Merge pull request #210 from effigies/fix/tests-py312-np2

TEST: Fix tests for Python 3.12, numpy 2.0, and pytest-xdist

Author: effigies

.github/workflows/pythonpackage.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9',  '3.10',  '3.11']
+        python-version: ['3.8', '3.9',  '3.10',  '3.11', '3.12']
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -91,8 +91,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.7
+    - name: Set up Python 3
       uses: actions/setup-python@v4
-      with:
-        python-version: 3.7
     - run: pipx run flake8 nitransforms

nitransforms/io/afni.py

@@ -237,7 +237,7 @@ def _is_oblique(affine, thres=OBLIQUITY_THRESHOLD_DEG):
     True
 
     """
-    return (obliquity(affine).max() * 180 / pi) > thres
+    return float(obliquity(affine).max() * 180 / pi) > thres
 
 
 def _afni_deobliqued_grid(oblique, shape):

nitransforms/io/base.py

@@ -76,12 +76,12 @@ class LinearParameters(LinearTransformStruct):
     Examples
     --------
     >>> lp = LinearParameters()
-    >>> np.all(lp.structarr['parameters'] == np.eye(4))
+    >>> np.array_equal(lp.structarr['parameters'], np.eye(4))
     True
 
     >>> p = np.diag([2., 2., 2., 1.])
     >>> lp = LinearParameters(p)
-    >>> np.all(lp.structarr['parameters'] == p)
+    >>> np.array_equal(lp.structarr['parameters'], p)
     True
 
     """

nitransforms/tests/test_cli.py

@@ -1,10 +1,18 @@
+import os
 from textwrap import dedent
 
 import pytest
 
 from ..cli import cli_apply, main as ntcli
 
+if os.getenv("PYTEST_XDIST_WORKER"):
+    breaks_on_xdist = pytest.mark.skip(reason="xdist is active; rerun without to run this test.")
+else:
+    def breaks_on_xdist(test):
+        return test
 
+
+@breaks_on_xdist
 def test_cli(capsys):
     # empty command
     with pytest.raises(SystemExit):

nitransforms/tests/test_version.py

@@ -1,10 +1,15 @@
 """Test _version.py."""
 import sys
 from collections import namedtuple
-from pkg_resources import DistributionNotFound
 from importlib import reload
+import pytest
 import nitransforms
 
+try:
+    from pkg_resources import DistributionNotFound
+except ImportError:
+    pytest.skip(allow_module_level=True)
+
 
 def test_version_scm0(monkeypatch):
     """Retrieve the version via setuptools_scm."""

setup.cfg

@@ -49,6 +49,7 @@ test =
     pytest-cov
     pytest-env
     codecov
+    lxml
 tests =
     %(test)s