marimo-flow 0.4.2__tar.gz → 0.4.4__tar.gz

{marimo_flow-0.4.2/src/marimo_flow.egg-info → marimo_flow-0.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marimo-flow
-Version: 0.4.2
+Version: 0.4.4
 Summary: Agentic scientific-computing platform: a reactive multi-agent team orchestrating PINA physics-informed neural-network workflows via pydantic-graph, with MLflow tracing/provenance and a marimo chat UI.
 Author-email: Björn Bethge <helloworld@synapticore.io>
 License-Expression: MIT
@@ -20,44 +20,44 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: marimo[lsp,mcp,recommended,sql]>=0.23.1
+Requires-Dist: marimo[lsp,mcp,recommended,sql]>=0.25.0
 Requires-Dist: mlflow[genai]>=3.16.1
 Requires-Dist: fastmcp>=4.0.9
-Requires-Dist: optuna>=4.8.0
-Requires-Dist: pina-mathlab>=0.2.6
-Requires-Dist: transformers[accelerate,tiktoken]>=5.5.4
-Requires-Dist: authlib>=1.6.9
-Requires-Dist: pillow>=12.2.0
-Requires-Dist: cryptography>=49.0.0
-Requires-Dist: langgraph>=1.1.8
+Requires-Dist: optuna>=5.0.0
+Requires-Dist: pina-mathlab>=0.3.2.post2609
+Requires-Dist: transformers[accelerate,tiktoken]>=5.17.0
+Requires-Dist: authlib>=1.8.0
+Requires-Dist: pillow>=12.3.0
+Requires-Dist: cryptography>=50.0.1
+Requires-Dist: langgraph>=1.2.12
 Requires-Dist: werkzeug>=3.1.8
 Requires-Dist: sqlparse>=0.6.0
 Requires-Dist: diskcache>=5.6.3
 Requires-Dist: protobuf>=6.33.6
-Requires-Dist: python-multipart>=0.0.27
-Requires-Dist: ujson>=5.12.0
-Requires-Dist: pyasn1>=0.6.3
-Requires-Dist: pyjwt>=2.12.1
+Requires-Dist: python-multipart>=0.0.32
+Requires-Dist: ujson>=6.0.0
+Requires-Dist: pyasn1>=0.6.4
+Requires-Dist: pyjwt>=2.15.0
 Requires-Dist: flask>=3.1.3
-Requires-Dist: gitpython>=3.1.59
-Requires-Dist: httpx2>=2.12.0
-Requires-Dist: httpcore2>=2.10.0
+Requires-Dist: gitpython>=3.1.62
+Requires-Dist: httpx2>=2.13.1
+Requires-Dist: httpcore2>=2.13.1
 Requires-Dist: lightning>=2.6.6
 Requires-Dist: aiohttp>=3.14.3
 Requires-Dist: accelerate>=1.15.0
-Requires-Dist: pymdown-extensions>=11.0.1
-Requires-Dist: optuna-integration[pytorch-lightning]>=4.8.0
-Requires-Dist: plotly[express,kaleido]>=6.7.0
-Requires-Dist: pydantic-ai-slim[ag-ui]>=2.10.0
+Requires-Dist: pymdown-extensions>=11.0.2
+Requires-Dist: optuna-integration[pytorch-lightning]>=5.0.0
+Requires-Dist: plotly[express,kaleido]>=7.1.0
+Requires-Dist: pydantic-ai-slim[ag-ui]>=2.49.0
 Requires-Dist: pyyaml>=6.0.3
-Requires-Dist: python-dotenv>=1.2.2
-Requires-Dist: typer>=0.24.1
+Requires-Dist: python-dotenv>=1.2.3
+Requires-Dist: typer>=0.27.2
 Requires-Dist: sympy>=1.14.0
 Requires-Dist: meshio>=5.3.5
-Requires-Dist: fasta2a>=0.6.1
+Requires-Dist: fasta2a>=2.0.1
 Provides-Extra: all
-Requires-Dist: torch>=2.11.0; extra == "all"
-Requires-Dist: torch-geometric>=2.7.0; extra == "all"
+Requires-Dist: torch>=2.14.0; extra == "all"
+Requires-Dist: torch-geometric>=2.8.0.post1; extra == "all"
 Dynamic: license-file
 
 # Marimo Flow 🌊

{marimo_flow-0.4.2 → marimo_flow-0.4.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "marimo-flow"
-version = "0.4.2"
+version = "0.4.4"
 description = "Agentic scientific-computing platform: a reactive multi-agent team orchestrating PINA physics-informed neural-network workflows via pydantic-graph, with MLflow tracing/provenance and a marimo chat UI."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -43,62 +43,62 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-    "marimo[lsp,recommended,sql,mcp]>=0.23.1",
+    "marimo[lsp,recommended,sql,mcp]>=0.25.0",
     # No [mcp] extra: it pins fastmcp<4, which pip resolves to fastmcp 2.x +
     # mcp 2.x (ImportError on McpError). We need the fastmcp client directly.
     "mlflow[genai]>=3.16.1",
     "fastmcp>=4.0.9",
-    "optuna>=4.8.0",
-    "pina-mathlab>=0.2.6",
-    "transformers[accelerate,tiktoken]>=5.5.4",
+    "optuna>=5.0.0",
+    "pina-mathlab>=0.3.2.post2609",
+    "transformers[accelerate,tiktoken]>=5.17.0",
     # security: explicit minimums for vulnerable transitive deps
-    "authlib>=1.6.9",
-    "pillow>=12.2.0",
-    "cryptography>=49.0.0",
-    "langgraph>=1.1.8",
+    "authlib>=1.8.0",
+    "pillow>=12.3.0",
+    "cryptography>=50.0.1",
+    "langgraph>=1.2.12",
     "werkzeug>=3.1.8",
     "sqlparse>=0.6.0",
     "diskcache>=5.6.3",
     "protobuf>=6.33.6",
-    "python-multipart>=0.0.27",
-    "ujson>=5.12.0",
-    "pyasn1>=0.6.3",
-    "pyjwt>=2.12.1",
+    "python-multipart>=0.0.32",
+    "ujson>=6.0.0",
+    "pyasn1>=0.6.4",
+    "pyjwt>=2.15.0",
     "flask>=3.1.3",
-    "gitpython>=3.1.59",
-    "httpx2>=2.12.0",
-    "httpcore2>=2.10.0",
+    "gitpython>=3.1.62",
+    "httpx2>=2.13.1",
+    "httpcore2>=2.13.1",
     "lightning>=2.6.6",
     "aiohttp>=3.14.3",
     "accelerate>=1.15.0",
-    "pymdown-extensions>=11.0.1",
-    "optuna-integration[pytorch-lightning]>=4.8.0",
-    "plotly[express,kaleido]>=6.7.0",
+    "pymdown-extensions>=11.0.2",
+    "optuna-integration[pytorch-lightning]>=5.0.0",
+    "plotly[express,kaleido]>=7.1.0",
     # pydantic-ai 2.x dropped the bundled `a2a` extra; A2A now comes via the
     # standalone `fasta2a` dep below (still the same agent_to_a2a API).
-    "pydantic-ai-slim[ag-ui]>=2.10.0",
+    "pydantic-ai-slim[ag-ui]>=2.49.0",
     "pyyaml>=6.0.3",
-    "python-dotenv>=1.2.2",
-    "typer>=0.24.1",
+    "python-dotenv>=1.2.3",
+    "typer>=0.27.2",
     "sympy>=1.14.0",
     "meshio>=5.3.5",
-    "fasta2a>=0.6.1",
+    "fasta2a>=2.0.1",
 ]
 
 [project.optional-dependencies]
 all = [
-    "torch>=2.11.0",
-    "torch-geometric>=2.7.0",
+    "torch>=2.14.0",
+    "torch-geometric>=2.8.0.post1",
 ]
 
 [dependency-groups]
 dev = [
-    "mypy>=1.20.1",
-    "pre-commit>=4.5.1",
-    "pytest>=9.0.3",
-    "pytest-asyncio>=1.3.0",
-    "pytest-cov>=7.0.0",
-    "ruff>=0.15.11",
+    "mypy>=2.3.1",
+    "pre-commit>=4.6.2",
+    "pytest>=9.1.1",
+    "pytest-asyncio>=1.4.0",
+    "pytest-cov>=7.1.0",
+    "ruff>=0.16.9",
 ]
 docs = [
     "sphinx>=9.0.4",

{marimo_flow-0.4.2 → marimo_flow-0.4.4}/src/marimo_flow/agents/toolsets/control.py

@@ -115,7 +115,11 @@ def closed_loop_simulation(
     true_dynamics_registry_key: str,
     n_steps: int = 20,
 ) -> dict[str, list[list[float]]]:
-    """Run a closed-loop rollout and return the state / control trajectory."""
+    """Run an offset-free closed-loop rollout.
+
+    Returns the state and control trajectories plus ``disturbance``, the
+    observer's estimate of the surrogate's bias at each step.
+    """
     from marimo_flow.control.mpc import simulate_closed_loop
 
     plan_model = ControlPlan.model_validate(plan)
@@ -135,4 +139,5 @@ def closed_loop_simulation(
     return {
         "states": traj["states"].tolist(),
         "controls": traj["controls"].tolist(),
+        "disturbance": traj["disturbance"].tolist(),
     }

{marimo_flow-0.4.2 → marimo_flow-0.4.4}/src/marimo_flow/control/heat_rod.py

@@ -119,8 +119,13 @@ def train_step_surrogate(
     epochs: int = 200,
     lr: float = 1e-3,
     batch_size: int = 256,
+    seed: int | None = None,
 ) -> PredictStepFn:
-    """Fit a small MLP on plant rollouts; return a numpy predict callable."""
+    """Fit a small MLP on plant rollouts; return a numpy predict callable.
+
+    ``seed`` makes weight init and batch shuffling reproducible without
+    touching torch's global RNG state.
+    """
     if inputs.ndim != 2 or inputs.shape[1] != 2:
         raise ValueError("inputs must have shape (n, 2)")
     if targets.ndim != 2 or targets.shape[1] != 1:
@@ -139,13 +144,23 @@ def train_step_surrogate(
     x_norm = (inputs - x_mean) / x_std
     y_norm = (targets - y_mean) / y_std
 
-    layers: list[nn.Module] = []
-    in_dim = 2
-    for width in hidden:
-        layers.extend([nn.Linear(in_dim, width), nn.Tanh()])
-        in_dim = width
-    layers.append(nn.Linear(in_dim, 1))
-    model = nn.Sequential(*layers)
+    generator = torch.Generator()
+    if seed is None:
+        generator.seed()
+    else:
+        generator.manual_seed(seed)
+
+    # nn.Linear initialises from the global RNG; fork it so a seeded run
+    # neither depends on nor changes the caller's torch RNG state.
+    with torch.random.fork_rng(devices=[]):
+        torch.manual_seed(generator.initial_seed())
+        layers: list[nn.Module] = []
+        in_dim = 2
+        for width in hidden:
+            layers.extend([nn.Linear(in_dim, width), nn.Tanh()])
+            in_dim = width
+        layers.append(nn.Linear(in_dim, 1))
+        model = nn.Sequential(*layers)
 
     x_t = torch.tensor(x_norm, dtype=torch.float32)
     y_t = torch.tensor(y_norm, dtype=torch.float32)
@@ -154,7 +169,7 @@ def train_step_surrogate(
 
     n = len(x_t)
     for _ in range(epochs):
-        perm = torch.randperm(n)
+        perm = torch.randperm(n, generator=generator)
         for start in range(0, n, batch_size):
             idx = perm[start : start + batch_size]
             pred = model(x_t[idx])

{marimo_flow-0.4.2 → marimo_flow-0.4.4}/src/marimo_flow/control/mpc.py

@@ -19,6 +19,13 @@ Returns:
   * ``state_trajectory``: shape ``(horizon, n_states)`` — predicted next states.
 """
 
+# Surrogates are usually torch networks evaluated in float32. SLSQP's default
+# finite-difference step (~1.5e-8) is below float32 resolution, so the
+# objective would not change, the gradient would be zero and the solver would
+# stop at the initial guess. sqrt(float32 eps) is the standard forward-
+# difference step for float32-noisy functions.
+_FD_REL_STEP = float(np.sqrt(np.finfo(np.float32).eps))
+
 
 def run_mpc_step(
     plan: ControlPlan,
@@ -26,12 +33,15 @@ def run_mpc_step(
     surrogate: SurrogateFn,
     *,
     prev_controls: np.ndarray | None = None,
+    disturbance: np.ndarray | None = None,
 ) -> tuple[np.ndarray, dict[str, float]]:
     """Solve one MPC horizon; return the chosen control sequence + info.
 
     Only the first control column is applied by the caller — the rest
     is the MPC's look-ahead. ``prev_controls`` warm-starts the solver
-    with the previous horizon shifted by one step.
+    with the previous horizon shifted by one step. ``disturbance`` (shape
+    ``(n_states,)``) is added to every predicted state — the output
+    disturbance estimate of offset-free MPC.
     """
     h = plan.horizon
     n_ctrl = len(plan.controls)
@@ -47,12 +57,13 @@ def run_mpc_step(
 
     targets = np.array([s.target if s.target is not None else 0.0 for s in plan.states])
     weights = np.array([s.weight for s in plan.states])
+    offset = np.zeros(n_state) if disturbance is None else disturbance
 
     def flat_to_seq(x: np.ndarray) -> np.ndarray:
         return x.reshape(h, n_ctrl)
 
     def objective(x: np.ndarray) -> float:
-        traj = surrogate(state_now, flat_to_seq(x))
+        traj = surrogate(state_now, flat_to_seq(x)) + offset
         err = traj - targets
         return float(np.sum(weights * (err**2)))
 
@@ -64,8 +75,9 @@ def run_mpc_step(
         objective,
         x0=x0.flatten(),
         method="SLSQP",
+        jac="2-point",
         bounds=bounds,
-        options={"maxiter": 50, "ftol": 1e-6},
+        options={"maxiter": 50, "ftol": 1e-6, "finite_diff_rel_step": _FD_REL_STEP},
     )
     return flat_to_seq(result.x), {
         "cost": float(result.fun),
@@ -81,25 +93,46 @@ def simulate_closed_loop(
     true_dynamics: SurrogateFn,
     *,
     n_steps: int,
+    offset_free: bool = True,
+    disturbance_gain: float = 0.3,
 ) -> dict[str, np.ndarray]:
     """Run n_steps of MPC + true-dynamics rollout; return the trajectory.
 
     ``true_dynamics`` plays the role of the real plant (for sim work).
     In production the caller replaces it with a measurement hook.
+
+    With ``offset_free`` (default) an integrating output-disturbance
+    observer corrects the surrogate: ``d += disturbance_gain * (measured -
+    (surrogate + d))``, and every horizon is planned on ``surrogate + d``.
+    A surrogate bias then leaves no steady-state error; ``d`` stays zero
+    when the surrogate matches the plant. A gain below 1 keeps the estimate
+    from chasing input-dependent (e.g. gain) model errors step by step,
+    which would make the loop oscillate.
+    Returns ``states`` and ``disturbance`` of shape ``(n_steps + 1,
+    n_states)`` and ``controls`` of shape ``(n_steps, n_controls)``.
     """
     n_ctrl = len(plan.controls)
+    n_state = len(plan.states)
     state = initial_state.copy()
     applied = np.zeros((n_steps, n_ctrl))
-    states = np.zeros((n_steps + 1, len(plan.states)))
+    states = np.zeros((n_steps + 1, n_state))
+    disturbances = np.zeros((n_steps + 1, n_state))
     states[0] = state
     prev = None
+    d = np.zeros(n_state)
     for k in range(n_steps):
-        ctrl_seq, _ = run_mpc_step(plan, state, surrogate, prev_controls=prev)
+        ctrl_seq, _ = run_mpc_step(
+            plan, state, surrogate, prev_controls=prev, disturbance=d
+        )
         applied[k] = ctrl_seq[0]
+        predicted = surrogate(state, ctrl_seq[:1])[0] + d
         state = true_dynamics(state, ctrl_seq[:1])[0]
+        if offset_free:
+            d = d + disturbance_gain * (state - predicted)
         states[k + 1] = state
+        disturbances[k + 1] = d
         prev = ctrl_seq
-    return {"states": states, "controls": applied}
+    return {"states": states, "controls": applied, "disturbance": disturbances}
 
 
 def _warm_start(plan: ControlPlan, prev_controls: np.ndarray | None) -> np.ndarray:

{marimo_flow-0.4.2 → marimo_flow-0.4.4/src/marimo_flow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marimo-flow
-Version: 0.4.2
+Version: 0.4.4
 Summary: Agentic scientific-computing platform: a reactive multi-agent team orchestrating PINA physics-informed neural-network workflows via pydantic-graph, with MLflow tracing/provenance and a marimo chat UI.
 Author-email: Björn Bethge <helloworld@synapticore.io>
 License-Expression: MIT
@@ -20,44 +20,44 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: marimo[lsp,mcp,recommended,sql]>=0.23.1
+Requires-Dist: marimo[lsp,mcp,recommended,sql]>=0.25.0
 Requires-Dist: mlflow[genai]>=3.16.1
 Requires-Dist: fastmcp>=4.0.9
-Requires-Dist: optuna>=4.8.0
-Requires-Dist: pina-mathlab>=0.2.6
-Requires-Dist: transformers[accelerate,tiktoken]>=5.5.4
-Requires-Dist: authlib>=1.6.9
-Requires-Dist: pillow>=12.2.0
-Requires-Dist: cryptography>=49.0.0
-Requires-Dist: langgraph>=1.1.8
+Requires-Dist: optuna>=5.0.0
+Requires-Dist: pina-mathlab>=0.3.2.post2609
+Requires-Dist: transformers[accelerate,tiktoken]>=5.17.0
+Requires-Dist: authlib>=1.8.0
+Requires-Dist: pillow>=12.3.0
+Requires-Dist: cryptography>=50.0.1
+Requires-Dist: langgraph>=1.2.12
 Requires-Dist: werkzeug>=3.1.8
 Requires-Dist: sqlparse>=0.6.0
 Requires-Dist: diskcache>=5.6.3
 Requires-Dist: protobuf>=6.33.6
-Requires-Dist: python-multipart>=0.0.27
-Requires-Dist: ujson>=5.12.0
-Requires-Dist: pyasn1>=0.6.3
-Requires-Dist: pyjwt>=2.12.1
+Requires-Dist: python-multipart>=0.0.32
+Requires-Dist: ujson>=6.0.0
+Requires-Dist: pyasn1>=0.6.4
+Requires-Dist: pyjwt>=2.15.0
 Requires-Dist: flask>=3.1.3
-Requires-Dist: gitpython>=3.1.59
-Requires-Dist: httpx2>=2.12.0
-Requires-Dist: httpcore2>=2.10.0
+Requires-Dist: gitpython>=3.1.62
+Requires-Dist: httpx2>=2.13.1
+Requires-Dist: httpcore2>=2.13.1
 Requires-Dist: lightning>=2.6.6
 Requires-Dist: aiohttp>=3.14.3
 Requires-Dist: accelerate>=1.15.0
-Requires-Dist: pymdown-extensions>=11.0.1
-Requires-Dist: optuna-integration[pytorch-lightning]>=4.8.0
-Requires-Dist: plotly[express,kaleido]>=6.7.0
-Requires-Dist: pydantic-ai-slim[ag-ui]>=2.10.0
+Requires-Dist: pymdown-extensions>=11.0.2
+Requires-Dist: optuna-integration[pytorch-lightning]>=5.0.0
+Requires-Dist: plotly[express,kaleido]>=7.1.0
+Requires-Dist: pydantic-ai-slim[ag-ui]>=2.49.0
 Requires-Dist: pyyaml>=6.0.3
-Requires-Dist: python-dotenv>=1.2.2
-Requires-Dist: typer>=0.24.1
+Requires-Dist: python-dotenv>=1.2.3
+Requires-Dist: typer>=0.27.2
 Requires-Dist: sympy>=1.14.0
 Requires-Dist: meshio>=5.3.5
-Requires-Dist: fasta2a>=0.6.1
+Requires-Dist: fasta2a>=2.0.1
 Provides-Extra: all
-Requires-Dist: torch>=2.11.0; extra == "all"
-Requires-Dist: torch-geometric>=2.7.0; extra == "all"
+Requires-Dist: torch>=2.14.0; extra == "all"
+Requires-Dist: torch-geometric>=2.8.0.post1; extra == "all"
 Dynamic: license-file
 
 # Marimo Flow 🌊

marimo_flow-0.4.4/src/marimo_flow.egg-info/requires.txt

@@ -0,0 +1,39 @@
+marimo[lsp,mcp,recommended,sql]>=0.25.0
+mlflow[genai]>=3.16.1
+fastmcp>=4.0.9
+optuna>=5.0.0
+pina-mathlab>=0.3.2.post2609
+transformers[accelerate,tiktoken]>=5.17.0
+authlib>=1.8.0
+pillow>=12.3.0
+cryptography>=50.0.1
+langgraph>=1.2.12
+werkzeug>=3.1.8
+sqlparse>=0.6.0
+diskcache>=5.6.3
+protobuf>=6.33.6
+python-multipart>=0.0.32
+ujson>=6.0.0
+pyasn1>=0.6.4
+pyjwt>=2.15.0
+flask>=3.1.3
+gitpython>=3.1.62
+httpx2>=2.13.1
+httpcore2>=2.13.1
+lightning>=2.6.6
+aiohttp>=3.14.3
+accelerate>=1.15.0
+pymdown-extensions>=11.0.2
+optuna-integration[pytorch-lightning]>=5.0.0
+plotly[express,kaleido]>=7.1.0
+pydantic-ai-slim[ag-ui]>=2.49.0
+pyyaml>=6.0.3
+python-dotenv>=1.2.3
+typer>=0.27.2
+sympy>=1.14.0
+meshio>=5.3.5
+fasta2a>=2.0.1
+
+[all]
+torch>=2.14.0
+torch-geometric>=2.8.0.post1

marimo_flow-0.4.2/src/marimo_flow.egg-info/requires.txt

@@ -1,39 +0,0 @@
-marimo[lsp,mcp,recommended,sql]>=0.23.1
-mlflow[genai]>=3.16.1
-fastmcp>=4.0.9
-optuna>=4.8.0
-pina-mathlab>=0.2.6
-transformers[accelerate,tiktoken]>=5.5.4
-authlib>=1.6.9
-pillow>=12.2.0
-cryptography>=49.0.0
-langgraph>=1.1.8
-werkzeug>=3.1.8
-sqlparse>=0.6.0
-diskcache>=5.6.3
-protobuf>=6.33.6
-python-multipart>=0.0.27
-ujson>=5.12.0
-pyasn1>=0.6.3
-pyjwt>=2.12.1
-flask>=3.1.3
-gitpython>=3.1.59
-httpx2>=2.12.0
-httpcore2>=2.10.0
-lightning>=2.6.6
-aiohttp>=3.14.3
-accelerate>=1.15.0
-pymdown-extensions>=11.0.1
-optuna-integration[pytorch-lightning]>=4.8.0
-plotly[express,kaleido]>=6.7.0
-pydantic-ai-slim[ag-ui]>=2.10.0
-pyyaml>=6.0.3
-python-dotenv>=1.2.2
-typer>=0.24.1
-sympy>=1.14.0
-meshio>=5.3.5
-fasta2a>=0.6.1
-
-[all]
-torch>=2.11.0
-torch-geometric>=2.7.0