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fix: create potentially missing .snakemake folder in case of very long command lines for spawned jobs#3894

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johanneskoester merged 1 commit intomainfrom
huge-command-shadow-minimal
Jan 8, 2026
Merged

fix: create potentially missing .snakemake folder in case of very long command lines for spawned jobs#3894
johanneskoester merged 1 commit intomainfrom
huge-command-shadow-minimal

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@Hocnonsense Hocnonsense commented Dec 20, 2025 •
edited by coderabbitai Bot
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will fix #3891 by force to create the .snakemake folder for the script

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

  • Bug Fixes

    • Enhanced robustness when executing shell commands with very long argument strings by ensuring proper directory initialization.

  • Tests

    • Added test coverage for handling extremely long command-line arguments in shadow mode.

✏️ Tip: You can customize this high-level summary in your review settings.

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coderabbitai Bot commented Dec 20, 2025 •
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📝 Walkthrough

Walkthrough

When shell commands exceed the maximum argument length, the code now ensures the .snakemake directory exists before creating temporary script files. This prevents failures when using shadow: "minimal" with large commands, and includes a test case demonstrating the fix.

Changes

Cohort / File(s) Summary
Shell command length handling
src/snakemake/shell.py		 Added .snakemake directory creation before writing temporary script files when shell command length exceeds MAX_ARG_LEN.
Shadow directive test coverage
tests/test_shadow/Snakefile		 Added minimal_huge_cmd rule generating test output with large concatenated shell command under shadow: "minimal", and updated minimal_ok rule to depend on new test output.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

  • src/snakemake/shell.py: Verify the directory creation logic correctly handles the .snakemake path and doesn't introduce race conditions or permission issues.
  • tests/test_shadow/Snakefile: Confirm the new rule follows established testing patterns and the huge_cmd variable generates a command exceeding system argument limits.
🚥 Pre-merge checks | ✅ 4 | ❌ 1
❌ Failed checks (1 warning)
Check name Status Explanation Resolution
Docstring Coverage ⚠️ Warning Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. You can run @coderabbitai generate docstrings to improve docstring coverage.
✅ Passed checks (4 passed)
Check name Status Explanation
Description check ✅ Passed Description includes the issue reference (#3891) and explains the fix (forcing .snakemake folder creation). Both QC checkboxes are marked complete, indicating test coverage and documentation assessment.
Linked Issues check ✅ Passed Changes directly address issue #3891 by ensuring .snakemake directory exists before creating temporary scripts [#3891], and include a test case with shadow 'minimal' and large commands [#3891].
Out of Scope Changes check ✅ Passed All changes are scoped to fixing issue #3891: the shell.py modification handles temporary directory creation, and the test additions verify the fix works with shadow 'minimal'.
Title check ✅ Passed The title accurately and specifically describes the main change: creating the .snakemake folder before handling very long command lines for spawned jobs.

✏️ Tip: You can configure your own custom pre-merge checks in the settings.

✨ Finishing touches
  • 📝 Generate docstrings

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@johanneskoester johanneskoester changed the title fix: huge command line in shadow: "minimal" fix: create potentially missing .snakemake folder in case of very long command lines for spawned jobs Jan 8, 2026
@johanneskoester johanneskoester merged commit 4b431dd into main Jan 8, 2026
61 checks passed
@johanneskoester johanneskoester deleted the huge-command-shadow-minimal branch January 8, 2026 16:28
@snakemake-bot snakemake-bot mentioned this pull request Jan 8, 2026
Merged
johanneskoester pushed a commit that referenced this pull request Jan 8, 2026
@snakemake-bot
chore(main): release 9.14.6 (#3893)
0130fc8 
🤖 I have created a release *beep* *boop*
---


##
[9.14.6](v9.14.5...v9.14.6)
(2026-01-08)


### Bug Fixes

* create local clone of git repos for source files from hosting
providers ([#3643](#3643))
([d2f8aba](d2f8aba))
* create potentially missing .snakemake folder in case of very long
command lines for spawned jobs
([#3894](#3894))
([4b431dd](4b431dd))
* make ilp solver enumeration lazy
([#3900](#3900))
([30e1509](30e1509))
* Prevent broken report_href links by using deterministic report IDs
with fixed prefix length
([#3889](#3889))
([6d8f4d8](6d8f4d8))
* refactor LoggerManager setup and scope
([#3851](#3851))
([f46d904](f46d904))
* yield proper error message in case a local git source file is not
retrievable
([#3892](#3892))
([ed79cae](ed79cae))


### Documentation

* explain how to pass nested config via CLI
([#3885](#3885))
([9d8c539](9d8c539))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
@Hocnonsense Hocnonsense self-assigned this Mar 18, 2026
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Successfully merging this pull request may close these issues.

Bug: edge case when there is a huge shell command with shadow: 'minimal'

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@Hocnonsense @johanneskoester