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

ReproNim / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers

https://www.repronim.org/neurodocker/

Apache License 2.0

325 stars 97 forks source link

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

Open yarikoptic opened 4 months ago

yarikoptic commented 4 months ago

More info:

https://github.com/ReproNim/neurodocker/issues/478#issuecomment-2023956277 Current show stopper since libpng12 from snapshots does not want that easily to install...
https://github.com/afni/afni/issues/596

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

codecov[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #601 +/- ## ======================================= Coverage 88.01% 88.01% ======================================= Files 11 11 Lines 1035 1035 ======================================= Hits 911 911 Misses 124 124 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

stebo85 commented 3 months ago

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

Remi-Gau commented 3 months ago

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 commented 3 months ago

Will fix the merge conflict

Remi-Gau commented 3 months ago

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 commented 1 month ago

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

mvdoc commented 1 month ago

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