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snakemake / snakeface

The snakemake interface, currently works like a notebook (under development)
https://snakeface.readthedocs.io/
Mozilla Public License 2.0
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Refactoring structure to keep settings in user home #22

Open vsoch opened 3 years ago

vsoch commented 3 years ago

This is a quick refactor to address some problems discussed in #21. I think the issue this user is facing is that the install was messy - we shouldn't require the user to clone and install locally, it should just work with pip install snakeface, and then we write whatever we need to the user home. This is optimized for the notebook use case, which (since we don't have other plugins for auth yet) I think is safe to focus on for now. This means that:

I think we could improve things by using ruamel.yaml (which preserves comments) but this should be good for a first. shot.

Signed-off-by: vsoch vsoch@users.noreply.github.com

iamh2o commented 3 years ago

snakeface init created the ~/.snakeface dir with the expected resources, specifically settings.yml.

But, when I edit the domain_host and domain_port, they do not get used when running snakeface again :-/ i can still set --port on the command line, but not change the IP

vsoch commented 3 years ago

Should be all set https://github.com/snakemake/snakeface/pull/22/commits/d27d59fd3aaecddcbba39b5299dc3373522d6173.

iamh2o commented 3 years ago

hi @vsoch -- Long time ! Sorry, for such a lag. But yes, it works fine now with init and editing the user home settings.yaml :-)

I did run via python 3.9, and had a problem with the pgsql binary that I could only fix with: mamba install -n SNKF2 psycopg2-binary

I also attempted to correct 2 dead links in the readme, but did not have permissions- you'll see them.

Thanks- I should have a little time to play around some more soon.

vsoch commented 2 years ago

So - you are ready to merge this? Or you'd like something else fixed?