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bvalot / pyMLST

whole genome MLST analysis
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Import function - Biopython module deprecated #27

Open marchoeppner opened 4 months ago

marchoeppner commented 4 months ago

Hi,

so I was just going to test out your tool - sounds very useful.

That said, installing the latest version on OSX via Conda yields:

/Users/myuser/miniforge3/envs/pymlst/lib/python3.11/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
Usage: wgMLST import [OPTIONS] DATABASE [SPECIES]...

  Creates a wgMLST DATABASE from an online resource.

  The research can be filtered by adding a SPECIES name.

Options:
  -f, --force             Overwrite alrealdy existing DATABASE
  --prompt / --no-prompt  Do not prompt if multiple choices are found, fail
                          instead.
  -h, --help              Show this message and exit.

I suspect this means that something has to be updated in your code perhaps?

/M

bvalot commented 4 months ago

Hi,

Yes, I correct the code on actual source code as explained here, but I have some other elements I want to change before release on conda.

For now, it is just a warning and the program can be run without problems.

Thanks for your comment.