environment-dev.yml

name: monai
channels:
  - pytorch
  - defaults
  - conda-forge
dependencies:
  - numpy>=1.17
  - pytorch>=1.6
  - coverage>=5.5
  - parameterized
  - setuptools>=50.3.0,!=60.0.0
  - ignite==0.4.8
  - gdown>=3.6.4
  - scipy
  - nibabel
  - pillow!=8.3.0  # https://github.com/python-pillow/Pillow/issues/5571
  - tensorboard
  - scikit-image>=0.14.2
  - tqdm>=4.47.0
  - python-lmdb
  - flake8>=3.8.1
  - flake8-bugbear
  - flake8-comprehensions
  - flake8-pyi
  - pylint
  - mccabe
  - pep8-naming
  - pycodestyle
  - pyflakes
  - isort
  - types-pkg_resources
  - ninja
  - torchvision
  - psutil
  - Sphinx==3.5.3
  - recommonmark==0.6.0
  - sphinx-autodoc-typehints==1.11.1
  - sphinx_rtd_theme==0.5.2
  - pandas
  - requests
  - einops
  - transformers
  - mlflow
  - tensorboardX
  - pip
  - pip:
    # pip for itk as conda-forge version only up to v5.1
    - itk>=5.2
    # black currently at v19 on conda vs v21 on pip
    - black
    # conda mypy v. slow
    - mypy>=0.790
    # OS-specific needs to be done via pip:
    #   https://github.com/conda/conda/issues/8089
    - pytype>=2020.6.1; platform_system != "Windows"
    - openslide-python==1.1.2
    - cucim>=21.8.2; platform_system == "Linux"
    - imagecodecs; platform_system == "Linux"
    - tifffile; platform_system == "Linux"
    - matplotlib!=3.5.0