ReproNim / containers

Containers "distribution" for reproducible neuroimaging
Apache License 2.0
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Add rudimentary testing of executability for freshly added containers #120

Open yarikoptic opened 1 month ago

yarikoptic commented 1 month ago

To prevent

We could seek --help output.

I ran

( export REPORTTIME=-1; COLUMNS=180 git log --stat | grep 'images/bids.*\.sing' | sed -e 's,sing .*,sing,g' | while read img; do echo -n "$img: "; singularity run $img --help >/dev/null 2>&1 && echo ok || echo FAIL; done; ) 2>&1 | tee containers--help.out

full output http://www.oneukrainian.com/tmp/containers--help.out

Here are the ones which FAILED ```shell ❯ grep FAIL containers--help.out | grep -v -e 'Adding' -e '=>' | sort | uniq images/bids/bids-aa--v0.2.0.sing: FAIL images/bids/bids-aslprep--0.5.1.sing: FAIL images/bids/bids-aslprep--0.6.0.sing: FAIL images/bids/bids-bidsmreye--0.3.0.sing: FAIL images/bids/bids-bidsmreye--dev.sing: FAIL images/bids/bids-broccoli--1.0.1.sing: FAIL images/bids/bids-broccoli--v1.0.1.sing: FAIL images/bids/bids-cpac--v1.1.0_14.sing: FAIL images/bids/bids-dmriprep--0.5.0.sing: FAIL images/bids/bids-fibredensityandcrosssection--v0.0.1.sing: FAIL images/bids/bids-freesurfer--v6.0.1-5.sing: FAIL images/bids/bids-hcppipelines--v3.17.0-18.sing: FAIL images/bids/bids-magetbrain--v0.3.sing: FAIL images/bids/bids-micapipe--0.0.1.sing: FAIL images/bids/bids-mindboggle--0.0.4-1.sing: FAIL images/bids/bids-mindboggle--0.0.4.sing: FAIL images/bids/bids-mriqc--23.1.1.sing: FAIL images/bids/bids-mriqc--24.0.0.sing: FAIL images/bids/bids-mrtrix3-connectome--0.4.1.sing: FAIL images/bids/bids-mrtrix3-connectome--0.4.2.sing: FAIL images/bids/bids-mrtrix3-connectome--0.5.0.sing: FAIL images/bids/bids-mrtrix3-connectome--0.5.1.sing: FAIL images/bids/bids-mrtrix3-connectome--0.5.2.sing: FAIL images/bids/bids-mrtrix3-connectome--0.5.3.sing: FAIL images/bids/bids-ndmg--v0.1.0.sing: FAIL images/bids/bids-niak--latest.sing: FAIL images/bids/bids-oppni--v0.7.0-1.sing: FAIL images/bids/bids-rshrf--1.0.1.sing: FAIL images/bids/bids-spm--0.0.15.sing: FAIL images/bids/bids-spm--v0.0.15.sing: FAIL images/bids/bids-xcp-d--0.6.1.sing: FAIL images/bids/bids-xcp-d--0.6.2.sing: FAIL images/bids/bids-xcp-d--0.6.3.sing: FAIL images/bids/bids-xcp-d--0.6.4.sing: FAIL images/bids/bids-xcp-d--0.7.0.sing: FAIL images/bids/bids-xcp-d--0.7.1.sing: FAIL ```

some are occasional (like mriqc) but some are chronic -- and needs to be troubleshooted and ideally addressed before we can reliably add --help checking.