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fix: Use 'snakemake.utils.update_config' instead of 'dict.update' #1126

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merged 23 commits into from Nov 25, 2021

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kpj
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@kpj kpj commented Aug 9, 2021

Description

When merging configs, Snakemake uses dict.update instead of snakemake.utils.update_config which is not recursive.
Nested config options can thus disappear unexpectedly.

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).

@kpj kpj marked this pull request as ready for review Aug 9, 2021
@kpj kpj requested a review from johanneskoester as a code owner Aug 9, 2021
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sonarcloud bot commented Aug 12, 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

@kpj
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kpj commented Aug 29, 2021

@johanneskoester Any thoughts on this? :-)

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@johanneskoester johanneskoester left a comment

Makes sense to me! Sorry for the late review.

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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

@johanneskoester
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johanneskoester commented Oct 21, 2021

Soemthing fails on windows now. Do you have a clue?

@kpj
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kpj commented Oct 21, 2021

Not really, and I don't have any Windows machine to investigate this :-(
Maybe something related to the quotation marks?

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sonarcloud bot commented Nov 24, 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

@johanneskoester johanneskoester merged commit 2658027 into snakemake:main Nov 25, 2021
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@johanneskoester
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johanneskoester commented Nov 25, 2021

Thanks a lot, finally done :-).

@kpj
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kpj commented Nov 25, 2021

Wonderful! Thanks a lot for the debugging as well :-)

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2 participants