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Optimize GCLDAModel with numba and Parallel #744

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Optimize GCLDAModel with numba and Parallel #744

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091b420
Use numba in for loop of _update_word_topic_assignments and _update_p…
JulioAPeraza Aug 24, 2022
4e7ca79
Convert staticmethod to function
JulioAPeraza Aug 24, 2022
daf4962
Disable numba execution to allow pytest-cov to detect coverage in fun…
JulioAPeraza Aug 24, 2022
0d86fba
`DISABLE_JIT=True` only for GCLDA tests
JulioAPeraza Aug 24, 2022
1502f2b
`DISABLE_JIT=True` inside GCLDA tests
JulioAPeraza Aug 24, 2022
6844ce0
`DISABLE_JIT=False` after GCLDA tests
JulioAPeraza Aug 24, 2022
d61fff7
Fix comments
JulioAPeraza Aug 24, 2022
63b46d4
Disable JIT using environment variable
JulioAPeraza Aug 24, 2022
2abaf9a
Lint issue
JulioAPeraza Aug 24, 2022
1e985e0
Try using `config.DISABLE_JIT` again
JulioAPeraza Aug 24, 2022
694a632
Set `nopython` mode to False
JulioAPeraza Aug 25, 2022
f263e32
Remove truncation of `probs_pdf`
JulioAPeraza Aug 30, 2022
e818cf9
Use Parallel in _update_peak_assignments
JulioAPeraza Sep 3, 2022
0c07abc
Speed parallelization by avoiding excessive `.copy()` across jobs
JulioAPeraza Sep 24, 2022
5870c3d
Create chunks of data to speed up Parallel
JulioAPeraza Oct 3, 2022
4e12046
Clean up the code
JulioAPeraza Oct 10, 2022
dc2ac6c
Use an array of seeds for multi-core reproducibility of default_rng()…
JulioAPeraza Oct 11, 2022
fc7c5e6
Update gclda.py
JulioAPeraza Oct 11, 2022
0d2939c
Parallelize `_update_word_topic_assignments()`
JulioAPeraza Oct 24, 2022
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10 changes: 7 additions & 3 deletions nimare/tests/test_annotate_gclda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,12 @@

from nimare import annotate, decode

# Disable numba execution to allow pytest-cov to detect coverage in functions with @jit
config.DISABLE_JIT = True


def test_gclda_symmetric(testdata_laird):
"""A smoke test for GCLDA with symmetric regions."""
# Disable numba execution to allow pytest-cov to detect coverage in functions with @jit
config.DISABLE_JIT = True

counts_df = annotate.text.generate_counts(
testdata_laird.texts,
text_column="abstract",
Expand Down Expand Up @@ -87,3 +87,7 @@ def test_gclda_asymmetric(testdata_laird):
# Encode text
encoded_img, _ = decode.encode.gclda_encode(model, "fmri activation")
assert isinstance(encoded_img, nib.Nifti1Image)


# Disable numba execution to allow pytest-cov to detect coverage in functions with @jit
config.DISABLE_JIT = False