environment.yml

name: mda-user-guide
channels:
  - jaimergp/label/unsupported-cudatoolkit-shim
  - conda-forge
  - plotly
  - defaults
dependencies:
  # mdanalysis dependencies
  - openmm>=7.0.0
  - parmed
  - scikit-learn>=1.1.2
  - pyedr>=0.7
  # building documentation
  - mdanalysis-sphinx-theme >=1.3.0
  - docutils
  - pandoc
  - pybtex
  - sphinx
  - sphinxcontrib-bibtex
  - tabulate
  # extensions
  - ipython
  - ipywidgets<8.0.0
  - jupyter_contrib_nbextensions
  - myst-parser
  - nbconvert # not called by any notebook explicitly but to download notebooks, or in nbsphinx
  - nbformat
  - nbsphinx
  - notebook<7
  # used for visualising/plotting
  - graphviz
  - ipygany
  - plotly
  - python-graphviz
  - pyvista
  - scikit-image
  - seaborn>=0.12.1
  # parallelization
  - distributed
  - dask
  # used for visualising/making movies of molecules;
  - nglview
  - moviepy
  # used for notebook testing
  - pytest
  - python=3.10
  - pip
  - pip:
      # extensions
      - sphinx-sitemap
      # used for notebook testing
      - nbval
      # developer tooling
      - pre-commit
      # doc generation dependency
      - pygithub
      # mdanalysis and its tests and test data
      - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=mdanalysis&subdirectory=package
      - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=MDAnalysisTests&subdirectory=testsuite
      - git+https://github.com/MDAnalysis/MDAnalysisData@master#egg=MDAnalysisData
      - syrupy # snapshot tests