fix: Prevent binary log files to crash snakemake execution with show-failed-logs#2827
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johanneskoester merged 2 commits intosnakemake:mainfrom Apr 28, 2024
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April 22, 2024 08:42
This replicates snakemake#2826 Unfortunately this test seems to currently crush the pytest test execution when failing. Given that it should not fail any more I think this may be acceptable.
Previously a binary log file would cause `show_logs` to crash the whole snakemake workflow execution with a `UnicodeDecodeError`. Closes snakemake#2826
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@test: I am not extremely happy about the test: currently the test is more on the integration test level, so I think it may be better to also add a unittest for |
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Sure, a follow-up PR in that direction would be appreciated. Maybe it would need synchronization with #2830 |
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🤖 I have created a release *beep* *boop* --- ## [8.11.1](v8.11.0...v8.11.1) (2024-04-29) ### Bug Fixes * check template rendering output for leaked input file paths ([#2850](#2850)) ([433302e](433302e)) * do not distinguish between local and remote rules in dryrun ([74b99ec](74b99ec)) * omit norun jobs when determining remote storage input file retrieval ([#2854](#2854)) ([37a7c7f](37a7c7f)) * Prevent binary log files to crash snakemake execution with `show-failed-logs` ([#2827](#2827)) ([8a80bda](8a80bda)) * replace pkg_resources for python 3.12 ([#2831](#2831)) ([ac144fc](ac144fc)) * return set instead of list when just --quiet ([#2829](#2829)) ([eeb57e2](eeb57e2)) * small typo in error ([#2853](#2853)) ([325a715](325a715)) * use keyword arguments in `_IOFile.open` ([#2847](#2847)) ([50c84dc](50c84dc)) ### Documentation * fix typo and link for RO Crate ([#2851](#2851)) ([cec0041](cec0041)) --- 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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Description
As described in #2826 currently the whole snakemake execution crashes if a log file is binary and
show-failed-logsis used.This fix prevents the crash by capturing the
UnicodeDecodeErrorand returning an error message that the log file is not a text instead.QC
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).