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fix: small bug in snakemake.executors #1440

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merged 1 commit into from Mar 1, 2022
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holtgrewe
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@holtgrewe holtgrewe commented Feb 28, 2022

Description

Fixing an issue where actually sys.stdout should have been used.

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).

@holtgrewe holtgrewe requested a review from johanneskoester as a code owner Feb 28, 2022
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holtgrewe commented Mar 1, 2022

Failure is unrelated and points towards a wrong or out of date assumption regarding temporary file creation @johanneskoester .

============================= test session starts ==============================
platform linux -- Python 3.9.10, pytest-7.0.1, pluggy-1.0.0 -- /usr/share/miniconda/envs/snakemake/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/snakemake/snakemake
plugins: requests-mock-1.9.3, cov-3.0.0
collecting ... collected 3 items

tests/test_google_lifesciences.py::test_google_lifesciences FAILED

=================================== FAILURES ===================================
___________________________ test_google_lifesciences ___________________________

    @google_credentials
    def test_google_lifesciences():
        bucket_name = "***-%s" % next(tempfile._get_candidate_names())
>       create_google_storage(bucket_name)

tests/test_google_lifesciences.py:57: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/test_google_lifesciences.py:51: in create_google_storage
    return client.create_bucket(bucket_name)
/usr/share/miniconda/envs/snakemake/lib/python3.9/site-packages/google/cloud/storage/client.py:934: in create_bucket
    bucket = self._bucket_arg_to_bucket(bucket_or_name)
/usr/share/miniconda/envs/snakemake/lib/python3.9/site-packages/google/cloud/storage/client.py:699: in _bucket_arg_to_bucket
    bucket = Bucket(self, name=bucket_or_name)
/usr/share/miniconda/envs/snakemake/lib/python3.9/site-packages/google/cloud/storage/bucket.py:609: in __init__
    name = _validate_name(name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

name = '***-dfvq2hu_'

    def _validate_name(name):
        """Pre-flight ``Bucket`` name validation.
    
        :type name: str or :data:`NoneType`
        :param name: Proposed bucket name.
    
        :rtype: str or :data:`NoneType`
        :returns: ``name`` if valid.
        """
        if name is None:
            return
    
        # The first and last characters must be alphanumeric.
        if not all([name[0].isalnum(), name[-1].isalnum()]):
>           raise ValueError("Bucket names must start and end with a number or letter.")
E           ValueError: Bucket names must start and end with a number or letter.

@holtgrewe holtgrewe changed the title Fixing small bug in snakemake.executors fix: small bug in snakemake.executors Mar 1, 2022
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sonarcloud bot commented Mar 1, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@johanneskoester johanneskoester merged commit 6e64292 into main Mar 1, 2022
7 checks passed
@johanneskoester johanneskoester deleted the holtgrewe-patch-1 branch Mar 1, 2022
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holtgrewe commented Mar 1, 2022

@johanneskoester could I get a patch release with this? ;-) my Slurm controller server would be very grateful

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2 participants