FIX: Add environment argument to TaskBase._run_task() and Workflow subclass

ghisvail commented 3 months ago

Types of changes

Bug fix (non-breaking change which fixes an issue)

Summary

I bumped the Pydra version used by Clinica to 0.23 and ran the test suite.

There are a few failures, but one caught my attention in particular:

----------------------------- Captured stdout call -----------------------------
in SUBM None
_run_task() got an unexpected keyword argument 'environment'

The first line is a residual print statement (removed by the first commit).

The second one suggests an interface mismatch (fixed by the second commit).

codecov[bot] commented 3 months ago

Codecov Report

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

Project coverage is 84.27%. Comparing base (e284b65) to head (14d1e19).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #739 +/- ## ========================================== - Coverage 84.28% 84.27% -0.01% ========================================== Files 26 26 Lines 5128 5127 -1 Branches 1447 1447 ========================================== - Hits 4322 4321 -1 Misses 800 800 Partials 6 6 ``` | [Flag](https://app.codecov.io/gh/nipype/pydra/pull/739/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/nipype/pydra/pull/739/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype) | `84.27% <100.00%> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype#carryforward-flags-in-the-pull-request-comment) to find out more.

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tclose commented 3 months ago

How did the environment kwarg get dropped? Was this something I introduced merging in my branches?

nipype / pydra