Add rudimentary testing of executability for freshly added containers

Open
#120 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Domain
infrastructure, testing-qa

Research direction

Start with the existing container layout under images/bids and reproduce the reported command that runs singularity run <image> --help against recently added .sing files. Define the check so newly added containers are tested for executability, then use the listed failures to verify that chronic failures are identified or addressed.

Written by the indexing model from the issue text.

Description

To prevent

  • #118
    from going undetected.

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 
❯ 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.

Dominant language
Python
Stars
32
Forks
17
Avg merge
12h 2m
Merged PRs (30d)
3

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from ReproNim/containers

All issues in ReproNim/containers

Similar issues

More Python issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.