Python 3.13 - ModuleNotFoundError: No module named 'pipes'

[rpetit3]

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]

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

[rpetit3]

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 conda-forge/executor-feedstock#8 , based on this PR xolox/python-executor#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]

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.

[rpetit3]

Heads up planning to work on dropping the wrapper and just going with subprocess directly

[apcamargo]

I've been using sh for a while now to simplify calling external programs. I guess it could replace Executor.