Unsuccessful installation, numpy version issue about genice HOT 6 CLOSED

Many thanks for providing this powerful tool to generate ice structures. Our paper utilizing GenIce is now published.
https://pubs.acs.org/doi/10.1021/acs.jctc.1c00357

from genice.

Thank you for your report.
The problem would be caused by pairlist library (also developed by myself).
I replaced the precompiled package in PyPI repository with a package without binaries. (PairList ver. 0.2.11.3)
I hope it will fix the problem.

from genice.

Hello Professor Matsumoto, thank you for your reply.
I'm now trying to use the "genice2-cif" plugin but had some similar issue with the numpy version.

As I install genice2 from the "pip" command, I still need to reinstall the numpy-1.21.0 version manually to make genice2 work properly.

Now after installing the "genice2-cif" from "pip", I had to reinstall the numpy-1.21.0 version again. However, the plugin complains about the numpy version.

% genice2
usage: genice2 [-h] [--version] [--rep REP REP REP] [--shift SHIFT SHIFT SHIFT] [--dens DENS] [--add_noise percent]
[--seed SEED] [--format name] [--water model] [--guest 14=me] [--Guest 13=me] [--Group 13=bu-:0]
[--anion 3=Cl] [--cation 3=Na] [--depol DEPOL] [--asis] [--debug] [--quiet] [--assess_cages]
Type
genice2: error: the following arguments are required: Type

It is fine to run without the plugin option.

% genice2 cif
INFO Extra lattice plugin: cif
INFO main: end.
INFO main: 41 ms
Traceback (most recent call last):
File "/home/raymond/miniconda3/envs/genice-cif/bin/genice2", line 8, in
sys.exit(main())
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/genice2/decorators.py", line 14, in _time_it
return func(*args, **kwargs)
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/genice2/decorators.py", line 34, in _banner
return func(*args, **kwargs)
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/genice2/cli/genice.py", line 214, in main
safe_import(
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/genice2/plugin.py", line 279, in safe_import
module = import_extra(category, name)
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/genice2/plugin.py", line 233, in import_extra
module = ep.load()
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/pkg_resources/init.py", line 2449, in load
self.require(*args, **kwargs)
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/pkg_resources/init.py", line 2472, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File "/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages/pkg_resources/init.py", line 777, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.21.0 (/home/raymond/miniconda3/envs/genice-cif/lib/python3.9/site-packages), Requirement.parse('numpy==1.19.3'), {'GenIce2'})

The issue came up.

In addition to this numpy version issue, I'm not sure about the syntax of that genice2-cif plugin. In the manual, it says "genice2 cif[RHO.cif]". So there is no space between "cif" and "[", am I correct? And the RHO.cif is a CIF file in my current folder? Thanks a lot.

from genice.

GenIce2 specifies the version of numpy to 1.19.3 just because it is (perhaps) necessary to run it on Apple M1 (i.e. my machine), but it would be rather harmful to other people. I will update the PIP packages not to specify the version of numpy.

The syntax is correct. However, some shells might react to the brackets after "cif". You might better put quotation marks around the argument like this: genice2 'cif[RHO.cif]'.

from genice.

I removed the version specification for numpy and deployed to PyPI as ver. 2.1.2. I hope it works for you.

from genice.

Thank you. The installation has no problem now.

from genice.