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rpetit3 / fastq-dl

Download FASTQ files from SRA or ENA repositories.
MIT License
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Python 3.13 - ModuleNotFoundError: No module named 'pipes' #33

Open rpetit3 opened 3 weeks ago

rpetit3 commented 3 weeks ago

I will need to make some fixes on the bioconda recipe. But in case you get the following erro

ModuleNotFoundError: No module named 'pipes'

The solution is to downgrade your Python version to 3.12 or earlier.

mbhall88 commented 3 weeks ago

Weird. We don't have a dependency on a module called pipes do we?

rpetit3 commented 3 weeks ago

Yep we do (and its not in the pyproject .toml which is another issue itself haha) , https://github.com/rpetit3/fastq-dl/blob/master/fastq_dl/utils.py#L11

I've submitted a PR here https://github.com/conda-forge/executor-feedstock/pull/8 , based on this PR https://github.com/xolox/python-executor/pull/22

Executor is a package I've used for years for simplifying the usage of subprocess. We can reconsider its usage going forward, but if the PR fixes it (substitutes pipes for shlex) then I think we just leave it as is.

mbhall88 commented 2 weeks ago

yeah I was going to say subprocess, which is in the standard library is pretty easy to work with so I think we could very easily transition to that.