Keep outer graph visible to the scan user function, including sequences

Sequences are now demoted to being just another constant in the Scan Op.
The user facing function creates the right indexing graph for iterating over sequences automatically.

Some extra logic is added in the `scan_to_loop` rewrite to avoid creating duplicated indexes,
while being on guard for Scans created elsewhere.

pytensor/loop/basic.py

@@ -1,12 +1,14 @@
+import functools
 from typing import List, Tuple
 
 import numpy as np
 
-from pytensor import Variable, as_symbolic
+from pytensor import Variable, as_symbolic, clone_replace
 from pytensor.graph import FunctionGraph
+from pytensor.graph.basic import Constant, truncated_graph_inputs
 from pytensor.loop.op import Scan
 from pytensor.scan.utils import until
-from pytensor.tensor import as_tensor, empty_like
+from pytensor.tensor import as_tensor, constant, empty_like, minimum
 
 
 def scan(
@@ -20,6 +22,8 @@ def scan(
     if sequences is None and n_steps is None:
         raise ValueError("Must provide n_steps when scanning without sequences")
 
+    # TODO: init_states should be made opaque to the inner function,
+    #  since any relationship to the outer graph no longer holds
     if init_states is None:
         init_states = []
     else:
@@ -34,20 +38,31 @@ def scan(
             sequences = [sequences]
         sequences = [as_tensor(s) for s in sequences]
 
+    if sequences:
+        leading_dims = [seq.shape[0] for seq in sequences]
+        shortest_dim = functools.reduce(minimum, leading_dims)
+        if n_steps is None:
+            n_steps = shortest_dim
+        else:
+            n_steps = minimum(n_steps, shortest_dim)
+
     if non_sequences is None:
         non_sequences = []
     else:
         if not isinstance(non_sequences, (tuple, list)):
             non_sequences = [non_sequences]
         non_sequences = [as_symbolic(n) for n in non_sequences]
 
+    # Create subsequence inputs for the inner function
+    idx = constant(0, dtype="int64", name="idx")
+    symbolic_idx = idx.type(name="idx")
+    subsequences = [s[symbolic_idx] for s in sequences]
     # Note: Old scan order is sequences + init + non_sequences
-    inner_sequences = [s[0] for s in sequences]
-    inner_inputs = [i.type() for i in init_states + inner_sequences + non_sequences]
-    inner_outputs = fn(*inner_inputs)
-    if not isinstance(inner_outputs, (tuple, list)):
-        inner_outputs = [inner_outputs]
-    next_states = [out for out in inner_outputs if not isinstance(out, until)]
+    fn_inputs = init_states + subsequences + non_sequences
+    fn_outputs = fn(*fn_inputs)
+    if not isinstance(fn_outputs, (tuple, list)):
+        fn_outputs = [fn_outputs]
+    next_states = [out for out in fn_outputs if not isinstance(out, until)]
 
     if len(next_states) > len(init_states):
         if not init_states:
@@ -61,27 +76,43 @@ def scan(
     prev_states = []
     for i, (init_state, next_state) in enumerate(zip(init_states, next_states)):
         if init_state is None:
+            # next_state may reference idx, let's replace that by the initial value
+            [next_state] = clone_replace(
+                output=[next_state], replace={symbolic_idx: idx}
+            )
             init_state = empty_like(next_state)
             init_state.name = "empty_init_state"
-            inner_inputs.insert(i, init_state.type())
         prev_states.append(init_state)
 
-    until_condition = [out.condition for out in inner_outputs if isinstance(out, until)]
+    until_condition = [out.condition for out in fn_outputs if isinstance(out, until)]
     if not until_condition:
         until_condition = [as_tensor(np.array(True))]
     if len(until_condition) > 1:
         raise ValueError("Only one until condition can be returned")
 
-    update_fg = FunctionGraph(
-        inputs=inner_inputs, outputs=until_condition + next_states
+    fgraph_inputs = [symbolic_idx] + prev_states + sequences + non_sequences
+    fgraph_outputs = until_condition + [symbolic_idx + 1] + next_states
+
+    all_fgraph_inputs = truncated_graph_inputs(
+        fgraph_outputs, ancestors_to_include=fgraph_inputs
+    )
+    extra_fgraph_inputs = [
+        inp
+        for inp in all_fgraph_inputs
+        if (not isinstance(inp, Constant) and inp not in fgraph_inputs)
+    ]
+    fgraph_inputs = fgraph_inputs + extra_fgraph_inputs
+    update_fg = FunctionGraph(inputs=fgraph_inputs, outputs=fgraph_outputs)
+
+    scan_op = Scan(update_fg=update_fg)
+    scan_outs = scan_op(
+        n_steps, idx, *prev_states, *sequences, *non_sequences, *extra_fgraph_inputs
     )
-    scan_op = Scan(update_fg=update_fg, n_sequences=len(sequences))
-    scan_outs = scan_op(n_steps, *prev_states, *sequences, *non_sequences)
     assert isinstance(scan_outs, list)
     last_states = scan_outs[: scan_op.n_states]
     traces = scan_outs[scan_op.n_states :]
-
-    return last_states, traces
+    # Don't return the inner index state
+    return last_states[1:], traces[1:]
 
 
 def map(