Comments (8)
Leads to simplify:
- includes somehow the dependency of niak on the brain connectivity toolbox and psom as part of the git release. Not sure whether that is possible but worth investigating. This would avoid pushing the niak release to nitrc altogether.
- Link the niak repo on docker with the niak repo on github. This will automatically build and release the xxxx and latest images.
- Which, btw, would be more efficient if the templates of niak where split into a separate repo, that would get updated less often. That way new niak images would typically change only by a very thin layer of pure .m code.
- Implement a version for targets separate from the niak version. The targets will be generated independently from niak, and much much more infrequently.
If all of that works, creating a new niak release would basically just include changing the niak version in niak_gb_vars.m, creating a new tag and pushing to github. The docker images would be created automatically. And if we use docker to run niak on servers, all we would need to do is invoke the latest niak image.
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Alright, so another fun fact. When making a new release of the target for the tests, it is necessary to change a new variable gb_niak_target_test
. It contains the version of the target (formatted like YYYY-MM-DD). BUT once the target is released on NITRC, it is assigned a random URL. This URL has to be manually added line 68 in niak_wget
. We need to move to a different place to release the targets, otherwise we will have to add this manual step for every new release of target data for tests.
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I have created a new repo for niak testing
https://github.com/SIMEXP/niak_test
I have also applied to early access to github large file support. I have installed the associated software and it's super easy to use. We'll use that repo to release new test data, which will appear on a predictable URL.
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Started testing automatic release on https://github.com/poquirion/docker_build.
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Since it is not that big, I will put the the target in niak_test. I will use tags make package and pull these package to run tests.
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Great! As soon as simexp get approved for lfs we will simply transfer them over.
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The release tool has now its own git repo.
To do the release, we still need to:
Add a valid psom_gb_vars_local.m
where the package is installed.
Manually trigger the a (not so) automatic docker image build here.
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Release issue should be posted on the release_tools site.
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Related Issues (20)
- user can't download niak because it is too big HOT 3
- Errors running NIAK pre-processing pipeline HOT 15
- NIAK ADHD-200 Data: Mean FD motion values
- niak_brick_anat2stereolin is not robust to spaces in the file name
- regress_confounds failure HOT 6
- verbose broken in `niak_brick_regress_confounds`
- missing parameter `nb_vol_min` in the doc of `niak_brick_regress_confounds`
- most of octave svds tests fails ( niak-cog docker) HOT 3
- running NIAK singularity with slurm system HOT 3
- crash using compcor
- qc_motion report crashing for erroneous subjects
- NIAK throws an error saying it can't find an image but still tries to preprocess image
- if the fieldname of files_in structure is too long psom throws an error saying the structure does not exist HOT 1
- niak clogs /tmp and kills the OS HOT 4
- test that niak does not leave files in the tmp HOT 1
- better bids-app and boutique support
- replace the bids parser by a call to pybids
- https online version of the doc is not working HOT 5
- Is motor fMRI data essential to the NIAK pipeline? HOT 1
- add support for non-uniformity correction
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