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fix: problem with spaces in path#3236

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johanneskoester merged 4 commits intosnakemake:mainfrom
kjohnsen:main
Dec 21, 2024
Merged

fix: problem with spaces in path#3236
johanneskoester merged 4 commits intosnakemake:mainfrom
kjohnsen:main

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@kjohnsen kjohnsen commented Dec 19, 2024 •
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Fixes #3235
Goes together with snakemake/snakemake-interface-executor-plugins#79
This PR updates tests to catch the bug (should break at least test_path_with_spaces and test_with_parentheses and snakemake/snakemake-interface-executor-plugins#79 actually fixes it

Summary by CodeRabbit

Summary by CodeRabbit

  • New Features
    • Introduced a new rule that generates an output file with a predefined string.
  • Tests
    • Added a test case to verify the handling of paths containing spaces.
    • Enhanced temporary directory naming for clarity during test execution.

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coderabbitai bot commented Dec 19, 2024 •
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📝 Walkthrough
📝 Walkthrough

Walkthrough

A new rule named default has been introduced in the Snakefile located in a directory with spaces. This rule specifies an output file named test.out and includes a run block that writes the string "hello there" to the output file. Additionally, a new test case has been added to verify the handling of paths containing spaces, ensuring that the system can process such paths correctly.

Changes

File Change Summary
tests/test_path with spaces/Snakefile Added default rule that writes "hello there" to test.out
tests/tests.py Added test case run(dpath("test_path with spaces")) to test path with spaces
tests/common.py Modified run function to include original_dirname for temp directory naming

Sequence Diagram

sequenceDiagram
    participant Test as Test Runner
    participant Snakefile as Snakefile
    participant File as Output File

    Test->>Snakefile: Execute default rule
    Snakefile->>File: Open test.out
    Snakefile->>File: Write "hello there"
    Snakefile->>File: Close file
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Assessment against linked issues

Objective Addressed Explanation
Ensure run directive handles paths with spaces correctly (#3235) ✅
Validate that the Snakefile can be executed without errors in paths with spaces (#3235) ✅
📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between d158320 and 75d7032.

📒 Files selected for processing (1)
  • tests/tests.py (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • tests/tests.py

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@kjohnsen kjohnsen changed the title add test Fix problem with spaces and parentheses in path Dec 19, 2024
@kjohnsen kjohnsen marked this pull request as draft December 19, 2024 18:09
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kjohnsen commented Dec 19, 2024

🚨Important🚨 the bug only shows up when I run snakemake from the command line; the automated test doesn't fail. i.e., this works:

pytest pytest tests/tests.py::test_path_with_spaces

but this doesn't:

snakemake --snakefile tests/test_path\ with\ spaces/Snakefile

I discovered this because I saw a pre-existing test should have covered my issue: test (with parenthese's). It passes via pytest but fails with SyntaxError when running from the terminal.

@kjohnsen kjohnsen changed the title Fix problem with spaces and parentheses in path Fix problem with spaces in path and inaccurate tests Dec 19, 2024
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kjohnsen commented Dec 19, 2024

The previous commit adds the test folder name to the temp folder. Now the parentheses and space tests do fail when I run from pytest

@kjohnsen kjohnsen changed the title Fix problem with spaces in path and inaccurate tests fix: problem with spaces in path Dec 19, 2024
@kjohnsen kjohnsen mentioned this pull request Dec 20, 2024
Merged
@kjohnsen kjohnsen marked this pull request as ready for review December 20, 2024 18:14
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sonarqubecloud bot commented Dec 21, 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 SonarQube Cloud

@johanneskoester johanneskoester merged commit 2d08c63 into snakemake:main Dec 21, 2024
@github-actions github-actions bot mentioned this pull request Dec 21, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Dec 23, 2024
@github-actions
chore(main): release 8.26.0 (#3229)
2cf0fbc 
🤖 I have created a release *beep* *boop*
---


##
[8.26.0](v8.25.5...v8.26.0)
(2024-12-23)


### Features

* add helpers for deferred input/output etc. item access
([#2927](#2927))
([2cca9bc](2cca9bc))


### Bug Fixes

* convert parameters so they can be serialized
([#2925](#2925))
([9e653fb](9e653fb))
* correct formatting of R preamble
([#2425](#2425))
([5380cae](5380cae))
* fix modification checks for scripts and and notebooks containing
wildcards or params in their paths
([#2751](#2751))
([773568d](773568d))
* Improved handling of missing output files in group job postprocessing,
accounting for temporary files.
([#1765](#1765))
([bac06ba](bac06ba))
* mtime of script or notebook not triggering workflow without metadata
([#3148](#3148))
([e8a0b83](e8a0b83))
* Pass `host` attribute to `GitlabFile` instantiation within class
methods ([#3155](#3155))
([9ef52de](9ef52de))
* problem with spaces in path
([#3236](#3236))
([2d08c63](2d08c63))
* require current yte release which contains an important bug fix for
cases where numpy/pandas data is passed to templates
([#3227](#3227))
([c3339da](c3339da))
* rerun jobs if previously failed but rule was changed afterwards
(thanks to [@laf070810](https://github.com/laf070810) for bringing this
up) ([#3237](#3237))
([1dc0084](1dc0084))
* use relpath for configfiles added to the source archive (thanks to
[@sposadac](https://github.com/sposadac) for the initial solution)
([#3240](#3240))
([bff3844](bff3844))

---
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>
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@github-actions @kjohnsen
chore(main): release 8.26.0 (snakemake#3229)
83cad95 
🤖 I have created a release *beep* *boop*
---


##
[8.26.0](snakemake/snakemake@v8.25.5...v8.26.0)
(2024-12-23)


### Features

* add helpers for deferred input/output etc. item access
([snakemake#2927](snakemake#2927))
([2cca9bc](snakemake@2cca9bc))


### Bug Fixes

* convert parameters so they can be serialized
([snakemake#2925](snakemake#2925))
([9e653fb](snakemake@9e653fb))
* correct formatting of R preamble
([snakemake#2425](snakemake#2425))
([5380cae](snakemake@5380cae))
* fix modification checks for scripts and and notebooks containing
wildcards or params in their paths
([snakemake#2751](snakemake#2751))
([773568d](snakemake@773568d))
* Improved handling of missing output files in group job postprocessing,
accounting for temporary files.
([snakemake#1765](snakemake#1765))
([bac06ba](snakemake@bac06ba))
* mtime of script or notebook not triggering workflow without metadata
([snakemake#3148](snakemake#3148))
([e8a0b83](snakemake@e8a0b83))
* Pass `host` attribute to `GitlabFile` instantiation within class
methods ([snakemake#3155](snakemake#3155))
([9ef52de](snakemake@9ef52de))
* problem with spaces in path
([snakemake#3236](snakemake#3236))
([2d08c63](snakemake@2d08c63))
* require current yte release which contains an important bug fix for
cases where numpy/pandas data is passed to templates
([snakemake#3227](snakemake#3227))
([c3339da](snakemake@c3339da))
* rerun jobs if previously failed but rule was changed afterwards
(thanks to [@laf070810](https://github.com/laf070810) for bringing this
up) ([snakemake#3237](snakemake#3237))
([1dc0084](snakemake@1dc0084))
* use relpath for configfiles added to the source archive (thanks to
[@sposadac](https://github.com/sposadac) for the initial solution)
([snakemake#3240](snakemake#3240))
([bff3844](snakemake@bff3844))

---
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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"Snakefile not found" when path contains a space, using run directive

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@kjohnsen @johanneskoester