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Reimplementation of cython code in numba - #7

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hsmaan wants to merge 30 commits into
mainfrom
scib_metrics
Open

Reimplementation of cython code in numba #7
hsmaan wants to merge 30 commits into
mainfrom
scib_metrics

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@hsmaan

@hsmaan hsmaan commented Apr 16, 2023

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  • Removed cython implementation and re-implemented expected mutual information using numba (utils/_emi.py)
  • Results are stable compared to the cython implementation (tested in scib_metrics_num_stab_testing branch)
  • Added non-install dependencies for notebooks in first cell
  • Added pre-commit configuration and all tests passing

hsmaan and others added 30 commits November 15, 2022 14:25
@hsmaan
removed notebooks and experiments
8fc594b
@hsmaan
modified dependencies to be minimal and non-restrictive
708690a
@hsmaan
passed assertions on new deps - removed completeness since invalid
829550b
@adamgayoso
Update __init__.py
4993b9a
@adamgayoso
Rename _emi_cython.pyx to _emi.py
5320536
@adamgayoso
Update _emi.py
6cd3f56
@adamgayoso
Update pyproject.toml
12d38b0
@adamgayoso
Update pyproject.toml
a08c62a
@adamgayoso
Update _emi.py
f7c6764
@adamgayoso
Merge branch 'scib_metrics' into emi_numba
99f201c
@adamgayoso
Update pyproject.toml
882de75
@hsmaan
removed unecessary imports
123a9af
@adamgayoso
Update _emi.py
f4faf33
@adamgayoso
Update _emi.py
f05df22
@hsmaan
replaced gammaln calls with lgamma (scipy.special not supported)
9fe1ee5
@hsmaan
typing fix
e4a804e
@hsmaan
typing fix (corrected)
12b8cf9
@adamgayoso
cleanup and fix numba
f1a9b36
@adamgayoso
loop indexing
7e410fa
@adamgayoso
update gitignore
2b2280b
@adamgayoso
proper poetry versioning
239b9de
@adamgayoso
amortize
25d89da
@hsmaan
cleanup files + tests
e5b5954
@hsmaan
Merge pull request #6 from adamgayoso/emi_numba
d6f2817 
Emi using numba and package cleanup.
@hsmaan
black/flake8 formatted
a2ae3a4
@hsmaan
Merge branch 'main' into scib_metrics
dc4a87a
@hsmaan
deleted hanging notebook
d3e0554
@hsmaan
readding prev notebook + pip installs for missing deps
1a29338
@hsmaan
black formatting
ea02c68
@hsmaan
added pre-commit
90bb6b3
@hsmaan hsmaan added the refactor Refactoring code for a feature or implementation label Apr 16, 2023
@hsmaan hsmaan self-assigned this Apr 16, 2023
@hsmaan hsmaan linked an issue Apr 16, 2023 that may be closed by this pull request
Cleanup package for dependency in scib-metrics #5
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This was referenced Apr 16, 2023
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refactor Refactoring code for a feature or implementation

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Cleanup package for dependency in scib-metrics

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@hsmaan @adamgayoso