nipype / pydra

Pydra Dataflow Engine
https://nipype.github.io/pydra/
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STY: Miscellaneous cleanups #645

Closed effigies closed 1 year ago

effigies commented 1 year ago

Types of changes

Summary

While looking into type checking failures, some style issues caught my eye. Rather than bundle them in, I am putting them in a standalone PR. This PR has three commits, each of which can be considered separately, if you disagree.

Closes #282.

Checklist

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 80.00% and project coverage change: -0.64 :warning:

Comparison is base (64bfa89) 81.77% compared to head (c1a8983) 81.13%.

:exclamation: Current head c1a8983 differs from pull request most recent head 4da0a35. Consider uploading reports for the commit 4da0a35 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #645 +/- ## ========================================== - Coverage 81.77% 81.13% -0.64% ========================================== Files 20 20 Lines 4394 4400 +6 Branches 1264 0 -1264 ========================================== - Hits 3593 3570 -23 - Misses 797 830 +33 + Partials 4 0 -4 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `81.13% <80.00%> (-0.64%)` | :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=None#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [pydra/engine/helpers\_file.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL2hlbHBlcnNfZmlsZS5weQ==) | `86.10% <ø> (ø)` | | | [pydra/engine/workers.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL3dvcmtlcnMucHk=) | `18.76% <33.33%> (ø)` | | | [pydra/engine/audit.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL2F1ZGl0LnB5) | `94.04% <66.66%> (-3.46%)` | :arrow_down: | | [pydra/\_\_init\_\_.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvX19pbml0X18ucHk=) | `90.90% <100.00%> (+0.43%)` | :arrow_up: | | [pydra/engine/core.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL2NvcmUucHk=) | `92.96% <100.00%> (-0.16%)` | :arrow_down: | | [pydra/engine/helpers\_state.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL2hlbHBlcnNfc3RhdGUucHk=) | `95.61% <100.00%> (ø)` | | | [pydra/engine/state.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvZW5naW5lL3N0YXRlLnB5) | `96.39% <100.00%> (ø)` | | | [pydra/mark/\_\_init\_\_.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvbWFyay9fX2luaXRfXy5weQ==) | `100.00% <100.00%> (ø)` | | | [pydra/utils/messenger.py](https://app.codecov.io/gh/nipype/pydra/pull/645?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHlkcmEvdXRpbHMvbWVzc2VuZ2VyLnB5) | `95.89% <100.00%> (ø)` | | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/nipype/pydra/pull/645/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None)

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djarecka commented 1 year ago

lgtm! thank you!

effigies commented 1 year ago

Are these random 3.11 failures expected?

djarecka commented 1 year ago

no, i didn't notice it... and it's not even test failure, but some INTERNALERROR...

effigies commented 1 year ago

It happened on 99df677708b1a25608b705daadb120202558971d as well, so at least I'm not introducing it with something I've done here. My guess is it's an out-of-memory error causing an xdist worker to get killed.