From d6b55f049833a14f6123dc8cbe048abfd82ad384 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 17 Jun 2026 05:45:47 +0000
Subject: [PATCH 1/4] Initial plan


From 9448a5e378a420df9075e28dead52cd94829ff7c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 17 Jun 2026 05:50:23 +0000
Subject: [PATCH 2/4] release-prep: tests, CI, plot_trajectories fix,
 packaging, README polish

---
 .github/workflows/ci.yml                      |  30 +++
 CITATION.cff                                  |   1 +
 README.md                                     |  78 ++++--
 __pycache__/engine.cpython-312.pyc            | Bin 0 -> 32552 bytes
 engine.py                                     |  48 +++-
 jump_diffusion_engine.egg-info/PKG-INFO       | 196 ++++++++++++++
 jump_diffusion_engine.egg-info/SOURCES.txt    |  10 +
 .../dependency_links.txt                      |   1 +
 jump_diffusion_engine.egg-info/requires.txt   |   6 +
 jump_diffusion_engine.egg-info/top_level.txt  |   1 +
 pyproject.toml                                |  26 ++
 release/CHANGELOG.md                          |  18 +-
 .../test_engine.cpython-312-pytest-9.1.0.pyc  | Bin 0 -> 41099 bytes
 tests/test_engine.py                          | 253 ++++++++++++++++++
 14 files changed, 644 insertions(+), 24 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 create mode 100644 __pycache__/engine.cpython-312.pyc
 create mode 100644 jump_diffusion_engine.egg-info/PKG-INFO
 create mode 100644 jump_diffusion_engine.egg-info/SOURCES.txt
 create mode 100644 jump_diffusion_engine.egg-info/dependency_links.txt
 create mode 100644 jump_diffusion_engine.egg-info/requires.txt
 create mode 100644 jump_diffusion_engine.egg-info/top_level.txt
 create mode 100644 pyproject.toml
 create mode 100644 tests/__pycache__/test_engine.cpython-312-pytest-9.1.0.pyc
 create mode 100644 tests/test_engine.py

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..edfa134
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,30 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v
diff --git a/CITATION.cff b/CITATION.cff
index 1087cf2..34c2db8 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,6 +1,7 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 title: "Jump Diffusion Engine"
+version: "0.1.0"
 abstract: "A universal framework for multistable stochastic control."
 type: software
 authors:
diff --git a/README.md b/README.md
index 326a53f..38c8496 100644
--- a/README.md
+++ b/README.md
@@ -1,47 +1,87 @@
-# Jump-Diffusion-Engine – Perfectly Balanced Stochastic Control
-**One set of inputs. Continuous, self-regulating outputs.**
+# Jump-Diffusion-Engine – Stochastic Stability Analysis
+**Simulate, analyse, and steer noisy nonlinear systems.**
 
-A universal stability port for any dynamic system with a Source (Λ(t)), a Medium (Δ), and a Sink (f(Δ)).
+A simulation framework for systems with a Source (Λ(t)), a Medium (Δ), and a nonlinear Sink (f(Δ))
+subject to continuous diffusion and discrete jump noise.
 
 ## Core Equation
 
 `dΔ = [Λ(t) − f(Δ)] dt + σ dW + J dN`
 
-- `Λ(t) = ε₀ + A·sin(ωt)` — the source, steady and singing
-- `f(Δ) = kΔ + gΔ²/(K²+Δ²)` — the sink, linear then saturating
-- `Δ* : Λ = f(Δ), f′(Δ*) > 0` — the bowl, the stable held place
+- `Λ(t) = ε₀ + A·sin(ωt)` — the source (constant or time-varying)
+- `f(Δ) = kΔ + gΔ²/(K²+Δ²)` — the nonlinear sink (linear + saturating)
+- `Δ* : Λ = f(Δ), f′(Δ*) > 0` — a stable equilibrium (basin centre)
 
-Use `engine.py` to **force** any stochastic system into its stable basin, then **verify** its resilience:
+Use `engine.py` to **analyse** stochastic systems and **steer** trajectories toward stable basins:
 
 | # | Action | Method | What it does |
 |:-|:---|:---|:---|
-| 1 | **FORCE** it into the bowl | `seat_and_release()` | Applies a transient push, then **releases control to zero**. The basin holds it forever. |
-| 2 | **BREATHE** with the noise | `adaptive_k()` | Dynamically stiffens when calm, relaxes when volatile. Prevents numerical blow-up while maximizing rejection. |
-| 3 | **MAP** where the bowls are | `find_fixed_points()` | Finds all stable (`f′>0`) and unstable equilibria before you force it. |
-| 4 | **MEASURE** how deep the bowl is | `basin_depth()` | Quantifies the energy barrier—how hard you'd have to push to knock it out. |
-| 5 | **PREDICT** escape risk | `escape_probability()` | Empirical escape rate over Monte Carlo trials. Should be near-zero after seating. |
-| 6 | **VISUALIZE** the long-term cloud | `stationary_density()` | The normalized PDF \( p(\Delta) \propto e^{-2V/\sigma^2} \)—where it lives once forced. |
+| 1 | **Seat** into a stable basin | `seat_and_release()` | Applies a transient corrective push, then releases control. Basin strength determines how well it holds. |
+| 2 | **Adapt** to volatility | `adaptive_k()` | Updates the reversion coefficient based on recent variance. |
+| 3 | **Map** equilibria | `find_fixed_points()` | Finds stable (`f′>0`) and unstable fixed points for a given Λ. |
+| 4 | **Measure** basin depth | `basin_depth()` | Quantifies the potential-energy barrier around each basin. |
+| 5 | **Estimate** escape risk | `escape_probability()` | Empirical escape rate via Monte Carlo trials. |
+| 6 | **Visualise** the stationary distribution | `stationary_density()` | Computes the Boltzmann-weighted PDF p(Δ) ∝ e^{−2V/σ²}. |
 
 ## Installation
 
-This project requires Python 3 and the libraries used by `engine.py`:
+**Standard install (recommended)**
 
-- `numpy`
-- `scipy`
-- `matplotlib`
+```bash
+pip install -e .
+```
+
+This installs the package and all dependencies from the root of the repository.
 
-Install them with pip:
+**Manual dependency install**
+
+If you prefer not to use the package install, install dependencies directly:
 
 ```bash
 pip install numpy scipy matplotlib
 ```
 
-Then import the engine in your Python code:
+Then add the repository root to your Python path and import:
 
 ```python
 from engine import JumpDiffusionEngine
 ```
 
+> **Note:** Packaging metadata lives in `packaging/pyproject.toml` (legacy) and the
+> root `pyproject.toml` (standard). Use the root `pyproject.toml` for `pip install -e .`.
+
+## Quick Start
+
+```python
+import numpy as np
+from engine import JumpDiffusionEngine
+
+# Define a source: constant with a small oscillation
+def lambda_func(t):
+    return 0.5 + 0.1 * np.sin(2 * np.pi * 0.1 * t)
+
+eng = JumpDiffusionEngine(lambda_func, sigma=0.3, jump_rate=0.05, seed=42)
+
+# 1. Find stable equilibria
+fps = eng.find_fixed_points(lambda_val=0.5)
+print("Fixed points:", fps)
+
+# 2. Simulate a few trajectories
+results = eng.simulate(t_max=20.0, x0=0.0, n_realizations=3)
+eng.plot_trajectories(results)
+
+# 3. Steer into a stable basin, then release control
+result = eng.seat_and_release(t_max=15.0, x0=3.0, lambda_val=0.5)
+print(f"Released at step {result['release_idx']}, seated at Δ* ≈ {result['x_star']:.3f}")
+
+# 4. Estimate escape probability from the basin
+p_escape = eng.escape_probability(threshold=2.0, t_max=10.0, n_trials=200)
+print(f"Empirical escape probability: {p_escape:.3f}")
+
+# 5. Stationary density
+x, p = eng.stationary_density(lambda_val=0.5)
+```
+
 ## Use Cases
 
 Use this on any system that needs to maintain a steady state while being bombarded by both constant noise and sudden, unpredictable shocks.
diff --git a/__pycache__/engine.cpython-312.pyc b/__pycache__/engine.cpython-312.pyc
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diff --git a/engine.py b/engine.py
index 5814fd5..c17a850 100644
--- a/engine.py
+++ b/engine.py
@@ -469,7 +469,10 @@ def seat_and_release(self, t_max: float, x0: float = 0.0,
     def stationary_density(self, lambda_val: float, x_range: Tuple[float, float] = (-10, 10), n_points: int = 2000):
         x = np.linspace(x_range[0], x_range[1], n_points)
         V = self.potential(x, lambda_val)
-        p = np.exp(-2 * V / (self.sigma ** 2 + 1e-12))
+        # Shift V by its minimum before exponentiation to avoid numerical overflow.
+        # The constant shift cancels exactly in the normalisation.
+        V_shifted = V - np.min(V)
+        p = np.exp(-2 * V_shifted / (self.sigma ** 2 + 1e-12))
         norm = np.trapezoid(p, x) if hasattr(np, 'trapezoid') else np.trapz(p, x)
         p /= (norm + 1e-12)
         return x, p
@@ -567,10 +570,47 @@ def _plot_sweep(self, results: List[Dict], param_name: str, metrics: List[str]):
         plt.tight_layout()
         plt.show()
 
-    # Plotting helpers (plot_trajectories, plot_potential, basin_analysis) unchanged
     def plot_trajectories(self, results: List[Dict], title: str = "Jump-Diffusion Trajectories", show_energy: bool = False):
-        # ... (standard implementation as before)
-        pass  # Replace with full from previous if needed
+        """Plot simulated trajectories from simulate().
+
+        Parameters
+        ----------
+        results : list of dicts returned by simulate()
+        title   : figure title
+        show_energy : if True and energy was recorded, add a second panel
+        """
+        has_energy = show_energy and any('energy' in r for r in results)
+        n_panels = 2 if has_energy else 1
+        fig, axes = plt.subplots(n_panels, 1, figsize=(10, 4 * n_panels), squeeze=False)
+        ax_traj = axes[0, 0]
+
+        for i, r in enumerate(results):
+            label = f"Run {i + 1}" if len(results) > 1 else None
+            ax_traj.plot(r['t'], r['x'], lw=0.8, alpha=0.7, label=label)
+
+        ax_traj.set_xlabel("Time")
+        ax_traj.set_ylabel("Δ")
+        ax_traj.set_title(title)
+        ax_traj.grid(True, alpha=0.3)
+        if len(results) > 1:
+            ax_traj.legend(fontsize=8)
+
+        if has_energy:
+            ax_en = axes[1, 0]
+            for i, r in enumerate(results):
+                if 'energy' in r:
+                    label = f"Run {i + 1}" if len(results) > 1 else None
+                    ax_en.plot(r['t'], r['energy'], lw=0.8, alpha=0.7, label=label)
+            ax_en.set_xlabel("Time")
+            ax_en.set_ylabel("Energy V(Δ)")
+            ax_en.set_title("Potential Energy")
+            ax_en.grid(True, alpha=0.3)
+            if len(results) > 1:
+                ax_en.legend(fontsize=8)
+
+        plt.tight_layout()
+        plt.show()
+        return fig
 
 # Quick test / usage
 if __name__ == "__main__":
diff --git a/jump_diffusion_engine.egg-info/PKG-INFO b/jump_diffusion_engine.egg-info/PKG-INFO
new file mode 100644
index 0000000..43aa37c
--- /dev/null
+++ b/jump_diffusion_engine.egg-info/PKG-INFO
@@ -0,0 +1,196 @@
+Metadata-Version: 2.4
+Name: jump-diffusion-engine
+Version: 0.1.0
+Summary: Jump diffusion simulation engine for stochastic control systems.
+Author: Sarah Marin
+License: Apache-2.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3.0,>=1.23
+Requires-Dist: scipy<2.0,>=1.10
+Requires-Dist: matplotlib<4.0,>=3.7
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# Jump-Diffusion-Engine – Stochastic Stability Analysis
+**Simulate, analyse, and steer noisy nonlinear systems.**
+
+A simulation framework for systems with a Source (Λ(t)), a Medium (Δ), and a nonlinear Sink (f(Δ))
+subject to continuous diffusion and discrete jump noise.
+
+## Core Equation
+
+`dΔ = [Λ(t) − f(Δ)] dt + σ dW + J dN`
+
+- `Λ(t) = ε₀ + A·sin(ωt)` — the source (constant or time-varying)
+- `f(Δ) = kΔ + gΔ²/(K²+Δ²)` — the nonlinear sink (linear + saturating)
+- `Δ* : Λ = f(Δ), f′(Δ*) > 0` — a stable equilibrium (basin centre)
+
+Use `engine.py` to **analyse** stochastic systems and **steer** trajectories toward stable basins:
+
+| # | Action | Method | What it does |
+|:-|:---|:---|:---|
+| 1 | **Seat** into a stable basin | `seat_and_release()` | Applies a transient corrective push, then releases control. Basin strength determines how well it holds. |
+| 2 | **Adapt** to volatility | `adaptive_k()` | Updates the reversion coefficient based on recent variance. |
+| 3 | **Map** equilibria | `find_fixed_points()` | Finds stable (`f′>0`) and unstable fixed points for a given Λ. |
+| 4 | **Measure** basin depth | `basin_depth()` | Quantifies the potential-energy barrier around each basin. |
+| 5 | **Estimate** escape risk | `escape_probability()` | Empirical escape rate via Monte Carlo trials. |
+| 6 | **Visualise** the stationary distribution | `stationary_density()` | Computes the Boltzmann-weighted PDF p(Δ) ∝ e^{−2V/σ²}. |
+
+## Installation
+
+**Standard install (recommended)**
+
+```bash
+pip install -e .
+```
+
+This installs the package and all dependencies from the root of the repository.
+
+**Manual dependency install**
+
+If you prefer not to use the package install, install dependencies directly:
+
+```bash
+pip install numpy scipy matplotlib
+```
+
+Then add the repository root to your Python path and import:
+
+```python
+from engine import JumpDiffusionEngine
+```
+
+> **Note:** Packaging metadata lives in `packaging/pyproject.toml` (legacy) and the
+> root `pyproject.toml` (standard). Use the root `pyproject.toml` for `pip install -e .`.
+
+## Quick Start
+
+```python
+import numpy as np
+from engine import JumpDiffusionEngine
+
+# Define a source: constant with a small oscillation
+def lambda_func(t):
+    return 0.5 + 0.1 * np.sin(2 * np.pi * 0.1 * t)
+
+eng = JumpDiffusionEngine(lambda_func, sigma=0.3, jump_rate=0.05, seed=42)
+
+# 1. Find stable equilibria
+fps = eng.find_fixed_points(lambda_val=0.5)
+print("Fixed points:", fps)
+
+# 2. Simulate a few trajectories
+results = eng.simulate(t_max=20.0, x0=0.0, n_realizations=3)
+eng.plot_trajectories(results)
+
+# 3. Steer into a stable basin, then release control
+result = eng.seat_and_release(t_max=15.0, x0=3.0, lambda_val=0.5)
+print(f"Released at step {result['release_idx']}, seated at Δ* ≈ {result['x_star']:.3f}")
+
+# 4. Estimate escape probability from the basin
+p_escape = eng.escape_probability(threshold=2.0, t_max=10.0, n_trials=200)
+print(f"Empirical escape probability: {p_escape:.3f}")
+
+# 5. Stationary density
+x, p = eng.stationary_density(lambda_val=0.5)
+```
+
+## Use Cases
+
+Use this on any system that needs to maintain a steady state while being bombarded by both constant noise and sudden, unpredictable shocks.
+
+---
+
+### 1. Renewable Energy Grid Management
+
+Power grids are dissipative systems because electricity is used up as soon as it is made.
+
+- **The Source (`Λ`):** The fluctuating energy from wind turbines or solar panels.
+- **The Sink (`f`):** The battery storage and consumer demand that drains the energy.
+- **The Jumps (`J`):** Sudden lightning strikes or a power plant going offline.
+- **Use Case:** Using your code to ensure the grid frequency stays in the bowl (for example, `60 Hz`) and does not crash during a sudden surge.
+
+---
+
+### 2. Biological Homeostasis (Synthetic Biology)
+
+In genetic engineering, scientists create circuits inside cells to produce insulin or other chemicals.
+
+- **The Source (`Λ`):** The nutrients fed to the cell.
+- **The Sink (`f`):** The metabolic rate at which the cell uses those nutrients.
+- **The Jumps (`J`):** Sudden changes in temperature or pH levels.
+- **Use Case:** Programming a cell to keep its internal chemical levels stable even if the environment becomes noisy or shocked.
+
+---
+
+### 3. Automated Financial Trading (Hedge Funds)
+
+Markets are the definition of jump-diffusion.
+
+- **The Source (`Λ`):** The underlying growth or drift of an asset.
+- **The Sink (`f`):** The mean-reverting force (investors selling when the price is too high).
+- **The Jumps (`J`):** A flash crash or a sudden news event.
+- **Use Case:** A trading bot that identifies the bowl (the fair value) and does not panic-sell during a Poisson shock, knowing the sink force will pull the price back.
+
+---
+
+### 4. Spacecraft Orientation & Satellite Control
+
+Satellites must point their antennas precisely at Earth while floating in noisy space.
+
+- **The Source (`Λ`):** The thrusters or reaction wheels.
+- **The Sink (`f`):** The friction of the gyroscopes or the magnetic pull of Earth.
+- **The Jumps (`J`):** Tiny meteoroid impacts or solar flares.
+- **Use Case:** An autopilot system that keeps the satellite centered in its orientation bowl regardless of constant vibrations or sudden bumps.
+
+---
+
+### 5. Supply Chain & Inventory Control
+
+A warehouse needs to keep enough stock in the bowl without overflowing or running out.
+
+- **The Source (`Λ`):** The incoming shipments of goods.
+- **The Sink (`f`):** The customer orders draining the inventory.
+- **The Jumps (`J`):** A sudden viral trend causing a massive spike in orders.
+- **Use Case:** An AI manager that uses your restoring-force logic to automatically adjust order rates so the warehouse does not stay empty after a shock.
+
+---
+
+### 6. Climate Modeling (Resilience Thresholds)
+
+Ecologists use these models to see whether a forest or ocean can survive climate change.
+
+- **The Source (`Λ`):** Rainfall and sunlight.
+- **The Sink (`f`):** Evaporation and consumption by animals.
+- **The Jumps (`J`):** Forest fires or extreme heatwaves.
+- **Use Case:** Determining the tipping point—how big a jump (`J`) it takes to push the system out of its bowl so that it can never recover.
+
+---
+
+### 7. AI Training & Safe Learning
+
+When training a robot to walk, you do not want it to explore so far that it breaks itself.
+
+- **The Source (`Λ`):** The robot's drive to move forward.
+- **The Sink (`f`):** A penalty in the code that gets stronger as the robot gets closer to falling.
+- **The Jumps (`J`):** A person pushing the robot or an uneven floor.
+- **Use Case:** Ensuring the robot's brain always stays within a safe operational basin.
+
+```bibtex
+@software{SarahMarin_JumpDiffusionEngine_2026,
+  author       = {Sarah Marin},
+  title        = {JumpDiffusionEngine: A Universal Framework for Multistable Stochastic Control},
+  year         = {2026},
+  publisher    = {GitHub},
+  url          = {https://github.com/beanapologist/Jump-Diffusion-Engine},
+  note         = {Versioned releases archived on Zenodo},
+  doi          = {10.5281/zenodo.XXXXXXX}
+}
+```
+
+## License
+
+This project is licensed under the **Apache License 2.0**. See the `LICENSE` file for details.
diff --git a/jump_diffusion_engine.egg-info/SOURCES.txt b/jump_diffusion_engine.egg-info/SOURCES.txt
new file mode 100644
index 0000000..88e3137
--- /dev/null
+++ b/jump_diffusion_engine.egg-info/SOURCES.txt
@@ -0,0 +1,10 @@
+LICENSE
+README.md
+engine.py
+pyproject.toml
+jump_diffusion_engine.egg-info/PKG-INFO
+jump_diffusion_engine.egg-info/SOURCES.txt
+jump_diffusion_engine.egg-info/dependency_links.txt
+jump_diffusion_engine.egg-info/requires.txt
+jump_diffusion_engine.egg-info/top_level.txt
+tests/test_engine.py
\ No newline at end of file
diff --git a/jump_diffusion_engine.egg-info/dependency_links.txt b/jump_diffusion_engine.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/jump_diffusion_engine.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/jump_diffusion_engine.egg-info/requires.txt b/jump_diffusion_engine.egg-info/requires.txt
new file mode 100644
index 0000000..12dbac7
--- /dev/null
+++ b/jump_diffusion_engine.egg-info/requires.txt
@@ -0,0 +1,6 @@
+numpy<3.0,>=1.23
+scipy<2.0,>=1.10
+matplotlib<4.0,>=3.7
+
+[dev]
+pytest>=7.0
diff --git a/jump_diffusion_engine.egg-info/top_level.txt b/jump_diffusion_engine.egg-info/top_level.txt
new file mode 100644
index 0000000..45a160d
--- /dev/null
+++ b/jump_diffusion_engine.egg-info/top_level.txt
@@ -0,0 +1 @@
+engine
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..d101839
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,26 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "jump-diffusion-engine"
+version = "0.1.0"
+description = "Jump diffusion simulation engine for stochastic control systems."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Sarah Marin" }]
+dependencies = [
+  "numpy>=1.23,<3.0",
+  "scipy>=1.10,<2.0",
+  "matplotlib>=3.7,<4.0",
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=7.0"]
+
+[tool.setuptools]
+py-modules = ["engine"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
diff --git a/release/CHANGELOG.md b/release/CHANGELOG.md
index db90dc6..a2bfb77 100644
--- a/release/CHANGELOG.md
+++ b/release/CHANGELOG.md
@@ -8,9 +8,25 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 ## [Unreleased]
 
 ### Added
-- Initial release scaffolding files in `release/`.
+- Root-level `pyproject.toml` for standard `pip install -e .` workflow.
+- `tests/test_engine.py` — automated test suite covering `find_fixed_points`,
+  `escape_probability`, `stationary_density`, `seat_and_release`, `simulate`,
+  and `plot_trajectories`.
+- `.github/workflows/ci.yml` — GitHub Actions CI running tests on Python 3.9–3.12.
+
+### Fixed
+- Implemented `plot_trajectories()`, which was previously a stub (`pass`).
+
+### Changed
+- README revised to use more precise, technically defensible language.
+- `CITATION.cff` now includes the `version` field (`0.1.0`).
 
 ## [0.1.0] - TBD
 
 ### Added
 - Initial public release of Jump-Diffusion-Engine.
+- Core SDE simulator (`simulate`), fixed-point analysis (`find_fixed_points`,
+  `basin_depth`, `potential`), escape probability estimation (`escape_probability`),
+  stationary density (`stationary_density`), and basin-seating control
+  (`seat_and_release`, `identify_boundary`).
+- Packaging files under `packaging/` and root `pyproject.toml`.
diff --git a/tests/__pycache__/test_engine.cpython-312-pytest-9.1.0.pyc b/tests/__pycache__/test_engine.cpython-312-pytest-9.1.0.pyc
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HcmV?d00001

diff --git a/tests/test_engine.py b/tests/test_engine.py
new file mode 100644
index 0000000..9084a5d
--- /dev/null
+++ b/tests/test_engine.py
@@ -0,0 +1,253 @@
+"""Tests for the JumpDiffusionEngine public API.
+
+All stochastic tests use a fixed seed (42) or rely on statistical invariants
+that hold with very high probability, to avoid brittle flakiness.
+"""
+import numpy as np
+import pytest
+import sys
+import os
+
+# Allow importing engine from the repo root when running with pytest from any cwd
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
+
+from engine import JumpDiffusionEngine
+
+
+# ---------------------------------------------------------------------------
+# Shared fixture
+# ---------------------------------------------------------------------------
+
+@pytest.fixture
+def engine():
+    """Standard engine with a constant lambda and deterministic seed."""
+    return JumpDiffusionEngine(
+        lambda_func=lambda t: 0.5,
+        sigma=0.3,
+        jump_rate=0.0,   # no jumps — keeps tests deterministic
+        dt=0.01,
+        seed=42,
+        k=0.8,
+        g=0.5,
+        K=2.0,
+    )
+
+
+# ---------------------------------------------------------------------------
+# find_fixed_points
+# ---------------------------------------------------------------------------
+
+class TestFindFixedPoints:
+    def test_returns_at_least_one_stable_point(self, engine):
+        fps = engine.find_fixed_points(lambda_val=0.5)
+        assert len(fps) > 0, "Expected at least one fixed point"
+
+    def test_stable_points_have_positive_f_prime(self, engine):
+        fps = engine.find_fixed_points(lambda_val=0.5)
+        stable = [fp for fp in fps if fp['stable']]
+        assert len(stable) > 0, "Expected at least one stable fixed point"
+        for fp in stable:
+            assert fp['f_prime'] > 0, "Stable fixed point must have f' > 0"
+
+    def test_fixed_point_satisfies_f_equals_lambda(self, engine):
+        lambda_val = 0.5
+        fps = engine.find_fixed_points(lambda_val=lambda_val)
+        for fp in fps:
+            residual = abs(engine.f_func(fp['x_star']) - lambda_val)
+            assert residual < 1e-4, f"Fixed point residual too large: {residual}"
+
+    def test_result_structure(self, engine):
+        fps = engine.find_fixed_points(lambda_val=0.5)
+        for fp in fps:
+            assert 'x_star' in fp
+            assert 'stable' in fp
+            assert 'f_prime' in fp
+            assert 'lambda_val' in fp
+
+    def test_no_fixed_points_returns_empty(self, engine):
+        # With a very large lambda_val that exceeds the sink's maximum,
+        # there should be no fixed points.
+        fps = engine.find_fixed_points(lambda_val=1e6)
+        assert fps == []
+
+    def test_different_lambda_shifts_fixed_point(self, engine):
+        fps_low = engine.find_fixed_points(lambda_val=0.1)
+        fps_high = engine.find_fixed_points(lambda_val=0.9)
+        x_low = sorted(fp['x_star'] for fp in fps_low if fp['stable'])
+        x_high = sorted(fp['x_star'] for fp in fps_high if fp['stable'])
+        # Higher lambda → fixed point shifts to higher x
+        if x_low and x_high:
+            assert x_high[0] > x_low[0]
+
+
+# ---------------------------------------------------------------------------
+# escape_probability
+# ---------------------------------------------------------------------------
+
+class TestEscapeProbability:
+    def test_returns_value_in_unit_interval(self, engine):
+        p = engine.escape_probability(threshold=5.0, t_max=10.0, n_trials=20)
+        assert 0.0 <= p <= 1.0
+
+    def test_large_threshold_gives_low_escape(self, engine):
+        # With a very large threshold, very few (if any) trials should escape.
+        p = engine.escape_probability(threshold=50.0, t_max=5.0, n_trials=30)
+        assert p < 0.5, f"Expected low escape probability with large threshold, got {p}"
+
+    def test_tiny_threshold_gives_high_escape(self, engine):
+        # With a near-zero threshold, almost every trial should "escape".
+        p = engine.escape_probability(threshold=1e-6, t_max=5.0, n_trials=30)
+        assert p > 0.5, f"Expected high escape probability with tiny threshold, got {p}"
+
+    def test_explicit_x0_and_x_star(self, engine):
+        fps = engine.find_fixed_points(0.5)
+        x_star = fps[0]['x_star'] if fps else 0.0
+        p = engine.escape_probability(
+            threshold=5.0, t_max=5.0, x0=x_star, x_star=x_star, n_trials=20
+        )
+        assert 0.0 <= p <= 1.0
+
+
+# ---------------------------------------------------------------------------
+# stationary_density
+# ---------------------------------------------------------------------------
+
+class TestStationaryDensity:
+    def test_returns_arrays_of_matching_length(self, engine):
+        x, p = engine.stationary_density(lambda_val=0.5)
+        assert len(x) == len(p)
+        assert len(x) > 0
+
+    def test_density_is_normalised(self, engine):
+        x, p = engine.stationary_density(lambda_val=0.5)
+        # Numerical integral should be approximately 1.
+        integral = (np.trapezoid(p, x) if hasattr(np, 'trapezoid') else
+                    np.trapz(p, x))
+        assert abs(integral - 1.0) < 0.05, f"Density not normalised: integral={integral}"
+
+    def test_density_is_non_negative(self, engine):
+        x, p = engine.stationary_density(lambda_val=0.5)
+        assert np.all(p >= 0), "Density contains negative values"
+
+    def test_peak_near_stable_fixed_point(self, engine):
+        lambda_val = 0.5
+        fps = engine.find_fixed_points(lambda_val)
+        stable = [fp for fp in fps if fp['stable']]
+        if not stable:
+            pytest.skip("No stable fixed point to compare against")
+        x_star = stable[0]['x_star']
+        x, p = engine.stationary_density(lambda_val=lambda_val)
+        peak_x = x[np.argmax(p)]
+        assert abs(peak_x - x_star) < 1.5, (
+            f"Density peak ({peak_x:.3f}) far from stable equilibrium ({x_star:.3f})"
+        )
+
+
+# ---------------------------------------------------------------------------
+# seat_and_release
+# ---------------------------------------------------------------------------
+
+class TestSeatAndRelease:
+    def test_returns_expected_keys(self, engine):
+        result = engine.seat_and_release(t_max=5.0, x0=3.0, lambda_val=0.5)
+        for key in ('t', 'x', 'control', 'boundary', 'x_star', 'settle_tol',
+                    'release_idx', 'released'):
+            assert key in result, f"Missing key: {key}"
+
+    def test_trajectory_length_matches_time(self, engine):
+        t_max = 5.0
+        result = engine.seat_and_release(t_max=t_max, x0=3.0, lambda_val=0.5)
+        expected_steps = int(t_max / engine.dt) + 1
+        assert len(result['t']) == expected_steps
+        assert len(result['x']) == expected_steps
+
+    def test_control_is_zero_after_release(self, engine):
+        result = engine.seat_and_release(t_max=5.0, x0=3.0, lambda_val=0.5)
+        if result['released'] and result['release_idx'] is not None:
+            post_control = result['control'][result['release_idx']:]
+            assert np.allclose(post_control, 0.0), "Control was non-zero after release"
+
+    def test_raises_without_stable_bowl(self):
+        """seat_and_release should raise when no stable bowl exists."""
+        eng = JumpDiffusionEngine(
+            lambda_func=lambda t: 1e6,  # extreme lambda → no fixed points
+            sigma=0.3, jump_rate=0.0, dt=0.01, seed=42,
+        )
+        with pytest.raises(ValueError, match="No stable bowl"):
+            eng.seat_and_release(t_max=1.0)
+
+    def test_trajectory_stays_bounded(self, engine):
+        # After seating, x should not wander to extreme values.
+        result = engine.seat_and_release(t_max=10.0, x0=1.0, lambda_val=0.5,
+                                         dwell=50)
+        assert np.all(np.abs(result['x']) < 30), "Trajectory left reasonable bounds"
+
+
+# ---------------------------------------------------------------------------
+# simulate (smoke / integration test)
+# ---------------------------------------------------------------------------
+
+class TestSimulate:
+    def test_single_realization_structure(self, engine):
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=1)
+        assert len(results) == 1
+        r = results[0]
+        assert 't' in r and 'x' in r
+        assert len(r['t']) == len(r['x'])
+
+    def test_multiple_realizations(self, engine):
+        n = 5
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=n)
+        assert len(results) == n
+
+    def test_seeded_reproducibility(self):
+        """Same seed → identical trajectory."""
+        def lf(t):
+            return 0.5
+
+        eng1 = JumpDiffusionEngine(lf, sigma=0.3, jump_rate=0.1, dt=0.01, seed=7)
+        eng2 = JumpDiffusionEngine(lf, sigma=0.3, jump_rate=0.1, dt=0.01, seed=7)
+        r1 = eng1.simulate(t_max=1.0, x0=0.0, n_realizations=1)[0]
+        r2 = eng2.simulate(t_max=1.0, x0=0.0, n_realizations=1)[0]
+        np.testing.assert_array_equal(r1['x'], r2['x'])
+
+    def test_trajectory_mean_reverting(self, engine):
+        """With no jumps and strong mean reversion, x should stay bounded."""
+        results = engine.simulate(t_max=20.0, x0=5.0, n_realizations=3,
+                                  record_energy=False)
+        for r in results:
+            assert np.all(np.abs(r['x']) < 50), "Trajectory diverged unexpectedly"
+
+    def test_energy_recorded_when_requested(self, engine):
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=1,
+                                  record_energy=True)
+        assert 'energy' in results[0]
+        assert len(results[0]['energy']) == len(results[0]['x'])
+
+    def test_energy_not_recorded_when_skipped(self, engine):
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=1,
+                                  record_energy=False)
+        assert 'energy' not in results[0]
+
+
+# ---------------------------------------------------------------------------
+# plot_trajectories (non-display smoke test)
+# ---------------------------------------------------------------------------
+
+class TestPlotTrajectories:
+    def test_returns_figure(self, engine, monkeypatch):
+        import matplotlib.pyplot as plt
+        # Suppress display in CI
+        monkeypatch.setattr(plt, "show", lambda: None)
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=2,
+                                  record_energy=True)
+        fig = engine.plot_trajectories(results, show_energy=True)
+        assert fig is not None
+
+    def test_accepts_single_realization(self, engine, monkeypatch):
+        import matplotlib.pyplot as plt
+        monkeypatch.setattr(plt, "show", lambda: None)
+        results = engine.simulate(t_max=1.0, x0=0.0, n_realizations=1,
+                                  record_energy=False)
+        fig = engine.plot_trajectories(results)
+        assert fig is not None

From 086c7cb3c99a1225600fda384b3d6f47df4ef3ca Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 17 Jun 2026 05:52:07 +0000
Subject: [PATCH 3/4] fix: align requires-python to >=3.9, add CI permissions,
 clarify README packaging note

---
 .github/workflows/ci.yml | 3 +++
 README.md                | 5 +++--
 pyproject.toml           | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index edfa134..35e62df 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [main]
 
+permissions:
+  contents: read
+
 jobs:
   test:
     runs-on: ubuntu-latest
diff --git a/README.md b/README.md
index 38c8496..0dbb632 100644
--- a/README.md
+++ b/README.md
@@ -47,8 +47,9 @@ Then add the repository root to your Python path and import:
 from engine import JumpDiffusionEngine
 ```
 
-> **Note:** Packaging metadata lives in `packaging/pyproject.toml` (legacy) and the
-> root `pyproject.toml` (standard). Use the root `pyproject.toml` for `pip install -e .`.
+> **Note:** A legacy `packaging/pyproject.toml` is also present in the repository.
+> For standard `pip install -e .` use the root `pyproject.toml`; the `packaging/`
+> directory is kept for historical reference and may be removed in a future release.
 
 ## Quick Start
 
diff --git a/pyproject.toml b/pyproject.toml
index d101839..7e9cbc1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ name = "jump-diffusion-engine"
 version = "0.1.0"
 description = "Jump diffusion simulation engine for stochastic control systems."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { text = "Apache-2.0" }
 authors = [{ name = "Sarah Marin" }]
 dependencies = [

From 8a0e7cfc15b5494b0ab6e6331942ad0377e90bf2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 17 Jun 2026 06:00:12 +0000
Subject: [PATCH 4/4] ci: add build job with wheel verification and upload
 artifact

---
 .github/workflows/ci.yml                      |  29 ++++++++++++++++++
 .gitignore                                    |  23 ++++++++++++++
 __pycache__/engine.cpython-312.pyc            | Bin 32552 -> 32552 bytes
 jump_diffusion_engine.egg-info/PKG-INFO       |   9 +++---
 pyproject.toml                                |   2 +-
 .../test_engine.cpython-312-pytest-9.1.0.pyc  | Bin 41099 -> 41099 bytes
 6 files changed, 58 insertions(+), 5 deletions(-)
 create mode 100644 .gitignore

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 35e62df..167cb44 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,3 +31,32 @@ jobs:
 
       - name: Run tests
         run: pytest tests/ -v
+
+  build:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: python -m pip install --upgrade pip build
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Verify wheel installs cleanly
+        run: |
+          pip install dist/*.whl
+          python -c "from engine import JumpDiffusionEngine; print('import OK')"
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..6d793b7
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,23 @@
+# Build / distribution artifacts
+*.egg-info/
+build/
+dist/
+
+# Python cache
+__pycache__/
+*.py[cod]
+*.pyo
+
+# Test / coverage artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Editor / OS
+.DS_Store
+*.swp
diff --git a/__pycache__/engine.cpython-312.pyc b/__pycache__/engine.cpython-312.pyc
index 20e88f319759e3c8458bc325727d38465b31dbcd..217d16f6c0c0b217e5fef27cb4e03520fc15c06f 100644
GIT binary patch
delta 21
bcmZ4Sk8#C6My}Jmyj%=G&}P1oORgROQ@sXV

delta 21
bcmZ4Sk8#C6My}Jmyj%=G&|$ifORgROQ@;jX

diff --git a/jump_diffusion_engine.egg-info/PKG-INFO b/jump_diffusion_engine.egg-info/PKG-INFO
index 43aa37c..b845ecf 100644
--- a/jump_diffusion_engine.egg-info/PKG-INFO
+++ b/jump_diffusion_engine.egg-info/PKG-INFO
@@ -3,8 +3,8 @@ Name: jump-diffusion-engine
 Version: 0.1.0
 Summary: Jump diffusion simulation engine for stochastic control systems.
 Author: Sarah Marin
-License: Apache-2.0
-Requires-Python: >=3.8
+License-Expression: Apache-2.0
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<3.0,>=1.23
@@ -63,8 +63,9 @@ Then add the repository root to your Python path and import:
 from engine import JumpDiffusionEngine
 ```
 
-> **Note:** Packaging metadata lives in `packaging/pyproject.toml` (legacy) and the
-> root `pyproject.toml` (standard). Use the root `pyproject.toml` for `pip install -e .`.
+> **Note:** A legacy `packaging/pyproject.toml` is also present in the repository.
+> For standard `pip install -e .` use the root `pyproject.toml`; the `packaging/`
+> directory is kept for historical reference and may be removed in a future release.
 
 ## Quick Start
 
diff --git a/pyproject.toml b/pyproject.toml
index 7e9cbc1..8521c24 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ version = "0.1.0"
 description = "Jump diffusion simulation engine for stochastic control systems."
 readme = "README.md"
 requires-python = ">=3.9"
-license = { text = "Apache-2.0" }
+license = "Apache-2.0"
 authors = [{ name = "Sarah Marin" }]
 dependencies = [
   "numpy>=1.23,<3.0",
diff --git a/tests/__pycache__/test_engine.cpython-312-pytest-9.1.0.pyc b/tests/__pycache__/test_engine.cpython-312-pytest-9.1.0.pyc
index 95d56f2a3ff250413e77a1c77d32deae1c20b132..8f48966e277d328d1499e97de27593a4bd40dfea 100644
GIT binary patch
delta 21
bcmeA^$kct1iR&~kFBbz4w3%<@YFq#SM~en8

delta 21
bcmeA^$kct1iR&~kFBbz4^qOwuYFq#SN2>-j