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fix: use short argument name for --chdir for compatibility with Slurm <=v17 #2040

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merged 2 commits into from Jan 16, 2023
Merged

fix: use short argument name for --chdir for compatibility with Slurm <=v17 #2040

merged 2 commits into from Jan 16, 2023

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@tdido tdido commented Dec 28, 2022

Description

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).

This would fix #2014 since the short argument is the same (-D) even if the long argument changed from --workdir to --chdir after Slurm 17:

https://slurm.schedmd.com/archive/slurm-17.02.0/sbatch.html
https://slurm.schedmd.com/sbatch.html

@tdido @johanneskoester
Add commenta and issue ref
c2eb102 
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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sonarcloud bot commented Jan 10, 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
0.0% 0.0% Duplication

@johanneskoester johanneskoester merged commit a9ed3ec into snakemake:main Jan 16, 2023
@github-actions github-actions bot mentioned this pull request Jan 16, 2023
Merged
johanneskoester pushed a commit that referenced this pull request Jan 18, 2023
@github-actions
chore(main): release 7.20.0 (#2018)
1c9ea65 
🤖 I have created a release *beep* *boop*
---


##
[7.20.0](v7.19.1...v7.20.0)
(2023-01-18)


### Features

* add tes token
([#1966](#1966))
([59a8fa0](59a8fa0))
* Add token auth to GitLab/GitHub hosting providers
([#1761](#1761))
([e03a3b4](e03a3b4)),
closes [#1301](#1301)
* allow for human friendly resource definitions (e.g. mem="5GB",
runtime="1d")
([#1861](#1861))
([24610ac](24610ac))


### Bug Fixes

* 🐛 - fix hyperlink
([#2046](#2046))
([9519d31](9519d31))
* Catch missing error stream in Slurm executor
([#2063](#2063))
([c21fc7e](c21fc7e))
* correctly parse empty values in config cli
([#2032](#2032))
([1b0689d](1b0689d))
* Correctly parse UserDicts in executors
([#2016](#2016))
([e3926fa](e3926fa))
* Fix handling of --jobs in no-exec state
([#2029](#2029))
([e8e8222](e8e8222))
* make `--show-failed-logs` handle empty log files
([#2039](#2039))
([683c6f2](683c6f2)),
closes [#2023](#2023)
* make python version check more robust
([#2058](#2058))
([e685621](e685621))
* parsing error when last line is comment
([#2054](#2054))
([a928dd4](a928dd4))
* prevent overriding of retries when set to 0
([#2053](#2053))
([a328f3e](a328f3e))
* propagate attempt count from group to subjobs
([#2052](#2052))
([da3f1c0](da3f1c0))
* remove overflow from rulegraph div in report
([9a0aaa7](9a0aaa7))
* skip type checks of missing dir in touch mode
([#2051](#2051))
([ae00c25](ae00c25))
* slurm default_resources quoting
([#2043](#2043))
([47d3fc3](47d3fc3))
* Update list of python versions in classifiers
([#2020](#2020))
([7a98100](7a98100))
* use short argument name for `--chdir` for compatibility with Slurm
&lt;=v17 ([#2040](#2040))
([a9ed3ec](a9ed3ec))


### Documentation

* Fix typo in SLURM help text
([#2049](#2049))
([79b7025](79b7025))
* mention XDG_CACHE_HOME
([#2057](#2057))
([ec2ef45](ec2ef45))

---
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>
jakevc pushed a commit to jakevc/snakemake that referenced this pull request Feb 7, 2023
@github-actions @jakevc
chore(main): release 7.20.0 (snakemake#2018)
bb07f59 
🤖 I have created a release *beep* *boop*
---


##
[7.20.0](snakemake/snakemake@v7.19.1...v7.20.0)
(2023-01-18)


### Features

* add tes token
([snakemake#1966](snakemake#1966))
([59a8fa0](snakemake@59a8fa0))
* Add token auth to GitLab/GitHub hosting providers
([snakemake#1761](snakemake#1761))
([e03a3b4](snakemake@e03a3b4)),
closes [snakemake#1301](snakemake#1301)
* allow for human friendly resource definitions (e.g. mem="5GB",
runtime="1d")
([snakemake#1861](snakemake#1861))
([24610ac](snakemake@24610ac))


### Bug Fixes

* 🐛 - fix hyperlink
([snakemake#2046](snakemake#2046))
([9519d31](snakemake@9519d31))
* Catch missing error stream in Slurm executor
([snakemake#2063](snakemake#2063))
([c21fc7e](snakemake@c21fc7e))
* correctly parse empty values in config cli
([snakemake#2032](snakemake#2032))
([1b0689d](snakemake@1b0689d))
* Correctly parse UserDicts in executors
([snakemake#2016](snakemake#2016))
([e3926fa](snakemake@e3926fa))
* Fix handling of --jobs in no-exec state
([snakemake#2029](snakemake#2029))
([e8e8222](snakemake@e8e8222))
* make `--show-failed-logs` handle empty log files
([snakemake#2039](snakemake#2039))
([683c6f2](snakemake@683c6f2)),
closes [snakemake#2023](snakemake#2023)
* make python version check more robust
([snakemake#2058](snakemake#2058))
([e685621](snakemake@e685621))
* parsing error when last line is comment
([snakemake#2054](snakemake#2054))
([a928dd4](snakemake@a928dd4))
* prevent overriding of retries when set to 0
([snakemake#2053](snakemake#2053))
([a328f3e](snakemake@a328f3e))
* propagate attempt count from group to subjobs
([snakemake#2052](snakemake#2052))
([da3f1c0](snakemake@da3f1c0))
* remove overflow from rulegraph div in report
([9a0aaa7](snakemake@9a0aaa7))
* skip type checks of missing dir in touch mode
([snakemake#2051](snakemake#2051))
([ae00c25](snakemake@ae00c25))
* slurm default_resources quoting
([snakemake#2043](snakemake#2043))
([47d3fc3](snakemake@47d3fc3))
* Update list of python versions in classifiers
([snakemake#2020](snakemake#2020))
([7a98100](snakemake@7a98100))
* use short argument name for `--chdir` for compatibility with Slurm
&lt;=v17 ([snakemake#2040](snakemake#2040))
([a9ed3ec](snakemake@a9ed3ec))


### Documentation

* Fix typo in SLURM help text
([snakemake#2049](snakemake#2049))
([79b7025](snakemake@79b7025))
* mention XDG_CACHE_HOME
([snakemake#2057](snakemake#2057))
([ec2ef45](snakemake@ec2ef45))

---
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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Using a slurm cluster that doesn't support --chdir=<folder>
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@tdido @johanneskoester