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fix: expand environment variables in --remote-job-local-storage-prefix within the remote job, not the main snakemake job #3222

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merged 1 commit into from
Nov 29, 2024
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fix: expand environment variables in --remote-job-local-storage-prefix within the remote job, not the main snakemake job #3222

merged 1 commit into from
Nov 29, 2024

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johanneskoester
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@johanneskoester johanneskoester commented Nov 29, 2024 •
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fixes #3049, snakemake/snakemake-storage-plugin-fs#22

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

    • No new features introduced.

  • Bug Fixes

    • Clarified help text for the --remote-job-local-storage-prefix argument.

  • Chores

    • Minor formatting adjustments and removal of unnecessary comments in the argument parser.

@johanneskoester
fix: expand environment variables given to --remote-job-local-storage…
cf27db7 
…-prefix within the remote job, not the main snakemake job
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coderabbitai bot commented Nov 29, 2024 •
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📝 Walkthrough

Walkthrough

The changes in this pull request modify the argument parser in the snakemake/cli.py file, specifically updating the type of the --remote-job-local-storage-prefix argument. The type was simplified from maybe_base64(expandvars(Path)) to maybe_base64(Path), eliminating unnecessary environment variable expansion. Additionally, the help text was revised to clarify the context of environment variable expansion. Minor formatting changes and the removal of extraneous comments were also made, but no new features were introduced, nor were any existing features removed.

Changes

File Change Summary
snakemake/cli.py Updated argument type for --remote-job-local-storage-prefix from maybe_base64(expandvars(Path)) to maybe_base64(Path); revised help text; minor formatting adjustments and comment removals.

Assessment against linked issues

Objective Addressed Explanation
$SLURM_JOB_ID not set correctly in remote-job-local-storage-prefix when running snakemake in a SLURM job context (3049) ✅

Possibly related PRs

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Reviewing files that changed from the base of the PR and between dea213d and cf27db7.

📒 Files selected for processing (1)
  • snakemake/cli.py (1 hunks)
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snakemake/cli.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
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🔇 Additional comments (1)
snakemake/cli.py (1)

1435-1441: LGTM! The changes correctly fix environment variable expansion timing.

The modification to remove expandvars from the argument type and update the help text is the right approach. This ensures that environment variables in the --remote-job-local-storage-prefix are expanded within the remote job context rather than prematurely in the parent job. This is particularly important for variables like $SLURM_JOB_ID that need to reflect the remote job"s environment.

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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 SonarQube Cloud

This was referenced Nov 29, 2024
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@johanneskoester johanneskoester changed the title fix: expand environment variables given to --remote-job-local-storage-prefix within the remote job, not the main snakemake job fix: expand environment variables in --remote-job-local-storage-prefix within the remote job, not the main snakemake job Nov 29, 2024
@johanneskoester johanneskoester merged commit 59c86a4 into main Nov 29, 2024
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@johanneskoester johanneskoester deleted the fix/envvar-expand-remote-job branch November 29, 2024 12:28
@github-actions github-actions bot mentioned this pull request Nov 29, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Nov 29, 2024
@github-actions
chore(main): release 8.25.5 (#3223)
45cb082 
🤖 I have created a release *beep* *boop*
---


##
[8.25.5](v8.25.4...v8.25.5)
(2024-11-29)


### Bug Fixes

* expand environment variables in --remote-job-local-storage-prefix
within the remote job, not the main snakemake job
([#3222](#3222))
([59c86a4](59c86a4))

---
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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