3.10.txt b/requirements/CI_3.10.txt deleted file mode 100644 index ab7298b6e6..0000000000 --- a/requirements/CI_3.10.txt +++ /dev/null @@ -1,463 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile -p 3.10 requirements/development.txt -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==0.7.16 - # via sphinx -asttokens==3.0.0 - # via stack-data -attrs==25.1.0 - # via - # -r requirements/minimal_install_requirements.txt - # demes - # flake8-bugbear - # hypothesis - # jsonschema - # jupyter-cache - # referencing -babel==2.17.0 - # via - # pydata-sphinx-theme - # sphinx -backports-tarfile==1.2.0 - # via jaraco-context -beautifulsoup4==4.13.3 - # via pydata-sphinx-theme -build==1.2.2.post1 - # via -r requirements/development.txt -certifi==2025.1.31 - # via requests -cffi==1.17.1 - # via cryptography -charset-normalizer==3.4.1 - # via requests -click==8.1.8 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -cmake==3.31.6 - # via -r requirements/build.txt -comm==0.2.2 - # via ipykernel -contourpy==1.3.1 - # via matplotlib -cryptography==44.0.2 - # via secretstorage -cycler==0.12.1 - # via matplotlib -debugpy==1.8.13 - # via ipykernel -decorator==5.2.1 - # via ipython -demes==0.2.2 - # via - # -r requirements/minimal_install_requirements.txt - # demesdraw - # msprime -demesdraw==0.4.0 - # via -r requirements/docs.txt -deprecated==1.2.18 - # via -r requirements/minimal_install_requirements.txt -docutils==0.18.1 - # via - # jupyter-book - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # readme-renderer - # sphinx - # sphinx-togglebutton - # sphinxcontrib-bibtex -exceptiongroup==1.2.2 - # via - # hypothesis - # ipython - # pytest -execnet==2.1.1 - # via pytest-xdist -executing==2.2.0 - # via stack-data -fastjsonschema==2.21.1 - # via nbformat -flake8==7.1.2 - # via - # -r requirements/development.txt - # flake8-bugbear -flake8-bugbear==24.12.12 - # via -r requirements/development.txt -fonttools==4.56.0 - # via matplotlib -greenlet==3.1.1 - # via sqlalchemy -hypothesis==6.56.4 - # via -r requirements/tests.txt -id==1.5.0 - # via twine -idna==3.10 - # via requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.6.1 - # via - # build - # jupyter-cache - # keyring - # myst-nb -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via myst-nb -ipython==8.33.0 - # via - # ipykernel - # myst-nb -jaraco-classes==3.4.0 - # via keyring -jaraco-context==6.0.1 - # via keyring -jaraco-functools==4.1.0 - # via keyring -jedi==0.19.2 - # via ipython -jeepney==0.9.0 - # via - # keyring - # secretstorage -jinja2==3.1.5 - # via - # jupyter-book - # myst-parser - # sphinx -jsonschema==4.23.0 - # via - # jupyter-book - # nbformat - # tskit -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-book==0.15.1 - # via -r requirements/docs.txt -jupyter-cache==0.6.1 - # via myst-nb -jupyter-client==8.6.3 - # via - # ipykernel - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -keyring==25.6.0 - # via twine -kiwisolver==1.4.8 - # via matplotlib -latexcodec==3.0.0 - # via pybtex -linkify-it-py==2.0.3 - # via jupyter-book -markdown-it-py==2.2.0 - # via - # mdit-py-plugins - # myst-parser - # rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.10.1 - # via - # -r requirements/docs.txt - # demesdraw -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.3.5 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -more-itertools==10.6.0 - # via - # jaraco-classes - # jaraco-functools -msprime==1.3.3 - # via - # -r requirements/docs.txt - # -r requirements/tests.txt -myst-nb==0.17.2 - # via jupyter-book -myst-parser==0.18.1 - # via myst-nb -nbclient==0.7.4 - # via - # jupyter-cache - # myst-nb -nbformat==5.10.4 - # via - # jupyter-cache - # myst-nb - # nbclient -nest-asyncio==1.6.0 - # via ipykernel -newick==1.9.0 - # via msprime -nh3==0.2.21 - # via readme-renderer -numpy==2.2.3 - # via - # -r requirements/minimal_install_requirements.txt - # contourpy - # demesdraw - # matplotlib - # msprime - # pandas - # scipy - # tskit -packaging==24.2 - # via - # build - # ipykernel - # matplotlib - # pydata-sphinx-theme - # pytest - # setuptools-scm - # sphinx - # twine -pandas==2.2.3 - # via -r requirements/docs.txt -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==11.1.0 - # via matplotlib -platformdirs==4.3.6 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prompt-toolkit==3.0.50 - # via ipython -psutil==7.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyarrow==19.0.1 - # via -r requirements/docs.txt -pybind11==2.12.0 - # via -r requirements/build.txt -pybind11-global==2.12.0 - # via pybind11 -pybtex==0.24.0 - # via - # pybtex-docutils - # sphinxcontrib-bibtex -pybtex-docutils==1.0.3 - # via sphinxcontrib-bibtex -pycodestyle==2.12.1 - # via flake8 -pycparser==2.22 - # via cffi -pydata-sphinx-theme==0.13.1 - # via - # -r requirements/docs.txt - # sphinx-book-theme -pyflakes==3.2.0 - # via flake8 -pygments==2.19.1 - # via - # accessible-pygments - # ipython - # pydata-sphinx-theme - # readme-renderer - # rich - # sphinx -pyparsing==3.2.1 - # via matplotlib -pyproject-hooks==1.2.0 - # via build -pytest==8.3.5 - # via - # -r requirements/tests.txt - # pytest-xdist -pytest-xdist==3.6.1 - # via -r requirements/tests.txt -python-dateutil==2.9.0.post0 - # via - # jupyter-client - # matplotlib - # pandas -pytz==2025.1 - # via pandas -pyyaml==6.0.2 - # via - # jupyter-book - # jupyter-cache - # myst-nb - # myst-parser - # pybtex - # sphinx-external-toc -pyzmq==26.2.1 - # via - # ipykernel - # jupyter-client -readme-renderer==43.0 - # via twine -referencing==0.36.2 - # via - # jsonschema - # jsonschema-specifications -requests==2.32.3 - # via - # id - # requests-toolbelt - # sphinx - # twine -requests-toolbelt==1.0.0 - # via twine -rfc3986==2.0.0 - # via twine -rich==13.9.4 - # via twine -rpds-py==0.23.1 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.10 - # via demes -ruamel-yaml-clib==0.2.12 - # via ruamel-yaml -scipy==1.15.2 - # via demesdraw -secretstorage==3.3.3 - # via keyring -setuptools==75.8.2 - # via - # setuptools-scm - # sphinx-togglebutton -setuptools-scm==7.1.0 - # via -r requirements/build.txt -six==1.17.0 - # via - # pybtex - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -sortedcontainers==2.4.0 - # via hypothesis -soupsieve==2.6 - # via beautifulsoup4 -sphinx==5.0.2 - # via - # jupyter-book - # myst-nb - # myst-parser - # pydata-sphinx-theme - # sphinx-book-theme - # sphinx-comments - # sphinx-copybutton - # sphinx-design - # sphinx-external-toc - # sphinx-issues - # sphinx-jupyterbook-latex - # sphinx-multitoc-numbering - # sphinx-thebe - # sphinx-togglebutton - # sphinxcontrib-bibtex -sphinx-book-theme==1.0.0 - # via jupyter-book -sphinx-comments==0.0.3 - # via jupyter-book -sphinx-copybutton==0.5.2 - # via jupyter-book -sphinx-design==0.3.0 - # via jupyter-book -sphinx-external-toc==0.3.1 - # via jupyter-book -sphinx-issues==5.0.0 - # via -r requirements/docs.txt -sphinx-jupyterbook-latex==0.5.2 - # via jupyter-book -sphinx-multitoc-numbering==0.1.3 - # via jupyter-book -sphinx-thebe==0.2.1 - # via jupyter-book -sphinx-togglebutton==0.3.2 - # via jupyter-book -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-bibtex==2.5.0 - # via jupyter-book -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -sqlalchemy==2.0.38 - # via jupyter-cache -stack-data==0.6.3 - # via ipython -svgwrite==1.4.3 - # via tskit -tabulate==0.9.0 - # via jupyter-cache -tomli==2.2.1 - # via - # build - # pytest - # setuptools-scm -tornado==6.4.2 - # via - # ipykernel - # jupyter-client -traitlets==5.14.3 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbformat -tskit==0.6.0 - # via - # -r requirements/minimal_install_requirements.txt - # msprime -twine==6.1.0 - # via -r requirements/development.txt -typing-extensions==4.12.2 - # via - # beautifulsoup4 - # ipython - # myst-nb - # myst-parser - # referencing - # rich - # setuptools-scm - # sqlalchemy -tzdata==2025.1 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -urllib3==2.3.0 - # via - # requests - # twine -wcwidth==0.2.13 - # via prompt-toolkit -wheel==0.45.1 - # via sphinx-togglebutton -wrapt==1.17.2 - # via deprecated -zipp==3.21.0 - # via importlib-metadata diff --git a/requirements/CI_3.11.txt b/requirements/CI_3.11.txt deleted file mode 100644 index ad9798d181..0000000000 --- a/requirements/CI_3.11.txt +++ /dev/null @@ -1,454 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile -p 3.11 requirements/development.txt -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==0.7.16 - # via sphinx -asttokens==3.0.0 - # via stack-data -attrs==25.1.0 - # via - # -r requirements/minimal_install_requirements.txt - # demes - # flake8-bugbear - # hypothesis - # jsonschema - # jupyter-cache - # referencing -babel==2.17.0 - # via - # pydata-sphinx-theme - # sphinx -backports-tarfile==1.2.0 - # via jaraco-context -beautifulsoup4==4.13.3 - # via pydata-sphinx-theme -build==1.2.2.post1 - # via -r requirements/development.txt -certifi==2025.1.31 - # via requests -cffi==1.17.1 - # via cryptography -charset-normalizer==3.4.1 - # via requests -click==8.1.8 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -cmake==3.31.6 - # via -r requirements/build.txt -comm==0.2.2 - # via ipykernel -contourpy==1.3.1 - # via matplotlib -cryptography==44.0.2 - # via secretstorage -cycler==0.12.1 - # via matplotlib -debugpy==1.8.13 - # via ipykernel -decorator==5.2.1 - # via ipython -demes==0.2.2 - # via - # -r requirements/minimal_install_requirements.txt - # demesdraw - # msprime -demesdraw==0.4.0 - # via -r requirements/docs.txt -deprecated==1.2.18 - # via -r requirements/minimal_install_requirements.txt -docutils==0.18.1 - # via - # jupyter-book - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # readme-renderer - # sphinx - # sphinx-togglebutton - # sphinxcontrib-bibtex -execnet==2.1.1 - # via pytest-xdist -executing==2.2.0 - # via stack-data -fastjsonschema==2.21.1 - # via nbformat -flake8==7.1.2 - # via - # -r requirements/development.txt - # flake8-bugbear -flake8-bugbear==24.12.12 - # via -r requirements/development.txt -fonttools==4.56.0 - # via matplotlib -greenlet==3.1.1 - # via sqlalchemy -hypothesis==6.56.4 - # via -r requirements/tests.txt -id==1.5.0 - # via twine -idna==3.10 - # via requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.6.1 - # via - # jupyter-cache - # keyring - # myst-nb -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via myst-nb -ipython==9.0.1 - # via - # ipykernel - # myst-nb -ipython-pygments-lexers==1.1.1 - # via ipython -jaraco-classes==3.4.0 - # via keyring -jaraco-context==6.0.1 - # via keyring -jaraco-functools==4.1.0 - # via keyring -jedi==0.19.2 - # via ipython -jeepney==0.9.0 - # via - # keyring - # secretstorage -jinja2==3.1.5 - # via - # jupyter-book - # myst-parser - # sphinx -jsonschema==4.23.0 - # via - # jupyter-book - # nbformat - # tskit -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-book==0.15.1 - # via -r requirements/docs.txt -jupyter-cache==0.6.1 - # via myst-nb -jupyter-client==8.6.3 - # via - # ipykernel - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -keyring==25.6.0 - # via twine -kiwisolver==1.4.8 - # via matplotlib -latexcodec==3.0.0 - # via pybtex -linkify-it-py==2.0.3 - # via jupyter-book -markdown-it-py==2.2.0 - # via - # mdit-py-plugins - # myst-parser - # rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.10.1 - # via - # -r requirements/docs.txt - # demesdraw -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.3.5 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -more-itertools==10.6.0 - # via - # jaraco-classes - # jaraco-functools -msprime==1.3.3 - # via - # -r requirements/docs.txt - # -r requirements/tests.txt -myst-nb==0.17.2 - # via jupyter-book -myst-parser==0.18.1 - # via myst-nb -nbclient==0.7.4 - # via - # jupyter-cache - # myst-nb -nbformat==5.10.4 - # via - # jupyter-cache - # myst-nb - # nbclient -nest-asyncio==1.6.0 - # via ipykernel -newick==1.9.0 - # via msprime -nh3==0.2.21 - # via readme-renderer -numpy==2.2.3 - # via - # -r requirements/minimal_install_requirements.txt - # contourpy - # demesdraw - # matplotlib - # msprime - # pandas - # scipy - # tskit -packaging==24.2 - # via - # build - # ipykernel - # matplotlib - # pydata-sphinx-theme - # pytest - # setuptools-scm - # sphinx - # twine -pandas==2.2.3 - # via -r requirements/docs.txt -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==11.1.0 - # via matplotlib -platformdirs==4.3.6 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prompt-toolkit==3.0.50 - # via ipython -psutil==7.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyarrow==19.0.1 - # via -r requirements/docs.txt -pybind11==2.12.0 - # via -r requirements/build.txt -pybind11-global==2.12.0 - # via pybind11 -pybtex==0.24.0 - # via - # pybtex-docutils - # sphinxcontrib-bibtex -pybtex-docutils==1.0.3 - # via sphinxcontrib-bibtex -pycodestyle==2.12.1 - # via flake8 -pycparser==2.22 - # via cffi -pydata-sphinx-theme==0.13.1 - # via - # -r requirements/docs.txt - # sphinx-book-theme -pyflakes==3.2.0 - # via flake8 -pygments==2.19.1 - # via - # accessible-pygments - # ipython - # ipython-pygments-lexers - # pydata-sphinx-theme - # readme-renderer - # rich - # sphinx -pyparsing==3.2.1 - # via matplotlib -pyproject-hooks==1.2.0 - # via build -pytest==8.3.5 - # via - # -r requirements/tests.txt - # pytest-xdist -pytest-xdist==3.6.1 - # via -r requirements/tests.txt -python-dateutil==2.9.0.post0 - # via - # jupyter-client - # matplotlib - # pandas -pytz==2025.1 - # via pandas -pyyaml==6.0.2 - # via - # jupyter-book - # jupyter-cache - # myst-nb - # myst-parser - # pybtex - # sphinx-external-toc -pyzmq==26.2.1 - # via - # ipykernel - # jupyter-client -readme-renderer==43.0 - # via twine -referencing==0.36.2 - # via - # jsonschema - # jsonschema-specifications -requests==2.32.3 - # via - # id - # requests-toolbelt - # sphinx - # twine -requests-toolbelt==1.0.0 - # via twine -rfc3986==2.0.0 - # via twine -rich==13.9.4 - # via twine -rpds-py==0.23.1 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.10 - # via demes -ruamel-yaml-clib==0.2.12 - # via ruamel-yaml -scipy==1.15.2 - # via demesdraw -secretstorage==3.3.3 - # via keyring -setuptools==75.8.2 - # via - # setuptools-scm - # sphinx-togglebutton -setuptools-scm==7.1.0 - # via -r requirements/build.txt -six==1.17.0 - # via - # pybtex - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -sortedcontainers==2.4.0 - # via hypothesis -soupsieve==2.6 - # via beautifulsoup4 -sphinx==5.0.2 - # via - # jupyter-book - # myst-nb - # myst-parser - # pydata-sphinx-theme - # sphinx-book-theme - # sphinx-comments - # sphinx-copybutton - # sphinx-design - # sphinx-external-toc - # sphinx-issues - # sphinx-jupyterbook-latex - # sphinx-multitoc-numbering - # sphinx-thebe - # sphinx-togglebutton - # sphinxcontrib-bibtex -sphinx-book-theme==1.0.0 - # via jupyter-book -sphinx-comments==0.0.3 - # via jupyter-book -sphinx-copybutton==0.5.2 - # via jupyter-book -sphinx-design==0.3.0 - # via jupyter-book -sphinx-external-toc==0.3.1 - # via jupyter-book -sphinx-issues==5.0.0 - # via -r requirements/docs.txt -sphinx-jupyterbook-latex==0.5.2 - # via jupyter-book -sphinx-multitoc-numbering==0.1.3 - # via jupyter-book -sphinx-thebe==0.2.1 - # via jupyter-book -sphinx-togglebutton==0.3.2 - # via jupyter-book -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-bibtex==2.5.0 - # via jupyter-book -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -sqlalchemy==2.0.38 - # via jupyter-cache -stack-data==0.6.3 - # via ipython -svgwrite==1.4.3 - # via tskit -tabulate==0.9.0 - # via jupyter-cache -tornado==6.4.2 - # via - # ipykernel - # jupyter-client -traitlets==5.14.3 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbformat -tskit==0.6.0 - # via - # -r requirements/minimal_install_requirements.txt - # msprime -twine==6.1.0 - # via -r requirements/development.txt -typing-extensions==4.12.2 - # via - # beautifulsoup4 - # ipython - # myst-nb - # myst-parser - # referencing - # setuptools-scm - # sqlalchemy -tzdata==2025.1 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -urllib3==2.3.0 - # via - # requests - # twine -wcwidth==0.2.13 - # via prompt-toolkit -wheel==0.45.1 - # via sphinx-togglebutton -wrapt==1.17.2 - # via deprecated -zipp==3.21.0 - # via importlib-metadata diff --git a/requirements/CI_3.12.txt b/requirements/CI_3.12.txt deleted file mode 100644 index 01ec765bad..0000000000 --- a/requirements/CI_3.12.txt +++ /dev/null @@ -1,450 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile -p 3.12 requirements/development.txt -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==0.7.16 - # via sphinx -asttokens==3.0.0 - # via stack-data -attrs==25.1.0 - # via - # -r requirements/minimal_install_requirements.txt - # demes - # flake8-bugbear - # hypothesis - # jsonschema - # jupyter-cache - # referencing -babel==2.17.0 - # via - # pydata-sphinx-theme - # sphinx -beautifulsoup4==4.13.3 - # via pydata-sphinx-theme -build==1.2.2.post1 - # via -r requirements/development.txt -certifi==2025.1.31 - # via requests -cffi==1.17.1 - # via cryptography -charset-normalizer==3.4.1 - # via requests -click==8.1.8 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -cmake==3.31.6 - # via -r requirements/build.txt -comm==0.2.2 - # via ipykernel -contourpy==1.3.1 - # via matplotlib -cryptography==44.0.2 - # via secretstorage -cycler==0.12.1 - # via matplotlib -debugpy==1.8.13 - # via ipykernel -decorator==5.2.1 - # via ipython -demes==0.2.2 - # via - # -r requirements/minimal_install_requirements.txt - # demesdraw - # msprime -demesdraw==0.4.0 - # via -r requirements/docs.txt -deprecated==1.2.18 - # via -r requirements/minimal_install_requirements.txt -docutils==0.18.1 - # via - # jupyter-book - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # readme-renderer - # sphinx - # sphinx-togglebutton - # sphinxcontrib-bibtex -execnet==2.1.1 - # via pytest-xdist -executing==2.2.0 - # via stack-data -fastjsonschema==2.21.1 - # via nbformat -flake8==7.1.2 - # via - # -r requirements/development.txt - # flake8-bugbear -flake8-bugbear==24.12.12 - # via -r requirements/development.txt -fonttools==4.56.0 - # via matplotlib -greenlet==3.1.1 - # via sqlalchemy -hypothesis==6.56.4 - # via -r requirements/tests.txt -id==1.5.0 - # via twine -idna==3.10 - # via requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.6.1 - # via - # jupyter-cache - # myst-nb -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via myst-nb -ipython==9.0.1 - # via - # ipykernel - # myst-nb -ipython-pygments-lexers==1.1.1 - # via ipython -jaraco-classes==3.4.0 - # via keyring -jaraco-context==6.0.1 - # via keyring -jaraco-functools==4.1.0 - # via keyring -jedi==0.19.2 - # via ipython -jeepney==0.9.0 - # via - # keyring - # secretstorage -jinja2==3.1.5 - # via - # jupyter-book - # myst-parser - # sphinx -jsonschema==4.23.0 - # via - # jupyter-book - # nbformat - # tskit -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-book==0.15.1 - # via -r requirements/docs.txt -jupyter-cache==0.6.1 - # via myst-nb -jupyter-client==8.6.3 - # via - # ipykernel - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -keyring==25.6.0 - # via twine -kiwisolver==1.4.8 - # via matplotlib -latexcodec==3.0.0 - # via pybtex -linkify-it-py==2.0.3 - # via jupyter-book -markdown-it-py==2.2.0 - # via - # mdit-py-plugins - # myst-parser - # rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.10.1 - # via - # -r requirements/docs.txt - # demesdraw -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.3.5 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -more-itertools==10.6.0 - # via - # jaraco-classes - # jaraco-functools -msprime==1.3.3 - # via - # -r requirements/docs.txt - # -r requirements/tests.txt -myst-nb==0.17.2 - # via jupyter-book -myst-parser==0.18.1 - # via myst-nb -nbclient==0.7.4 - # via - # jupyter-cache - # myst-nb -nbformat==5.10.4 - # via - # jupyter-cache - # myst-nb - # nbclient -nest-asyncio==1.6.0 - # via ipykernel -newick==1.9.0 - # via msprime -nh3==0.2.21 - # via readme-renderer -numpy==2.2.3 - # via - # -r requirements/minimal_install_requirements.txt - # contourpy - # demesdraw - # matplotlib - # msprime - # pandas - # scipy - # tskit -packaging==24.2 - # via - # build - # ipykernel - # matplotlib - # pydata-sphinx-theme - # pytest - # setuptools-scm - # sphinx - # twine -pandas==2.2.3 - # via -r requirements/docs.txt -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==11.1.0 - # via matplotlib -platformdirs==4.3.6 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prompt-toolkit==3.0.50 - # via ipython -psutil==7.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyarrow==19.0.1 - # via -r requirements/docs.txt -pybind11==2.12.0 - # via -r requirements/build.txt -pybind11-global==2.12.0 - # via pybind11 -pybtex==0.24.0 - # via - # pybtex-docutils - # sphinxcontrib-bibtex -pybtex-docutils==1.0.3 - # via sphinxcontrib-bibtex -pycodestyle==2.12.1 - # via flake8 -pycparser==2.22 - # via cffi -pydata-sphinx-theme==0.13.1 - # via - # -r requirements/docs.txt - # sphinx-book-theme -pyflakes==3.2.0 - # via flake8 -pygments==2.19.1 - # via - # accessible-pygments - # ipython - # ipython-pygments-lexers - # pydata-sphinx-theme - # readme-renderer - # rich - # sphinx -pyparsing==3.2.1 - # via matplotlib -pyproject-hooks==1.2.0 - # via build -pytest==8.3.5 - # via - # -r requirements/tests.txt - # pytest-xdist -pytest-xdist==3.6.1 - # via -r requirements/tests.txt -python-dateutil==2.9.0.post0 - # via - # jupyter-client - # matplotlib - # pandas -pytz==2025.1 - # via pandas -pyyaml==6.0.2 - # via - # jupyter-book - # jupyter-cache - # myst-nb - # myst-parser - # pybtex - # sphinx-external-toc -pyzmq==26.2.1 - # via - # ipykernel - # jupyter-client -readme-renderer==43.0 - # via twine -referencing==0.36.2 - # via - # jsonschema - # jsonschema-specifications -requests==2.32.3 - # via - # id - # requests-toolbelt - # sphinx - # twine -requests-toolbelt==1.0.0 - # via twine -rfc3986==2.0.0 - # via twine -rich==13.9.4 - # via twine -rpds-py==0.23.1 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.10 - # via demes -ruamel-yaml-clib==0.2.12 - # via ruamel-yaml -scipy==1.15.2 - # via demesdraw -secretstorage==3.3.3 - # via keyring -setuptools==75.8.2 - # via - # setuptools-scm - # sphinx-togglebutton -setuptools-scm==7.1.0 - # via -r requirements/build.txt -six==1.17.0 - # via - # pybtex - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -sortedcontainers==2.4.0 - # via hypothesis -soupsieve==2.6 - # via beautifulsoup4 -sphinx==5.0.2 - # via - # jupyter-book - # myst-nb - # myst-parser - # pydata-sphinx-theme - # sphinx-book-theme - # sphinx-comments - # sphinx-copybutton - # sphinx-design - # sphinx-external-toc - # sphinx-issues - # sphinx-jupyterbook-latex - # sphinx-multitoc-numbering - # sphinx-thebe - # sphinx-togglebutton - # sphinxcontrib-bibtex -sphinx-book-theme==1.0.0 - # via jupyter-book -sphinx-comments==0.0.3 - # via jupyter-book -sphinx-copybutton==0.5.2 - # via jupyter-book -sphinx-design==0.3.0 - # via jupyter-book -sphinx-external-toc==0.3.1 - # via jupyter-book -sphinx-issues==5.0.0 - # via -r requirements/docs.txt -sphinx-jupyterbook-latex==0.5.2 - # via jupyter-book -sphinx-multitoc-numbering==0.1.3 - # via jupyter-book -sphinx-thebe==0.2.1 - # via jupyter-book -sphinx-togglebutton==0.3.2 - # via jupyter-book -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-bibtex==2.5.0 - # via jupyter-book -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -sqlalchemy==2.0.38 - # via jupyter-cache -stack-data==0.6.3 - # via ipython -svgwrite==1.4.3 - # via tskit -tabulate==0.9.0 - # via jupyter-cache -tornado==6.4.2 - # via - # ipykernel - # jupyter-client -traitlets==5.14.3 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbformat -tskit==0.6.0 - # via - # -r requirements/minimal_install_requirements.txt - # msprime -twine==6.1.0 - # via -r requirements/development.txt -typing-extensions==4.12.2 - # via - # beautifulsoup4 - # myst-nb - # myst-parser - # referencing - # setuptools-scm - # sqlalchemy -tzdata==2025.1 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -urllib3==2.3.0 - # via - # requests - # twine -wcwidth==0.2.13 - # via prompt-toolkit -wheel==0.45.1 - # via sphinx-togglebutton -wrapt==1.17.2 - # via deprecated -zipp==3.21.0 - # via importlib-metadata diff --git a/requirements/CI_3.13.txt b/requirements/CI_3.13.txt deleted file mode 100644 index 448b9ff055..0000000000 --- a/requirements/CI_3.13.txt +++ /dev/null @@ -1,447 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile -p 3.13 requirements/development.txt -accessible-pygments==0.0.5 - # via pydata-sphinx-theme -alabaster==0.7.16 - # via sphinx -asttokens==3.0.0 - # via stack-data -attrs==25.1.0 - # via - # -r requirements/minimal_install_requirements.txt - # demes - # flake8-bugbear - # hypothesis - # jsonschema - # jupyter-cache - # referencing -babel==2.17.0 - # via - # pydata-sphinx-theme - # sphinx -beautifulsoup4==4.13.3 - # via pydata-sphinx-theme -build==1.2.2.post1 - # via -r requirements/development.txt -certifi==2025.1.31 - # via requests -cffi==1.17.1 - # via cryptography -charset-normalizer==3.4.1 - # via requests -click==8.1.8 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -cmake==3.31.6 - # via -r requirements/build.txt -comm==0.2.2 - # via ipykernel -contourpy==1.3.1 - # via matplotlib -cryptography==44.0.2 - # via secretstorage -cycler==0.12.1 - # via matplotlib -debugpy==1.8.13 - # via ipykernel -decorator==5.2.1 - # via ipython -demes==0.2.2 - # via - # -r requirements/minimal_install_requirements.txt - # demesdraw - # msprime -demesdraw==0.4.0 - # via -r requirements/docs.txt -deprecated==1.2.18 - # via -r requirements/minimal_install_requirements.txt -docutils==0.18.1 - # via - # jupyter-book - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # readme-renderer - # sphinx - # sphinx-togglebutton - # sphinxcontrib-bibtex -execnet==2.1.1 - # via pytest-xdist -executing==2.2.0 - # via stack-data -fastjsonschema==2.21.1 - # via nbformat -flake8==7.1.2 - # via - # -r requirements/development.txt - # flake8-bugbear -flake8-bugbear==24.12.12 - # via -r requirements/development.txt -fonttools==4.56.0 - # via matplotlib -greenlet==3.1.1 - # via sqlalchemy -hypothesis==6.56.4 - # via -r requirements/tests.txt -id==1.5.0 - # via twine -idna==3.10 - # via requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.6.1 - # via - # jupyter-cache - # myst-nb -iniconfig==2.0.0 - # via pytest -ipykernel==6.29.5 - # via myst-nb -ipython==9.0.1 - # via - # ipykernel - # myst-nb -ipython-pygments-lexers==1.1.1 - # via ipython -jaraco-classes==3.4.0 - # via keyring -jaraco-context==6.0.1 - # via keyring -jaraco-functools==4.1.0 - # via keyring -jedi==0.19.2 - # via ipython -jeepney==0.9.0 - # via - # keyring - # secretstorage -jinja2==3.1.5 - # via - # jupyter-book - # myst-parser - # sphinx -jsonschema==4.23.0 - # via - # jupyter-book - # nbformat - # tskit -jsonschema-specifications==2024.10.1 - # via jsonschema -jupyter-book==0.15.1 - # via -r requirements/docs.txt -jupyter-cache==0.6.1 - # via myst-nb -jupyter-client==8.6.3 - # via - # ipykernel - # nbclient -jupyter-core==5.7.2 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -keyring==25.6.0 - # via twine -kiwisolver==1.4.8 - # via matplotlib -latexcodec==3.0.0 - # via pybtex -linkify-it-py==2.0.3 - # via jupyter-book -markdown-it-py==2.2.0 - # via - # mdit-py-plugins - # myst-parser - # rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.10.1 - # via - # -r requirements/docs.txt - # demesdraw -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.3.5 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -more-itertools==10.6.0 - # via - # jaraco-classes - # jaraco-functools -msprime==1.3.3 - # via - # -r requirements/docs.txt - # -r requirements/tests.txt -myst-nb==0.17.2 - # via jupyter-book -myst-parser==0.18.1 - # via myst-nb -nbclient==0.7.4 - # via - # jupyter-cache - # myst-nb -nbformat==5.10.4 - # via - # jupyter-cache - # myst-nb - # nbclient -nest-asyncio==1.6.0 - # via ipykernel -newick==1.9.0 - # via msprime -nh3==0.2.21 - # via readme-renderer -numpy==2.2.3 - # via - # -r requirements/minimal_install_requirements.txt - # contourpy - # demesdraw - # matplotlib - # msprime - # pandas - # scipy - # tskit -packaging==24.2 - # via - # build - # ipykernel - # matplotlib - # pydata-sphinx-theme - # pytest - # setuptools-scm - # sphinx - # twine -pandas==2.2.3 - # via -r requirements/docs.txt -parso==0.8.4 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==11.1.0 - # via matplotlib -platformdirs==4.3.6 - # via jupyter-core -pluggy==1.5.0 - # via pytest -prompt-toolkit==3.0.50 - # via ipython -psutil==7.0.0 - # via ipykernel -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyarrow==19.0.1 - # via -r requirements/docs.txt -pybind11==2.12.0 - # via -r requirements/build.txt -pybind11-global==2.12.0 - # via pybind11 -pybtex==0.24.0 - # via - # pybtex-docutils - # sphinxcontrib-bibtex -pybtex-docutils==1.0.3 - # via sphinxcontrib-bibtex -pycodestyle==2.12.1 - # via flake8 -pycparser==2.22 - # via cffi -pydata-sphinx-theme==0.13.1 - # via - # -r requirements/docs.txt - # sphinx-book-theme -pyflakes==3.2.0 - # via flake8 -pygments==2.19.1 - # via - # accessible-pygments - # ipython - # ipython-pygments-lexers - # pydata-sphinx-theme - # readme-renderer - # rich - # sphinx -pyparsing==3.2.1 - # via matplotlib -pyproject-hooks==1.2.0 - # via build -pytest==8.3.5 - # via - # -r requirements/tests.txt - # pytest-xdist -pytest-xdist==3.6.1 - # via -r requirements/tests.txt -python-dateutil==2.9.0.post0 - # via - # jupyter-client - # matplotlib - # pandas -pytz==2025.1 - # via pandas -pyyaml==6.0.2 - # via - # jupyter-book - # jupyter-cache - # myst-nb - # myst-parser - # pybtex - # sphinx-external-toc -pyzmq==26.2.1 - # via - # ipykernel - # jupyter-client -readme-renderer==43.0 - # via twine -referencing==0.36.2 - # via - # jsonschema - # jsonschema-specifications -requests==2.32.3 - # via - # id - # requests-toolbelt - # sphinx - # twine -requests-toolbelt==1.0.0 - # via twine -rfc3986==2.0.0 - # via twine -rich==13.9.4 - # via twine -rpds-py==0.23.1 - # via - # jsonschema - # referencing -ruamel-yaml==0.18.10 - # via demes -scipy==1.15.2 - # via demesdraw -secretstorage==3.3.3 - # via keyring -setuptools==75.8.2 - # via - # setuptools-scm - # sphinx-togglebutton -setuptools-scm==7.1.0 - # via -r requirements/build.txt -six==1.17.0 - # via - # pybtex - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -sortedcontainers==2.4.0 - # via hypothesis -soupsieve==2.6 - # via beautifulsoup4 -sphinx==5.0.2 - # via - # jupyter-book - # myst-nb - # myst-parser - # pydata-sphinx-theme - # sphinx-book-theme - # sphinx-comments - # sphinx-copybutton - # sphinx-design - # sphinx-external-toc - # sphinx-issues - # sphinx-jupyterbook-latex - # sphinx-multitoc-numbering - # sphinx-thebe - # sphinx-togglebutton - # sphinxcontrib-bibtex -sphinx-book-theme==1.0.0 - # via jupyter-book -sphinx-comments==0.0.3 - # via jupyter-book -sphinx-copybutton==0.5.2 - # via jupyter-book -sphinx-design==0.3.0 - # via jupyter-book -sphinx-external-toc==0.3.1 - # via jupyter-book -sphinx-issues==5.0.0 - # via -r requirements/docs.txt -sphinx-jupyterbook-latex==0.5.2 - # via jupyter-book -sphinx-multitoc-numbering==0.1.3 - # via jupyter-book -sphinx-thebe==0.2.1 - # via jupyter-book -sphinx-togglebutton==0.3.2 - # via jupyter-book -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-bibtex==2.5.0 - # via jupyter-book -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -sqlalchemy==2.0.38 - # via jupyter-cache -stack-data==0.6.3 - # via ipython -svgwrite==1.4.3 - # via tskit -tabulate==0.9.0 - # via jupyter-cache -tornado==6.4.2 - # via - # ipykernel - # jupyter-client -traitlets==5.14.3 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbformat -tskit==0.6.0 - # via - # -r requirements/minimal_install_requirements.txt - # msprime -twine==6.1.0 - # via -r requirements/development.txt -typing-extensions==4.12.2 - # via - # beautifulsoup4 - # myst-nb - # myst-parser - # setuptools-scm - # sqlalchemy -tzdata==2025.1 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -urllib3==2.3.0 - # via - # requests - # twine -wcwidth==0.2.13 - # via prompt-toolkit -wheel==0.45.1 - # via sphinx-togglebutton -wrapt==1.17.2 - # via deprecated -zipp==3.21.0 - # via importlib-metadata diff --git a/requirements/build.txt b/requirements/build.txt deleted file mode 100644 index 7758b65b73..0000000000 --- a/requirements/build.txt +++ /dev/null @@ -1,5 +0,0 @@ -# VERY minimal requirements -# to build the package -pybind11[global] == 2.12.0 -cmake >= 3.27.2 -setuptools_scm<8 diff --git a/requirements/conda_minimal_deps.txt b/requirements/conda_minimal_deps.txt deleted file mode 100644 index 6d47bc9c74..0000000000 --- a/requirements/conda_minimal_deps.txt +++ /dev/null @@ -1,14 +0,0 @@ -pybind11==2.11.1 -numpy -scipy -attrs>=0.19.2 -tskit -msprime -gsl -boost -pytest -pytest-xdist -setuptools_scm -demes==0.2.2 -rust==1.62.1 -hypothesis diff --git a/requirements/conda_minimal_deps_Linux.txt b/requirements/conda_minimal_deps_Linux.txt deleted file mode 100644 index c1be8d2992..0000000000 --- a/requirements/conda_minimal_deps_Linux.txt +++ /dev/null @@ -1 +0,0 @@ -gxx_linux-64 diff --git a/requirements/conda_minimal_deps_macOS.txt b/requirements/conda_minimal_deps_macOS.txt deleted file mode 100644 index 18eae1de18..0000000000 --- a/requirements/conda_minimal_deps_macOS.txt +++ /dev/null @@ -1 +0,0 @@ -clangxx_osx-64 diff --git a/requirements/development.txt b/requirements/development.txt deleted file mode 100644 index 05ac305cb6..0000000000 --- a/requirements/development.txt +++ /dev/null @@ -1,15 +0,0 @@ -# NOTE: any pinning should also be coordinated -# with requirements.in and doc/requirements.in -# and may require regenerating the .txt files. --r build.txt --r minimal_install_requirements.txt --r tests.txt --r docs.txt - -build -twine - -#below are for formatting, linting, -#etc. -flake8 -flake8-bugbear diff --git a/requirements/docs.txt b/requirements/docs.txt deleted file mode 100644 index 77727538e3..0000000000 --- a/requirements/docs.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Docs -jupyter-book~=0.15.1 -pydata-sphinx-theme==0.13.1 -matplotlib -msprime -pandas -# pyarrow will be a requirement of pandas soon. -# right now, not having it raises a warning -pyarrow -sphinx-issues -demesdraw~=0.4.0 - diff --git a/requirements/minimal_install_requirements.txt b/requirements/minimal_install_requirements.txt deleted file mode 100644 index 1fe4856643..0000000000 --- a/requirements/minimal_install_requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -attrs >= 20.30.0 -demes == 0.2.2 -numpy >= 1.23.5 -tskit >= 0.5.6 -Deprecated diff --git a/requirements/tests.txt b/requirements/tests.txt deleted file mode 100644 index 2296fcfda3..0000000000 --- a/requirements/tests.txt +++ /dev/null @@ -1,6 +0,0 @@ -#below are for building package -#and running tests -pytest -pytest-xdist -hypothesis==6.56.4 -msprime ~= 1.3.0 diff --git a/requirements/wheel_building_workflow.txt b/requirements/wheel_building_workflow.txt deleted file mode 100644 index 3e54a3077d..0000000000 --- a/requirements/wheel_building_workflow.txt +++ /dev/null @@ -1,5 +0,0 @@ -# This is intended to be the minimal -# requirements file needed to generate -# a successful wheel installation -# in the "test wheels" step of .github/workflows/wheels.yml --r minimal_install_requirements.txt diff --git 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