Add installatoin instructions for pyteomics for conda from the bioconda channel

levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.

http://pyteomics.readthedocs.io

Apache License 2.0

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Add installatoin instructions for pyteomics for conda from the bioconda channel #88

Closed fabianegli closed 1 year ago

fabianegli commented 1 year ago

It would be great to also promote the possibility to install via bioconda, athough now the version on bioconda is not the latest (4.5.5 in bioconda instead of 4.5.6 on PyPI). Would a PR be welcome to add these installation instructions?

levitsky commented 1 year ago

A PR would be welcome! The installation instructions reside in INSTALL.

fabianegli commented 1 year ago

@levitsky Would you mind if I restructure the Installation instructions? I am tempted to remove OS specific language and reduce it to installations with pip and conda and link to the instructions to the respective tooling. But I am also happy to just add a conda related section at the end.

levitsky commented 1 year ago

Separate Windows instructions don't make a lot of sense to me, but mentioning alternative installation sources like AUR doesn't hurt IMHO. What do you think?

fabianegli commented 1 year ago

I am not familiar with AUR - and can't form a serious opinion on wether it is useful or not. I just think the installation instructions for package management tools can be deferred the tools themselves.

Additional notes/questions:

Some URLs are still http instead of https which is supported on all linked websites in the INSTALL file. (https://github.com/levitsky/pyteomics/pull/89)
I find suggesting to use sudo for the installation of a python package disturbing and would like to remove it together with Ubuntu specific instructions.
The docs say all dependencies are optional - but the installation instructions say that the dependencies should be installed and explicitly lists some in the pip install command. I am a bit confused as to how optional these dependencies are.

levitsky commented 1 year ago

[x] I am all for updating the URLs.
[x] Ubuntu-specific and Windows-specific instructions can be removed.
[x] Dependencies are optional. We can just leave pip install pyteomics there.
[x] The list of those dependencies is not complete and should be extended. There are also spectrum_utils, h5py,hdf5plugin, psims.
[x] Speaking of which, perhaps we should document the extras as defined in setup.py.

levitsky commented 1 year ago

I went ahead and implemented the rest of the items we discussed. @fabianegli please feel free to improve or comment!

fabianegli commented 1 year ago

Cool! I think you covered it all. 🥳