Fix Scan JAX dispatcher

pytensor/link/jax/dispatch/scan.py

 import jax
 import jax.numpy as jnp
 
-from pytensor.graph.fg import FunctionGraph
 from pytensor.link.jax.dispatch.basic import jax_funcify
 from pytensor.scan.op import Scan
-from pytensor.scan.utils import ScanArgs
 
 
 @jax_funcify.register(Scan)
-def jax_funcify_Scan(op, **kwargs):
-    inner_fg = FunctionGraph(op.inputs, op.outputs)
-    jax_at_inner_func = jax_funcify(inner_fg, **kwargs)
+def jax_funcify_Scan(op: Scan, **kwargs):
+    info = op.info
 
-    def scan(*outer_inputs):
-        scan_args = ScanArgs(
-            list(outer_inputs), [None] * op.info.n_outs, op.inputs, op.outputs, op.info
+    if info.as_while:
+        raise NotImplementedError("While Scan cannot yet be converted to JAX")
+
+    if info.n_mit_mot:
+        raise NotImplementedError(
+            "Scan with MIT-MOT (gradients of scan) cannot yet be converted to JAX"
         )
 
-        # `outer_inputs` is a list with the following composite form:
-        # [n_steps]
-        # + outer_in_seqs
-        # + outer_in_mit_mot
-        # + outer_in_mit_sot
-        # + outer_in_sit_sot
-        # + outer_in_shared
-        # + outer_in_nit_sot
-        # + outer_in_non_seqs
-        n_steps = scan_args.n_steps
-        seqs = scan_args.outer_in_seqs
-
-        # TODO: mit_mots
-        mit_mot_in_slices = []
-
-        mit_sot_in_slices = []
-        for tap, seq in zip(scan_args.mit_sot_in_slices, scan_args.outer_in_mit_sot):
-            neg_taps = [abs(t) for t in tap if t < 0]
-            pos_taps = [abs(t) for t in tap if t > 0]
-            max_neg = max(neg_taps) if neg_taps else 0
-            max_pos = max(pos_taps) if pos_taps else 0
-            init_slice = seq[: max_neg + max_pos]
-            mit_sot_in_slices.append(init_slice)
-
-        sit_sot_in_slices = [seq[0] for seq in scan_args.outer_in_sit_sot]
+    # Optimize inner graph
+    rewriter = op.mode_instance.optimizer
+    rewriter(op.fgraph)
+    scan_inner_func = jax_funcify(op.fgraph, **kwargs)
+
+    def scan(*outer_inputs):
+        # Extract JAX scan inputs
+        outer_inputs = list(outer_inputs)
+        n_steps = outer_inputs[0]  # JAX `length`
+        seqs = op.outer_seqs(outer_inputs)  # JAX `xs`
+
+        mit_sot_init = []
+        for tap, seq in zip(op.info.mit_sot_in_slices, op.outer_mitsot(outer_inputs)):
+            init_slice = seq[: abs(min(tap))]
+            mit_sot_init.append(init_slice)
+
+        sit_sot_init = [seq[0] for seq in op.outer_sitsot(outer_inputs)]
 
         init_carry = (
-            mit_mot_in_slices,
-            mit_sot_in_slices,
-            sit_sot_in_slices,
-            scan_args.outer_in_shared,
-            scan_args.outer_in_non_seqs,
-        )
+            mit_sot_init,
+            sit_sot_init,
+            op.outer_shared(outer_inputs),
+            op.outer_non_seqs(outer_inputs),
+        )  # JAX `init`
+
+        def jax_args_to_inner_func_args(carry, x):
+            """Convert JAX scan arguments into format expected by scan_inner_func.
+
+            scan(carry, x) -> scan_inner_func(seqs, mit_sot, sit_sot, shared, non_seqs)
+            """
 
-        def jax_args_to_inner_scan(op, carry, x):
-            # `carry` contains all inner-output taps, non_seqs, and shared
-            # terms
+            # `carry` contains all inner taps, shared terms, and non_seqs
             (
-                inner_in_mit_mot,
-                inner_in_mit_sot,
-                inner_in_sit_sot,
-                inner_in_shared,
-                inner_in_non_seqs,
+                inner_mit_sot,
+                inner_sit_sot,
+                inner_shared,
+                inner_non_seqs,
             ) = carry
 
-            # `x` contains the in_seqs
-            inner_in_seqs = x
-
-            # `inner_scan_inputs` is a list with the following composite form:
-            # inner_in_seqs
-            # + sum(inner_in_mit_mot, [])
-            # + sum(inner_in_mit_sot, [])
-            # + inner_in_sit_sot
-            # + inner_in_shared
-            # + inner_in_non_seqs
-            inner_in_mit_sot_flatten = []
-            for array, index in zip(inner_in_mit_sot, scan_args.mit_sot_in_slices):
-                inner_in_mit_sot_flatten.extend(array[jnp.array(index)])
-
-            inner_scan_inputs = sum(
-                [
-                    inner_in_seqs,
-                    inner_in_mit_mot,
-                    inner_in_mit_sot_flatten,
-                    inner_in_sit_sot,
-                    inner_in_shared,
-                    inner_in_non_seqs,
-                ],
-                [],
-            )
+            # `x` contains the inner sequences
+            inner_seqs = x
+
+            mit_sot_flatten = []
+            for array, index in zip(inner_mit_sot, op.info.mit_sot_in_slices):
+                mit_sot_flatten.extend(array[jnp.array(index)])
+
+            inner_scan_inputs = [
+                *inner_seqs,
+                *mit_sot_flatten,
+                *inner_sit_sot,
+                *inner_shared,
+                *inner_non_seqs,
+            ]
 
             return inner_scan_inputs
 
-        def inner_scan_outs_to_jax_outs(
-            op,
+        def inner_func_outs_to_jax_outs(
             old_carry,
             inner_scan_outs,
         ):
+            """Convert inner_scan_func outputs into format expected by JAX scan.
+
+            old_carry + (mit_sot_outs, sit_sot_outs, nit_sot_outs, shared_outs) -> (new_carry, ys)
+            """
             (
-                inner_in_mit_mot,
-                inner_in_mit_sot,
-                inner_in_sit_sot,
-                inner_in_shared,
-                inner_in_non_seqs,
+                inner_mit_sot,
+                inner_sit_sot,
+                inner_shared,
+                inner_non_seqs,
             ) = old_carry
 
-            def update_mit_sot(mit_sot, new_val):
-                return jnp.concatenate([mit_sot[1:], new_val[None, ...]], axis=0)
-
-            inner_out_mit_sot = [
-                update_mit_sot(mit_sot, new_val)
-                for mit_sot, new_val in zip(inner_in_mit_sot, inner_scan_outs)
+            inner_mit_sot_outs = op.inner_mitsot_outs(inner_scan_outs)
+            inner_sit_sot_outs = op.inner_sitsot_outs(inner_scan_outs)
+            inner_nit_sot_outs = op.inner_nitsot_outs(inner_scan_outs)
+            inner_shared_outs = op.inner_shared_outs(inner_scan_outs)
+
+            # Replace the oldest mit_sot tap by the newest value
+            inner_mit_sot_new = [
+                jnp.concatenate([old_mit_sot[1:], new_val[None, ...]], axis=0)
+                for old_mit_sot, new_val in zip(
+                    inner_mit_sot,
+                    inner_mit_sot_outs,
+                )
             ]
 
-            # This should contain all inner-output taps, non_seqs, and shared
-            # terms
-            if not inner_in_sit_sot:
-                inner_out_sit_sot = []
-            else:
-                inner_out_sit_sot = inner_scan_outs
+            # Nothing needs to be done with sit_sot
+            inner_sit_sot_new = inner_sit_sot_outs
+
+            inner_shared_new = inner_shared
+            # Replace old shared inputs by new shared outputs
+            inner_shared_new[: len(inner_shared_outs)] = inner_shared_outs
+
             new_carry = (
-                inner_in_mit_mot,
+                inner_mit_sot_new,
+                inner_sit_sot_new,
+                inner_shared_new,
+                inner_non_seqs,
+            )
+
+            # Shared variables and non_seqs are not traced
+            traced_outs = [
+                *inner_mit_sot_outs,
+                *inner_sit_sot_outs,
+                *inner_nit_sot_outs,
+            ]
+
+            return new_carry, traced_outs
+
+        def jax_inner_func(carry, x):
+            inner_args = jax_args_to_inner_func_args(carry, x)
+            inner_scan_outs = list(scan_inner_func(*inner_args))
+            new_carry, traced_outs = inner_func_outs_to_jax_outs(carry, inner_scan_outs)
+            return new_carry, traced_outs
+
+        # Extract PyTensor scan outputs
+        final_carry, traces = jax.lax.scan(
+            jax_inner_func, init_carry, seqs, length=n_steps
+        )
+
+        def get_partial_traces(traces):
+            """Convert JAX scan traces to PyTensor traces.
+
+            We need to:
+                1. Prepend initial states to JAX output traces
+                2. Slice final traces if Scan was instructed to only keep a portion
+            """
+
+            init_states = mit_sot_init + sit_sot_init + [None] * op.info.n_nit_sot
+            buffers = (
+                op.outer_mitsot(outer_inputs)
+                + op.outer_sitsot(outer_inputs)
+                + op.outer_nitsot(outer_inputs)
+            )
+            partial_traces = []
+            for init_state, trace, buffer in zip(init_states, traces, buffers):
+                if init_state is not None:
+                    # MIT-SOT and SIT-SOT: The final output should be as long as the input buffer
+                    full_trace = jnp.concatenate(
+                        [jnp.atleast_1d(init_state), jnp.atleast_1d(trace)],
+                        axis=0,
+                    )
+                    buffer_size = buffer.shape[0]
+                else:
+                    # NIT-SOT: Buffer is just the number of entries that should be returned
+                    full_trace = jnp.atleast_1d(trace)
+                    buffer_size = buffer
+
+                partial_trace = full_trace[-buffer_size:]
+                partial_traces.append(partial_trace)
+
+            return partial_traces
+
+        def get_shared_outs(final_carry):
+            """Retrive last state of shared_outs from final_carry.
+
+            These outputs cannot be traced in PyTensor Scan
+            """
+            (
                 inner_out_mit_sot,
                 inner_out_sit_sot,
-                inner_in_shared,
+                inner_out_shared,
                 inner_in_non_seqs,
-            )
+            ) = final_carry
 
-            return new_carry
+            shared_outs = inner_out_shared[: info.n_shared_outs]
+            return list(shared_outs)
 
-        def jax_inner_func(carry, x):
-            inner_args = jax_args_to_inner_scan(op, carry, x)
-            inner_scan_outs = list(jax_at_inner_func(*inner_args))
-            new_carry = inner_scan_outs_to_jax_outs(op, carry, inner_scan_outs)
-            return new_carry, inner_scan_outs
-
-        _, scan_out = jax.lax.scan(jax_inner_func, init_carry, seqs, length=n_steps)
-
-        # We need to prepend the initial values so that the JAX output will
-        # match the raw `Scan` `Op` output and, thus, work with a downstream
-        # `Subtensor` `Op` introduced by the `scan` helper function.
-        def append_scan_out(scan_in_part, scan_out_part):
-            return jnp.concatenate([scan_in_part[:-n_steps], scan_out_part], axis=0)
-
-        if scan_args.outer_in_mit_sot:
-            scan_out_final = [
-                append_scan_out(init, out)
-                for init, out in zip(scan_args.outer_in_mit_sot, scan_out)
-            ]
-        elif scan_args.outer_in_sit_sot:
-            scan_out_final = [
-                append_scan_out(init, out)
-                for init, out in zip(scan_args.outer_in_sit_sot, scan_out)
-            ]
+        scan_outs_final = get_partial_traces(traces) + get_shared_outs(final_carry)
 
-        if len(scan_out_final) == 1:
-            scan_out_final = scan_out_final[0]
-        return scan_out_final
+        if len(scan_outs_final) == 1:
+            scan_outs_final = scan_outs_final[0]
+        return scan_outs_final
 
     return scan

tests/link/jax/test_scan.py

+import re
+
 import numpy as np
 import pytest
-from packaging.version import parse as version_parse
 
 import pytensor.tensor as at
+from pytensor import function, shared
+from pytensor.compile import get_mode
 from pytensor.configdefaults import config
 from pytensor.graph.fg import FunctionGraph
+from pytensor.scan import until
 from pytensor.scan.basic import scan
+from pytensor.scan.op import Scan
+from pytensor.tensor import random
 from pytensor.tensor.math import gammaln, log
-from pytensor.tensor.type import ivector, lscalar, scalar
+from pytensor.tensor.type import lscalar, scalar, vector
 from tests.link.jax.test_basic import compare_jax_and_py
 
 
 jax = pytest.importorskip("jax")
 
 
-@pytest.mark.xfail(
-    version_parse(jax.__version__) >= version_parse("0.2.12"),
-    reason="Omnistaging cannot be disabled",
-)
-def test_jax_scan_multiple_output():
+@pytest.mark.parametrize("view", [None, (-1,), slice(-2, None, None)])
+def test_scan_sit_sot(view):
+    x0 = at.scalar("x0", dtype="float64")
+    xs, _ = scan(
+        lambda xtm1: xtm1 + 1,
+        outputs_info=[x0],
+        n_steps=10,
+    )
+    if view:
+        xs = xs[view]
+    fg = FunctionGraph([x0], [xs])
+    test_input_vals = [np.e]
+    compare_jax_and_py(fg, test_input_vals)
+
+
+@pytest.mark.parametrize("view", [None, (-1,), slice(-4, -1, None)])
+def test_scan_mit_sot(view):
+    x0 = at.vector("x0", dtype="float64", shape=(3,))
+    xs, _ = scan(
+        lambda xtm3, xtm1: xtm3 + xtm1 + 1,
+        outputs_info=[{"initial": x0, "taps": [-3, -1]}],
+        n_steps=10,
+    )
+    if view:
+        xs = xs[view]
+    fg = FunctionGraph([x0], [xs])
+    test_input_vals = [np.full((3,), np.e)]
+    compare_jax_and_py(fg, test_input_vals)
+
+
+@pytest.mark.parametrize("view_x", [None, (-1,), slice(-4, -1, None)])
+@pytest.mark.parametrize("view_y", [None, (-1,), slice(-4, -1, None)])
+def test_scan_multiple_mit_sot(view_x, view_y):
+    x0 = at.vector("x0", dtype="float64", shape=(3,))
+    y0 = at.vector("y0", dtype="float64", shape=(4,))
+
+    def step(xtm3, xtm1, ytm4, ytm2):
+        return xtm3 + ytm4 + 1, xtm1 + ytm2 + 2
+
+    [xs, ys], _ = scan(
+        fn=step,
+        outputs_info=[
+            {"initial": x0, "taps": [-3, -1]},
+            {"initial": y0, "taps": [-4, -2]},
+        ],
+        n_steps=10,
+    )
+    if view_x:
+        xs = xs[view_x]
+    if view_y:
+        ys = ys[view_y]
+
+    fg = FunctionGraph([x0, y0], [xs, ys])
+    test_input_vals = [np.full((3,), np.e), np.full((4,), np.pi)]
+    compare_jax_and_py(fg, test_input_vals)
+
+
+@pytest.mark.parametrize("view", [None, (-2,), slice(None, None, 2)])
+def test_scan_nit_sot(view):
+    rng = np.random.default_rng(seed=49)
+
+    xs = at.vector("x0", dtype="float64", shape=(10,))
+
+    ys, _ = scan(
+        lambda x: at.exp(x),
+        outputs_info=[None],
+        sequences=[xs],
+    )
+    if view:
+        ys = ys[view]
+    fg = FunctionGraph([xs], [ys])
+    test_input_vals = [rng.normal(size=10)]
+    # We need to remove pushout rewrites, or the whole scan would just be
+    # converted to an Elemwise on xs
+    jax_fn, _ = compare_jax_and_py(
+        fg, test_input_vals, jax_mode=get_mode("JAX").excluding("scan_pushout")
+    )
+    scan_nodes = [
+        node for node in jax_fn.maker.fgraph.apply_nodes if isinstance(node.op, Scan)
+    ]
+    assert len(scan_nodes) == 1
+
+
+@pytest.mark.xfail(raises=NotImplementedError)
+def test_scan_mit_mot():
+    xs = at.vector("xs", shape=(10,))
+    ys, _ = scan(
+        lambda xtm2, xtm1: (xtm2 + xtm1),
+        outputs_info=[{"initial": xs, "taps": [-2, -1]}],
+        n_steps=10,
+    )
+    grads_wrt_xs = at.grad(ys.sum(), wrt=xs)
+    fg = FunctionGraph([xs], [grads_wrt_xs])
+    compare_jax_and_py(fg, [np.arange(10)])
+
+
+def test_scan_update():
+    sh_static = shared(np.array(0.0), name="sh_static")
+    sh_update = shared(np.array(1.0), name="sh_update")
+
+    xs, update = scan(
+        lambda sh_static, sh_update: (
+            sh_static + sh_update,
+            {sh_update: sh_update * 2},
+        ),
+        outputs_info=[None],
+        non_sequences=[sh_static, sh_update],
+        strict=True,
+        n_steps=7,
+    )
+
+    jax_fn = function([], xs, updates=update, mode="JAX")
+    np.testing.assert_array_equal(jax_fn(), np.array([1, 2, 4, 8, 16, 32, 64]) + 0.0)
+
+    sh_static.set_value(1.0)
+    np.testing.assert_array_equal(
+        jax_fn(), np.array([128, 256, 512, 1024, 2048, 4096, 8192]) + 1.0
+    )
+
+    sh_static.set_value(2.0)
+    sh_update.set_value(1.0)
+    np.testing.assert_array_equal(jax_fn(), np.array([1, 2, 4, 8, 16, 32, 64]) + 2.0)
+
+
+def test_scan_rng_update():
+    rng = shared(np.random.default_rng(190), name="rng")
+
+    def update_fn(rng):
+        new_rng, x = random.normal(rng=rng).owner.outputs
+        return x, {rng: new_rng}
+
+    xs, update = scan(
+        update_fn,
+        outputs_info=[None],
+        non_sequences=[rng],
+        strict=True,
+        n_steps=10,
+    )
+
+    # Without updates
+    with pytest.warns(
+        UserWarning,
+        match=re.escape("[rng] will not be used in the compiled JAX graph"),
+    ):
+        jax_fn = function([], [xs], updates=None, mode="JAX")
+
+    res1, res2 = jax_fn(), jax_fn()
+    assert np.unique(res1).size == 10
+    assert np.unique(res2).size == 10
+    np.testing.assert_array_equal(res1, res2)
+
+    # With updates
+    with pytest.warns(
+        UserWarning,
+        match=re.escape("[rng] will not be used in the compiled JAX graph"),
+    ):
+        jax_fn = function([], [xs], updates=update, mode="JAX")
+
+    res1, res2 = jax_fn(), jax_fn()
+    assert np.unique(res1).size == 10
+    assert np.unique(res2).size == 10
+    assert np.all(np.not_equal(res1, res2))
+
+
+@pytest.mark.xfail(raises=NotImplementedError)
+def test_scan_while():
+    xs, _ = scan(
+        lambda x: (x + 1, until(x < 10)),
+        outputs_info=[at.zeros(())],
+        n_steps=100,
+    )
+
+    fg = FunctionGraph([], [xs])
+    compare_jax_and_py(fg, [])
+
+
+def test_scan_SEIR():
     """Test a scan implementation of a SEIR model.
 
     SEIR model definition:
@@ -38,8 +216,8 @@ def test_jax_scan_multiple_output():
         return binomln(n, value) + value * log(p) + (n - value) * log(1 - p)
 
     # sequences
-    at_C = ivector("C_t")
-    at_D = ivector("D_t")
+    at_C = vector("C_t", dtype="int32", shape=(8,))
+    at_D = vector("D_t", dtype="int32", shape=(8,))
     # outputs_info (initial conditions)
     st0 = lscalar("s_t0")
     et0 = lscalar("e_t0")
@@ -108,11 +286,7 @@ def test_jax_scan_multiple_output():
     compare_jax_and_py(out_fg, test_input_vals)
 
 
-@pytest.mark.xfail(
-    version_parse(jax.__version__) >= version_parse("0.2.12"),
-    reason="Omnistaging cannot be disabled",
-)
-def test_jax_scan_tap_output():
+def test_scan_mitsot_with_nonseq():
     a_at = scalar("a")
 
     def input_step_fn(y_tm1, y_tm3, a):