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Hamming distance implementation with Numba #512

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Aug 19, 2024
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bad62d8
take static methods out of tcrdist
felixpetschko Apr 29, 2024
72565bf
made _tcrdist_mat a normal class method
felixpetschko Apr 29, 2024
add8e7f
parent method NumbaDistanceCalculator extracted
felixpetschko Apr 29, 2024
e9c0642
numba version of hamming distance implemented
felixpetschko Apr 29, 2024
68e0493
hamming numba tests passed and reference test added
felixpetschko Apr 29, 2024
ef0fa7d
hamming numba distance calculator implemented and tested
felixpetschko Apr 29, 2024
0b15f8b
n_jobs parameter handling done in NumbaDistanceCalculator superclass
felixpetschko Apr 29, 2024
46bfc14
documentation adapted
felixpetschko Apr 29, 2024
e339e14
removed unnecessary import
felixpetschko Apr 29, 2024
7da4519
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 29, 2024
82b0259
hamming distance with numba parallelization implemented
felixpetschko May 2, 2024
b2d28d3
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko May 2, 2024
249e626
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 2, 2024
2fccc6a
imports fixed
felixpetschko May 2, 2024
9ee1a2b
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko May 2, 2024
a68ab53
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 2, 2024
d68a10b
implemented parallelization with n_jobs and n_blocks for hamming and …
felixpetschko May 6, 2024
0005e63
performance optimization for hamming and tcrdist
felixpetschko May 6, 2024
6f16a3e
more documentation added
felixpetschko May 6, 2024
6b32311
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko May 6, 2024
ad13f52
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 6, 2024
08ad838
documentation adapted
felixpetschko May 7, 2024
a8d9846
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko May 7, 2024
b86030c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 7, 2024
2fb8254
documentation adapted
felixpetschko May 7, 2024
bb0f430
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko May 7, 2024
80ae271
signature of _calc_dist_mat_block changed
felixpetschko Aug 7, 2024
91c1dea
the alphabet for the hamming distance is now the unique characters oc…
felixpetschko Aug 7, 2024
899e2eb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 7, 2024
a0627b4
Merge branch 'main' into numba_hamming
grst Aug 8, 2024
d5dbe8e
normalized hamming distance added
felixpetschko Aug 9, 2024
5a6ef24
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 9, 2024
3060314
renaming test
felixpetschko Aug 9, 2024
6b2b025
histogram creation for hamming distance added
felixpetschko Aug 9, 2024
fc24ac5
merge
felixpetschko Aug 9, 2024
5670a84
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 9, 2024
53d542e
refactored
felixpetschko Aug 9, 2024
fe31be7
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 9, 2024
59a3c9d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 9, 2024
c1d9d51
hamming histogram adjustments
felixpetschko Aug 9, 2024
ce4f3f3
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 9, 2024
5419d0b
reference test cases added for normalized hamming and hamming histogram
felixpetschko Aug 11, 2024
effee43
Merge branch 'main' into numba_hamming
grst Aug 13, 2024
da07aff
Update src/scirpy/ir_dist/metrics.py
felixpetschko Aug 15, 2024
a934743
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 15, 2024
c0e0381
test cases for normalized hamming and hamming histogram adapted
felixpetschko Aug 15, 2024
6a220a7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 15, 2024
8683ab6
docstring for normalized hamming distance and tcrdist distance added
felixpetschko Aug 15, 2024
bfe35fd
adapted default parameters and tests for n_jobs and n_blocks
felixpetschko Aug 15, 2024
a91130a
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 15, 2024
15c04bd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 15, 2024
d45ab64
test_sequence_dist_all_metrics adaptions
felixpetschko Aug 15, 2024
1730b3f
n_jobs default value set to -1
felixpetschko Aug 15, 2024
8f18210
docstring of ir_dist for n_jobs adapted
felixpetschko Aug 15, 2024
d62c1c8
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 15, 2024
8cfc1c6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 15, 2024
efbc37b
docstring change to test cicd pipeline
felixpetschko Aug 15, 2024
ae3121a
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 15, 2024
9398d7c
docstring for n_jobs of _ir_dist changed
felixpetschko Aug 15, 2024
66d6f70
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 15, 2024
afc03ba
docstring for n_jobs of _ir_dist changed
felixpetschko Aug 15, 2024
def8b1e
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 15, 2024
dc8dae4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 15, 2024
758feed
moved histogram creation to parent class of hamming distance calculator
felixpetschko Aug 16, 2024
04d0db7
histogram computation adaptions
felixpetschko Aug 16, 2024
b7ed4ca
test case test_tcrdist_histogram_not_implemented added
felixpetschko Aug 16, 2024
d40e193
documentation for histogram adapted
felixpetschko Aug 16, 2024
f2c32af
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 16, 2024
54c0cc2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 16, 2024
b16c705
reformatted doc string
felixpetschko Aug 16, 2024
3aab445
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 16, 2024
2419bfb
handling of symmetric matrices with respect to histogram variable cha…
felixpetschko Aug 16, 2024
e516a86
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 16, 2024
20c14eb
retrieval of usable cpus for numba adapted
felixpetschko Aug 16, 2024
7c2cc06
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 16, 2024
f566211
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 16, 2024
f68dd70
more documentation for histogram and (hamming) normalize added
felixpetschko Aug 19, 2024
3955eb1
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scir…
felixpetschko Aug 19, 2024
d9dd20e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 19, 2024
edf6900
Update CHANGELOG and tweak docs
grst Aug 19, 2024
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