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snakemake.io._IOFile.open method doesn't use it's keyword arguments #2846

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J-Wall opened this issue Apr 26, 2024 · 0 comments · Fixed by #2847
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snakemake.io._IOFile.open method doesn't use it's keyword arguments #2846

J-Wall opened this issue Apr 26, 2024 · 0 comments · Fixed by #2847
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@J-Wall
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J-Wall commented Apr 26, 2024

Snakemake version
Checked this issue is in the master branch

Describe the bug

I am trying to open a file (output of a checkpoint rule) using the .open() method while specifying the mode. However, it just gets opened in text mode which leads to an error downstream in my code.

I had a look at the code in the master branch, and the method has call signature

def open(self, mode="r", buffering=-1, encoding=None, errors=None, newline=None):

however, in the body of the function it just calls

f = open(self)

I think this should instead be

f = open(self, mode=mode, buffering=buffering, encoding=encoding, errors=errors, newline=newline)
@J-Wall J-Wall added the bug Something isn't working label Apr 26, 2024
J-Wall added a commit to J-Wall/snakemake that referenced this issue Apr 26, 2024
@J-Wall
use keyword arguments in _IOFile.open
2a7c8d5 
fixes snakemake#2846
@J-Wall J-Wall mentioned this issue Apr 26, 2024
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johanneskoester added a commit that referenced this issue Apr 29, 2024
@J-Wall @johanneskoester
fix: use keyword arguments in _IOFile.open (#2847)
50c84dc 
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 <johannes.koester@tu-dortmund.de>
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fix: use keyword arguments in _IOFile.open J-Wall/snakemake
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