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Support using container entrypoints for shell tasks #822

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@tclose tclose commented May 5, 2025

Types of changes

  • New feature (non-breaking change which adds functionality)

Summary

When executing shell commands in Docker/Singularity containers, permit setting executable to None in order to use the entrypoint of the container.

Checklist

  • I have added tests to cover my changes (if necessary)
  • I have updated documentation (if necessary)

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codecov bot commented May 5, 2025

Codecov Report

Attention: Patch coverage is 16.07143% with 47 lines in your changes missing coverage. Please review.

Project coverage is 64.11%. Comparing base (058d793) to head (38a1db8).

Files with missing lines Patch % Lines
pydra/environments/tests/test_environments.py 13.04% 20 Missing ⚠️
pydra/environments/base.py 21.42% 11 Missing ⚠️
pydra/compose/shell/builder.py 12.50% 7 Missing ⚠️
pydra/compose/shell/task.py 14.28% 6 Missing ⚠️
pydra/environments/docker.py 0.00% 1 Missing ⚠️
pydra/environments/native.py 0.00% 1 Missing ⚠️
pydra/environments/singularity.py 0.00% 1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (058d793) and HEAD (38a1db8). Click for more details.

HEAD has 16 uploads less than BASE
Flag BASE (058d793) HEAD (38a1db8)
23 7
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #822       +/-   ##
===========================================
- Coverage   88.76%   64.11%   -24.66%     
===========================================
  Files          84       84               
  Lines       17890    17907       +17     
  Branches     3483     1556     -1927     
===========================================
- Hits        15880    11481     -4399     
- Misses       1640     6024     +4384     
- Partials      370      402       +32     

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@tclose tclose force-pushed the container-entrypoint branch from dd382ca to d7a9b2a Compare May 6, 2025 00:13
@tclose tclose force-pushed the container-entrypoint branch from 6f08e7b to 38a1db8 Compare May 13, 2025 04:52
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