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Speed up clonotype distance calculation #470

Merged
merged 63 commits into from
Sep 8, 2024
Merged

Speed up clonotype distance calculation #470

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6dd0e0b
compute_distances new version added
felixpetschko Jan 7, 2024
c90ac96
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 7, 2024
9a1474b
Merge branch 'main' into compute_distances
grst Jan 9, 2024
10f2ffa
Merge branch 'main' of https://github.com/scverse/scirpy into compute…
felixpetschko Aug 11, 2024
e09d33a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 11, 2024
c122273
data type for csr max computation set to int16 to allow negative values
felixpetschko Aug 12, 2024
63211ff
data type also for csr_min set to int16 to allow negative values
felixpetschko Aug 12, 2024
b117aca
raise AssertainError instead of assert False
felixpetschko Aug 13, 2024
39abc5e
matrix shape changed in lookup function
felixpetschko Aug 13, 2024
cf6eb09
array size changed for v-gene and column matching
felixpetschko Aug 13, 2024
af1fd38
naming conventions
felixpetschko Aug 13, 2024
0e325ac
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 13, 2024
f471092
use self._chain_count2 for asymmetric matrix for filter_chain_count
felixpetschko Aug 13, 2024
ae4678d
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Aug 13, 2024
58f05ad
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 13, 2024
6d86d9a
reverse table assignment adjusted in lookup function
felixpetschko Aug 14, 2024
c08d13e
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Aug 14, 2024
86eaab9
changed AssertionError to NotImplementedError
felixpetschko Aug 19, 2024
3c7cc64
removed unnecessary for loop
felixpetschko Aug 19, 2024
719961b
refactored lookup function
felixpetschko Aug 19, 2024
c59119d
refactored lookup function and added docstring
felixpetschko Aug 19, 2024
2ad79b4
adapted docsting of lookup function
felixpetschko Aug 19, 2024
55611cc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 19, 2024
3a76eb1
j_gene matching implemented
felixpetschko Aug 19, 2024
ce59cc3
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Aug 19, 2024
522cf2e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 19, 2024
b1d80cf
fixes typo in j_gene parameter
felixpetschko Aug 19, 2024
840f41e
bind loop variables in function match_gene_segment
felixpetschko Aug 19, 2024
f1a1e3e
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Aug 19, 2024
9c11c59
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 19, 2024
b59abc0
Merge branch 'main' into compute_distances
grst Aug 19, 2024
e6b2011
set datatypes of csr matrix arrays explicitely
felixpetschko Aug 20, 2024
ec5c50a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 20, 2024
bb245e6
docstring and data type checks added for csr_min and csr_max
felixpetschko Aug 20, 2024
0e8ff42
Changed data types of indices and indptr arrays for the csr matrices …
felixpetschko Aug 30, 2024
3b38e0e
Changed data type checks to max value checks
felixpetschko Aug 30, 2024
3685162
merge
felixpetschko Aug 30, 2024
a7cbc4c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 30, 2024
291ad5c
documentation adaptions
felixpetschko Aug 30, 2024
fb8d8d4
update pre-commit config
grst Aug 30, 2024
1db5c9a
reformat
grst Aug 30, 2024
aaef3a2
Merge remote-tracking branch 'origin/main' into compute_distances
grst Aug 30, 2024
f2055de
deleted print statement
felixpetschko Sep 5, 2024
360130c
Implemented allowing graph partitioning method "fastgreedy"
felixpetschko Sep 5, 2024
21b1023
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Sep 5, 2024
d951dc6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 5, 2024
b8fcf05
test case for j_gene added
felixpetschko Sep 5, 2024
7a6d3e3
Merge branch 'main' of https://github.com/scverse/scirpy into compute…
felixpetschko Sep 5, 2024
9775616
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Sep 5, 2024
36152da
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 5, 2024
1260aa3
refactored filter_chain_count and added documentation
felixpetschko Sep 5, 2024
e380da4
documentation and refactoring
felixpetschko Sep 5, 2024
0b1afee
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Sep 5, 2024
4e1ad60
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 5, 2024
437ed18
documentation
felixpetschko Sep 5, 2024
a00de91
Merge branch 'compute_distances' of https://github.com/felixpetschko/…
felixpetschko Sep 5, 2024
ca31f74
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 5, 2024
f8b5979
Rerun tutorial
grst Sep 8, 2024
20d2696
Update CHANGELOG
grst Sep 8, 2024
ea210e5
Attempt to fix conda CI
grst Sep 8, 2024
911ff2c
update conda CI
grst Sep 8, 2024
06857ae
Fix python version conda ci
grst Sep 8, 2024
130ab81
override python version
grst Sep 8, 2024
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