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Update B2RIO for latest neurolang and nilearn compatibility (Python ≥ 3.12) #9

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Update B2RIO for latest neurolang and nilearn compatibility (Python ≥ 3.12) #9

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c3cc61e
Initial plan
Copilot Apr 18, 2026
abba721
Update B2RIO for latest neurolang and Python >= 3.12 compatibility
Copilot Apr 18, 2026
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30 changes: 20 additions & 10 deletions b2rio/b2rio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,22 @@
config.disable_probabilistic_solver_check_unate()
import argparse
import warnings
from pathlib import Path

from neurolang.frontend import NeurolangPDL
from neurolang.frontend.neurosynth_utils import (
get_ns_mni_peaks_reported, get_ns_term_study_associations)
from nilearn import datasets, image

try:
from nilearn.datasets.utils import _fetch_files, _get_dataset_dir
except ImportError:
# nilearn >= 0.11: functions were moved and renamed
from nilearn.datasets._utils import (
fetch_files as _fetch_files,
get_dataset_dir as _get_dataset_dir,
)

warnings.simplefilter(action='ignore', category=FutureWarning)


Expand All @@ -23,7 +33,7 @@ def run():
parser.add_argument("--resample", nargs='?', type=int, default=1)
parser.add_argument("--frac_sample", nargs='?', type=int, default=0.7)
parser.add_argument("--radius", nargs='?', type=int, default=4)
parser.add_argument("--tfIdf", nargs='?', type=str, default='1e-3')
parser.add_argument("--tfIdf", nargs='?', type=float, default=1e-3)
parser.add_argument("--output_file", nargs=1, type=str, default=None)
parser.add_argument("--only_topconcepts", nargs='?', type=bool, default=False)
parser.add_argument("--output_summary", nargs='?', type=bool, default=False)
Expand Down Expand Up @@ -91,8 +101,8 @@ def run():
return


ns_terms = get_ns_term_study_associations('./', tfidf_threshold=tfIdf)[['id', 'term']]
ns_data = get_ns_mni_peaks_reported('./')
ns_terms = get_ns_term_study_associations(Path('./'), tfidf_threshold=tfIdf)[['id', 'term']]
ns_data = get_ns_mni_peaks_reported(Path('./'))
ns_docs = ns_data[['id']].drop_duplicates()

ijk_positions = (
Expand All @@ -108,8 +118,8 @@ def run():
ns_data['id'] = ns_data.id.astype(int)
ns_data = ns_data[['id', 'i', 'j', 'k']].values

cogAt = datasets.utils._fetch_files(
datasets.utils._get_dataset_dir('CogAt'),
cogAt = _fetch_files(
_get_dataset_dir('CogAt'),
[
(
'cogat.xml',
Expand Down Expand Up @@ -296,7 +306,7 @@ def run_probabilistic():
parser.add_argument("--resample", nargs='?', type=int, default=1)
parser.add_argument("--frac_sample", nargs='?', type=int, default=0.7)
parser.add_argument("--radius", nargs='?', type=int, default=4)
parser.add_argument("--tfIdf", nargs='?', type=str, default='1e-3')
parser.add_argument("--tfIdf", nargs='?', type=float, default=1e-3)
parser.add_argument("--output_file", nargs=1, type=str, default=None)
parser.add_argument("--only_topconcepts", nargs='?', type=bool, default=False)
parser.add_argument("--output_summary", nargs='?', type=bool, default=False)
Expand Down Expand Up @@ -364,8 +374,8 @@ def run_probabilistic():
print('The nifti file must contain 3 or 4 dimensions')
return

ns_terms = get_ns_term_study_associations('./', tfidf_threshold=tfIdf)[['id', 'term']]
ns_data = get_ns_mni_peaks_reported('./')
ns_terms = get_ns_term_study_associations(Path('./'), tfidf_threshold=tfIdf)[['id', 'term']]
ns_data = get_ns_mni_peaks_reported(Path('./'))
ns_docs = ns_data[['id']].drop_duplicates()

ijk_positions = (
Expand All @@ -382,8 +392,8 @@ def run_probabilistic():
ns_data = ns_data[['id', 'i', 'j', 'k']].values


cogAt = datasets.utils._fetch_files(
datasets.utils._get_dataset_dir('CogAt'),
cogAt = _fetch_files(
_get_dataset_dir('CogAt'),
[
(
'cogat.xml',
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
description ='Brain t(w)o Reverse Inference Ontology',
license ='MIT',
packages = find_packages(),
python_requires='>3.8',
python_requires='>=3.12',
entry_points ={
'console_scripts': [
'b2rio = b2rio.b2rio:run',
Expand Down