fix: Pandas deprecations (#906)

* chore(tox): Add UV_EXTRA_INDEX_URL for pre-releases

* fix: Copy correlation values before zeroing diagonal

* fix: Pandas deprecation

* chore(tox): Pass environment variables

* chore(ci): Enable Python 3.13 tests

* chore: Disable 3.13. runs until traits is figured out

.github/workflows/pythonpackage.yml

@@ -94,7 +94,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"] #, "3.13"]
         dependencies: [latest, pre]
         include:
           - python-version: "3.9"

niworkflows/interfaces/utility.py

@@ -251,8 +251,7 @@ class AddTSVHeader(SimpleInterface):
     >>> addheader.inputs.in_file = 'data.tsv'
     >>> addheader.inputs.columns = ['a', 'b', 'c', 'd', 'e']
     >>> res = addheader.run()
-    >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,
-    ...                  index_col=None)
+    >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None)
     >>> df.columns.ravel().tolist()
     ['a', 'b', 'c', 'd', 'e']
 
@@ -311,7 +310,7 @@ class JoinTSVColumns(SimpleInterface):
     >>> join.inputs.in_file = 'data.tsv'
     >>> join.inputs.join_file = 'add.tsv'
     >>> res = join.run()
-    >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,
+    >>> df = pd.read_csv(res.outputs.out_file, sep='\s+',
     ...                  index_col=None, dtype=float, header=None)
     >>> df.columns.ravel().tolist() == list(range(5))
     True
@@ -328,8 +327,7 @@ class JoinTSVColumns(SimpleInterface):
     >>> res = join.run()
     >>> res.outputs.out_file  # doctest: +ELLIPSIS
     '...data_joined.tsv'
-    >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,
-    ...                  index_col=None)
+    >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None)
     >>> df.columns.ravel().tolist()
     ['a', 'b', 'c', 'd', 'e']
 
@@ -342,8 +340,7 @@ class JoinTSVColumns(SimpleInterface):
     >>> join.inputs.side = 'left'
     >>> join.inputs.columns = ['a', 'b', 'c', 'd', 'e']
     >>> res = join.run()
-    >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,
-    ...                  index_col=None)
+    >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None)
     >>> df.columns.ravel().tolist()
     ['a', 'b', 'c', 'd', 'e']
 

niworkflows/viz/plots.py

@@ -926,7 +926,11 @@ def confounds_correlation_plot(
     gs_descending = gs_descending[:max_dim]
     features = [p for p in corr.columns if p in gs_descending]
     corr = corr.loc[features, features]
-    np.fill_diagonal(corr.values, 0)
+
+    # Modifying in-place is no longer supported
+    corr_vals = corr.to_numpy(copy=True)
+    np.fill_diagonal(corr_vals, 0)
+    corr.iloc[:, :] = corr_vals
 
     if figure is None:
         plt.figure(figsize=(15, 5))

tox.ini

@@ -14,6 +14,7 @@ python =
   3.10: py310
   3.11: py311
   3.12: py312
+  3.13: py313
 
 [gh-actions:env]
 DEPENDS =
@@ -27,6 +28,20 @@ labels = test
 pip_pre =
   pre: true
 pass_env =
+  TEMPLATEFLOW_HOME
+  # Freesurfer variables searched for
+  FREESURFER_HOME
+  SUBJECTS_DIR
+  FS_LICENSE
+  # CI variables
+  TEST_DATA_HOME
+  TEST_OUTPUT_DIR
+  TEST_WORK_DIR
+  FMRIPREP_REGRESSION_SOURCE
+  CACHED_WORK_DIRECTORY
+  # CircleCI-specific
+  CIRCLE_NPROCS
+  SAVE_CIRCLE_ARTIFACTS
   # getpass.getuser() sources for Windows:
   LOGNAME
   USER
@@ -39,9 +54,12 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
   PYTHON_GIL
+deps =
+  py313: traits @ git+https://github.com/enthought/traits.git@10954eb
 extras = tests
 setenv =
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 uv_resolution =
   min: lowest-direct
 
@@ -91,7 +109,6 @@ set_env =
   # https://github.com/pypa/pip/issues/11684
   # https://github.com/pypa/pip/issues/12243
   strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
-commands_pre =
 commands =
   python -m build
   python -m twine check dist/*