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benjefferybenjeffery
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Pyproject reqs
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‎.circleci/config.yml‎

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@@ -17,16 +17,17 @@ jobs:
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name: Install dependencies and set PATH
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command: |
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sudo apt-get update
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sudo apt-get install libgsl-dev libcap-dev libnuma-dev libcunit1-dev \
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libconfig-dev ninja-build valgrind clang python3-pip
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sudo apt-get install libcap-dev libnuma-dev libcunit1-dev \
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libconfig-dev ninja-build valgrind clang
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# set path persistently https://circleci.com/docs/2.0/env-vars/#setting-path
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echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
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- run:
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name: Install development dependencies
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name: Install test dependencies
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command: |
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pyenv global 3.9
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pip install -r requirements/CI-tests-complete/requirements.txt --user
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pip install uv
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uv pip install --system -r pyproject.toml --extra test
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pyenv rehash
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- save_cache:

‎.github/workflows/docs.yml‎

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@@ -8,8 +8,7 @@ on:
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merge_group:
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jobs:
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Docs:
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uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@main
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uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
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with:
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requirements-path: requirements/CI-docs/requirements.txt
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additional-setup: sudo apt-get install -y tabix
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make-command: make all
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make-command: make all

‎.github/workflows/tests.yml‎

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@@ -20,7 +20,6 @@ jobs:
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with:
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python-version: '3.10'
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- name: install clang-format
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if: steps.clang_format.outputs.cache-hit != 'true'
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run: |
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sudo pip install clang-format==6.0.1
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sudo ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-6.0
@@ -48,70 +47,39 @@ jobs:
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with:
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submodules: true
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- name: Cache conda and dependancies
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id: cache
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uses: actions/[email protected]
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@v6
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with:
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path: ${{ env.CONDA }}/envs
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key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v5-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}}
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- name: Install Miniconda with Mamba
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uses: conda-incubator/[email protected]
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if: steps.cache.outputs.cache-hit != 'true'
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with:
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activate-environment: anaconda-client-env
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python-version: ${{ matrix.python }}
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channels: conda-forge
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# channel-priority: strict
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auto-update-conda: true
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# mamba-version: "*"
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# use-mamba: true
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version: "0.8.15"
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- name: Fix windows .profile
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if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
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- name: Setup venv
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run: |
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cp ~/.bash_profile ~/.profile
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# Work around weird issues on OSX possibly caused by mixed compilers
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# https://github.com/tskit-dev/tsinfer/issues/376
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- name: Install compiler from conda
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if: steps.cache.outputs.cache-hit != 'true'
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shell: bash -l {0} #We need a login shell to get conda
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run: conda install --yes c-compiler
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- name: Install conda deps
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if: steps.cache.outputs.cache-hit != 'true'
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shell: bash -l {0} #We need a login shell to get conda
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run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
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uv venv
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- name: Install cyvcf2 #Fails if done via conda due to no windows support.
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if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest'
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if: matrix.os != 'windows-latest'
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run: |
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source ~/.profile
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conda activate anaconda-client-env
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#Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
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pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3
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uv pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3
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- name: Install sgkit only on windows
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if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
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if: matrix.os == 'windows-latest'
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run: |
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source ~/.profile
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conda activate anaconda-client-env
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#Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
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pip install sgkit==0.9.0
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uv pip install sgkit==0.9.0
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- name: Install pip deps
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run: |
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uv pip install -r pyproject.toml --extra test
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- name: Build module
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run: |
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source ~/.profile
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conda activate anaconda-client-env
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# Use numpy2 to build the module
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pip install "numpy>=2"
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python setup.py build_ext --inplace
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uv pip install "numpy>=2"
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uv run --no-sync python setup.py build_ext --inplace
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- name: Run tests
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run: |
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source ~/.profile
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conda activate anaconda-client-env
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# Test with numpy<2 for numba
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pip install "numpy<2"
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python -m pytest -xv
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uv pip install "numpy<2"
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uv run --no-sync python -m pytest -xv

‎pyproject.toml‎

Lines changed: 72 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ dependencies = [
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"humanize",
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"daiquiri",
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"tskit>=0.5.3",
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"numcodecs>=0.6",
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"numcodecs>=0.6,<0.15.1", #Pinned due to https://github.com/zarr-developers/numcodecs/issues/733
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"zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2,<3",
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"lmdb",
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"sortedcontainers",
@@ -73,6 +73,77 @@ Changelog = "https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html"
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[project.scripts]
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tsinfer = "tsinfer.__main__:main"
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[project.optional-dependencies]
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test = [
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"build==1.2.2.post1",
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"colorama==0.4.6",
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"daiquiri==3.2.5.1",
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"humanize==4.12.1",
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"lmdb==1.6.2",
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"matplotlib==3.9.4",
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"meson==1.7.0",
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"msprime==1.3.4",
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"pytest==8.3.5",
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"pytest-cov==6.0.0",
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"seaborn==0.13.2",
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"sgkit[vcf]==0.9.0; sys_platform != 'win32'",
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"tskit==0.6.0",
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"tqdm==4.67.1",
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"twine==6.1.0"
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]
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95+
docs = [
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"jupyter-book==1.0.4.post1",
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"sphinx-issues==5.0.0",
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"sphinx-argparse==0.5.2",
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"humanize==4.12.1",
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"lmdb==1.6.2",
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"tqdm==4.67.1",
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"daiquiri==3.3.0",
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"msprime==1.3.3",
104+
"sgkit[vcf]==0.9.0",
105+
"ipywidgets==8.1.5",
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"Bio==1.7.1",
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"bio2zarr==0.1.4",
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"sphinx-book-theme",
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"pyfaidx==0.8.1.3"
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]
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112+
dev = [
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"attrs",
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"codecov",
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"coverage",
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"flake8",
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"six",
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"tqdm",
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"humanize",
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"daiquiri",
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"msprime>=1.0.0",
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"tskit>=0.5.3",
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"lmdb",
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"pre-commit",
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"pytest",
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"pytest-coverage",
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"h5py",
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"sortedcontainers",
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"python-prctl; sys_platform == 'linux'",
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"numa; sys_platform == 'linux'",
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"sphinx",
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"sphinx-argparse",
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"sphinx_rtd_theme",
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"setuptools>=45",
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"setuptools_scm",
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"matplotlib",
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"seaborn",
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"colorama",
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"sgkit[vcf]",
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"sphinx-book-theme",
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"jupyter-book",
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"sphinx-issues",
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"ipywidgets",
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"pyfaidx"
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]
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[tool.setuptools]
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packages = ["tsinfer"]
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include-package-data = true

‎requirements/CI-docs/requirements.txt‎

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‎requirements/CI-tests-complete/requirements.txt‎

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‎requirements/CI-tests-conda/requirements.txt‎

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‎requirements/development.txt‎

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