From 4e2abf0f86e4f8b25202f0931e7b811a0c03725b Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sat, 22 Jun 2024 10:31:20 +0900
Subject: [PATCH 1/3] TEST: Fix tests for PY312, NP2

---
 nitransforms/io/afni.py            | 2 +-
 nitransforms/io/base.py            | 4 ++--
 nitransforms/tests/test_version.py | 7 ++++++-
 setup.cfg                          | 1 +
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/nitransforms/io/afni.py b/nitransforms/io/afni.py
index 06eaf432..7c66d434 100644
--- a/nitransforms/io/afni.py
+++ b/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):
diff --git a/nitransforms/io/base.py b/nitransforms/io/base.py
index d86c8539..3c923426 100644
--- a/nitransforms/io/base.py
+++ b/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
 
     """
diff --git a/nitransforms/tests/test_version.py b/nitransforms/tests/test_version.py
index a0723e9a..bc4c4a0a 100644
--- a/nitransforms/tests/test_version.py
+++ b/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."""
diff --git a/setup.cfg b/setup.cfg
index 20fe531e..79e47f47 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,6 +49,7 @@ test =
     pytest-cov
     pytest-env
     codecov
+    lxml
 tests =
     %(test)s
 

From 06f8a274a8c19ee7c0f058c4fa83ff8ef12584e3 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sat, 22 Jun 2024 11:00:45 +0900
Subject: [PATCH 2/3] TEST: Disable test_cli if xdist is enabled

---
 nitransforms/tests/test_cli.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nitransforms/tests/test_cli.py b/nitransforms/tests/test_cli.py
index 7f16a1de..58867131 100644
--- a/nitransforms/tests/test_cli.py
+++ b/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):

From 4d2f4c7b7c0a5ace5ca5dae9ca774bda16b83379 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sat, 22 Jun 2024 11:01:03 +0900
Subject: [PATCH 3/3] CI: Add Python 3.12 tests, unpin the flake8 Python
 version

---
 .github/workflows/pythonpackage.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 97c4984e..71a1494b 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.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