Singularity def file for dipy1.4.0.dev0 & patch2self

[pcamach2]

Description

I wanted to set up a Singularity container to run patch2self , so I followed the guidance in this post to install dipy1.4.0.dev0, which includes patch2self.

Here is the Singularity def file contents:

Bootstrap: docker
From: python:3.6.0

%runscript

    exec /usr/local/bin/python "$@"


%post

    apt-get update
    apt-get install -y vim
    pip3 install --upgrade pip
    pip3 install scikit-learn 
    pip3 install tqdm>=4.30.0 nibabel>=3.0.0 h5py>=2.5.0
    pip3 install -i https://pypi.anaconda.org/scipy-wheels-nightly/simple dipy==1.4.0.dev0
    mkdir -p /scratch
    mkdir -p /local-scratch

Say someone names this file patch2self_def, they can build the container with: sudo singularity build patch2self.sif patch2self_def

I originally opened an issue on the patch2self repo and @Garyfallidis recommended I bring this over to dipy as well in case it is useful for other folks.

Cheers

[pcamach2]

I feel comfortable closing this issue since it has been over a year and dipy has updated.

[skoudoro]

Hi @pcamach2,

Indeed, we have it on another repo, but I want to keep this issue open.

I would like to have an official singularity and docker set up on the main repo. I will close it back when it is done.

Thank you

[pcamach2]

Hi @skoudoro,

Totally understandable! Let me know if you want any help with the singularity and docker set up!

Cheers, Paul

[arokem]

@skoudoro : We have a pretty straightforward docker GitHub actions setup over on pyAFQ.

Take a look at:

https://github.com/yeatmanlab/pyAFQ/blob/master/.github/workflows/docker_pyafq.yml https://github.com/yeatmanlab/pyAFQ/tree/master/pyafq_docker

Which runs a build on pull requests and merges to master, and pushes tagged versions to ghcr.

I think that we can borrow most of that here.

[skoudoro]

Thank you Ariel! it looks great!

I will have a deeper look after the DIPY workshop, so the two first weeks of April. We will also need to document it somewhere.

I see that you are storing the docker build in GitHub and not the docker hub. is there any limitation with that choice?