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dev: comment and cleanup environment.yml #295

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Aug 22, 2023
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dev: comment and cleanup environment.yml #295

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dev: comment and cleanup environment.yml
jandom Aug 8, 2023
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review: comments by Irfan
jandom Aug 18, 2023
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review: comments from Lily
jandom Aug 18, 2023
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Update environment.yml
jandom Aug 20, 2023
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jandom Aug 20, 2023
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75 changes: 39 additions & 36 deletions environment.yml
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Expand Up @@ -5,57 +5,60 @@ channels:
- plotly
- defaults
dependencies:
- cython
- distributed==2021.1.0
- dask==2021.1.0
- python-graphviz
- pytest
- decorator
- docutils
- graphviz
- ipywidgets<8.0.0
- ipython
- ipygany
- jedi
- jinja2
- jupyter_contrib_nbextensions
# mdanalysis dependencies
- matplotlib
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- nbclient
- nbconvert
- nbformat
- nbsphinx
- networkx
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- nglview
- notebook
- numpy
- openmm>=7.0.0
- packaging
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- parmed
- parso
- pip
- plotly
- pybtex
- python=3.9
- pyvista
- scikit-image
- scikit-learn>=1.1.2
- threadpoolctl
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- pyedr>=0.7
# building documentation
- docutils
- pandoc
- pybtex
- sphinx
- sphinxcontrib-bibtex
- threadpoolctl
# used by custom_parallel_analysis.ipynb
- graphviz
- tabulate
- widgetsnbextension
- ipycytoscape>=1.3.0
- python-graphviz
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Could you move this down to #visualisation?

# extensions
- jupyter_contrib_nbextensions
- nbconvert # not called by any notebook explicitly but to download notebooks, or in nbsphinx
- nbformat
- notebook<7
# used for visualising/plotting
- plotly
- ipygany
- pyvista
- scikit-image
- seaborn>=0.12.1
- openmm>=7.0.0
- pandoc
# parallelization
- distributed==2021.1.0
- dask==2021.1.0
# used for visualising/making movies of molecules;
- nglview
- moviepy
- ipyvtklink
# used in conf.py
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I mostly think of these as sphinx "extensions" -- we use the ipython directive in some docs, nbsphinx to render notebooks, etc. If they're imported/used in conf.py it would generally be in their role as extensions.

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Thanks, yeah, easy to change

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Thanks @jandom -- could you please move these up to the #extensions then?

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Just this to go -- nbsphinx, ipywidgets and the like are used to render notebooks, and IIRC ipython to use the ipython sphinx directive. If they're imported in conf.py it's to configure settings but, otherwise they fall into the same category as other extensions, e.g. sphinx bibtex.

- ipython
- ipywidgets<8.0.0
- nbsphinx
# used for notebook testing
- pytest
- python=3.9
- pip
- pip:
- sphinx_rtd_theme
# used in conf.py
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- msmb_theme
- sphinx_rtd_theme
- sphinx-sitemap
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# used for notebook testing
- nbval
# developer tooling
- pre-commit
- pyedr>=0.7
# 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