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[WIP][ENH] add Dockerfile for python version og GLM single #46

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@Remi-Gau Remi-Gau commented Apr 11, 2022

Will need to use a containerized version of glmsingle to build on top of so in case this is useful, here is how to do it for glmsingle alone.

Feel free to reject / close.

  1. make Dockerfile will create a Dockerfile for the python implementation using neurodocker
  2. make docker_buildwill run 1 and then create the docker image
  3. make docker_run will run 2 and then run the docker image and open jupyter lab to use it

Once again this is based on the same initial commit as #43 and #44

TODO

  • fix import error

Currently the examples notebook cannot run and throw this error and pip list does shows GLMsingle 0.0.1

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Input In [1], in <cell line: 15>()
     12 from pprint import pprint
     13 warnings.filterwarnings('ignore')
---> 15 from glmsingle.glmsingle import GLM_single

ModuleNotFoundError: No module named 'glmsingle'

Remi-Gau added 3 commits April 7, 2022 13:12
Common base for the matlab and python testing branch to minimize merge conflicts down the line
Comment on lines +1 to +9
# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.8.0
# Timestamp: 2022/04/11 12:55:39 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/ReproNim/neurodocker
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This file is automatically generated via the Makefile

Comment on lines +123 to +134
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base python:3.9.12-slim-buster \
--pkg-manager apt \
--install "build-essential" \
--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /glmsingle/ \
--workdir /glmsingle \
--run "pip install ." \
--run "pip install jupyterlab" \
--expose 8888 \
--user neuro \
--workdir /home/neuro \
--copy examples /home/neuro/examples > Dockerfile
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This is the neurodocker command to build the Dockerfile for GLMsingle

@kendrickkay
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Hmm... I'm not sure what the action item is here. Perhaps earmark for a discussion soon.

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@Remi-Gau Remi-Gau left a comment

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  • add doc explaining how to build and run the docker image
  • add singularity image

Current problem when building the singularity def file: neurodocker related.
Issue raised: ReproNim/neurodocker#447

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2 participants