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fix: patch LocalSourceFile to work with containerize #1211

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@mfansler mfansler commented Oct 9, 2021

Description

Fixes #1210 by implementing the os.PathLike interface (__fspath__()). Updates interface usage. Adds test to demonstrate fix.

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

@mfansler mfansler requested a review from johanneskoester as a code owner Oct 9, 2021
@mfansler mfansler changed the title Patch LocalSourceFile to work with containerize fix: patch LocalSourceFile to work with containerize Oct 9, 2021
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mfansler commented Oct 11, 2021

@johanneskoester please let me know if you'd like a different direction for this. I realized after submitting that we don't need to add __fspath__ to LocalSourceFile, but could instead just modify all the env.file references to env.file.get_path_or_uri(). Personally, I think it makes semantic sense for LocalSourceFile to implement os.PathLike, unless one can imagine a local source file without a path.

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@johanneskoester johanneskoester left a comment

Thank you!

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sonarcloud bot commented Oct 21, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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johanneskoester commented Oct 26, 2021

I have some additional related fixes in #1236. Thanks a lot for your work here, I've integrated it into the other PR (I will reference you in the release notes).

johanneskoester added a commit that referenced this pull request Oct 26, 2021
…#1233 and #1211). (#1236)

* fix: more informative nothing to be done message

* fmt

* fmt, fixes and additional tests

* implement fspath
pvandyken pushed a commit to pvandyken/snakemake that referenced this pull request Nov 15, 2021
…snakemake#1233 and snakemake#1211). (snakemake#1236)

* fix: more informative nothing to be done message

* fmt

* fmt, fixes and additional tests

* implement fspath
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--containerize is broken
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