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base repository: snakemake/snakemake
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base: v8.11.0
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head repository: snakemake/snakemake
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compare: v8.11.1
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  • 10 commits
  • 14 files changed
  • 10 contributors

Commits on Apr 26, 2024

  1. Configuration menu
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Commits on Apr 28, 2024

  1. fix: check template rendering output for leaked input file paths (#2850)

    <!--Add a description of your PR here-->
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] 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).
    johanneskoester authored Apr 28, 2024
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  2. fix: small typo in error (#2853)

    <!--Add a description of your PR here-->
    This is just a small typo fix. 
    Working on a fix for
    snakemake/snakemake-executor-plugin-kubernetes#19
    and eventually ended up at the following error when deploying to
    kubernetes:
    ```
    Error: Error when applying default storage provider gcs to upload workflow sources. {query_validity}
    ```
    Fixing this here so the error is more clear since it looks like
    kubernetes uses the docker container from main.
    jjjermiah authored Apr 28, 2024
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  3. docs: fix typo and link for RO Crate (#2851)

    Fixes a typo that breaks the link and link text for RO Crate in the
    docs.
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [ ] **N/A** The PR contains a test case for the changes or the changes
    are already covered by an existing test case.
    * [x] 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).
    sdruskat authored Apr 28, 2024
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  4. fix: return set instead of list when just --quiet (#2829)

    ### Description
    
    Fixes #2825. `parse_quietness` should return a set since that is what
    `setup_logger()` expects.
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] 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).
    cademirch authored Apr 28, 2024
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  5. fix: replace pkg_resources for python 3.12 (#2831)

    ### Description
    
    Follow up to #2312, Python 3.12 also
    [removed](https://docs.python.org/3.12/whatsnew/3.12.html#removed)
    bundled `setuptools` (aka `pkg_resources`)
    
    ### QC
    
    <!-- Make sure that you can tick the boxes below. -->
    
    - [ ] 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).
    
    Co-authored-by: Johannes Köster <[email protected]>
    branchv and johanneskoester authored Apr 28, 2024
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  6. fix: Prevent binary log files to crash snakemake execution with `show…

    …-failed-logs` (#2827)
    
    ### Description
    
    As described in #2826 currently the whole snakemake execution crashes if
    a log file is binary and `show-failed-logs` is used.
    
    This fix prevents the crash by capturing the `UnicodeDecodeError` and
    returning an error message that the log file is not a text instead.
    
    ### QC
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] 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).
    
    ---------
    
    Co-authored-by: Vito Zanotelli <[email protected]>
    votti and Vito Zanotelli authored Apr 28, 2024
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Commits on Apr 29, 2024

  1. fix: omit norun jobs when determining remote storage input file retri…

    …eval (#2854)
    
    <!--Add a description of your PR here-->
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] 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).
    johanneskoester authored Apr 29, 2024
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  2. fix: use keyword arguments in _IOFile.open (#2847)

    fixes #2846
    
    Previously, keword arguments to `.open` were not actually used leading
    to unexpected (by me) behaviour. I don't think the documentation needs
    to change to reflect this, because it's what one would expect in the
    first place.
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [ ] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] 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).
    
    ---------
    
    Co-authored-by: Johannes Köster <[email protected]>
    J-Wall and johanneskoester authored Apr 29, 2024
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  3. chore(main): release 8.11.1 (#2849)

    🤖 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>
    github-actions[bot] authored Apr 29, 2024
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