dev-requirements-py36.yml

name: kipoi-dev
channels:
  - bioconda
  - pytorch
  - conda-forge
  - defaults
dependencies:
  - python=3.6
  # general packages
  # - git-lfs 
  # General
  - numpy>=1.13.0
  - pandas
  - pytest>=3.3.1
  - pytest-cov>=2.6.1
  - h5py=2.10.0 # h5py >= 3.* is incompatible with keras 
  - matplotlib
  - importlib_metadata=4.8.1
  - tinydb=4.7.0
  # Bio
  - pybigwig>=0.3.10
  # could not pin pydedtools ins conda
  - 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
  - zarr 
  - numcodecs
  # singularity
  #- singularity
  - git
  - git-lfs
  - cookiecutter>=1.6.0
  - wheel
  - gitpython
  - pip=21.3.1 
  - pip:
    - kipoi-utils>=0.7.5
    - kipoi-conda
    - kipoi-interpret>=0.1.2
    - kipoiseq
    - concise>=0.6.5
    - joblib==0.17.0
    - typing-extensions==4.1.1
    - sorted-nearest<=0.0.33