kipoi/dev-requirements-py37.yml at master · bytewife/kipoi · GitHub

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name: kipoi-dev
channels:
  - bioconda
  - pytorch
  - conda-forge
  - defaults
dependencies:
  - python=3.7
  - numpy>=1.13.0
  - pandas
  - pytest>=3.3.1
  - pytest-cov>=2.6.1
  - h5py=2.10.0 # h5py >= 3.* is incompatible with keras
  - scipy>=1.0.0
  - pybigwig>=0.3.10
  - pybedtools>=0.7.10
  - pyvcf>=0.6.8
  - pysam>=0.14.0
  - pyfaidx>=0.5.5.2
  - cython=0.29.23
  - cyvcf2>=0.8.4
  - bedtools>=2.27.1
  - htslib>=1.7
  # ML
  - scikit-learn>=0.19.1,<=0.22
  - tensorflow==1.13.1
  - pytorch-cpu>=0.3.1
  - keras>=2.2.4
  # for plugins (double check)
  - fastparquet
  - pyarrow=7.0.0
  - zarr
  - numcodecs
  - tinydb>=3.12.2
  # singularity
  #- singularity
  - git
  - git-lfs
  - cookiecutter>=1.6.0
  - wheel
  - gitpython
  - pip
  - matplotlib
  - pip:
    - kipoi-utils>=0.7.5
    - kipoi-conda
    - kipoi-interpret>=0.1.2
    - kipoiseq
    - concise>=0.6.5
    - joblib==0.17.0
    - sorted-nearest<=0.0.33