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hpc-carpentry / old-hpc-workflows

Scaling studies on high-performance clusters using Snakemake workflows
https://www.hpc-carpentry.org/old-hpc-workflows/
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Add versions to requirements.txt #20

Open bkmgit opened 2 years ago

bkmgit commented 2 years ago

Adding version of libraries supported and tested on to requirements.txt will make setup easier. It would also allow running CI to check that the scripts used work. This is motivated by dropping of dropping of collections.MutableMapping from Python 3.10 and above, see https://stackoverflow.com/questions/70943244/attributeerror-module-collections-has-no-attribute-mutablemapping

bkmgit commented 2 years ago

Also https://docs.python.org/3/library/collections.abc.html

ocaisa commented 2 years ago

I don't know what to do about this. Where is the requirement for collections coming from (it's not amdahl, unless that is indirectly via mpi4py which is it's only dependency).

ocaisa commented 2 years ago

Ah, it is from https://github.com/carpentries-incubator/hpc-workflows/blob/gh-pages/code/plotcount.py#L8 so that makes me worry less about this. I believe we have a pretty simple use case and we'll need to rewrite that file anyway so I suspect this requirement will disappear.

ocaisa commented 2 years ago

In general, this is a good idea, we should maintain a requirements.txt

bkmgit commented 2 years ago

Tested using Python 3.10.5 with snakemake==7.12.0 matplotlib==3.5.2 numpy==1.23.1 graphviz==0.20.1