environment.yml

# Conda environment, that includes all packages that are necessary for
# the complete Biotite development process.

name: biotite-dev

channels:
  - anaconda
  - conda-forge
  - salilab
  - bioconda

dependencies:
  - python =3.10
  # Package building
  - cython >=3.0
  - pip >=10.0
  - setuptools >=30.0
  - wheel >=0.30
  # Biotite dependencies
  - msgpack-python >=0.5.6
  - networkx >=2.0
  - numpy >=1.15, <2.0
  - requests >=2.12
  # Testing
  - mdtraj >=1.9.3, <1.10
  - pytest >=7.0
  # Interfaced software in biotite.application (can also be installed separately)
  - autodock-vina
  - clustalo
  - dssp
  - mafft
  - muscle =3
  - sra-tools
  - tantan
  - viennarna >=2.5.0
  # Documentation building
  - pydata-sphinx-theme =0.15
  - matplotlib >=3.3
  - numpydoc >=0.8
  - jupyter-sphinx >=0.5.3
  - sphinx >=7.0
  - sphinxcontrib-bibtex >=2.3
  - sphinx-copybutton >=0.5
  - sphinx-design >=0.5
  - sphinx-gallery =0.15.0
  - sphinx-notfound-page >=1.0
  # Extra packages used in example gallery
  - pandas >=1.5.2
  - pydot >=1.4
  - scikit-learn >=0.18
  - scipy >=1.8.0