
# Install PyTorch manually with index
torch==2.1.0+cpu --index-url https://download.pytorch.org/whl/cpu

# Pytorch geometric dependencies with correct torch version
torch-scatter -f https://data.pyg.org/whl/torch-2.1.0+cpu.html
torch-sparse -f https://data.pyg.org/whl/torch-2.1.0+cpu.html
torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cpu.html
torch-geometric

# Standard packages
torchmetrics==1.3.2
numpy
pandas
matplotlib
scikit-learn

install_requires =
    importlib-metadata; python_version<="3.8"
    numpy>=1.21,<2.0
    pandas>=1.3,<2.0
    #scikit-learn>=0.24,<1.3
    matplotlib>=3.4,<4.0
    tqdm>=4.66.5
    opencv-python>=4.5,<5.0
    #torch
    #==2.6.0
    setuptools==59.5.0
    sphinx>=3.2.1
    torch >= 2.0
    torchmetrics >= 0.11
    pytorch-lightning>=2.0
    #umap-learn[parametric_umap]>=0.5.2;platform_system!='Darwin'
    #tensorflow >= 2.12;platform_system=='Linux'
    #tensorflow-macos;platform_system=='Darwin'
    keras
    #tqdm
    #matplotlib
    #numpy
    fbm
    scipy
    #pandas
    #tifffile>=2023.4.12,<2024.0.0
    #trackpy>=0.5,<0.6
    plotly>=5.24.1,<5.25.0
    seaborn>=0.13.2,<0.14.0
    pillow>=10.4.0,<10.5.0
    absl-py==2.1.0
    aicsimageio==4.13.0
    aiobotocore==2.5.4
    aiohttp==3.9.3
    aioitertools==0.11.0
    aiosignal==1.3.1
    alabaster==0.7.13
    alembic
    #==1.13.1
    amqp==5.2.0
    annotated-types==0.6.0
    app-model
    #==0.2.5
    appdirs==1.4.4
    asciitree==0.3.3
    asttokens==2.4.1
    astunparse==1.6.3
    async-timeout==4.0.3
    attrs==23.2.0
    Babel==2.14.0
    backcall==0.2.0
    backports.zoneinfo==0.2.1
    billiard==3.6.4.0
    botocore==1.31.17
    build==1.1.1
    cachelib==0.12.0
    cachetools==5.3.3
    cachey==0.2.1
    celery==5.2.6
    certifi==2024.2.2
    charset-normalizer==3.3.2
    click==8.1.7
    click-didyoumean==0.3.0
    click-plugins==1.1.1
    click-repl==0.3.0
    cloudpickle==3.0.0
    cmake==3.28.3
    comm==0.2.2
    cycler==0.12.1
    dask==2023.5.0
    dask-image==2023.3.0
    debugpy==1.8.1
    decorator==5.1.1
    Deprecated==1.2.14
    distributed==2023.5.0
    dm-tree==0.1.8
    docstring_parser==0.16
    docutils==0.20.1
    elementpath==4.4.0
    environs==9.5.0
    exceptiongroup==1.2.0
    executing==2.0.1
    fasteners==0.19
    fbm==0.3.0
    filelock==3.13.1
    Flask==2.0.0
    Flask-Cors==3.0.10
    Flask-Migrate==3.1.0
    Flask-Session==0.4.0
    Flask-SQLAlchemy==2.5.1
    flatbuffers==24.3.7
    fonttools==4.50.0
    freetype-py==2.4.0
    frozenlist==1.4.1
    fsspec==2023.6.0
    gast==0.4.0
    google-auth==2.28.2
    google-auth-oauthlib==1.0.0
    google-pasta==0.2.0
    gratin==0.1.11
    greenlet==3.0.3
    grpcio==1.62.1
    gunicorn==20.1.0
    h5py==3.10.0
    HeapDict==1.0.1
    hsluv==5.0.4
    idna==3.6
    imagecodecs==2023.3.16
    imageio==2.34.0
    imageio-ffmpeg==0.4.9
    imagesize==1.4.1
    importlib_metadata==7.0.2
    importlib_resources==6.3.2
    in-n-out==0.2.0
    iniconfig==2.0.0
    ipykernel==6.29.3
    ipython==8.12.3
    itsdangerous==2.1.2
    jedi==0.19.1
    Jinja2==3.1.3
    jmespath==1.0.1
    joblib==1.3.2
    jsonschema==4.21.1
    jsonschema-specifications==2023.12.1
    jupyter_client==8.6.1
    jupyter_core==5.7.2
    keras==2.13.1
    kiwisolver==1.4.5
    kombu==5.3.5
    lazy_loader==0.3
    libclang==18.1.1
    lightning-utilities
    #==0.11.0
    lit==18.1.1
    llvmlite==0.41.1
    locket==1.0.0
    looseversion==1.3.0
    lxml==4.9.4
    magicgui
    #==0.8.2
    Mako==1.3.2
    Markdown==3.6
    markdown-it-py==3.0.0
    MarkupSafe==2.1.5
    marshmallow==3.21.1
    matplotlib==3.5.0
    matplotlib-inline==0.1.6
    mdurl==0.1.2
    mpmath==1.3.0
    msgpack==1.0.8
    multidict==6.0.5
    munkres==1.1.4
    napari
    #==0.4.19.post1
    napari-aicsimageio==0.2.0
    napari-console==0.0.9
    napari-plugin-engine==0.2.0
    napari-svg==0.1.10
    nest-asyncio==1.6.0
    networkx==3.1
    npe2==0.7.4
    numba==0.58.1
    numcodecs==0.12.1
    #numpy==1.24.0
    numpydoc==1.6.0
    #nvidia-cublas-cu11==11.10.3.66
    #nvidia-cuda-cupti-cu11==11.7.101
    #nvidia-cuda-nvrtc-cu11==11.7.99
    #nvidia-cuda-runtime-cu11==11.7.99
    #nvidia-cudnn-cu11==8.5.0.96
    #nvidia-cufft-cu11==10.9.0.58
    #nvidia-curand-cu11==10.2.10.91
    #nvidia-cusolver-cu11==11.4.0.1
    #nvidia-cusparse-cu11==11.7.4.91
    #nvidia-nccl-cu11==2.14.3
    #nvidia-nvtx-cu11==11.7.91
    oauthlib==3.2.2
    ome-types==0.5.1
    ome-zarr==0.8.3
    opt-einsum==3.3.0
    packaging==24.0
    palm-tools @ git+https://gitlab.pasteur.fr/tramway/palm-tools.git@ffefdc2558b37d57f871897ed1b2452ba1b6ea28
    palmari==0.3.0
    pandas==1.3.4
    parso==0.8.3
    partd==1.4.1
    pexpect==4.9.0
    pickleshare==0.7.5
    #pillow==10.2.0
    PIMS==0.6.1
    Pint==0.21.1
    pkgutil_resolve_name==1.3.10
    platformdirs==4.2.0
    pluggy==1.4.0
    pooch==1.8.1
    prometheus-flask-exporter==0.23.0
    prometheus_client==0.20.0
    prompt-toolkit==3.0.43
    protobuf==4.25.3
    psutil==5.9.8
    psygnal==0.10.2
    ptyprocess==0.7.0
    pure-eval==0.2.2
    pyasn1==0.5.1
    pyasn1-modules==0.3.0
    pyconify==0.1.6
    pydantic
    #==2.6.4
    pydantic-compat==0.1.2
    pydantic_core
    #==2.16.3
    Pygments==2.17.2
    pynndescent==0.5.11
    PyOpenGL==3.1.7
    pyparsing==3.1.2
    pyproject_hooks==1.0.0
    PyQt6-sip==13.6.0
    pytest==8.1.1
    python-dateutil==2.9.0.post0
    python-dotenv==1.0.1
    #pytorch-lightning
    #==2.2.1
    pytz==2024.1
    PyWavelets==1.4.1
    PyYAML==6.0.1
    pyzmq==25.1.2
    qtconsole==5.5.1
    QtPy==2.4.1
    redis==4.2.2
    referencing==0.34.0
    requests==2.31.0
    requests-oauthlib==1.4.0
    resource-backed-dask-array
    #==0.1.0
    rich==13.7.1
    rpds-py==0.18.0
    rsa==4.9
    s3fs==2023.6.0
    scikit-image==0.21.0
    scikit-learn==1.3.2
    scipy==1.10.1
    setuptools-scm
    #==8.0.4
    six==1.16.0
    slicerator==1.1.0
    snowballstemmer==2.2.0
    sortedcontainers==2.4.0
    Sphinx==7.1.2
    sphinxcontrib-applehelp==1.0.4
    sphinxcontrib-devhelp==1.0.2
    sphinxcontrib-htmlhelp==2.0.1
    sphinxcontrib-jsmath==1.0.1
    sphinxcontrib-qthelp==1.0.3
    sphinxcontrib-serializinghtml==1.1.5
    SQLAlchemy==1.4.35
    stack-data==0.6.3
    superqt
    #==0.6.2
    sympy==1.12
    tabulate==0.9.0
    tblib==3.0.0
    tensorboard==2.13.0
    tensorboard-data-server==0.7.2
    tensorflow==2.13.1
    tensorflow-estimator==2.13.0
    tensorflow-io-gcs-filesystem==0.34.0
    tensorflow-probability
    termcolor==2.4.0
    threadpoolctl==3.3.0
    tifffile==2023.2.28
    toml==0.10.2
    tomli==2.0.1
    tomli_w==1.0.0
    toolz==0.12.1
    #torch
    #--index-url https://download.pytorch.org/whl/cpu
    #torch-cluster
    #==1.6.0
    #torch-geometric
    #==2.1.0.post1
    #torch-scatter
    #==2.0.9
    #torch-sparse
    #==0.6.18
    #torch-spline-conv
    #==1.2.1
    #torchmetrics
    #==1.3.2
    tornado==6.4
    #tqdm==4.66.2
    trackpy==0.6.2
    # Editable install with no version control (tracktor-back==0.1)
    traitlets==5.14.2
    #triton==2.0.0
    typer
    #==0.9.0
    typing_extensions
    #>4.7
    tzdata==2024.1
    umap-learn==0.5.5
    urllib3==1.26.18
    vine==5.1.0
    vispy==0.14.2
    wcwidth==0.2.13
    Werkzeug==2.0.3
    wrapt==1.16.0
    xarray==2023.1.0
    xmlschema==3.1.0
    xsdata==24.3.1
    yarl==1.9.4
    zarr==2.15.0
    zict==3.0.0
    zipp==3.18.1
    Flask==2.0
    Flask-Migrate==3.1.0
    Flask-Session==0.4.0
    Flask-SQLAlchemy==2.5.1
    Flask-Cors==3.0.10
    #pandas==1.3.4
    #numpy==1.19.5
    Werkzeug==2.0.3
    #matplotlib==3.5.0
    celery==5.2.6
    environs==9.5.0
    sqlalchemy==1.4.35
    gunicorn==20.1.0
    SQLAlchemy==1.4.35
    #git+https://pip:JRyeMBUcrJCw8FVAc7D7@gitlab.pasteur.fr/hverdier/palm-tools.git
    environs==9.5.0
    #torch==1.11.0
    redis==4.2.2
