Numpy 2.0 compability (#6238)

.github/workflows/test.yaml

@@ -85,15 +85,21 @@ jobs:
         run: |
           MATRIX=$(jq -nsc '{
               "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
-              "environment": ["test-39", "test-312"]
+              "environment": ["test-39", "test-312"],
+              "include": [
+                { "os": "ubuntu-latest", "environment": "test-numpy" }
+              ]
           }')
           echo "MATRIX=$MATRIX" >> $GITHUB_ENV
       - name: Set test matrix with 'full' option
         if: env.MATRIX_OPTION == 'full'
         run: |
           MATRIX=$(jq -nsc '{
               "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
-              "environment": ["test-39", "test-310", "test-311", "test-312"]
+              "environment": ["test-39", "test-310", "test-311", "test-312"],
+              "include": [
+                { "os": "ubuntu-latest", "environment": "test-numpy" }
+              ]
           }')
           echo "MATRIX=$MATRIX" >> $GITHUB_ENV
       - name: Set test matrix with 'downstream' option

examples/conftest.py

@@ -1,6 +1,7 @@
 import os
 import platform
 import sys
+from importlib.util import find_spec
 
 import bokeh
 import pandas as pd
@@ -62,6 +63,22 @@
         "user_guide/Plotting_with_Matplotlib.ipynb",
     ]
 
+# 2024-05: Numpy 2.0
+if find_spec("datashader") is None:
+    collect_ignore_glob += [
+        "reference/elements/matplotlib/ImageStack.ipynb",
+        "reference/elements/plotly/ImageStack.ipynb",
+        "user_guide/15-Large_Data.ipynb",
+        "user_guide/16-Streaming_Data.ipynb",
+        "user_guide/Linked_Brushing.ipynb",
+        "user_guide/Network_Graphs.ipynb",
+    ]
+
+if find_spec("scikit-image"):
+    collect_ignore_glob += [
+        "user_guide/Network_Graphs.ipynb",
+    ]
+
 
 def pytest_runtest_makereport(item, call):
     """

holoviews/core/sheetcoords.py

@@ -365,7 +365,7 @@ def __new__(cls, bounds, sheet_coordinate_system, force_odd=False,
         else:
             slicespec=Slice._boundsspec2slicespec(bounds.lbrt(),sheet_coordinate_system)
         # Using numpy.int32 for legacy reasons
-        a = np.array(slicespec, dtype=np.int32, copy=False).view(cls)
+        a = np.asarray(slicespec, dtype=np.int32).view(cls)
         return a
 
 

holoviews/core/util.py

@@ -50,6 +50,9 @@
 _PANDAS_ROWS_LARGE = 1_000_000
 _PANDAS_SAMPLE_SIZE = 1_000_000
 
+numpy_version = Version(Version(np.__version__).base_version)
+NUMPY_GE_200 = numpy_version >= Version("2")
+
 pandas_version = Version(pd.__version__)
 try:
     if pandas_version >= Version('1.3.0'):

holoviews/tests/core/test_dimensions.py

@@ -5,6 +5,7 @@
 import pandas as pd
 
 from holoviews.core import Dimension, Dimensioned
+from holoviews.core.util import NUMPY_GE_200
 from holoviews.element.comparison import ComparisonTestCase
 
 from ..utils import LoggingComparisonTestCase
@@ -243,7 +244,10 @@ def test_tuple_clone(self):
 class DimensionDefaultTest(ComparisonTestCase):
 
     def test_validate_default_against_values(self):
-        msg = r"Dimension\('A'\) default 1\.1 not found in declared values: \[0, 1\]"
+        if NUMPY_GE_200:
+            msg = r"Dimension\('A'\) default 1\.1 not found in declared values: \[np\.int64\(0\), np\.int64\(1\)\]"
+        else:
+            msg = r"Dimension\('A'\) default 1\.1 not found in declared values: \[0, 1\]"
         with self.assertRaisesRegex(ValueError, msg):
             Dimension('A', values=[0, 1], default=1.1)
 

holoviews/tests/element/test_comparisondimension.py

@@ -2,6 +2,7 @@
 Test cases for Dimension and Dimensioned object comparison.
 """
 from holoviews.core import Dimension, Dimensioned
+from holoviews.core.util import NUMPY_GE_200
 from holoviews.element.comparison import ComparisonTestCase
 
 
@@ -74,7 +75,11 @@ def test_dimension_comparison_values_unequal(self):
         try:
             self.assertEqual(self.dimension4, self.dimension8)
         except AssertionError as e:
-            self.assertEqual(str(e), "Dimension parameter 'values' mismatched: [] != ['a', 'b']")
+            if NUMPY_GE_200:
+                msg = "Dimension parameter 'values' mismatched: [] != [np.str_('a'), np.str_('b')]"
+            else:
+                msg = "Dimension parameter 'values' mismatched: [] != ['a', 'b']"
+            self.assertEqual(str(e), msg)
 
     def test_dimension_comparison_types_unequal(self):
         try:

holoviews/tests/test_streams.py

@@ -11,7 +11,7 @@
 
 import holoviews as hv
 from holoviews.core.spaces import DynamicMap
-from holoviews.core.util import Version
+from holoviews.core.util import NUMPY_GE_200, Version
 from holoviews.element import Curve, Histogram, Points, Polygons, Scatter
 from holoviews.element.comparison import ComparisonTestCase
 from holoviews.streams import *  # noqa (Test all available streams)
@@ -1421,6 +1421,7 @@ def test_selection_expr_stream_hist_invert_xaxis_yaxis(self):
 
 
     def test_selection_expr_stream_polygon_index_cols(self):
+        # TODO: Should test both spatialpandas and shapely
         # Create SelectionExpr on element
         try: import shapely # noqa
         except ImportError:
@@ -1444,10 +1445,12 @@ def test_selection_expr_stream_polygon_index_cols(self):
         self.assertIsNone(expr_stream.bbox)
         self.assertIsNone(expr_stream.selection_expr)
 
+        fmt = lambda x: list(map(np.str_, x)) if NUMPY_GE_200 else x
+
         expr_stream.input_streams[2].event(index=[0, 1])
         self.assertEqual(
             repr(expr_stream.selection_expr),
-            repr(dim('cat').isin(['a', 'b']))
+            repr(dim('cat').isin(fmt(['a', 'b'])))
         )
         self.assertEqual(expr_stream.bbox, None)
         self.assertEqual(len(events), 1)
@@ -1456,23 +1459,23 @@ def test_selection_expr_stream_polygon_index_cols(self):
         expr_stream.input_streams[0].event(bounds=(0, 0, 4, 1))
         self.assertEqual(
             repr(expr_stream.selection_expr),
-            repr(dim('cat').isin(['a', 'b']))
+            repr(dim('cat').isin(fmt(['a', 'b'])))
         )
         self.assertEqual(len(events), 1)
 
         # Ensure geometry event does trigger another update
         expr_stream.input_streams[1].event(geometry=np.array([(0, 0), (4, 0), (4, 2), (0, 2)]))
         self.assertEqual(
             repr(expr_stream.selection_expr),
-            repr(dim('cat').isin(['a', 'b', 'c']))
+            repr(dim('cat').isin(fmt(['a', 'b', 'c'])))
         )
         self.assertEqual(len(events), 2)
 
         # Ensure index event does trigger another update
         expr_stream.input_streams[2].event(index=[1, 2])
         self.assertEqual(
             repr(expr_stream.selection_expr),
-            repr(dim('cat').isin(['b', 'c']))
+            repr(dim('cat').isin(fmt(['b', 'c'])))
         )
         self.assertEqual(expr_stream.bbox, None)
         self.assertEqual(len(events), 3)

pixi.toml

@@ -15,6 +15,7 @@ test-311 = ["py311", "test-core", "test", "example", "test-example", "test-unit-
 test-312 = ["py312", "test-core", "test", "example", "test-example", "test-unit-task"]
 test-ui = ["py312", "test-core", "test", "test-ui"]
 test-core = ["py312", "test-core", "test-unit-task"]
+test-numpy = ["py312", "test-core", "test-unit-task", "numpy2", "test-example"]
 test-gpu = ["py311", "test-core", "test", "test-gpu"]
 docs = ["py311", "example", "doc"]
 build = ["py311", "build"]
@@ -134,6 +135,39 @@ rmm = { version = "*", channel = "rapidsai" }
 [feature.test-gpu.tasks]
 test-gpu = { cmd = "pytest holoviews/tests --gpu", env = { NUMBA_CUDA_LOW_OCCUPANCY_WARNINGS = '0' } }
 
+[feature.numpy2]
+channels = ["pyviz/label/dev", "conda-forge/label/numpy_rc", "numba/label/dev", "conda-forge"]
+
+[feature.numpy2.dependencies]
+numpy = "2.*"
+numba = { version = "0.60.*", channel = "numba/label/dev" }
+llvmlite = { version = "*", channel = "numba/label/dev" }
+
+# test dependencies
+cftime = "*"
+contourpy = "*"
+dask-core = "*"
+datashader = ">=0.11.1"
+ffmpeg = "*"
+ibis-sqlite = "*"
+nbconvert = "*"
+networkx = "*"
+pillow = "*"
+scipy = ">=1.10" # Python 3.9 + Windows downloads 1.9
+selenium = "*"
+shapely = "*"
+# spatialpandas = "*"
+xarray = ">=0.10.4"
+xyzservices = "*"
+
+# Examples (removed duplicates)
+# netcdf4 = "*"
+notebook = "*"
+pooch = "*"
+# pyarrow = "*"
+# scikit-image = "*"
+streamz = ">=0.5.0"
+
 # =============================================
 # =================== DOCS ====================
 # =============================================

pyproject.toml

@@ -90,7 +90,7 @@ filterwarnings = [
     # 2023-01: Sqlalchemy 2.0 warning:
     "ignore: Deprecated API features detected:DeprecationWarning:ibis.backends.base.sql.alchemy", # https://github.com/ibis-project/ibis/issues/5048
     # 2023-03: Already handling the nested sequence
-    "ignore:Creating an ndarray from ragged nested sequences:numpy.VisibleDeprecationWarning:holoviews.core.data.spatialpandas",
+    "ignore:Creating an ndarray from ragged nested sequences::holoviews.core.data.spatialpandas",
     # 2023-09: Dash needs to update their code to use the comm module and pkg_resources
     "ignore:The `.+?` class has been deprecated:DeprecationWarning:dash._jupyter",
     "ignore:pkg_resources is deprecated as an API:DeprecationWarning:dash.dash",