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Attempt to adjust template for AFNI binary to make it work on Debian #601

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yarikoptic
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More info:

Some initial commit which moves to use snapshot is generally useful since otherwise URL is just 404

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i -e 's,http.*libxp6_1.0.2-2_amd64.deb,https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb,g' neurodocker/templates/afni.yaml neurodocker/templates/ants.yaml neurodocker/templates/bids_validator.yaml neurodocker/templates/cat12.yaml neurodocker/templates/convert3d.yaml neurodocker/templates/dcm2niix.yaml neurodocker/templates/freesurfer.yaml neurodocker/templates/fsl.yaml neurodocker/templates/_header.yaml neurodocker/templates/jq.yaml neurodocker/templates/matlabmcr.yaml neurodocker/templates/minc.yaml neurodocker/templates/miniconda.yaml neurodocker/templates/mricron.yaml neurodocker/templates/mrtrix3.yaml neurodocker/templates/ndfreeze.yaml neurodocker/templates/neurodebian.yaml neurodocker/templates/niftyreg.yaml neurodocker/templates/petpvc.yaml neurodocker/templates/spm12.yaml neurodocker/templates/vnc.yaml",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
@yarikoptic yarikoptic marked this pull request as draft March 27, 2024 20:51
yarikoptic added a commit to yarikoptic/dsst-defacing-pipeline that referenced this pull request Mar 27, 2024
It is not yet finished
- did not even try FSL installation
- AFNI installation relies on incomplete fixes proposed in
  ReproNim/neurodocker#601
- moved away attempt to install bids-validator (would be useful) due
  those failing too ATM
yarikoptic added a commit to yarikoptic/dsst-defacing-pipeline that referenced this pull request Mar 27, 2024
It is not yet finished
- did not even try FSL installation
- AFNI installation relies on incomplete fixes proposed in
  ReproNim/neurodocker#601
- moved away attempt to install bids-validator (would be useful) due
  those failing too ATM
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codecov bot commented Mar 27, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.01%. Comparing base (0f6fc2e) to head (7c81b80).
Report is 1 commits behind head on master.

Additional details and impacted files
@@           Coverage Diff           @@
##           master     #601   +/-   ##
=======================================
  Coverage   88.01%   88.01%           
=======================================
  Files          11       11           
  Lines        1035     1035           
=======================================
  Hits          911      911           
  Misses        124      124           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@stebo85
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stebo85 commented Apr 1, 2024

does anyone understand why the black formatting fails? @Remi-Gau maybe?

@Remi-Gau
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Remi-Gau commented Apr 2, 2024

The black failure is not new and given the dates it started happening at, I suspect this is because of the new version of black released in January.

I can take care of fixing in a separate PR. Will probably do a refactor of the linting stuff to channel everything via pre-commit that encourages us to pin the formatting tool versions.

@Remi-Gau Remi-Gau mentioned this pull request Apr 2, 2024
@Remi-Gau
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Remi-Gau commented Apr 3, 2024

Will fix the merge conflict

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "pre-commit run yamlfmt --files neurodocker/templates/afni.yaml neurodocker/templates/spm12.yaml",
 "exit": 1,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
@Remi-Gau
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Remi-Gau commented Apr 3, 2024

Note: some of our tests are flaky and require rerunning for them to pass.

  • FAILED neurodocker/cli/tests/test_build_images_with_cli.py::test_build_image_from_registered[yum-centos:7-singularity]
  • FAILED neurodocker/cli/tests/test_build_images_with_cli.py::test_build_image_from_registered[yum-centos:7-singularity]

@mvdoc
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mvdoc commented Jun 22, 2024

Is anything else needed here? I just tried installing AFNI and it blew :(, it would be great to have this merged

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mvdoc commented Jun 22, 2024

Unfortunately it's still not working :\ AFNI got installed without issues but then it complains about libpng12

(base) root@78262ef97a5f:/# 3dvolreg
3dvolreg: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

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4 participants