Add support for TypedList in numba backend

Note: Numba object mode fallback is not safe with lists

Author: ricardoV94

pytensor/link/numba/dispatch/__init__.py

@@ -17,6 +17,7 @@
 import pytensor.link.numba.dispatch.sparse
 import pytensor.link.numba.dispatch.subtensor
 import pytensor.link.numba.dispatch.tensor_basic
+import pytensor.link.numba.dispatch.typed_list
 
 
 # isort: on

pytensor/link/numba/dispatch/basic.py

@@ -23,6 +23,7 @@
 from pytensor.tensor.random.type import RandomGeneratorType
 from pytensor.tensor.type import TensorType
 from pytensor.tensor.utils import hash_from_ndarray
+from pytensor.typed_list import TypedListType
 
 
 def _filter_numba_warnings():
@@ -132,6 +133,8 @@ def get_numba_type(
             return CSCMatrixType(numba_dtype)
     elif isinstance(pytensor_type, RandomGeneratorType):
         return numba.types.NumPyRandomGeneratorType("NumPyRandomGeneratorType")
+    elif isinstance(pytensor_type, TypedListType):
+        return numba.types.List(get_numba_type(pytensor_type.ttype))
     else:
         raise NotImplementedError(f"Numba type not implemented for {pytensor_type}")
 
@@ -260,7 +263,10 @@ def numba_typify(data, dtype=None, **kwargs):
 
 
 def generate_fallback_impl(op, node, storage_map=None, **kwargs):
-    """Create a Numba compatible function from a Pytensor `Op`."""
+    """Create a Numba compatible function from a Pytensor `Op`.
+
+    Note limitations: https://numba.pydata.org/numba-doc/dev/user/withobjmode.html#the-objmode-context-manager
+    """
 
     warnings.warn(
         f"Numba will use object mode to run {op}'s perform method. "

pytensor/link/numba/dispatch/typed_list.py

@@ -0,0 +1,219 @@
+import numba
+import numpy as np
+
+import pytensor.link.numba.dispatch.basic as numba_basic
+from pytensor.link.numba.dispatch.basic import register_funcify_default_op_cache_key
+from pytensor.link.numba.dispatch.compile_ops import numba_deepcopy
+from pytensor.tensor.type_other import SliceType
+from pytensor.typed_list import (
+    Append,
+    Count,
+    Extend,
+    GetItem,
+    Index,
+    Insert,
+    Length,
+    MakeList,
+    Remove,
+    Reverse,
+)
+
+
+def numba_all_equal(x, y):
+    if isinstance(x, np.ndarray) or isinstance(y, np.ndarray):
+        if not (isinstance(x, np.ndarray) and isinstance(y, np.ndarray)):
+            return False
+        return (x == y).all()
+    if isinstance(x, list) or isinstance(y, list):
+        if not (isinstance(x, list) and isinstance(y, list)):
+            return False
+        if len(x) != len(y):
+            return False
+        return all(numba_all_equal(xi, yi) for xi, yi in zip(x, y))
+    return x == y
+
+
+@numba.extending.overload(numba_all_equal)
+def list_all_equal(x, y):
+    all_equal = None
+
+    if isinstance(x, numba.types.List) and isinstance(y, numba.types.List):
+
+        def all_equal(x, y):
+            if len(x) != len(y):
+                return False
+            for xi, yi in zip(x, y):
+                if not numba_all_equal(xi, yi):
+                    return False
+            return True
+
+    if isinstance(x, numba.types.Array) and isinstance(y, numba.types.Array):
+
+        def all_equal(x, y):
+            return (x == y).all()
+
+    if isinstance(x, numba.types.Number) and isinstance(y.numba.types.Number):
+
+        def all_equal(x, y):
+            return x == y
+
+    return all_equal
+
+
+@numba.extending.overload(numba_deepcopy)
+def numba_deepcopy_list(x):
+    if isinstance(x, numba.types.List):
+
+        def deepcopy_list(x):
+            return [numba_deepcopy(xi) for xi in x]
+
+        return deepcopy_list
+
+
+@register_funcify_default_op_cache_key(MakeList)
+def numba_funcify_make_list(op, node, **kwargs):
+    @numba_basic.numba_njit
+    def make_list(*args):
+        return [numba_deepcopy(arg) for arg in args]
+
+    return make_list
+
+
+@register_funcify_default_op_cache_key(Length)
+def numba_funcify_list_length(op, node, **kwargs):
+    @numba_basic.numba_njit
+    def list_length(x):
+        return np.array(len(x), dtype=np.int64)
+
+    return list_length
+
+
+@register_funcify_default_op_cache_key(GetItem)
+def numba_funcify_list_get_item(op, node, **kwargs):
+    if isinstance(node.inputs[1].type, SliceType):
+
+        @numba_basic.numba_njit
+        def list_get_item_slice(x, index):
+            return x[index]
+
+        return list_get_item_slice
+
+    else:
+
+        @numba_basic.numba_njit
+        def list_get_item_index(x, index):
+            return x[index.item()]
+
+        return list_get_item_index
+
+
+@register_funcify_default_op_cache_key(Reverse)
+def numba_funcify_list_reverse(op, node, **kwargs):
+    inplace = op.inplace
+
+    @numba_basic.numba_njit
+    def list_reverse(x):
+        if inplace:
+            z = x
+        else:
+            z = numba_deepcopy(x)
+        z.reverse()
+        return z
+
+    return list_reverse
+
+
+@register_funcify_default_op_cache_key(Append)
+def numba_funcify_list_append(op, node, **kwargs):
+    inplace = op.inplace
+
+    @numba_basic.numba_njit
+    def list_append(x, to_append):
+        if inplace:
+            z = x
+        else:
+            z = numba_deepcopy(x)
+        z.append(numba_deepcopy(to_append))
+        return z
+
+    return list_append
+
+
+@register_funcify_default_op_cache_key(Extend)
+def numba_funcify_list_extend(op, node, **kwargs):
+    inplace = op.inplace
+
+    @numba_basic.numba_njit
+    def list_extend(x, to_append):
+        if inplace:
+            z = x
+        else:
+            z = numba_deepcopy(x)
+        z.extend(numba_deepcopy(to_append))
+        return z
+
+    return list_extend
+
+
+@register_funcify_default_op_cache_key(Insert)
+def numba_funcify_list_insert(op, node, **kwargs):
+    inplace = op.inplace
+
+    @numba_basic.numba_njit
+    def list_insert(x, index, to_insert):
+        if inplace:
+            z = x
+        else:
+            z = numba_deepcopy(x)
+        z.insert(index.item(), numba_deepcopy(to_insert))
+        return z
+
+    return list_insert
+
+
+@register_funcify_default_op_cache_key(Index)
+def numba_funcify_list_index(op, node, **kwargs):
+    @numba_basic.numba_njit
+    def list_index(x, elem):
+        for idx, xi in enumerate(x):
+            if numba_all_equal(xi, elem):
+                break
+        return np.array(idx, dtype=np.int64)
+
+    return list_index
+
+
+@register_funcify_default_op_cache_key(Count)
+def numba_funcify_list_count(op, node, **kwargs):
+    @numba_basic.numba_njit
+    def list_count(x, elem):
+        c = 0
+        for xi in x:
+            if numba_all_equal(xi, elem):
+                c += 1
+        return np.array(c, dtype=np.int64)
+
+    return list_count
+
+
+@register_funcify_default_op_cache_key(Remove)
+def numba_funcify_list_remove(op, node, **kwargs):
+    inplace = op.inplace
+
+    @numba_basic.numba_njit
+    def list_remove(x, to_remove):
+        if inplace:
+            z = x
+        else:
+            z = numba_deepcopy(x)
+        index_to_remove = -1
+        for i, zi in enumerate(z):
+            if numba_all_equal(zi, to_remove):
+                index_to_remove = i
+                break
+        if index_to_remove == -1:
+            raise ValueError("list.remove(x): x not in list")
+        z.pop(index_to_remove)
+        return z
+
+    return list_remove

tests/link/numba/test_typed_list.py

@@ -0,0 +1,46 @@
+import numpy as np
+
+from pytensor.tensor import matrix
+from pytensor.typed_list import make_list
+from tests.link.numba.test_basic import compare_numba_and_py
+
+
+def test_list_basic_ops():
+    x = matrix("x", shape=(3, None), dtype="int64")
+    l = make_list([x[0], x[2]])
+
+    x_test = np.arange(12).reshape(3, 4)
+    compare_numba_and_py([x], [l, l.length()], [x_test])
+
+    # Test nested list
+    ll = make_list([l, l, l])
+    compare_numba_and_py([x], [ll, ll.length()], [x_test])
+
+
+def test_make_list_index_ops():
+    x = matrix("x", shape=(3, None), dtype="int64")
+    l = make_list([x[0], x[2]])
+
+    x_test = np.arange(12).reshape(3, 4)
+    compare_numba_and_py([x], [l[-1], l[:-1], l.reverse()], [x_test])
+
+
+def test_make_list_extend_ops():
+    x = matrix("x", shape=(3, None), dtype="int64")
+    l = make_list([x[0], x[2]])
+
+    x_test = np.arange(12).reshape(3, 4)
+    compare_numba_and_py(
+        [x], [l.append(x[1]), l.extend(l), l.insert(0, x[1])], [x_test]
+    )
+
+
+def test_make_list_find_ops():
+    # Remove requires to first find it
+    x = matrix("x", shape=(3, None), dtype="int64")
+    y = x[0].type("y")
+    l = make_list([x[0], x[2], x[0], x[2]])
+
+    x_test = np.arange(12).reshape(3, 4)
+    test_y = x_test[2]
+    compare_numba_and_py([x, y], [l.ind(y), l.count(y), l.remove(y)], [x_test, test_y])