nimare 0.5.0rc2__tar.gz → 0.5.1rc1__tar.gz

{nimare-0.5.0rc2/nimare.egg-info → nimare-0.5.1rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nimare
-Version: 0.5.0rc2
+Version: 0.5.1rc1
 Summary: NiMARE: Neuroimaging Meta-Analysis Research Environment
 Home-page: https://github.com/neurostuff/NiMARE
 Author: NiMARE developers

{nimare-0.5.0rc2 → nimare-0.5.1rc1}/nimare/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-04-25T13:22:39-0500",
+ "date": "2025-05-14T18:30:31-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "9e3b73cbb6235b31a4fab7a9a118e32c1d2f9932",
- "version": "0.5.0rc2"
+ "full-revisionid": "0d38f6753997f345fc39e3eddb079655f87077b2",
+ "version": "0.5.1rc1"
 }
 '''  # END VERSION_JSON
 

{nimare-0.5.0rc2 → nimare-0.5.1rc1}/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-0.5.1rc1/nimare/tests/test_extract.py

@@ -0,0 +1,76 @@
+"""Test nimare.extract."""
+
+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.
+
+    Taken from the Neurosynth Python package.
+    """
+    tmpdir = tmp_path_factory.mktemp("test_fetch_neurosynth")
+    data_files = nimare.extract.fetch_neurosynth(
+        data_dir=tmpdir,
+        version="7",
+        overwrite=False,
+        source="abstract",
+        vocab="terms",
+    )
+    # 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
+
+
+@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(
+        data_dir=tmpdir,
+        version="1",
+        overwrite=False,
+        source="abstract",
+        vocab="neuroquery7547",
+        type="count",
+    )
+    files = glob(os.path.join(tmpdir, "neuroquery", "*"))
+    assert len(files) == 4
+
+    # 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-0.5.0rc2 → nimare-0.5.1rc1}/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-0.5.0rc2 → nimare-0.5.1rc1/nimare.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nimare
-Version: 0.5.0rc2
+Version: 0.5.1rc1
 Summary: NiMARE: Neuroimaging Meta-Analysis Research Environment
 Home-page: https://github.com/neurostuff/NiMARE
 Author: NiMARE developers

nimare-0.5.0rc2/nimare/tests/test_extract.py

@@ -1,46 +0,0 @@
-"""Test nimare.extract."""
-
-import os
-from glob import glob
-
-import nimare
-
-
-def test_fetch_neurosynth(tmp_path_factory):
-    """Smoke test for extract.fetch_neurosynth.
-
-    Taken from the Neurosynth Python package.
-    """
-    tmpdir = tmp_path_factory.mktemp("test_fetch_neurosynth")
-    data_files = nimare.extract.fetch_neurosynth(
-        data_dir=tmpdir,
-        version="7",
-        overwrite=False,
-        source="abstract",
-        vocab="terms",
-    )
-    files = glob(os.path.join(tmpdir, "neurosynth", "*"))
-    assert len(files) == 4
-
-    # One set of files found
-    assert isinstance(data_files, list)
-    assert len(data_files) == 1
-
-
-def test_fetch_neuroquery(tmp_path_factory):
-    """Smoke test for extract.fetch_neuroquery."""
-    tmpdir = tmp_path_factory.mktemp("test_fetch_neuroquery")
-    data_files = nimare.extract.fetch_neuroquery(
-        data_dir=tmpdir,
-        version="1",
-        overwrite=False,
-        source="abstract",
-        vocab="neuroquery7547",
-        type="count",
-    )
-    files = glob(os.path.join(tmpdir, "neuroquery", "*"))
-    assert len(files) == 4
-
-    # One set of files found
-    assert isinstance(data_files, list)
-    assert len(data_files) == 1