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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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Right now `looper.pep_config` isn't working if the path given is a pephub path. #424

Closed donaldcampbelljr closed 6 months ago

donaldcampbelljr commented 8 months ago

I believe that, during loading via the function read_looper_config_file, the attribute pep_config becomes config_file in the returned dictionary: https://github.com/pepkit/looper/blob/6523e4b525570aa0f7b3013d19a049d1866a28df/looper/utils.py#L472-L476

which is why the pephub path is not accessible later via looper.pep_config

donaldcampbelljr commented 8 months ago

Actually, when building the looper namespace, it appears as though: settings["pep_config"] = self.prj.config_file

In testing hello_looper with pephub, this does not appear to actually point to the config file (.looper_pephub.yaml) but rather, the directory containing the config file.

Either way looper.pep_config should be accessible but it may not be pointing to the proper file.

donaldcampbelljr commented 8 months ago

OK, I found where this was not being set (during Project creation) and have fixed it to properly point to the pephub registry path via looper.pep_config