Merge pull request #1527 from brian-team/numpy2_compat

Numpy 2 compatibility

.github/workflows/publish.yml

@@ -83,7 +83,6 @@ jobs:
       - name: Build source tarball
         run: |
           python -m pip install --upgrade pip build
-          python -m pip install "cython>=0.29" oldest-supported-numpy "setuptools>=61" "setuptools_scm[toml]>=6.2"
           python -m build --sdist --config-setting=--formats=gztar --config-setting=--with-cython --config-setting=--fail-on-error
         if: ${{ matrix.arch == 'auto64' }}
       - name: Set up QEMU

README.md

@@ -40,8 +40,8 @@ Try out Brian on the [mybinder](https://mybinder.org/) service:
 ## Dependencies
 The following packages need to be installed to use Brian 2 (cf. [`pyproject.toml`](pyproject.toml)):
 
-* Python >= 3.9
-* NumPy >=1.21
+* Python >= 3.10
+* NumPy >=1.23
 * SymPy >= 1.2
 * Cython >= 0.29.21
 * PyParsing

brian2/codegen/runtime/numpy_rt/numpy_rt.py

@@ -127,11 +127,13 @@ def __iter__(self):
             return iter(self.indices)
 
     # Allow conversion to a proper array with np.array(...)
-    def __array__(self, dtype=None):
+    def __array__(self, dtype=None, copy=None):
+        if copy is False:
+            raise ValueError("LazyArange does not support copy=False")
         if self.indices is None:
-            return np.arange(self.start, self.stop)
+            return np.arange(self.start, self.stop, dtype=dtype)
         else:
-            return self.indices + self.start
+            return (self.indices + self.start).astype(dtype)
 
     # Allow basic arithmetics (used when shifting stuff for subgroups)
     def __add__(self, other):

brian2/core/variables.py

@@ -1337,11 +1337,13 @@ def set_with_index_array(self, item, value, check_units):
         variable.get_value()[indices] = value
 
     # Allow some basic calculations directly on the ArrayView object
-    def __array__(self, dtype=None):
+    def __array__(self, dtype=None, copy=None):
         try:
             # This will fail for subexpressions that refer to external
             # parameters
-            self[:]
+            values = self[:]
+            # Never hand over copy = None
+            return np.array(values, dtype=dtype, copy=copy is not False, subok=True)
         except ValueError:
             var = self.variable.name
             raise ValueError(
@@ -1350,7 +1352,6 @@ def __array__(self, dtype=None):
                 f"variables, use 'group.{var}[:]' instead of "
                 f"'group.{var}'"
             )
-        return np.asanyarray(self[:], dtype=dtype)
 
     def __array__ufunc__(self, ufunc, method, *inputs, **kwargs):
         if method == "__call__":
@@ -1434,6 +1435,13 @@ def __iadd__(self, other):
         self[:] = rhs
         return self
 
+    # Support matrix multiplication with @
+    def __matmul__(self, other):
+        return self.get_item(slice(None), level=1) @ np.asanyarray(other)
+
+    def __rmatmul__(self, other):
+        return np.asanyarray(other) @ self.get_item(slice(None), level=1)
+
     def __isub__(self, other):
         if isinstance(other, str):
             raise TypeError(

brian2/parsing/rendering.py

@@ -1,6 +1,7 @@
 import ast
 import numbers
 
+import numpy as np
 import sympy
 
 from brian2.core.functions import DEFAULT_CONSTANTS, DEFAULT_FUNCTIONS
@@ -87,6 +88,9 @@ def render_Name(self, node):
         return node.id
 
     def render_Constant(self, node):
+        if isinstance(node.value, np.number):
+            # repr prints the dtype in numpy 2.0
+            return repr(node.value.item())
         return repr(node.value)
 
     def render_Call(self, node):
@@ -344,7 +348,7 @@ def render_Constant(self, node):
         elif node.value is False:
             return "false"
         else:
-            return repr(node.value)
+            return super().render_Constant(node)
 
     def render_Name(self, node):
         if node.id == "inf":

brian2/tests/test_codegen.py

@@ -10,6 +10,7 @@
 from brian2 import _cache_dirs_and_extensions, clear_cache, prefs
 from brian2.codegen.codeobject import CodeObject
 from brian2.codegen.cpp_prefs import compiler_supports_c99, get_compiler_and_args
+from brian2.codegen.generators.cython_generator import CythonNodeRenderer
 from brian2.codegen.optimisation import optimise_statements
 from brian2.codegen.runtime.cython_rt import CythonCodeObject
 from brian2.codegen.statements import Statement
@@ -22,6 +23,7 @@
 from brian2.core.functions import DEFAULT_CONSTANTS, DEFAULT_FUNCTIONS, Function
 from brian2.core.variables import ArrayVariable, Constant, Subexpression, Variable
 from brian2.devices.device import auto_target, device
+from brian2.parsing.rendering import CPPNodeRenderer, NodeRenderer, NumpyNodeRenderer
 from brian2.parsing.sympytools import str_to_sympy, sympy_to_str
 from brian2.units import ms, second
 from brian2.units.fundamentalunits import Unit
@@ -618,6 +620,25 @@ def test_msvc_flags():
     assert len(previously_stored_flags[hostname])
 
 
+@pytest.mark.codegen_independent
+@pytest.mark.parametrize(
+    "renderer",
+    [
+        NodeRenderer(),
+        NumpyNodeRenderer(),
+        CythonNodeRenderer(),
+        CPPNodeRenderer(),
+    ],
+)
+def test_number_rendering(renderer):
+    import ast
+
+    for number in [0.5, np.float32(0.5), np.float64(0.5)]:
+        # In numpy 2.0, repr(np.float64(0.5)) is 'np.float64(0.5)'
+        node = ast.Constant(value=number)
+        assert renderer.render_node(node) == "0.5"
+
+
 if __name__ == "__main__":
     test_auto_target()
     test_analyse_identifiers()

examples/advanced/stochastic_odes.py

@@ -55,8 +55,8 @@ def exact_solution(t, dt):
 methods = ['milstein', 'heun']
 dts = [1*ms, 0.5*ms, 0.2*ms, 0.1*ms, 0.05*ms, 0.025*ms, 0.01*ms, 0.005*ms]
 
-rows = floor(sqrt(len(dts)))
-cols = ceil(1.0 * len(dts) / rows)
+rows = int(sqrt(len(dts)))
+cols = int(ceil(1.0 * len(dts) / rows))
 errors = dict([(method, zeros(len(dts))) for method in methods])
 for dt_idx, dt in enumerate(dts):
     print('dt: %s' % dt)

pyproject.toml

@@ -5,9 +5,9 @@ authors = [
     {name = 'Dan Goodman'},
     {name ='Romain Brette'}
 ]
-requires-python = '>=3.9'
+requires-python = '>=3.10'
 dependencies = [
-    'numpy>=1.21',
+    'numpy>=1.23.5',
     'cython>=0.29.21',
     'sympy>=1.2',
     'pyparsing',
@@ -60,10 +60,11 @@ fallback_version = 'unknown'
 [build-system]
 requires = [
     "setuptools>=61",
-    "numpy>=1.10",
+    # By building against numpy 2.0, we make sure that the wheel is compatible with
+    # both numpy 2.0 and numpy>=1.23
+    "numpy>=2.0.0rc1",
     "wheel",
     "Cython",
-    "oldest-supported-numpy",
     "setuptools_scm[toml]>=6.2"
 ]
 build-backend = "setuptools.build_meta"

versions.md

@@ -6,7 +6,6 @@ This file contains a list of other files where versions of packages are specifie
 In the future it would be advantageous to implement an automated way of keep versions synchronised across files e.g. https://github.com/pre-commit/pre-commit/issues/945#issuecomment-527603460 or preferably parsing `.pre-commit-config.yaml` and using it to `pip install` requirements (see discussion here: https://github.com/brian-team/brian2/pull/1449#issuecomment-1372476018). Until then, the files are listed below for manual checking and updating. 
 
 * [`README.md`](https://github.com/brian-team/brian2/blob/master/README.md)
-* [`setup.py`](https://github.com/brian-team/brian2/blob/master/setup.py)
 * [`rtd-requirements.txt`](https://github.com/brian-team/brian2/blob/master/rtd-requirements.txt)
 * [`pyproject.toml`](https://github.com/brian-team/brian2/blob/master/pyproject.toml)
 * [`.pre-commit-config.yaml`](https://github.com/brian-team/brian2/blob/master/.pre-commit-config.yaml)