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51 reduce memory burden of pipeline #95

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merged 24 commits into from
Sep 18, 2024
+424 −182
Merged

51 reduce memory burden of pipeline #95

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356696c
low memory pasisng test
geoffwoollard Sep 4, 2024
5e3591f
tests passing for low memory mode t and f
geoffwoollard Sep 10, 2024
7c8e247
l2, corr, bioem working
geoffwoollard Sep 11, 2024
14805d7
fsc low memory working
geoffwoollard Sep 11, 2024
6f5e09e
tests passing checking identical output
geoffwoollard Sep 11, 2024
a7290aa
all metrics implemented and test passing for matched results
geoffwoollard Sep 11, 2024
22ec5a5
all metrics implemented and test passing for matched results
geoffwoollard Sep 11, 2024
de3cddc
all metrics implemented and test passing for matched results
geoffwoollard Sep 11, 2024
f20344e
flags for masking and not masking
geoffwoollard Sep 11, 2024
6def1bf
tests for masking and normalization
geoffwoollard Sep 11, 2024
c0f2f83
code duplication for norm
geoffwoollard Sep 17, 2024
f1f8cd8
tests passing. vmap over sub batch
geoffwoollard Sep 17, 2024
61608cb
tests passing. get_sub_distance_matrix
geoffwoollard Sep 17, 2024
1440d84
tests passing with hard coded instantiation
geoffwoollard Sep 17, 2024
555a39f
map_to_map_distance.distance_matrix_precomputation
geoffwoollard Sep 17, 2024
b71e52b
chunk_size_low_memory
geoffwoollard Sep 17, 2024
76fdb46
on the fly sub batch normalization
geoffwoollard Sep 17, 2024
0a2efc0
normalization and masking on the fly in sub batch
geoffwoollard Sep 17, 2024
42525f4
tests passing
geoffwoollard Sep 17, 2024
e472372
tests passing for low memory off
geoffwoollard Sep 17, 2024
3077f6a
tests passing. time to delete separate low memory
geoffwoollard Sep 18, 2024
cb7085e
all tests passing
geoffwoollard Sep 18, 2024
1f4057e
remove low memory versions
geoffwoollard Sep 18, 2024
b33a6a0
update configs to remove low memory metrics
geoffwoollard Sep 18, 2024
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4 changes: 1 addition & 3 deletions src/cryo_challenge/_commands/run_map2map_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,7 @@ def main(args):
warnexists(config["output"])
mkbasedir(os.path.dirname(config["output"]))

run(config)

return
return run(config)


if __name__ == "__main__":
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