biotite/environment.yml at main · biotite-dev/biotite · GitHub

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

name: biotite-dev

channels:
  - conda-forge
  - bioconda

dependencies:
  - python =3.12
  # 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
  - packaging >=24.0
  - requests >=2.12
  # Testing
  - pytest >=7.0
  - pytest-codspeed >=2.0
  # Code style, keep in sync with the versions in pyproject.toml
  - ruff =0.9.7
  - numpydoc =1.8.0
  # Interfaced software in biotite.application (can also be installed separately)
  - autodock-vina
  - clustalo
  - dssp =4
  - libcifpp  # Makes sure that the used version of libcifpp contains this fix: https://github.com/bioconda/bioconda-recipes/pull/57869
  - mafft
  - muscle =3
  - sra-tools =3
  - tantan
  - viennarna >=2.5.0
  # Interfaced packages in biotite.interface (can also be installed separately)
  - pymol-open-source >=2
  - ffmpeg  # Required for video rendering in PyMOL
  - imagemagick  # Required for video rendering in PyMOL
  - openmm >=8
  # Documentation building
  - pydata-sphinx-theme =0.15
  - matplotlib >=3.3
  - ipython <8.29  # jupyter-sphinx is not compatible with the newest IPython versions
  - jupyter-sphinx >=0.5.3
  - sphinx >=7.0
  - sphinxcontrib-bibtex >=2.3
  - sphinx-copybutton >=0.5
  - sphinx-design >=0.5
  - sphinx-gallery =0.18.0
  - 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
  - pip:
    # Conda provides no recent version of RDKit (required for biotite.interface)
    - rdkit >=2024.09.1