Attempt to adjust template for AFNI binary to make it work on Debian #601
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=== 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 ^^^
…be pulled by -dev AFAIK)
yarikoptic
added a commit
to yarikoptic/dsst-defacing-pipeline
that referenced
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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
6 tasks
Codecov ReportAll modified and coverable lines are covered by tests ✅
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. |
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does anyone understand why the black formatting fails? @Remi-Gau maybe? |
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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. |
Closed
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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 ^^^
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Note: some of our tests are flaky and require rerunning for them to pass.
|
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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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Unfortunately it's still not working :\ AFNI got installed without issues but then it complains about libpng12 |
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More info:
Current show stopper since libpng12 from snapshots does not want that easily to install...
Some initial commit which moves to use snapshot is generally useful since otherwise URL is just 404