From 9e6de79c122ba4c5d654006553a2ddbc9c0edb30 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:03 +0200
Subject: [PATCH 01/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_bssfp.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_bssfp.py b/src/torchsim/_functional/_bssfp.py
index 7e3cf754..de0c4d15 100644
--- a/src/torchsim/_functional/_bssfp.py
+++ b/src/torchsim/_functional/_bssfp.py
@@ -2,6 +2,8 @@
 
 __all__ = ["bssfp_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -15,15 +17,16 @@ def bssfp_sim(
     TR: float,
     T1: float | npt.ArrayLike,
     T2: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     phase_inc: float = 180.0,
     B0: float | npt.ArrayLike = 0.0,
     chemshift: float | npt.ArrayLike = 0.0,
     M0: float | npt.ArrayLike = 1.0,
-    device: str | torch.device = None,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
-    SPoiled Gradient Recalled echo simulator wrapper.
+    Balanced steady-state free-precession simulator wrapper.
 
     Parameters
     ----------
@@ -49,6 +52,10 @@ def bssfp_sim(
         Chemical shift in Hz, default is ``0.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -76,4 +83,5 @@ def bssfp_sim(
         TR=TR,
         TE=TE,
         phase_inc=phase_inc,
+        **values,
     )

From 6a473f821306421bc60382df977d7e06a97f99aa Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:06 +0200
Subject: [PATCH 02/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_spgr.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/torchsim/_functional/_spgr.py b/src/torchsim/_functional/_spgr.py
index 95b9b291..15c6febe 100644
--- a/src/torchsim/_functional/_spgr.py
+++ b/src/torchsim/_functional/_spgr.py
@@ -2,6 +2,8 @@
 
 __all__ = ["spgr_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -15,11 +17,12 @@ def spgr_sim(
     TR: float,
     T1: float | npt.ArrayLike,
     T2star: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     B0: float | npt.ArrayLike = 0.0,
     chemshift: float | npt.ArrayLike = 0.0,
     M0: float | npt.ArrayLike = 1.0,
-    device: str | torch.device = None,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     SPoiled Gradient Recalled echo simulator wrapper.
@@ -45,6 +48,10 @@ def spgr_sim(
         Chemical shift in Hz, default is ``0.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -71,4 +78,5 @@ def spgr_sim(
         flip=flip,
         TR=TR,
         TE=TE,
+        **values,
     )

From 95521ee5814a2dde16ac487e83a0a2b9e3c6dcdf Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:09 +0200
Subject: [PATCH 03/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_fse.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/torchsim/_functional/_fse.py b/src/torchsim/_functional/_fse.py
index 2ca9ee69..d4751649 100644
--- a/src/torchsim/_functional/_fse.py
+++ b/src/torchsim/_functional/_fse.py
@@ -2,6 +2,8 @@
 
 __all__ = ["fse_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -18,11 +20,12 @@ def fse_sim(
     TR: float | npt.ArrayLike = 1e6,
     exc_flip: float = 90.0,
     exc_phase: float = 90.0,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     B1: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
     states: int = 10,
-    device: str | torch.device = None,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     Fast Spin Echo simulator wrapper.
@@ -35,7 +38,7 @@ def fse_sim(
         Echo spacing in milliseconds.
     phases : float | npt.ArrayLike, optional
         Refocusing flip angle phases in degrees.
-        The default is ``90.0``.
+        The default is ``0.0``.
     TR : float | npt.ArrayLike, optional
         Repetition time in milliseconds.
         The default is ``1e6``.
@@ -44,7 +47,7 @@ def fse_sim(
         The default is ``90.0``.
     exc_phase : float, optional
         Excitation flip angle phase in degrees.
-        The default is ``0.0``.
+        The default is ``90.0``.
     T1 : float | npt.ArrayLike
         Longitudinal relaxation time in milliseconds.
     T2 : float | npt.ArrayLike
@@ -64,6 +67,12 @@ def fse_sim(
     states : int, optional
         Number of EPG states to be retained.
         The default is ``10``.
+    phases : float or array-like, optional
+        Sequence phase schedule in degrees. The default is ``0.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -93,4 +102,5 @@ def fse_sim(
         exc_flip=exc_flip,
         exc_phase=exc_phase,
         states=states,
+        **values,
     )

From ca7aec33965e684dc342c4e13930c7c9bd173055 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:12 +0200
Subject: [PATCH 04/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_mprage.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/torchsim/_functional/_mprage.py b/src/torchsim/_functional/_mprage.py
index b29db986..b110c4c4 100644
--- a/src/torchsim/_functional/_mprage.py
+++ b/src/torchsim/_functional/_mprage.py
@@ -2,6 +2,8 @@
 
 __all__ = ["mprage_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -15,10 +17,12 @@ def mprage_sim(
     TRspgr: float,
     nshots: int | npt.ArrayLike,
     T1: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     inv_efficiency: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
-    device: str | torch.device = None,
+    phases: float | npt.ArrayLike = 0.0,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     MPRAGE simulator wrapper.
@@ -49,6 +53,12 @@ def mprage_sim(
     TI : float | npt.ArrayLike, optional
         Inversion time in milliseconds.
         The default is ``0.0``.
+    phases : float or array-like, optional
+        Sequence phase schedule in degrees. The default is ``0.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -74,4 +84,6 @@ def mprage_sim(
         flip=flip,
         TRspgr=TRspgr,
         nshots=nshots,
+        phases=phases,
+        **values,
     )

From cc51fe57dfd3f2bd0753d7c2efce4734e05be2df Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:15 +0200
Subject: [PATCH 05/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_mp2rage.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/torchsim/_functional/_mp2rage.py b/src/torchsim/_functional/_mp2rage.py
index 11b41094..c33c0230 100644
--- a/src/torchsim/_functional/_mp2rage.py
+++ b/src/torchsim/_functional/_mp2rage.py
@@ -2,6 +2,8 @@
 
 __all__ = ["mp2rage_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -16,10 +18,12 @@ def mp2rage_sim(
     TRmp2rage: float,
     nshots: int | npt.ArrayLike,
     T1: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     inv_efficiency: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
-    device: str | torch.device = None,
+    phases: float | npt.ArrayLike = 0.0,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     MP2RAGE simulator wrapper.
@@ -52,6 +56,12 @@ def mp2rage_sim(
     TI : float | npt.ArrayLike, optional
         Inversion time in milliseconds.
         The default is ``0.0``.
+    phases : float or array-like, optional
+        Sequence phase schedule in degrees. The default is ``0.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -78,4 +88,6 @@ def mp2rage_sim(
         TRspgr=TRspgr,
         TRmp2rage=TRmp2rage,
         nshots=nshots,
+        phases=phases,
+        **values,
     )

From 0cb901f88be4307af93d2f561baf2fd48a973092 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:18 +0200
Subject: [PATCH 06/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_mpnrage.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/torchsim/_functional/_mpnrage.py b/src/torchsim/_functional/_mpnrage.py
index 1c04e6cb..9bb4ddf2 100644
--- a/src/torchsim/_functional/_mpnrage.py
+++ b/src/torchsim/_functional/_mpnrage.py
@@ -2,6 +2,8 @@
 
 __all__ = ["mpnrage_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -14,12 +16,14 @@ def mpnrage_sim(
     flip: npt.ArrayLike,
     TR: float | npt.ArrayLike,
     T1: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     B1: float | npt.ArrayLike = 1.0,
     inv_efficiency: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
     TI: float = 0.0,
-    device: str | torch.device = None,
+    phases: float | npt.ArrayLike = 0.0,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     MPnRAGE simulator wrapper.
@@ -46,6 +50,12 @@ def mpnrage_sim(
     TI : float | npt.ArrayLike, optional
         Inversion time in milliseconds.
         The default is ``0.0``.
+    phases : float or array-like, optional
+        Sequence phase schedule in degrees. The default is ``0.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -72,4 +82,6 @@ def mpnrage_sim(
         flip=flip,
         TR=TR,
         TI=TI,
+        phases=phases,
+        **values,
     )

From 432d59486def4bbfa4fdd8127447900ade99f7d2 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:22 +0200
Subject: [PATCH 07/25] api: bring functional wrappers up to Simulator

---
 src/torchsim/_functional/_mrf.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_mrf.py b/src/torchsim/_functional/_mrf.py
index f7fb4f23..1b116333 100644
--- a/src/torchsim/_functional/_mrf.py
+++ b/src/torchsim/_functional/_mrf.py
@@ -2,6 +2,8 @@
 
 __all__ = ["mrf_sim"]
 
+from typing import Any
+
 import numpy.typing as npt
 import torch
 
@@ -14,14 +16,16 @@ def mrf_sim(
     TR: float | npt.ArrayLike,
     T1: float | npt.ArrayLike,
     T2: float | npt.ArrayLike,
-    diff: str | tuple[str] = None,
+    diff: str | tuple[str, ...] | None = None,
     B1: float | npt.ArrayLike = 1.0,
     inv_efficiency: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
     TI: float = 0.0,
+    phases: float | npt.ArrayLike = 0.0,
     states: int = 10,
     nreps: int = 1,
-    device: str | torch.device = None,
+    device: str | torch.device | None = None,
+    **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
     """
     SSFP MR Fingerprinting simulator wrapper.
@@ -54,6 +58,12 @@ def mrf_sim(
     nreps : int, optional
         Number of simulation repetitions.
         The default is ``1``.
+    phases : float or array-like, optional
+        Sequence phase schedule in degrees. The default is ``0.0``.
+    **values : optional
+        Additional tissue, protocol or run settings accepted by the corresponding
+        ``Simulator`` class. Explicit wrapper arguments remain available for
+        backwards compatibility.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).
@@ -80,6 +90,7 @@ def mrf_sim(
         flip=flip,
         TR=TR,
         TI=TI,
+        phases=phases,
         states=states,
-        repetitions=nreps,
+        **{"repetitions": nreps, **values},
     )

From 1730a258aceee29da7cb597e3b34b3a8766f7da1 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:47 +0200
Subject: [PATCH 08/25] api: correct FSE wrapper documentation

---
 src/torchsim/_functional/_fse.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/torchsim/_functional/_fse.py b/src/torchsim/_functional/_fse.py
index d4751649..62bad0ab 100644
--- a/src/torchsim/_functional/_fse.py
+++ b/src/torchsim/_functional/_fse.py
@@ -57,18 +57,11 @@ def fse_sim(
         The default is ``None`` (no differentation).
     B1 : float | npt.ArrayLike, optional
         Flip angle scaling map, default is ``1.0``.
-    inv_efficiency : float | npt.ArrayLike, optional
-        Inversion efficiency map, default is ``1.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
-    TI : float | npt.ArrayLike, optional
-        Inversion time in milliseconds.
-        The default is ``0.0``.
     states : int, optional
         Number of EPG states to be retained.
         The default is ``10``.
-    phases : float or array-like, optional
-        Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
         Additional tissue, protocol or run settings accepted by the corresponding
         ``Simulator`` class. Explicit wrapper arguments remain available for

From dfe920889eed3feb45a5830d4fb44a1ddf92109e Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:50 +0200
Subject: [PATCH 09/25] api: correct prepared-GRE wrapper documentation

---
 src/torchsim/_functional/_mprage.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/torchsim/_functional/_mprage.py b/src/torchsim/_functional/_mprage.py
index b110c4c4..4095f2f8 100644
--- a/src/torchsim/_functional/_mprage.py
+++ b/src/torchsim/_functional/_mprage.py
@@ -50,9 +50,6 @@ def mprage_sim(
         Inversion efficiency map, default is ``1.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
-    TI : float | npt.ArrayLike, optional
-        Inversion time in milliseconds.
-        The default is ``0.0``.
     phases : float or array-like, optional
         Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional

From 669ff138bae2641ebf1d8ac11dcd821281655e49 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:53 +0200
Subject: [PATCH 10/25] api: correct prepared-GRE wrapper documentation


From 477b514942736becd2bab4d7ea3a95c2f05211bc Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:56 +0200
Subject: [PATCH 11/25] api: fix functional wrapper docstrings

---
 src/torchsim/_functional/_bssfp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/torchsim/_functional/_bssfp.py b/src/torchsim/_functional/_bssfp.py
index de0c4d15..26cf66f4 100644
--- a/src/torchsim/_functional/_bssfp.py
+++ b/src/torchsim/_functional/_bssfp.py
@@ -48,7 +48,7 @@ def bssfp_sim(
         The default is ``180.0``
     B0 : float | npt.ArrayLike, optional
         Frequency offset map in Hz, default is ``0.0.``
-    chemshift : float | npt.ArrayLik, optional
+    chemshift : float | npt.ArrayLike, optional
         Chemical shift in Hz, default is ``0.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.

From c36e25609a62a4ce9101b3d6897bd8f43d635289 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:38:58 +0200
Subject: [PATCH 12/25] api: fix functional wrapper docstrings

---
 src/torchsim/_functional/_spgr.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/torchsim/_functional/_spgr.py b/src/torchsim/_functional/_spgr.py
index 15c6febe..6b052505 100644
--- a/src/torchsim/_functional/_spgr.py
+++ b/src/torchsim/_functional/_spgr.py
@@ -44,7 +44,7 @@ def spgr_sim(
         The default is ``None`` (no differentation).
     B0 : float | npt.ArrayLike, optional
         Frequency offset map in Hz, default is ``0.0.``
-    chemshift : float | npt.ArrayLik, optional
+    chemshift : float | npt.ArrayLike, optional
         Chemical shift in Hz, default is ``0.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.

From 0f622f7a93b0e355095a9ba49fe1bbcb972cbf0c Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:39:18 +0200
Subject: [PATCH 13/25] test: cover functional wrapper protocol parity

---
 tests/functionals/test_mrf_func.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tests/functionals/test_mrf_func.py b/tests/functionals/test_mrf_func.py
index 0e8b1978..b73d6788 100644
--- a/tests/functionals/test_mrf_func.py
+++ b/tests/functionals/test_mrf_func.py
@@ -41,3 +41,21 @@ def test_scalar_gradient(flip):
 def test_multiple_gradient(flip):
     _, grad = mrf_sim(flip, TR=10.0, T1=(200, 500, 1000.0), T2=100.0, diff=("T1", "T2"))
     assert grad.shape == (3, 2, 100)
+
+def test_current_simulator_protocol_arguments_pass_through(flip):
+    """The convenience call accepts protocol fields added to MRFSimulator."""
+    from torchsim.simulators import MRFSimulator
+
+    phases = np.linspace(0.0, 117.0, flip.size, dtype=np.float32)
+    got = mrf_sim(
+        flip,
+        TR=10.0,
+        T1=1000.0,
+        T2=100.0,
+        phases=phases,
+        B0=23.0,
+    )
+    expected = MRFSimulator(flip=flip, TR=10.0, phases=phases).simulate(
+        T1=1000.0, T2=100.0, B0=23.0
+    )
+    np.testing.assert_allclose(got, expected)

From 62e87a674c33cb7b4ed29fee990ab0664e0e70be Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:39:22 +0200
Subject: [PATCH 14/25] test: cover functional wrapper physics parity

---
 tests/functionals/test_fse_func.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/tests/functionals/test_fse_func.py b/tests/functionals/test_fse_func.py
index 1e4af953..2c621600 100644
--- a/tests/functionals/test_fse_func.py
+++ b/tests/functionals/test_fse_func.py
@@ -41,3 +41,24 @@ def test_scalar_gradient(flip):
 def test_multiple_gradient(flip):
     _, grad = fse_sim(flip, ESP=1.0, T1=(200, 500, 1000.0), T2=100.0, diff=("T1", "T2"))
     assert grad.shape == (3, 2, 100)
+
+def test_current_simulator_physics_passes_through(flip):
+    """The convenience call does not hide physics the Simulator accepts."""
+    from torchsim.simulators import FSESimulator
+
+    got = fse_sim(
+        flip,
+        ESP=5.0,
+        T1=1000.0,
+        T2=100.0,
+        B0=17.0,
+        crusher_dephasing_rad=2 * np.pi,
+        voxel_size_m=1e-3,
+    )
+    expected = FSESimulator(
+        flip=flip,
+        ESP=5.0,
+        crusher_dephasing_rad=2 * np.pi,
+        voxel_size_m=1e-3,
+    ).simulate(T1=1000.0, T2=100.0, B0=17.0)
+    np.testing.assert_allclose(got, expected)

From 587de427aa828b6098fa3492ebafc58d50d78bed Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:39:57 +0200
Subject: [PATCH 15/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_bssfp.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_bssfp.py b/src/torchsim/_functional/_bssfp.py
index 26cf66f4..277b657e 100644
--- a/src/torchsim/_functional/_bssfp.py
+++ b/src/torchsim/_functional/_bssfp.py
@@ -53,9 +53,9 @@ def bssfp_sim(
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From c93dd21bd4f87c7ed64acfc9d859dc939c0e7e6c Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:11 +0200
Subject: [PATCH 16/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_spgr.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_spgr.py b/src/torchsim/_functional/_spgr.py
index 6b052505..91d25435 100644
--- a/src/torchsim/_functional/_spgr.py
+++ b/src/torchsim/_functional/_spgr.py
@@ -49,9 +49,9 @@ def spgr_sim(
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From 2e0a9db8c7faaba1f66c42a27b8b949e6cc481a6 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:13 +0200
Subject: [PATCH 17/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_fse.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_fse.py b/src/torchsim/_functional/_fse.py
index 62bad0ab..9e565a3d 100644
--- a/src/torchsim/_functional/_fse.py
+++ b/src/torchsim/_functional/_fse.py
@@ -63,9 +63,9 @@ def fse_sim(
         Number of EPG states to be retained.
         The default is ``10``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From 440267c0cb584480697a7a36311f10d78d3decb6 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:17 +0200
Subject: [PATCH 18/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_mprage.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_mprage.py b/src/torchsim/_functional/_mprage.py
index 4095f2f8..01126b74 100644
--- a/src/torchsim/_functional/_mprage.py
+++ b/src/torchsim/_functional/_mprage.py
@@ -53,9 +53,9 @@ def mprage_sim(
     phases : float or array-like, optional
         Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From 7f66477cdf3994cb77ad085cfbee66fbcd2960ed Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:20 +0200
Subject: [PATCH 19/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_mp2rage.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_mp2rage.py b/src/torchsim/_functional/_mp2rage.py
index c33c0230..f77a1077 100644
--- a/src/torchsim/_functional/_mp2rage.py
+++ b/src/torchsim/_functional/_mp2rage.py
@@ -59,9 +59,9 @@ def mp2rage_sim(
     phases : float or array-like, optional
         Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From 41e3118f42d37a5b556cb81dda998f86d0d6ea83 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:23 +0200
Subject: [PATCH 20/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_mpnrage.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_mpnrage.py b/src/torchsim/_functional/_mpnrage.py
index 9bb4ddf2..2d9a33c8 100644
--- a/src/torchsim/_functional/_mpnrage.py
+++ b/src/torchsim/_functional/_mpnrage.py
@@ -53,9 +53,9 @@ def mpnrage_sim(
     phases : float or array-like, optional
         Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From f1c135cf8a07aece99fa98c03a8c88af40254b4c Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:26 +0200
Subject: [PATCH 21/25] api: clarify functional pass-through scope

---
 src/torchsim/_functional/_mrf.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/torchsim/_functional/_mrf.py b/src/torchsim/_functional/_mrf.py
index 1b116333..97979448 100644
--- a/src/torchsim/_functional/_mrf.py
+++ b/src/torchsim/_functional/_mrf.py
@@ -61,9 +61,9 @@ def mrf_sim(
     phases : float or array-like, optional
         Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
-        Additional tissue, protocol or run settings accepted by the corresponding
-        ``Simulator`` class. Explicit wrapper arguments remain available for
-        backwards compatibility.
+        Additional call-time tissue, protocol or run settings accepted by
+        ``Simulator.simulate``. Settings fixed only at simulator construction
+        remain class-interface features.
     device : str | torch.device, optional
         Computational device for simulation.
         The default is ``None`` (infer from input).

From 53979235793ad6571db970d29849c234070049cf Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:40:29 +0200
Subject: [PATCH 22/25] test: keep wrapper parity to call-time settings

---
 tests/functionals/test_fse_func.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/functionals/test_fse_func.py b/tests/functionals/test_fse_func.py
index 2c621600..200cf727 100644
--- a/tests/functionals/test_fse_func.py
+++ b/tests/functionals/test_fse_func.py
@@ -52,13 +52,9 @@ def test_current_simulator_physics_passes_through(flip):
         T1=1000.0,
         T2=100.0,
         B0=17.0,
-        crusher_dephasing_rad=2 * np.pi,
-        voxel_size_m=1e-3,
     )
     expected = FSESimulator(
         flip=flip,
         ESP=5.0,
-        crusher_dephasing_rad=2 * np.pi,
-        voxel_size_m=1e-3,
     ).simulate(T1=1000.0, T2=100.0, B0=17.0)
     np.testing.assert_allclose(got, expected)

From 502263ce19e1bafdcd3999b67ff01b18a55a1139 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:45:07 +0200
Subject: [PATCH 23/25] style: apply pre-commit formatting

---
 tests/functionals/test_fse_func.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/functionals/test_fse_func.py b/tests/functionals/test_fse_func.py
index 200cf727..82c1e4de 100644
--- a/tests/functionals/test_fse_func.py
+++ b/tests/functionals/test_fse_func.py
@@ -42,6 +42,7 @@ def test_multiple_gradient(flip):
     _, grad = fse_sim(flip, ESP=1.0, T1=(200, 500, 1000.0), T2=100.0, diff=("T1", "T2"))
     assert grad.shape == (3, 2, 100)
 
+
 def test_current_simulator_physics_passes_through(flip):
     """The convenience call does not hide physics the Simulator accepts."""
     from torchsim.simulators import FSESimulator

From aed068fc26a2a47a25108a3e230a264e515cdb29 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 11:45:10 +0200
Subject: [PATCH 24/25] style: apply pre-commit formatting

---
 tests/functionals/test_mrf_func.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/functionals/test_mrf_func.py b/tests/functionals/test_mrf_func.py
index b73d6788..1af564bc 100644
--- a/tests/functionals/test_mrf_func.py
+++ b/tests/functionals/test_mrf_func.py
@@ -42,6 +42,7 @@ def test_multiple_gradient(flip):
     _, grad = mrf_sim(flip, TR=10.0, T1=(200, 500, 1000.0), T2=100.0, diff=("T1", "T2"))
     assert grad.shape == (3, 2, 100)
 
+
 def test_current_simulator_protocol_arguments_pass_through(flip):
     """The convenience call accepts protocol fields added to MRFSimulator."""
     from torchsim.simulators import MRFSimulator

From 5f71f3593d69567f1e67ad923012d827750170e8 Mon Sep 17 00:00:00 2001
From: Matteo Cencini <83717049+mcencini@users.noreply.github.com>
Date: Mon, 5 Oct 2026 12:00:13 +0200
Subject: [PATCH 25/25] fix: keep MP2RAGE wrapper to supported closed-form
 arguments

---
 src/torchsim/_functional/_mp2rage.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/torchsim/_functional/_mp2rage.py b/src/torchsim/_functional/_mp2rage.py
index f77a1077..76d18311 100644
--- a/src/torchsim/_functional/_mp2rage.py
+++ b/src/torchsim/_functional/_mp2rage.py
@@ -21,7 +21,6 @@ def mp2rage_sim(
     diff: str | tuple[str, ...] | None = None,
     inv_efficiency: float | npt.ArrayLike = 1.0,
     M0: float | npt.ArrayLike = 1.0,
-    phases: float | npt.ArrayLike = 0.0,
     device: str | torch.device | None = None,
     **values: Any,
 ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
@@ -53,11 +52,6 @@ def mp2rage_sim(
         Inversion efficiency map, default is ``1.0``.
     M0 : float or array-like, optional
         Proton density scaling factor, default is ``1.0``.
-    TI : float | npt.ArrayLike, optional
-        Inversion time in milliseconds.
-        The default is ``0.0``.
-    phases : float or array-like, optional
-        Sequence phase schedule in degrees. The default is ``0.0``.
     **values : optional
         Additional call-time tissue, protocol or run settings accepted by
         ``Simulator.simulate``. Settings fixed only at simulator construction
@@ -88,6 +82,5 @@ def mp2rage_sim(
         TRspgr=TRspgr,
         TRmp2rage=TRmp2rage,
         nshots=nshots,
-        phases=phases,
         **values,
     )