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 =3.11
  # Package building
  - cython >=3.0
  - pip >=10.0
  - hatchling
  - hatch-vcs == 0.4
  - wheel >=0.30
  # Biotite dependencies
  - biotraj >=1.0,<2.0
  - msgpack-python >=0.5.6
  - networkx >=2.0
  - numpy >=2.0
  - requests >=2.12
  # Testing
  - pytest >=7.0
  - pytest-codspeed >=2.0
  # Code style
  - ruff =0.5.2
  # 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