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Implement fast ZETA test #22

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Implement fast ZETA test #22

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mmagnuski
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@mmagnuski mmagnuski commented May 30, 2024 •
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TODO:

  • > 2 conditions
  • gumbel function (numpy should be fast enough)
  • test against zetapy (results similarity and speedup)
  • high-level API
  • backend to select the numba version
  • function to download the zeta example data
  • cache numba functions
  • clean up numpy and numba code (function and variable names, docstrings, making some functions private etc.)
  • create a test
  • example on same data as zetapy

@mmagnuski
STY: use njit instead of jit(nopython=True)
f49db9f
@mmagnuski
ENH: add numba _monotonic_find_first and _select_spikes
a06f321
@mmagnuski
FIX: compat with new ttest_ind_no_p in borsar (for some reason does n…
6453fb1 
…ot work with xarray
@mmagnuski
ENH: some new numba functions + tests
6ce43f1
@mmagnuski
zeta test, part 1
8126c9c
@mmagnuski
zeta test, part 2, multi-unit
06a5989
@mmagnuski
small changes
ceda829
@mmagnuski
DOC: improve gumbel docstring
f89465d
@mmagnuski
separate compute_pvalues function
c201e27
@mmagnuski
towards unified API for numpy and numba versions
6f15277
@mmagnuski
updates
6f8ef1c
@mmagnuski
ENH: n-condition ZETA for numba
953ac81
@mmagnuski
ENH: make numpy backend working for 2 and n conditions
f76817e
@mmagnuski
ENH: switch to object arrays of trial-level spike arrays in numpy
c7d8e34
@mmagnuski
ENH: add subsample, return reference_times in the dict
613e631
@mmagnuski
DOC: add docstring to ZETA function
588db85
@mmagnuski
small changes
c9787fe
@mmagnuski
STY: rename functions
cb8e774
@mmagnuski
DOC: add some docstrings
ace9049
@mmagnuski
do not subsample by default
ed8156c
@mmagnuski
STY: remove unused functions, improve docstring
0cd4993
@mmagnuski
ENH: function to read the zeta example data
8a733ab
@mmagnuski
ENH: cache numba functions, improve function and variable names
8bd8e97
@mmagnuski
STY: whitespace
c9fc74e
@mmagnuski
FIX TST: fix so that searched 9 is always in the array
75f90cf
@mmagnuski
FIX: better output of _monotonic_find_first when value is not found
7eb94ef
@mmagnuski
small cleanup
723867b
@mmagnuski
FIX, ENH: use var in numba implementation for N-condition cases too
16af2ac
@mmagnuski
TST: add test for ZETA
17e3d81
@mmagnuski
DEV: move pylabianca._zeta.ZETA to pylabianca.selectivity.zeta_test
67f67a9
@mmagnuski
small changes
e16895e
@mmagnuski
STY: rename functions
ed37485
@mmagnuski
DOC: add some docstrings
3e86011
@mmagnuski
do not subsample by default
cf09d56
@mmagnuski
STY: remove unused functions, improve docstring
bd1b139
@mmagnuski
ENH: function to read the zeta example data
fe82bef
@mmagnuski
ENH: cache numba functions, improve function and variable names
8f3ffd6
@mmagnuski
STY: whitespace
e460fad
@mmagnuski
FIX TST: fix so that searched 9 is always in the array
6d34cb2
@mmagnuski
FIX: better output of _monotonic_find_first when value is not found
254bc89
@mmagnuski
small cleanup
e8eade4
@mmagnuski
FIX, ENH: use var in numba implementation for N-condition cases too
0c722d4
@mmagnuski
TST: add test for ZETA
82367a3
@mmagnuski
DEV: move pylabianca._zeta.ZETA to pylabianca.selectivity.zeta_test
00a5de4
@mmagnuski
TST: adapt tests to the move
710df78
@mmagnuski
TST, DEV: reorganize tests
b4b5c27
@mmagnuski
DOC: update whats_new.md
625d89e
@mmagnuski
FIX empirical pvalues calculation
0e92941
@mmagnuski
ENH: make sure each cell has the same permutation structure
0daff30
@mmagnuski
TST: fix tests
875a0f7
@mmagnuski
FIX: event_id can be a single value
774cf39
@codecov Codecov
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codecov bot commented Sep 3, 2024

Codecov Report

Attention: Patch coverage is 73.53952% with 77 lines in your changes missing coverage. Please review.

@@           Coverage Diff           @@
##            main     #22     +/-   ##
=======================================
+ Coverage   64.9%   65.5%   +0.6%     
=======================================
  Files         11      13      +2     
  Lines       3392    3681    +289     
=======================================
+ Hits        2202    2412    +210     
- Misses      1190    1269     +79

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@mmagnuski