raphael-group / chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
BSD 3-Clause "New" or "Revised" License
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Minor restructuring/tests/GH Actions integration #18

Closed vineetbansal closed 3 years ago

vineetbansal commented 3 years ago

In the process of testing chisel code to be able to tease out the phase processing, I've had to make minor adjustments to the folder structure and add some basic tests. A lot of this is very similar to what we did for HATCHet, except that in the case of chisel, I've also rooted the source tree under a top-level src/chisel folder.

Until now, chisel, when installed, would show up in the site-packages folder as 2 independent folders - bin, and src. These are somewhat dangerous names to go with, and they will likely interfere with other packages installed in the same environment as chisel. This also means that any scripts using chisel would have to do from bin import .. or from src import .. which is again not very robust long-term. With this restructuring, one can simply do a from chisel..bin import .., which we in fact do in these newly-introduced tests.

Nothing should break in the documentation or the tests, but this PR should probably stay open till the Github Actions tests pass successfully.