environment.yml

name: seqlike-dev
channels:
  - conda-forge
  - bioconda
dependencies:
  - python<=3.9 # 18 Nov 2021: A super esoteric issue leads to us pinning env at 3.9.
  # For more information, see: https://github.com/conda/conda-pack/issues/196#issuecomment-971790933
  - pip
  - scikit-learn
  - biopython
  - numpy
  - pandas
  - pytest
  - pytest-regtest
  - weblogo
  - requests
  - pillow
  - black # for code formatting
  - mafft # necessary for multiple sequence alignemnt tests.
  - multipledispatch
  - ipykernel
  - hypothesis
  - interrogate
  - matplotlib
  - bokeh>=3.0.2
  - ghostscript
  - python-codon-tables
  - pyprojroot
  # Code quality
  - pre-commit
  - darglint
  # Docs dependencies
  - mkdocs
  - mkdocs-material=8.1.3
  - mkdocstrings
  - mkdocstrings-python-legacy
  # Infrastructural
  - bump2version
  # Dependencies of mknotebooks
  - gitpython
  - jupyter
  - markdown
  - nbconvert
  - mypy
  - flake8
  - pydocstyle
  - pip:
      - mknotebooks # for notebooks in docs
      - build
      - lazy-loader