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fix: Allow hyphens in config keys given on the command line.#2998

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johanneskoester merged 2 commits intosnakemake:mainfrom
cmkobel:main
Aug 13, 2024
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fix: Allow hyphens in config keys given on the command line.#2998
johanneskoester merged 2 commits intosnakemake:mainfrom
cmkobel:main

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@cmkobel cmkobel commented Aug 4, 2024 •
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It is possible to use hyphens when specifying config keys given in the configfile, but when given on the command line as --config key-with-hyphens=value, it fails. With this PR, hyphens are allowed in the middle of config keys, when given on the command line.

As far as I understand, hyphens are valid for keys in the yaml specification: https://yaml.org/spec/1.2.2/ https://www.yaml.info/learn/bestpractices.html

I have been using this code in my projects for a while and I don't think it introduces any problems, especially since hyphens have been allowed in the config file for a very long time.

The motivation for me to use hyphens in the command line config is discussed here: #2986

Best, Carl

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).

Summary by CodeRabbit

  • New Features
    • Enhanced configuration key validation to allow hyphens in key names, increasing flexibility for user configurations.

@cmkobel cmkobel changed the title Allow hyphens in config keys given on the command line. Fix: Allow hyphens in config keys given on the command line. Aug 4, 2024
@cmkobel cmkobel changed the title Fix: Allow hyphens in config keys given on the command line. fix: Allow hyphens in config keys given on the command line. Aug 4, 2024
@cmkobel cmkobel marked this pull request as ready for review August 4, 2024 14:16
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coderabbitai bot commented Aug 13, 2024 •
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Walkthrough

The recent changes enhance the parse_config function in the snakemake/cli.py file by updating the regular expression used to validate configuration keys. The new regex allows for hyphens in key names, expanding the range of valid formats and improving flexibility in configuration entry. This adjustment aims to accommodate diverse naming requirements in configuration files.

Changes

File Change Summary
snakemake/cli.py Modified the regex in parse_config to allow hyphens in configuration keys, enhancing flexibility.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant CLI
    participant ConfigParser

    User->>CLI: Submit configuration
    CLI->>ConfigParser: Parse configuration
    ConfigParser-->>CLI: Validate keys with regex
    CLI-->>User: Return success/failure
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Poem

In the meadow, the rabbit hops,
With keys that dance and never stop.
Hyphens now join the joyful spree,
Configs are free, as they ought to be!
So let's all cheer, with a little twitch,
For flexible keys, without a hitch! 🐇✨

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@johanneskoester johanneskoester enabled auto-merge (squash) August 13, 2024 09:54
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sonarqubecloud bot commented Aug 13, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@johanneskoester johanneskoester merged commit b70c0db into snakemake:main Aug 13, 2024
@github-actions github-actions bot mentioned this pull request Aug 13, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Aug 13, 2024
@github-actions
chore(main): release 8.17.0 (#2960)
7e2d075 
🤖 I have created a release *beep* *boop*
---


##
[8.17.0](v8.16.0...v8.17.0)
(2024-08-13)


### Features

* fix job rate limiting with --max-jobs-per-second and introduce the
more flexible --max-jobs-per-timespan
([#3010](#3010))
([9c31257](9c31257))


### Bug Fixes

* Allow hyphens in config keys given on the command line.
([#2998](#2998))
([b70c0db](b70c0db))
* allowing trailing '+' in name patterns
([#3002](#3002))
([59150d3](59150d3))
* print message if not yet enough resources for executing further jobs
([b8df036](b8df036))
* unawaited coroutine sanitize_local_storage_copies
([#2972](#2972))
([715c572](715c572))


### Documentation

* Change sha256 checksum in docs to more realistic example
([#2987](#2987))
([16a5cf2](16a5cf2))
* Make it more clear that the cluster commands now require a plugin
([#2976](#2976))
([74134cf](74134cf))
* Update installation.rst to recommend Miniforge instead of Mambaforge
([#2975](#2975))
([0fc7619](0fc7619))
* use plain monospace font instead of theme default that changes &gt;=
into ≥
([cc17fc1](cc17fc1))

---
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>
This was referenced Aug 13, 2024
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@coderabbitai coderabbitai bot mentioned this pull request Sep 9, 2024
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@coderabbitai coderabbitai bot mentioned this pull request Mar 10, 2025
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@durr1602 durr1602 mentioned this pull request Jan 6, 2026
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