Merge pull request #1134 from effigies/maint/lock

MNT: Lock test environment, update with dependabot

Author: effigies

.github/dependabot.yml

@@ -5,7 +5,15 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"
   - package-ecosystem: "gitsubmodule"
     directory: "/"
     schedule:
       interval: "weekly"
+  - package-ecosystem: uv
+    directory: "/"
+    schedule:
+      interval: weekly

.github/workflows/build-test-deploy.yml

@@ -74,6 +74,7 @@ jobs:
           - python-version: '3.10'
             dependencies: pre
       fail-fast: false
+    continue-on-error: ${{ matrix.dependencies == 'pre' }}
 
     env:
       DEPENDS: ${{ matrix.dependencies }}

MANIFEST.in

@@ -3,5 +3,7 @@ graft tests
 graft doc
 
 include tox.ini
+# Include uv.lock so that tox can run from sdist
+include uv.lock
 
 recursive-exclude src README.md

src/bids/modeling/tests/test_statsmodels.py

@@ -304,7 +304,7 @@ def test_missing_value_fill():
 
     # Assert that there are no missing values
     outputs = graph.nodes['run'].outputs_
-    assert not np.isnan(outputs[0].model_spec.X).any().any()
+    assert not outputs[0].model_spec.X.isna().any().any()
 
     # Check that missing_values='error' raises an error
     with pytest.raises(ValueError):
@@ -314,4 +314,4 @@ def test_missing_value_fill():
     graph.run_graph(missing_values='ignore')
 
     outputs = graph.nodes['run'].outputs_
-    assert np.isnan(outputs[0].model_spec.X).any().any()
+    assert outputs[0].model_spec.X.isna().any().any()

src/bids/modeling/tests/test_transformations.py

@@ -278,12 +278,12 @@ def test_split(collection):
     rt_post_onsets = np.r_[collection['RT.respcat[0]'].onset,
                            collection['RT.respcat[-1]'].onset,
                            collection['RT.respcat[1]'].onset]
-    assert np.array_equal(rt_pre_onsets.sort(), rt_post_onsets.sort())
+    assert np.array_equal(np.sort(rt_pre_onsets), np.sort(rt_post_onsets))
 
     rt_post_values = np.r_[collection['RT.respcat[0]'].values.values,
                            collection['RT.respcat[-1]'].values.values,
                            collection['RT.respcat[1]'].values.values]
-    assert np.array_equal(rt_pre_values.sort(), rt_post_values.sort())
+    assert np.array_equal(np.sort(rt_pre_values), np.sort(rt_post_values))
 
     # Grouping SparseEventVariable by multiple columns
     transform.Split(collection, variables=['RT_2'], by=['loss', 'respcat'])

src/bids/tests/test_cli.py

@@ -15,8 +15,12 @@ def runner():
 
 def test_cli_entrypoint(runner):
     res = runner.invoke(cli, catch_exceptions=False)
-    assert "Command-line interface for PyBIDS operations" in res.stdout
-    assert runner.invoke(cli, ['-h'], catch_exceptions=False).stdout == res.stdout
+    if res.exit_code == 2:  # click 8.2+
+        help_text = res.stderr
+    elif res.exit_code == 0:
+        help_text = res.stdout
+    assert "Command-line interface for PyBIDS operations" in help_text
+    assert runner.invoke(cli, ['-h'], catch_exceptions=False).stdout == help_text
     # verify versioning
     assert runner.invoke(cli, ['--version'], catch_exceptions=False).stdout.startswith('pybids')
 
@@ -65,4 +69,4 @@ def is_success(res):
         ],
         catch_exceptions=False,
     )
-    assert is_success(res)
+    assert is_success(res)

src/bids/variables/variables.py

@@ -371,7 +371,9 @@ def __init__(self, name, data, run_info, source, **kwargs):
                             % repr(run_info))
         self.run_info = run_info
         for sc in self._property_columns:
-            setattr(self, sc, data.pop(sc).values)
+            arr = data.pop(sc).values
+            arr.flags['WRITEABLE'] = True
+            setattr(self, sc, arr)
         super(SparseRunVariable, self).__init__(name, data, source, **kwargs)
 
     def get_duration(self):

tests/data/ds005/derivatives/events/dataset_description.json

@@ -1,7 +1,7 @@
 {
-    "PipelineDescription": {
+    "GeneratedBy": [{
         "Name": "events"
-      },
+    }],
     "BIDSVersion": "1.7.1",
     "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
     "Name": "Mixed-gambles task",

tests/data/ds005/derivatives/fmriprep/dataset_description.json

@@ -2,7 +2,6 @@
     "Name": "fMRIPrep - fMRI PREProcessing workflow",
     "BIDSVersion": "1.4.0",
     "DatasetType": "derivative",
-    "PipelineDescription": {"Name": "ds000003 Pipeline"},
     "GeneratedBy": [
         {
             "Name": "fMRIPrep",

tests/data/ds005_derivs/dummy-vx.x.x/dataset_description.json

@@ -1,7 +1,7 @@
 {
-    "PipelineDescription": {
+    "GeneratedBy": [{
         "Name": "dummy"
-      },
+     }],
     "BIDSVersion": "1.0.0rc2",
     "Name": "Mixed-gambles task -- dummy derivative",
     "ReferencesAndLinks": "Tom, S.M., Fox, C.R., Trepel, C., Poldrack, R.A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315(5811):515-8",