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#1 2020-03-04 12:17:07

E3LDDfrK
Member
Registered: 2019-10-24
Posts: 17

[Solved] Python package's dependencies not available

Hi,

Quick questions.

I'm interested in the packages python-mdanalysis and python2-mdanalysis in AUR.
Some of their dependencies are not packaged for Arch:

  • for python-mdanalysis: python-mmtf

  • for python2-mdanalysis: python2-biopython, python2-joblib, python2-mmtf, python2-netcdf4

There is also a dependency not listed on AUR, a python package named "gsd".

My questions are:

  1. I wonder what's the policy here? Since I don't think anyone is willing to maintain the unavailable packages.

  2. Why are those packages listed as optional dependencies? I don't know much python, but when I try to import MDAnalysis (python-mdanalysis), it outputs "ModuleNotFoundError: No module named 'mmtf'". Surely it means these dependencies are not optional.

Last edited by E3LDDfrK (2020-03-04 16:17:55)

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#2 2020-03-04 13:07:35

loqs
Member
Registered: 2014-03-06
Posts: 10,071

Re: [Solved] Python package's dependencies not available

The python2 versions of the following packages were dropped from the repositories as python2 is EOL.
https://git.archlinux.org/svntogit/comm … 5ed0c0662d
https://git.archlinux.org/svntogit/comm … 39048ec009
https://git.archlinux.org/svntogit/comm … af578d0bcd
Do you need both python3 and python2 support?

man 5 PKGBUILD wrote:

       optdepends (array)
           An array of packages (and accompanying reasons) that are not
           essential for base functionality, but may be necessary to make full
           use of the contents of this package.

The package maintainers response to your question https://aur.archlinux.org/packages/pyth … ent-727691 should answer why python-mmtf is listed as an optdepends.
You could leave a message for python2-mdanalysis package maintainer about the issues.

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#3 2020-03-04 16:11:07

E3LDDfrK
Member
Registered: 2019-10-24
Posts: 17

Re: [Solved] Python package's dependencies not available

Hi Ioqs.

loqs wrote:

The python2 versions of the following packages were dropped from the repositories as python2 is EOL.

Just to clarify, all python2- packages will be gone soon?

loqs wrote:

The package maintainers response to your question https://aur.archlinux.org/packages/pyth … ent-727691 should answer why python-mmtf is listed as an optdepends.
You could leave a message for python2-mdanalysis package maintainer about the issues.

I didn't see the response. Did he make a comment that for some reason that I can't see? My point is, isn't "import MDAnalysis" a base functionality? If I can't do that without all of those "optional" packages, are they really that optional? And optional or not, both python-mmtf and gsd are not available in Arch right now.

Last edited by E3LDDfrK (2020-03-04 16:12:49)

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#4 2020-03-04 16:12:50

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,513

Re: [Solved] Python package's dependencies not available

E3LDDfrK wrote:

Hi Ioqs.

loqs wrote:

The python2 versions of the following packages were dropped from the repositories as python2 is EOL.

Just to clarify, all python2- packages will be gone soon?

As soon as is practical. There's still a lot of things that need python2 and will for some time to come.

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#5 2020-03-04 16:17:30

E3LDDfrK
Member
Registered: 2019-10-24
Posts: 17

Re: [Solved] Python package's dependencies not available

Well, thanks for the answers, Scimmia and loqs. So the solution is for someone to maintain python-mmtf again, and the gsd package. I'll mark it solved.

Last edited by E3LDDfrK (2020-03-04 16:23:44)

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