Package Details: python-mdanalysis 2.7.0-2

Git Clone URL: https://aur.archlinux.org/python-mdanalysis.git (read-only, click to copy)
Package Base: python-mdanalysis
Description: An object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.
Upstream URL: http://www.mdanalysis.org/
Keywords: analysis chemistry science
Licenses: GPL
Submitter: hseara
Maintainer: hseara (vedranmiletic)
Last Packager: hseara
Votes: 2
Popularity: 0.080272
First Submitted: 2017-06-11 16:27 (UTC)
Last Updated: 2024-10-11 07:35 (UTC)

Pinned Comments

vedranmiletic commented on 2025-03-03 12:34 (UTC)

Thanks for the reports and the note that 2.8 is released. I will look into packaging it soon.

Latest Comments

vedranmiletic commented on 2025-03-03 12:34 (UTC)

Thanks for the reports and the note that 2.8 is released. I will look into packaging it soon.

physkets commented on 2025-02-10 05:01 (UTC)

My build stops with the following error:

ERROR Missing dependencies:
        numpy<2.0; python_version >= "3.13"

Isn't the current numpy version 2.2.2? Why is that the dependency?

Do I have to install an older numpy?

nihil39 commented on 2024-05-21 09:29 (UTC) (edited on 2024-05-21 09:30 (UTC) by nihil39)

Here is a working version of the pkgbuild, just the -Wno-incompatible-pointer-types CFLAGS was added

https://dpaste.org/MWt9w

Please update the official pkgbuild.

Thank you

nihil39 commented on 2024-05-20 14:37 (UTC)

Package is failing with this error message https://dpaste.org/4ndL9

MDAnalysis/lib/formats/src/xdrfile.c:2535:17: error: initialization of ‘unsigned int (*)(XDR *)’ from incompatible pointer type ‘int64_t (*)(XDR *)’ {aka ‘long int (*)(XDR *)’} [-Wincompatible-pointer-types] 2535 | xdrstdio_getpos, /* get offset in the stream */ | ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2535:17: note: (near initialization for ‘xdrstdio_ops.x_getpostn’) MDAnalysis/lib/formats/src/xdrfile.c:2536:17: error: initialization of ‘int (*)(XDR *, unsigned int)’ from incompatible pointer type ‘int (*)(XDR *, int64_t, int)’ {aka ‘int (*)(XDR *, long int, int)’} [-Wincompatible-pointer-types] 2536 | xdrstdio_setpos, /* set offset in the stream */ | ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2536:17: note: (near initialization for ‘xdrstdio_ops.x_setpostn’) error: command '/usr/bin/gcc' failed with exit code 1

Apparently the -Wno-incompatible-pointer-types should be added to CFLAGS.

Thanks to Antonio Rojas

vedranmiletic commented on 2023-05-27 13:15 (UTC)

@vale this should be fixed now. Enjoy!

vale commented on 2022-05-28 14:25 (UTC)

python-biopython is also required as of sometime recently; thank you!

vale commented on 2021-02-19 22:57 (UTC)

looks like python-tqdm is also required; thank you for packaging!

hseara commented on 2021-01-20 21:48 (UTC)

Hi guys. The list of hard dependencies of MDAnalysis is growing. Moreover, they do no longer provide the list of compulsory ones. I have created two new packages that are required and added them as such to depends:

  • python-mmtf
  • python-gsd

I am not sure if the optional ones are more than are really required. If you find any, please let me know, and I will make the appropriate changes.

FoPref commented on 2021-01-20 18:39 (UTC)

Basically all the "optional" dependencies here are mandatory to make mdanalysis run. Sadly, python-mmtf is not available and needs to be installed via pip. Also 'gsd' pip package needs to be installed.

E3LDDfrK commented on 2020-02-04 00:24 (UTC) (edited on 2020-02-04 17:33 (UTC) by E3LDDfrK)

edit: And it seems, a python package called "gsd" is also a dependency.

Is python-mmtf really an optional dependency? Trying to import MDAnalysis, I got this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.8/site-packages/MDAnalysis/__init__.py", line 183, in <module>
    from .lib import log
  File "/usr/lib/python3.8/site-packages/MDAnalysis/lib/__init__.py", line 36, in <module>
    from . import util
  File "/usr/lib/python3.8/site-packages/MDAnalysis/lib/util.py", line 174, in <module>
    import mmtf
ModuleNotFoundError: No module named 'mmtf'