nimare 0.5.0rc1__py3-none-any.whl → 0.5.1rc1__py3-none-any.whl

nimare/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-03-13T11:20:33-0500",
+ "date": "2025-05-14T18:30:31-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "71d779964e5756b89c6237e1550112d9c8a77498",
- "version": "0.5.0rc1"
+ "full-revisionid": "0d38f6753997f345fc39e3eddb079655f87077b2",
+ "version": "0.5.1rc1"
 }
 '''  # END VERSION_JSON
 

nimare/meta/utils.py

@@ -33,7 +33,7 @@ def _convolve_sphere(kernel, ijks, index, max_shape):
 
     def np_all_axis1(x):
         """Numba compatible version of np.all(x, axis=1)."""
-        out = np.ones(x.shape[0], dtype=np.bool8)
+        out = np.ones(x.shape[0], dtype=np.bool_)
         for i in range(x.shape[1]):
             out = np.logical_and(out, x[:, i])
         return out

nimare/reports/base.py

@@ -540,7 +540,7 @@ class Report:
                             rowvar=True,
                         )
                 else:
-                    corr = self.inputs_["corr_matrix"]
+                    corr = self.results.estimator.inputs_["corr_matrix"]
 
                 similarity_table = pd.DataFrame(
                     index=ids_,

nimare/tests/test_extract.py

@@ -2,10 +2,28 @@
 
 import os
 from glob import glob
+from io import BytesIO
+from unittest.mock import patch
 
 import nimare
 
 
+def mock_urlopen(url):
+    """Mock URL opener that returns appropriate mock data based on file type."""
+    if "coordinates.tsv.gz" in url:
+        mock_data = b"x\ty\tz\n1\t2\t3\n4\t5\t6"
+    elif "metadata.tsv.gz" in url:
+        mock_data = b"id\ttitle\n1\tStudy 1\n2\tStudy 2"
+    elif "features.npz" in url:
+        mock_data = b"mock npz content"
+    elif "vocabulary.txt" in url:
+        mock_data = b"term1\nterm2\nterm3"
+    else:
+        mock_data = b"Mock file content"
+    return BytesIO(mock_data)
+
+
+@patch("nimare.extract.extract.urlopen", side_effect=mock_urlopen)
 def test_fetch_neurosynth(tmp_path_factory):
     """Smoke test for extract.fetch_neurosynth.
 
@@ -19,15 +37,20 @@ def test_fetch_neurosynth(tmp_path_factory):
         source="abstract",
         vocab="terms",
     )
-    files = glob(os.path.join(tmpdir, "neurosynth", "*"))
-    assert len(files) == 4
-
-    # One set of files found
+    # Check data_files structure
     assert isinstance(data_files, list)
     assert len(data_files) == 1
 
+    # Verify expected files in data_files
+    files_dict = data_files[0]
+    assert "coordinates" in files_dict
+    assert "metadata" in files_dict
+    assert "features" in files_dict
+    assert len(files_dict["features"]) == 1
+
 
-def test_fetch_neuroquery(tmp_path_factory):
+@patch("nimare.extract.extract.urlopen", side_effect=mock_urlopen)
+def test_fetch_neuroquery(mock_url, tmp_path_factory):
     """Smoke test for extract.fetch_neuroquery."""
     tmpdir = tmp_path_factory.mktemp("test_fetch_neuroquery")
     data_files = nimare.extract.fetch_neuroquery(
@@ -44,3 +67,10 @@ def test_fetch_neuroquery(tmp_path_factory):
     # One set of files found
     assert isinstance(data_files, list)
     assert len(data_files) == 1
+
+    # Verify mock was called with expected URLs
+    assert mock_url.call_count > 0  # Should be called for each file download
+    for call in mock_url.call_args_list:
+        url = call[0][0]
+        assert "neuroquery/neuroquery_data/blob" in url
+        assert "?raw=true" in url

nimare/tests/test_reports.py

@@ -108,3 +108,25 @@ def test_reports_ibma_smoke(tmp_path_factory, testdata_ibma, aggressive_mask):
     filename = "report.html"
     outpath = op.join(hedges_dir, filename)
     assert op.isfile(outpath)
+
+
+def test_reports_ibma_multiple_contrasts_smoke(tmp_path_factory, testdata_ibma_multiple_contrasts):
+    """Smoke test for IBMA reports for multiple contrasts."""
+    tmpdir = tmp_path_factory.mktemp("test_reports_ibma_smoke")
+
+    # Generate a report with z maps as inputs
+    stouffers_dir = op.join(tmpdir, "stouffers")
+    workflow = IBMAWorkflow(
+        estimator=Stouffers(aggressive_mask=True),
+        corrector="fdr",
+        diagnostics="jackknife",
+        voxel_thresh=3.2,
+        output_dir=stouffers_dir,
+    )
+    results = workflow.fit(testdata_ibma_multiple_contrasts)
+
+    run_reports(results, stouffers_dir)
+
+    filename = "report.html"
+    outpath = op.join(stouffers_dir, filename)
+    assert op.isfile(outpath)

nimare/utils.py

@@ -1286,9 +1286,9 @@ def b_spline_bases(masker_voxels, spacing, margin=10):
     x_spline_coords = x_spline.nonzero()
     y_spline_coords = y_spline.nonzero()
     z_spline_coords = z_spline.nonzero()
-    x_spline_sparse = sparse.COO(x_spline_coords, x_spline[x_spline_coords])
-    y_spline_sparse = sparse.COO(y_spline_coords, y_spline[y_spline_coords])
-    z_spline_sparse = sparse.COO(z_spline_coords, z_spline[z_spline_coords])
+    x_spline_sparse = sparse.COO(x_spline_coords, x_spline[x_spline_coords], shape=x_spline.shape)
+    y_spline_sparse = sparse.COO(y_spline_coords, y_spline[y_spline_coords], shape=y_spline.shape)
+    z_spline_sparse = sparse.COO(z_spline_coords, z_spline[z_spline_coords], shape=z_spline.shape)
 
     # create spatial design matrix by tensor product of spline bases in 3 dimesion
     # Row sums of X are all 1=> There is no need to re-normalise X

{nimare-0.5.0rc1.dist-info → nimare-0.5.1rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nimare
-Version: 0.5.0rc1
+Version: 0.5.1rc1
 Summary: NiMARE: Neuroimaging Meta-Analysis Research Environment
 Home-page: https://github.com/neurostuff/NiMARE
 Author: NiMARE developers

{nimare-0.5.0rc1.dist-info → nimare-0.5.1rc1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 benchmarks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 benchmarks/bench_cbma.py,sha256=fg_EER8hohi6kD1Hno_uXsFntKuCLTvseu-6OqkHkoU,1382
 nimare/__init__.py,sha256=HHIq3EimSZSf3zJSDwuTjBig1GbRwHGYfRLSqI3yleE,802
-nimare/_version.py,sha256=B-yG1ELidF5YmffvLhUktR130qlkvoRlzyFTb5ItxHw,500
+nimare/_version.py,sha256=wKqr4KLFDBfby4GFFBohLjmyONhzWdP50R86OZ2SCak,500
 nimare/base.py,sha256=9DlcRB2mW759p7XqpKG3wRE-MmPsEPiYTbq6V1Yile4,7826
 nimare/cli.py,sha256=Zvy5jN2KopH_MBke-gm8A0DbBZmIFGvnE1tjhbYib9I,3695
 nimare/correct.py,sha256=2eI0jR6_odND-2CzSlaxRU2um6ccLSapd7ERAYteBnE,17110
@@ -14,7 +14,7 @@ nimare/nimads.py,sha256=2s5QnaLvrBt-kMrImGhG_p6r0unysufIIcPczr2bG0c,24342
 nimare/results.py,sha256=7szcyR6PkZAXBqbIGGWrw1nW9j9QCdpdl4MxUK_1Wzc,8190
 nimare/stats.py,sha256=XhXfFj6KHTPVSTXhbEid0qt8HLqJD82Bl5T23qmaf40,10098
 nimare/transforms.py,sha256=_kZO8N3IEHxd6Ir4IcewZtkWHpFknnjEnjsaD9b-1pg,30136
-nimare/utils.py,sha256=BJOOKgQuubamE0RBMJVubggQfaPgIH9wZ9Oou9DKvbU,46936
+nimare/utils.py,sha256=rMuT1mhEYrb3R_2EAsz5A_f5VPWXzqRkH_saQTFybm4,47002
 nimare/annotate/__init__.py,sha256=hTla1yFYTJ8PDjm72ReeHa3qf0Que50Ww0fqz3Z86JI,434
 nimare/annotate/cogat.py,sha256=xzrepAuTkRenbECn4XYwgyul45r0tIMxCDKQV_ZFVb8,7457
 nimare/annotate/gclda.py,sha256=P2OQjuJn3DX0GVPte_VIVZf0LfO-yE_OhLbs6DwMaHQ,42592
@@ -35,13 +35,13 @@ nimare/meta/cbmr.py,sha256=h9CNMHW4KUh-YQYyGDRzqPN7G1tkHYAhrSgxrP8E61s,47769
 nimare/meta/ibma.py,sha256=qVw3ZhOlK6hgTdZZwa7TPDpfrGLf52dN00wH2Gw-Z8c,65442
 nimare/meta/kernel.py,sha256=5wN-6dbLkzqQ0WUSTrC0DJPSbbyGiZCls9M_TAYhNGY,19169
 nimare/meta/models.py,sha256=0QPlQTjWaNTeI8qTX-DHMXVjQSRD72SfJ2RZIYBZnCg,47054
-nimare/meta/utils.py,sha256=fvnFz4ek8APjQHhYBS441WYXE1N9huHaTiOO0Bvui4Q,18083
+nimare/meta/utils.py,sha256=84T4I-wn-HTx7zwMqh0TdvzUbBe_vcpxIU4jA_pfuFU,18083
 nimare/meta/cbma/__init__.py,sha256=bWLrv5tL03U2ITttnnz3yerbg74w44qkZgdy32QMhqQ,219
 nimare/meta/cbma/ale.py,sha256=ZNjXC4MXhfSHvrTRppY04NkGtz_Iri696k5QMuBog7o,39273
 nimare/meta/cbma/base.py,sha256=-gJ4hW6_6T5oto3pre9GbWodHWRmPS2WZ1LJjB0BtMI,38382
 nimare/meta/cbma/mkda.py,sha256=V5vSQodiLZoZhkYPhous0a_-1pZoRjAIL8gmGyyoezc,60397
 nimare/reports/__init__.py,sha256=zGfrOPlMq2lTorKNEpyPblArFCnsvz3dRsvOHy_Ciag,428
-nimare/reports/base.py,sha256=DPYr1lTuS740pSv5Q-tE0UegU0mckG0JMI-2TKVe64Y,23489
+nimare/reports/base.py,sha256=_PYM_zq5ATYden5CiuppURrZX_y54u_h5-DL5UFi_KM,23507
 nimare/reports/default.yml,sha256=zTcWUlC9ntvacMcIIUAJPoFV8XrvPGqCH2uwovwB4Wc,6003
 nimare/reports/figures.py,sha256=MCsjDR53475Jz1_anktKvNOh0qUNPMx-dfvP6Vy0uUc,19783
 nimare/reports/report.tpl,sha256=ZweYiJF80zdaIwK1iawAl1pwmBZdPjpxXxY5C0U5yVs,5518
@@ -72,7 +72,7 @@ nimare/tests/test_decode_continuous.py,sha256=KmdkulIIBBpjbao-TdFTVFuRd6lUx_-3Qq
 nimare/tests/test_decode_discrete.py,sha256=NL__uEvMori4HtmoZUVdj465lW4Qwr4ndgyOz5rB7dY,3293
 nimare/tests/test_diagnostics.py,sha256=VrfR_8nQKn2VF7dFdnTM7ZQy3Ou5eHdpaLhml5T6Pb0,6467
 nimare/tests/test_estimator_performance.py,sha256=tbK2Qr83rB0in-pB6MccnjLg4iHSyfilx-hTNDWQfe4,12749
-nimare/tests/test_extract.py,sha256=XJSxZTdy_hAej1J9CFK9zQk29rAM5KPiZKlopmUVCJ4,1206
+nimare/tests/test_extract.py,sha256=nPaL07G9paLRCJzPOv79jH3mhOPs2YvQdghoLfcDz5A,2348
 nimare/tests/test_generate.py,sha256=LSh2APJsg87u2s2zydkrre3RVk_ZGpoB4d7uuvIPWYE,7318
 nimare/tests/test_io.py,sha256=QKr_zRGu8tyrpiLoLAjCV9ektxCTHRlKPWgyJRqQ9T8,10397
 nimare/tests/test_meta_ale.py,sha256=hccXSNzLGUgj6E4tCsiHZpuUFoBxXkP293-vtUS5jdE,11791
@@ -81,7 +81,7 @@ nimare/tests/test_meta_ibma.py,sha256=Yw4F0_pr3cpVSe7oeMlK0-btg1Uw58cenklOsIw87P
 nimare/tests/test_meta_kernel.py,sha256=Edk6lOsnqokg86mp9jAkokA203K61R7pjJEmyEEzV7E,8450
 nimare/tests/test_meta_mkda.py,sha256=9PuzNUKrTBjbCHdSnuOAToXbV7wp1O0TCdD537qGQkA,9206
 nimare/tests/test_nimads.py,sha256=3yzCO8rmUVfEYAt3HNnJcyAENorJ5BOWdJXY3hjrdP0,9807
-nimare/tests/test_reports.py,sha256=Qdz-PHjQwOneRmSCo0ac2d67BeGypWJIMi4OoiQrNik,3293
+nimare/tests/test_reports.py,sha256=KIihXTAsIntsEG6xk3crMFLoQGiI5EOr0mesCne48CA,4030
 nimare/tests/test_stats.py,sha256=_GhpUC1u4hnFR2SZ-sHQqkJ5MwsyPsvwPEd2GkQmsHY,4030
 nimare/tests/test_transforms.py,sha256=mzEnufefhybs4r_dfRY6zQUAShepPMwKFY7S5amq3cs,10378
 nimare/tests/test_utils.py,sha256=JaJYexM_xJOa-Jhv5OdbQBZ-3IWba1-Dmf1-V580ACo,6443
@@ -111,9 +111,9 @@ nimare/workflows/cbma.py,sha256=2jYJs9kH7_LzFP6d7-oTHiTTgAFbtmiBNtBXSCSZPjg,7052
 nimare/workflows/ibma.py,sha256=lAkWtqSqnZiUUV460Bh046U9LeGhnry3bl8BFi-tx7s,4289
 nimare/workflows/macm.py,sha256=mVUBeKbTawhU93ApnkunZSUXZWo7qBPrM3dMGWfl0ik,2531
 nimare/workflows/misc.py,sha256=OWgHlSAnRI0-5Seii-bd48piIYsfEAF_aNKGorH1yJQ,1827
-nimare-0.5.0rc1.dist-info/LICENSE,sha256=PWPXnCGWh-FMiBZ61OnQ2BHFjPPlJJ7F0kFx_ryzp-M,1074
-nimare-0.5.0rc1.dist-info/METADATA,sha256=YyiKFKuawdfsp9SIW5pJ6nVgibwk27EYr8bKIointfA,4698
-nimare-0.5.0rc1.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
-nimare-0.5.0rc1.dist-info/entry_points.txt,sha256=3w_hk9N2PWnKZkCaJyDlc0_kdn3rh35aiI21rSdvsuA,44
-nimare-0.5.0rc1.dist-info/top_level.txt,sha256=XnOcEXMs0BxdI8t3_ksTl96T8hykn9L7-bxLLraVrTI,18
-nimare-0.5.0rc1.dist-info/RECORD,,
+nimare-0.5.1rc1.dist-info/LICENSE,sha256=PWPXnCGWh-FMiBZ61OnQ2BHFjPPlJJ7F0kFx_ryzp-M,1074
+nimare-0.5.1rc1.dist-info/METADATA,sha256=z9_jAt6fncG6KjI6Fi_A3ktJyuY1gAAUEsU-cvZBn5U,4698
+nimare-0.5.1rc1.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+nimare-0.5.1rc1.dist-info/entry_points.txt,sha256=3w_hk9N2PWnKZkCaJyDlc0_kdn3rh35aiI21rSdvsuA,44
+nimare-0.5.1rc1.dist-info/top_level.txt,sha256=XnOcEXMs0BxdI8t3_ksTl96T8hykn9L7-bxLLraVrTI,18
+nimare-0.5.1rc1.dist-info/RECORD,,