fix installation instructions and recommend mamba instead of conda #370
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contributions to the PR are welcome! |
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@orbeckst I might either take over or overwrite this PR later today - I had started working on my own update earlier. |
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By all means. |
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Where are you with the update that you mentioned @IAlibay ? |
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@yuxuanzhuang if you want to do a quick minimal update to the instructions then we can at least get a quick-fix into the user guide. This PR already introduces mamba; you could add your changes to this PR. |
doc/source/contributing_code.rst
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| @@ -243,7 +249,7 @@ First we need to install dependencies. You'll need a mix of conda and pip instal | |||
| 'mda-xdrlib' | |||
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| # documentation dependencies | |||
| conda install -c conda-forge 'mdanalysis-sphinx-theme>=1.3.0' docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils | |||
| mamba install -c conda-forge 'mdanalysis-sphinx-theme>=1.3.0' docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils | |||
| python -m pip install docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils | |||
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Is there a reason these deps are installed both with mamba and pip here?
Sorry I'm travelling / handling work things - I'll be free to do MDAnalysis things, including this, over the weekend. |
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@yuxuanzhuang @RMeli we do need this PR to be merged so that we have some instructions for the hackathon. (Ideally we also get a release of the User Guide but that's probably a different thing.) |
doc/source/contributing_code.rst
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| an isolated environment without touching your base Python installation, and without | ||
| touching existing environments that may have stable versions of MDAnalysis. : | ||
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| .. code-block:: bash | ||
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| conda create --name mdanalysis-dev "python>=3.9" | ||
| mamba create --name mdanalysis-dev "python>=3.10" |
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Should we recommend the latest supported Python here instead? We will have three version changes before the docs going out of date. ;)
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Ok. Can I ask you to try out the installation instructions below for the version you want to put here?
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I'm sorry but I'm AFK until Friday morning (UTC+2). Please discard my comment if this needs to be merged quickly, it was just a "nice to have" suggestion.
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tried it with 3.12 and it works, added 3.12
doc/source/contributing_code.rst
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| You can also install the following optional dependencies, although please note | ||
| that they many not all be available for your machine type. Specifically; | ||
| hole2, and distopia are only available on linux + x86_64 machines, and openmm | ||
| is not available for windows. |
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Maybe add "Remove the packages listed as incompatible from the command below and run it again."
Alternatively, we can show example code for different os with sphinxcontrib.osexample (https://sublime-and-sphinx-guide.readthedocs.io/en/latest/code_blocks.html)
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added something similar
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sphinxcontrib.osexample as used in https://sublime-and-sphinx-guide.readthedocs.io/en/latest/code_blocks.html#code-examples-in-multiple-languages looks like a neat addition. Maybe open new issue?
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And all tests pass so I am going to merge. Thanks for the reviews & contributions! |
📚 Documentation preview 📚: https://mdanalysisuserguide--370.org.readthedocs.build/en/370/