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feat: add support for Kubernetes service account name spec #2254

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merged 8 commits into from Aug 3, 2023
Merged

feat: add support for Kubernetes service account name spec #2254

merged 8 commits into from Aug 3, 2023

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hnawar
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@hnawar hnawar commented May 9, 2023 •
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Description

Add support for Custom Kubernetes service account which enables the use of GKE Autopilot and other Kuberenetes clusters using Workload identity

QC

I tested it with a GATK pipeline but will add relevant test cases

  • 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).

@hnawar hnawar marked this pull request as draft May 9, 2023 12:36
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hnawar commented May 9, 2023

Hi @johanneskoester ,
It's been a while since I used snakemake, but I was trying to use it with GKE Autopilot when I ran into some issues. This PR enables the use of GKE autopilot and clusters configured with Workload identity.

Can you let me know your thoughts and I will start adding test cases and documentation.

Please note that there is a limit on ephemeral storage per pod of 10GiB which does limit the pipelines you can run.
This is not an urgent PR

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hnawar commented May 9, 2023

I noticed that docs should be added automatically by the CLI parser, so I'm assuming I don't need to add any more documentation unless you want me to add a note about Kubernetes workload identity.
Are there any examples of tests that would be needed. I've already tested with multiple snakefiles on different clusters using workload identity

@hnawar hnawar changed the title Add support for Kubernetes service account name spec [WIP] Add support for Kubernetes service account name spec May 9, 2023
@hnawar hnawar marked this pull request as ready for review May 9, 2023 16:23
johanneskoester
johanneskoester approved these changes May 12, 2023
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Thanks a lot!

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May I ask you to fix the formatting with black?

@johanneskoester johanneskoester changed the title Add support for Kubernetes service account name spec feat: add support for Kubernetes service account name spec May 12, 2023
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hnawar commented May 17, 2023

Hi Johannes, thanks for reviewing. Did you mean the missing parmeter type? I have added that and updated the branch so it can be merged.

Thanks

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sonarcloud bot commented May 17, 2023

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
No Duplication information No Duplication information

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You have to run black on the source code to get the formatting fixed according to the best practices. This is what the failing test means.

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sonarcloud bot commented Aug 2, 2023

Please retry analysis of this Pull-Request directly on SonarCloud.

@johanneskoester johanneskoester merged commit 3370426 into snakemake:main Aug 3, 2023
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@github-actions github-actions bot mentioned this pull request Aug 3, 2023
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johanneskoester pushed a commit that referenced this pull request Aug 3, 2023
@github-actions
chore(main): release 7.32.0 (#2388)
2e42866 
🤖 I have created a release *beep* *boop*
---


##
[7.32.0](v7.31.1...v7.32.0)
(2023-08-03)


### Features

* add support for Kubernetes service account name spec
([#2254](#2254))
([3370426](3370426))


### Bug Fixes

* Enable values with an = sign in default_resources
([#2340](#2340))
([c1c9229](c1c9229))
* Escape workdir paths for potential spaces in paths
([#2196](#2196))
([9261f7e](9261f7e))
* ga4gh executor resources
([#2042](#2042))
([ad6eaef](ad6eaef))
* print exceptions when job is not a shell job
([#2385](#2385))
([8a37b85](8a37b85))
* remote-azblob-sasToken-Authorization
([#1800](#1800))
([bc854a7](bc854a7))
* wms-monitor now gets data in correct json format
([#2347](#2347))
([7fafa7a](7fafa7a))


### Documentation

* fix a copy&paste (?) mistake
([#2386](#2386))
([d878847](d878847))

---
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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