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Add setup.py, python API#1

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CFGrote wants to merge 3 commits intoFangfeiLi05:masterfrom
mpievolbio-scicomp:master
Open

Add setup.py, python API#1
CFGrote wants to merge 3 commits intoFangfeiLi05:masterfrom
mpievolbio-scicomp:master

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@CFGrote
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@CFGrote CFGrote commented Jun 19, 2020

This PR adds a basic setup.py for easy installation via pip install . from the repo's root. This also allows installation of pyfitseq as a dependency in other python packages via a requirements.py (pip) or environments.yml (conda).
pyfitseq.py and evo_simulator.py are moved to the src directory PyFitSeq/.

The second change affects the signature of pyfitseq.main(). With this change, one can run pyfitseq directly from within a python script or notebook without having to exit to the terminal. Output data from pyfitseq are returned as a pandas.DataFrame to the caller and written to csv file if requested.

In a python script or notebook, one would:

from PyFitSeq import pyfitseq
...

estimates = pyfitseq.main(input=..., t_seq=[0, 1, 2, ...], ...)

@darachm
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darachm commented May 8, 2021

@FangfeiLi05

@darachm
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darachm commented Sep 14, 2021

@FangfeiLi05 I just want to point out that this is not yet merged... do you want me to help merge the cherry-picked edits for the setup.py ??

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darachm commented Oct 13, 2021

@FangfeiLi05 I would recommend rejecting this. I am making another pull request that fetches from Carsten's repo to cherry-pick the setup.py change you told me you wanted, then you can pull that request. I believe/hope this will still reflect Carsten's writing of the setup.py file.....

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CFGrote commented Oct 14, 2021 via email

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3 participants