NumPy 2 compatibility for tests and tools

.github/workflows/headless-tests.yml

@@ -31,10 +31,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install numpy "vtk<9.3" pillow pytest traitsui
+        python -m pip install numpy "vtk<9.3" pillow pytest pytest-timeout traitsui
     - name: Install mayavi and tvtk
-      run: python -m pip install -v .
-    - name: Test tvtk package
-      run: pytest -v --pyargs tvtk
+      run: python -m pip install --no-build-isolation -v .
     - name: Test Mayavi package
-      run: pytest -v --pyargs mayavi
+      run: pytest -v --timeout=10 --pyargs mayavi
+    - name: Test tvtk package
+      run: pytest -v --timeout=60 --pyargs tvtk

.github/workflows/run-mayavi-tests.yml

@@ -43,6 +43,22 @@ jobs:
             qt-api: 'pyside6'
             os: macos-13
             vtk: 'vtk<9.3'
+          # Some old NumPys
+          - python-version: '3.12'
+            qt-api: 'pyside6'
+            os: ubuntu-latest
+            vtk: 'vtk>=9.3'
+            numpy: 'numpy==1.26.4'
+          - python-version: '3.12'
+            qt-api: 'pyside6'
+            os: windows-latest
+            vtk: 'vtk>=9.3'
+            numpy: 'numpy==2.0.2'
+          - python-version: '3.12'
+            qt-api: 'pyside6'
+            os: windows-latest
+            vtk: 'vtk>=9.3'
+            numpy: 'numpy==1.26.4'
       fail-fast: false
     defaults:
       run:
@@ -69,14 +85,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      shell: bash
       run: |
         set -exo pipefail
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --upgrade "${{ matrix.qt-api }}" numpy "${{ matrix.vtk }}" pillow pytest traits traitsui
+        python -m pip install --upgrade "${{ matrix.qt-api }}" "${{ matrix.numpy || 'numpy' }}" "${{ matrix.vtk }}" pillow pytest pytest-timeout traits traitsui --only-binary="numpy,vtk"
     - name: Install mayavi and tvtk
-      run: python -um pip install -ve .[app]
+      run: python -um pip install --no-build-isolation -ve .[app]
     - name: Test Mayavi package
-      run: pytest -v mayavi
+      run: pytest -v --timeout=10 mayavi
     - name: Test tvtk package
-      run: pytest -sv tvtk
+      run: pytest -sv --timeout=60 tvtk

.gitignore

@@ -16,4 +16,5 @@ docs/build/
 
 docs/html.zip
 tvtk/tvtk_classes.zip
+tvtk/tvtk_classes/
 mayavi/images/m2_about.jpg

mayavi/__init__.py

@@ -9,13 +9,15 @@
 
 __requires__ = [
     'apptools',
+    'configobj',
     'envisage',
     'numpy',
     'pyface>=6.1.1',
     'pygments',  # This is only needed for the Qt backend but we add it anyway.
     'traits>=6.0.0',
     'traitsui>=7.0.0',
     'packaging',
+    'importlib_resources; python_version<"3.11"',
     'vtk'
 ]
 

mayavi/preferences/preference_manager.py

@@ -21,7 +21,7 @@
 
 # Standard library imports
 from os.path import join
-import pkg_resources
+import importlib.resources
 
 # Enthought library imports.
 from traits.etsconfig.api import ETSConfig
@@ -106,12 +106,11 @@ def _load_preferences(self):
             for pkg in ('mayavi.preferences',
                         'tvtk.plugins.scene'):
                 pref = 'preferences.ini'
-                pref_file = pkg_resources.resource_stream(pkg, pref)
-
+                pref_file = importlib.resources.files(pkg).joinpath(pref)
                 preferences = self.preferences
                 default = preferences.node('default/')
-                default.load(pref_file)
-                pref_file.close()
+                with open(pref_file, 'rb') as fid:
+                    default.load(fid)
         finally:
             # Set back the application home.
             ETSConfig.application_home = app_home
@@ -126,4 +125,3 @@ def _preferences_changed(self, preferences):
 # A Global preference manager that all other modules can use.
 
 preference_manager = PreferenceManager()
-

mayavi/tests/test_csv_sniff.py

@@ -12,7 +12,7 @@
 import tempfile
 from unittest import SkipTest
 
-from numpy import array, ndarray
+from numpy import array, ndarray, isnan
 
 from mayavi.tools.data_wizards.csv_sniff import \
      Sniff, loadtxt, loadtxt_unknown, array2dict
@@ -33,8 +33,8 @@ def assertAllClose(self, x, y):
 
     def assertClose(self, a, b):
         if isinstance(a, (int, float)):
-            if repr(a) == 'nan':
-                self.assertTrue(repr(b) == 'nan')
+            if isnan(a):
+                self.assertTrue(isnan(b), '%r != %r' % (a ,b))
             else:
                 self.assertTrue(abs(a - b) < 1e-6 * max(1, abs(a)),
                              '%r != %r  %r' % (a, b, abs(a - b)))

mayavi/tests/test_mlab_source.py

@@ -171,7 +171,7 @@ def test_set(self):
         self.check_traits()
         self.check_dataset()
 
-    def test_strange_shape(self):
+    def test_basic_strange_shape(self):
         " Test the MGlyphSource with strange shapes for the arguments "
         x, y, z, v, s, src = self.get_data()
         x = y = z = v = s = 0

mayavi/tools/data_wizards/loadtxt.py

@@ -23,7 +23,7 @@ def _getconv(dtype):
         return lambda x: int(float(x))
     elif issubclass(typ, np.floating):
         return float
-    elif issubclass(typ, np.complex_):
+    elif issubclass(typ, np.complexfloating):
         return complex
     else:
         return str

setup.cfg

@@ -4,5 +4,7 @@ addopts =
 filterwarnings =
     # Currently unsatisfiable
     ignore:Workbench will be moved from pyface:PendingDeprecationWarning
+    # Should be fixed in traits
+    ignore: module 'sre_.+' is deprecated:DeprecationWarning
     # We call deprecated methods and classes in our tests, and there are many variants for how the parentheticals are formatted
     ignore:Call to deprecated .*. \((This|Use|Please|Deprecated|Deprecating|Removed|Part|no|renamed) .*\) -- Deprecated since version.*:DeprecationWarning

setup.py

@@ -130,8 +130,8 @@ def example_files(self):
         mlab_ref_dir = join(DEFAULT_INPUT_DIR, 'mayavi', 'auto')
 
         source_path = join('examples', 'mayavi')
-        sources = '(\.py)|(\.rst)$'
-        excluded_dirs = '^\.'
+        sources = r'(\.py)|(\.rst)$'
+        excluded_dirs = r'^\.'
         target_path = mlab_ref_dir
         target_time = self.latest_modified(target_path,
                                            ignore_dirs=excluded_dirs)[0]

tvtk/array_handler.py

@@ -197,9 +197,9 @@ def get_vtk_array_type(numeric_array_type):
         numpy.dtype(ULONG_TYPE_CODE): vtkConstants.VTK_UNSIGNED_LONG,
         numpy.dtype(LONG_TYPE_CODE): vtkConstants.VTK_LONG,
     }
-    for t in _extra:
+    for t, val in _extra.items():
         if t not in _arr_vtk:
-            _arr_vtk[t] = _extra[t]
+            _arr_vtk[t] = val
 
     try:
         return _arr_vtk[numeric_array_type]

tvtk/code_gen.py

@@ -1,13 +1,16 @@
 """This module generates tvtk (Traited VTK) classes from the VTK-Python API.
 
-This can be evoked for example by:
+This can be evoked for example by running from the ``mayavi`` root:
 
 ..code-block:: console
 
-    $ python -ic "from tvtk.code_gen import main; main()" -szv
+    $ python -m tvtk.code_gen -szvno $PWD/tvtk
 
 On failures you can then for example do ``import pdb; pdb.pm()`` to do
 post-mortem debugging.
+
+Exceptions to behaviors based on VTK versions and bugs etc. live in ``wrapper_gen.py``
+and ``tvtk_parser.py``.
 """
 # Author: Prabhu Ramachandran
 # Copyright (c) 2004-2020, Enthought, Inc.

tvtk/tests/test_array_ext.py

@@ -5,12 +5,16 @@
 # Copyright (c) 2005, Enthought, Inc.
 # License: BSD Style.
 
+import pytest
 import unittest
 
 import numpy
 
 from tvtk.array_handler import ID_TYPE_CODE, set_id_type_array_py
-from tvtk.array_ext import set_id_type_array
+try:
+    from tvtk.array_ext import set_id_type_array
+except ModuleNotFoundError:  # not compiled
+    pytest.skip("array_ext not found", allow_module_level=True)
 
 
 class TestArrayExt(unittest.TestCase):

tvtk/tests/test_array_handler.py

@@ -29,6 +29,7 @@ def mysum(arr):
 class TestArrayHandler(unittest.TestCase):
     def _check_arrays(self, arr, vtk_arr):
         self.assertEqual(vtk_arr.GetNumberOfTuples(), len(arr))
+        msg = f"\n{vtk_arr}"
         if len(arr.shape) == 2:
             dim1 = arr.shape[1]
             self.assertEqual(vtk_arr.GetNumberOfComponents(), dim1)
@@ -45,8 +46,7 @@ def _check_arrays(self, arr, vtk_arr):
                     self.assertEqual(chr(int(vtk_arr.GetTuple1(i))), arr[i])
             else:
                 for i in range(len(arr)):
-                    self.assertEqual(vtk_arr.GetTuple1(i), arr[i])
-
+                    self.assertEqual(vtk_arr.GetTuple1(i), arr[i], msg=msg)
 
     def test_array2vtk(self):
         """Test Numeric array to VTK array conversion and vice-versa."""
@@ -63,6 +63,7 @@ def test_array2vtk(self):
         t_z.append(numpy.array([-2147483648, 0, 2147483647], numpy.int32))
         t_z.append(numpy.array([
             -9223372036854775808, 0, 9223372036854775807], numpy.int64))
+        assert t_z[-1][0] == -9223372036854775808
         t_z.append(numpy.array([0, 255], numpy.uint8))
         t_z.append(numpy.array([0, 65535], numpy.uint16))
         t_z.append(numpy.array([0, 4294967295], numpy.uint32))
@@ -160,13 +161,16 @@ def test_array2vtk(self):
         self.assertEqual(vtk_arr.GetValue(2), 0)
         self.assertEqual(vtk_arr.GetValue(3), 1)
 
-        # Make sure the code at least runs for all the non-complex
-        # numerical dtypes in numpy.
-        float_types = [x for x in numpy.sctypes['float']
-                       if x().dtype.name not in ('float16', 'float128')]
-        for dtype in (numpy.sctypes['int'] + numpy.sctypes['uint'] +
-                      float_types):
-            array_handler.array2vtk(numpy.zeros((1,), dtype=dtype))
+        # Make sure the code at least runs for all
+        # numerical dtypes in numpy
+        # except for half, longdouble and complexfloating
+        int_types = ['byte', 'short', 'int', 'intc', 'int_', 'long', 'longlong']
+        uint_types = ['ubyte', 'ushort', 'uintc', 'uint', 'ulong',
+                      'ulonglong']
+        float_types = ['single', 'double']
+        for dtype in int_types + uint_types + float_types:
+            array_handler.array2vtk(numpy.zeros((1,),
+                                    dtype=numpy.dtype(dtype)))
 
     def test_arr2cell_array(self):
         """Test Numeric array to vtkCellArray conversion."""
@@ -201,17 +205,15 @@ def test_arr2cell_array(self):
         cells = array_handler.array2vtkCellArray(a)
         arr = array_handler.vtk2array(cells.GetData())
         expect = numpy.array([3, 0, 1, 2]*3, int)
-        self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)),
-                         True)
+        self.assertTrue(numpy.all(numpy.equal(arr, expect)))
         self.assertEqual(cells.GetNumberOfCells(), N)
 
         # Test if a list of Numeric arrays of different cell lengths works.
         l_a = [a[:,:1], a, a[:2,:2]]
         cells = array_handler.array2vtkCellArray(l_a)
         arr = array_handler.vtk2array(cells.GetData())
         expect = numpy.array([1, 0]*3 + [3, 0, 1, 2]*3 + [2, 0,1]*2, int)
-        self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)),
-                         True)
+        self.assertTrue(numpy.all(numpy.equal(arr, expect)))
         self.assertEqual(cells.GetNumberOfCells(), N*2 + 2)
 
         # This should not take a long while.  This merely tests if a

tvtk/wrapper_gen.py

@@ -679,6 +679,10 @@ def _gen_state_methods(self, klass, out):
 
             if not vtk_val:
                 default = self._reform_name(meths[m][0][0])
+                # Weirdness on NumPy 2.1 and vtk >= 9.3 that this does not show up as
+                # an option and creates problems
+                if klass.__name__ == "vtkPoints" and m == "DataType" and sys.platform == "win32":
+                    d["int32"] = vtk.VTK_ID_TYPE
                 if extra_val is None:
                     t_def = """tvtk_base.RevPrefixMap(%(d)s, default_value='%(default)s')""" % locals()
                 elif hasattr(extra_val, '__iter__'):
@@ -1591,22 +1595,22 @@ def _write_trait_with_range(self, klass, out, vtk_attr_name):
     #         the code for this trait,
     #         i.e. getattr(self, name_of_method)(...)
     special_traits = {
-        '[a-zA-Z0-9]+\.Output$': (
+        r'[a-zA-Z0-9]+\.Output$': (
             False, False, '_write_any_output'),
-        '[a-zA-Z0-9]+\.Source$': (
+        r'[a-zA-Z0-9]+\.Source$': (
             False, False, '_write_any_source'),
-        '[a-zA-Z0-9]+\.ScalarType$': (
+        r'[a-zA-Z0-9]+\.ScalarType$': (
             False, False, '_write_any_scalar_type'),
 
         # In VTK > 4.5, Set/GetInput have multiple signatures
-        '[a-zA-Z0-9]+\.Input$': (
+        r'[a-zA-Z0-9]+\.Input$': (
             False, False, '_write_any_input'),
 
-        '[a-zA-Z0-9]+\.InputConnection$': (
+        r'[a-zA-Z0-9]+\.InputConnection$': (
             False, False, '_write_any_input_connection'),
-        '[a-zA-Z0-9\.]+FileName$': (
+        r'[a-zA-Z0-9\.]+FileName$': (
             True, False, '_write_any_something_file_name'),
-        '[a-zA-Z0-9\.]+FilePrefix$': (
+        r'[a-zA-Z0-9\.]+FilePrefix$': (
             True, False, '_write_any_something_file_prefix'),
         'vtkImageReader2.HeaderSize$': (
             True, False, '_write_image_reader2_header_size'),