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bigginlab / ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
GNU General Public License v3.0
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Installation failed #26

Closed EricChen521 closed 3 weeks ago

EricChen521 commented 4 months ago

Hi, I experienced an error related to Scipy using mamba env create --file environment.yml. Any idea why?

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for scipy
ERROR: Could not build wheels for scipy, which is required to install pyproject.toml-based projects

failed
RiesBen commented 4 months ago

@EricChen521 hej Eric, this looks weird! looking into it :)

ErikZhang-9762 commented 4 months ago

Hi, I have the same problem.

The error should occur when installing MDRestraintsGenerator using pip

The problem can be reproduced using the following command

pip install MDRestraintsGenerator

and scipy version is 1.7.3

conda list | grep scipy
scipy                     1.7.3           py310hea5193d_0    conda-forge

Is there a solution to this problem now?

RiesBen commented 4 months ago

Hej, it took some time, till I had time to look into this.

I updated the environment.yml and pinned the numpy version to 1.22, now at least the CI works. how does that look on your end? :)

RobertArbon commented 3 weeks ago

Just FYI - i've managed to install this perfectly fine on my system (ubuntu 22): 


          mamba version : 1.5.8
     active environment : abfe
    active env location : /home/lex/miniforge3/envs/abfe
            shell level : 2
       user config file : /home/lex/.condarc
 populated config files : /home/lex/miniforge3/.condarc
          conda version : 24.3.0
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen2
                          __conda=24.3.0=0
                          __cuda=12.2=0
                          __glibc=2.35=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /home/lex/miniforge3  (writable)
      conda av data dir : /home/lex/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/lex/miniforge3/pkgs
                          /home/lex/.conda/pkgs
       envs directories : /home/lex/miniforge3/envs
                          /home/lex/.conda/envs
               platform : linux-64
             user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/6.8.0-48-generic ubuntu/22.04.5 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
philbiggin commented 3 weeks ago

OK - its a been a few months now so in the absence of information saying otherwise I think this is fixed.