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==0.23.4
  - pytest>=3.3.1
  - pytest-xdist
  - pytest-sugar
  - pytest-cov>=2.6.1
  - deprecation>=2.0.6
  #- coveralls
  - h5py>=2.7.0
  - scipy>=1.0.0
  - attrs>=18.2.0
  - matplotlib
  - tinydb>=3.12.2
  # 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
  # - intervaltree
  - cyvcf2>=0.8.4
  - bedtools>=2.27.1
  - htslib>=1.7
  - genomelake>=0.1.4
  # ML
  - scikit-learn>=0.19.1
  - tensorflow>=1.4.0
  - pytorch-cpu>=0.3.1
  - keras>=2.2.4
  # for plugins (double check)
  - fastparquet
  - zarr 
  - numcodecs
  # singularity
  #- singularity
  - git
  - git-lfs
  - cookiecutter>=1.6.0
  - wheel
  - gitpython
  - pip>=18.0
  - pip:
    - kipoi-utils>=0.1.12
    - kipoi-conda>=0.1.6
    - kipoi-interpret>=0.1.2
    # - kipoi-veff>=0.3.0
    - kipoiseq>=0.2.3
    - concise>=0.6.5