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fix: Setting the value of ignore_incomplete Fixes #2556 #2654

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MarwanMabrouk
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Description

setting ignore_incomplete to True to fix a few functions that run before ExecutionSettings is initialized because ExecutionSettings is only initialized in execute_workflow

fixes:

  • printdag
  • printrulegraph
  • conda_create_envs
  • conda_cleanup_envs
  • container_cleanup_images

which all run before execute_workflow

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).

@MarwanMabrouk MarwanMabrouk changed the title Setting the value of ignore_incomplete Fixes #2556 fix: Setting the value of ignore_incomplete Fixes #2556 Jan 26, 2024
@cademirch
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Looks like this covers the PR I opened yesterday, #2654, but you've covered a few more functions. I'm still not sure if ignore_incomplete should be True or False for these functions, but we can wait until @johanneskoester responds.

If you don't mind, I can add the tests from my PR to this one and then close mine? Can also incorporate your changes into mine, don't think the order of operations matters.

@johanneskoester
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Thank you so much!

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sonarcloud bot commented Jan 29, 2024

Quality Gate Passed Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

@johanneskoester johanneskoester merged commit 05dac64 into snakemake:main Jan 29, 2024
34 checks passed
johanneskoester pushed a commit that referenced this pull request Jan 29, 2024
🤖 I have created a release *beep* *boop*
---


##
[8.4.0](v8.3.2...v8.4.0)
(2024-01-29)


### Features

* add cols argument to lookup function; fix various minor bugs on
cluster systems
([#2651](#2651))
([ca7a602](ca7a602))


### Bug Fixes

* batch bug [#2643](#2643)
([#2650](#2650))
([2ecb21b](2ecb21b))
* f-string in a more robust style?
([#2649](#2649))
([2a50dc0](2a50dc0))
* set ignore_incomplete to False in create_conda_envs
([#2653](#2653))
([4834a42](4834a42))
* Setting the value of ignore_incomplete Fixes
[#2556](#2556)
([#2654](#2654))
([05dac64](05dac64))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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3 participants