phaseprobe 0.2.0__py3-none-any.whl

phaseprobe/types.py

@@ -0,0 +1,131 @@
+"""Typed public model-adapter and result interfaces."""
+
+from __future__ import annotations
+
+from collections.abc import Mapping, Sequence
+from dataclasses import dataclass
+from typing import Literal, Protocol, TypeAlias, runtime_checkable
+
+Scalar: TypeAlias = float | int | str
+State: TypeAlias = tuple[float, ...]
+Parameters: TypeAlias = Mapping[str, float]
+ModelConfig: TypeAlias = Mapping[str, object]
+Tolerances: TypeAlias = Mapping[str, float]
+ReplayMode: TypeAlias = Literal["exact", "tolerance"]
+
+
+@dataclass(frozen=True, slots=True)
+class TracePoint:
+    """One retained point from a bounded simulation trace."""
+
+    step: int
+    time: float
+    state: State
+    observations: Mapping[str, Scalar]
+
+
+@dataclass(frozen=True, slots=True)
+class InvariantResult:
+    """Result of evaluating a declared model invariant or boundedness rule."""
+
+    name: str
+    passed: bool
+    measured: float
+    tolerance: float
+    detail: str
+
+
+@dataclass(frozen=True, slots=True)
+class SimulationTrace:
+    """One completed trajectory-level simulation before engine retention.
+
+    ``metadata`` contains JSON-serializable execution evidence supplied by the adapter. It must
+    describe solver termination and the numerical environment without embedding callable code.
+    """
+
+    points: tuple[TracePoint, ...]
+    final_state: State
+    success: bool
+    status: int
+    message: str
+    metadata: Mapping[str, object]
+
+
+@runtime_checkable
+class ModelAdapter(Protocol):
+    """Small interface implemented by built-in and downstream simulation adapters.
+
+    The explicit state tuple makes perturbation, serialization, and finite-value validation
+    deterministic. Classifiers and invariants receive declared tolerances rather than hiding
+    thresholds inside the engine.
+    """
+
+    name: str
+    identity: str
+    dimensions: tuple[str, ...]
+
+    def initial_state(self, config: ModelConfig, seed: int) -> State:
+        """Return a deterministic initial state for ``config`` and ``seed``."""
+
+    def step(self, state: State, parameters: Parameters, dt: float) -> State:
+        """Advance exactly one declared step."""
+
+    def observe(self, state: State) -> Mapping[str, Scalar]:
+        """Expose bounded scalar observables used in reports and classification."""
+
+    def classify(self, trace: Sequence[TracePoint], tolerances: Tolerances) -> str:
+        """Return a qualitative class using only retained trace evidence."""
+
+    def invariants(
+        self,
+        trace: Sequence[TracePoint],
+        parameters: Parameters,
+        tolerances: Tolerances,
+    ) -> list[InvariantResult]:
+        """Evaluate declared invariants or boundedness conditions."""
+
+
+@runtime_checkable
+class TrajectoryAdapter(Protocol):
+    """Optional protocol for solvers that naturally integrate a whole trajectory.
+
+    The engine dispatches this protocol without manufacturing a fake fixed-step loop. Search,
+    perturbation, policy, artifact, replay, and reporting code is shared with ``ModelAdapter``.
+    """
+
+    name: str
+    identity: str
+    dimensions: tuple[str, ...]
+
+    @property
+    def replay_mode(self) -> ReplayMode:
+        """Declare whether numerical replay is exact or tolerance-based."""
+
+    def initial_state(self, config: ModelConfig, seed: int) -> State:
+        """Return the declared initial state for ``config`` and ``seed``."""
+
+    def simulate(
+        self,
+        initial_state: State,
+        parameters: Parameters,
+        config: ModelConfig,
+        seed: int,
+    ) -> SimulationTrace:
+        """Integrate once and return a finite, serializable trajectory."""
+
+    def observe(self, trace: SimulationTrace) -> Mapping[str, Scalar]:
+        """Return bounded summary observables for the completed trajectory."""
+
+    def classify(self, trace: SimulationTrace, tolerances: Tolerances) -> str:
+        """Return a qualitative class from retained trajectory evidence."""
+
+    def invariants(
+        self,
+        trace: SimulationTrace,
+        parameters: Parameters,
+        tolerances: Tolerances,
+    ) -> list[InvariantResult]:
+        """Evaluate declared invariants or boundedness conditions."""
+
+    def configuration(self) -> Mapping[str, object]:
+        """Serialize adapter settings and explicit identity, never callable source."""

phaseprobe-0.2.0.dist-info/METADATA

@@ -0,0 +1,275 @@
+Metadata-Version: 2.4
+Name: phaseprobe
+Version: 0.2.0
+Summary: Find reproducible qualitative simulation transitions and turn them into regression tests.
+Project-URL: Documentation, https://github.com/aliengineering-byte/phaseprobe#readme
+Project-URL: Issues, https://github.com/aliengineering-byte/phaseprobe/issues
+Project-URL: Source, https://github.com/aliengineering-byte/phaseprobe
+Author: Ali
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: dynamical-systems,regression-testing,reproducibility,simulation,testing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Testing
+Requires-Python: >=3.10
+Provides-Extra: demo
+Requires-Dist: pillow==11.3.0; extra == 'demo'
+Provides-Extra: dev
+Requires-Dist: build==1.3.0; extra == 'dev'
+Requires-Dist: mypy==1.17.1; extra == 'dev'
+Requires-Dist: pytest-cov==6.2.1; extra == 'dev'
+Requires-Dist: pytest==8.4.1; extra == 'dev'
+Requires-Dist: ruff==0.12.7; extra == 'dev'
+Provides-Extra: scipy
+Requires-Dist: numpy<2.5,>=1.23.5; extra == 'scipy'
+Requires-Dist: scipy<1.19,>=1.15; extra == 'scipy'
+Description-Content-Type: text/markdown
+
+# PhaseProbe
+
+> Find a simulation behavior boundary. Preserve it as a replay. Turn it into a test.
+
+Maintaining a simulation is risky when a tiny parameter or initial-condition change can cross a qualitative boundary while ordinary numeric assertions still look plausible. PhaseProbe runs a bounded, deterministic search, records exactly what it tested, and emits an offline report plus an executable pytest regression.
+
+```console
+$ python -m pip install .
+$ phaseprobe scan --example logistic
+QUALITATIVE TRANSITION FOUND
+
+Model: logistic-map
+Search dimension: r
+Baseline regime: period-2
+Changed regime: period-4
+Replay: .phaseprobe/runs/<run-id>/replay.json
+
+$ phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
+$ python -m pytest -q tests/generated
+1 passed
+```
+
+[![Terminal demo: scan, refine, replay, and generated pytest](assets/demo-static.png)](assets/demo.gif)
+
+No API key, LLM, GPU, Docker, account, telemetry, network connection, or hosted service is required at runtime. PhaseProbe's base installation has no third-party runtime dependencies; NumPy and SciPy are isolated in the optional `scipy` extra.
+
+## Five-minute quick start
+
+Requires Python 3.10 or newer on Windows or Linux.
+
+```bash
+python -m pip install .
+phaseprobe scan --example logistic
+phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
+phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
+python -m pytest -q tests/generated
+phaseprobe report .phaseprobe/runs/<run-id>
+```
+
+Replace `<run-id>` with the directory printed by `scan`. The scan returns `0` when it successfully finds a transition. Add `--fail-on-finding` only when a finding should fail CI.
+
+The quick-start evidence is empirical: the built-in classifier finds a finite-time period-2/period-4 bracket for the logistic map, performs bounded binary refinement, repeats both endpoints, saves trace hashes and a versioned fixture, and generates a fixed pytest template. It does not claim an exact bifurcation point.
+
+## Use with SciPy
+
+SciPy integrates trajectories. PhaseProbe searches declared dimensions, preserves qualitative
+boundaries, and creates regressions. PhaseProbe is an independent project and does not imply
+endorsement by SciPy.
+
+Five-minute path:
+
+[![SciPy demo: solve_ivp evidence, tolerance replay, and generated pytest](assets/scipy-demo-static.png)](assets/scipy-demo.gif)
+
+The verified command transcript is [assets/scipy-demo-session.txt](assets/scipy-demo-session.txt),
+with a self-contained [HTML example report](examples/scipy/report.html).
+
+```bash
+python -m pip install "phaseprobe[scipy]"
+phaseprobe perturb --config examples/scipy/lorenz.json
+phaseprobe check --config examples/scipy/predator-prey.json
+phaseprobe replay .phaseprobe/runs/<run-id>/replay.json
+phaseprobe generate-test .phaseprobe/runs/<run-id>/replay.json
+python -m pytest -q tests/generated
+```
+
+The Lorenz command searches a declared initial-`x` perturbation and reports only finite-time
+divergence evidence. `examples/scipy/lorenz-negative.json` is its short-window negative control.
+The predator–prey command checks the declared first integral with tightly resolved DOP853 settings;
+`examples/scipy/predator-prey-coarse.json` deliberately fails the same policy with loose RK23
+settings.
+
+For a direct Python API:
+
+```python
+from phaseprobe import run_perturbation
+from phaseprobe.adapters.scipy import SolveIVPAdapter
+
+adapter = SolveIVPAdapter(
+    name="lorenz-scipy",
+    identity="my-lorenz-v1",
+    rhs=lorenz_rhs,
+    state_names=("x", "y", "z"),
+    initial_state=(1.0, 1.0, 1.0),
+    t_span=(0.0, 25.0),
+    t_eval=1001,
+    method="DOP853",
+    rtol=1e-9,
+    atol=1e-12,
+    max_step=0.05,
+    classifier=classify_lorenz,
+)
+
+outcome = run_perturbation(adapter, config)
+```
+
+JSON CLI configurations name an absolute dotted Python module and factory. Running, replaying, or
+generating from that configuration executes the selected trusted Python code; validation alone
+does not import it. See [the audited contract](docs/SCIPY_SOLVE_IVP_AUDIT.md),
+[architecture](ARCHITECTURE.md), and [security boundary](SECURITY.md).
+
+## Commands
+
+| command | job | normal success |
+| --- | --- | --- |
+| `scan` | Bounded one-dimensional parameter scan, adjacent class-change detection, and stable bracket refinement | Finding or no finding, exit `0` |
+| `perturb` | Baseline/perturbed twin runs over bounded initial-state changes | Finding or no finding, exit `0` |
+| `check` | Execute a declared configuration policy for CI | Exit `1` only when policy fails |
+| `replay` | Validate fixture integrity and re-execute model, parameters, seed, initial state, tolerances, and retention | Declared `exact` or `tolerance` comparison passes |
+| `generate-test` | Validate and copy a fixture into a non-extensible pytest template | Executable test under `tests/generated/` |
+| `report` | Regenerate terminal, versioned JSON, and self-contained offline HTML evidence | Local report files |
+
+Common options:
+
+```console
+phaseprobe scan --config examples/configs/logistic-scan.json
+phaseprobe perturb --example lorenz --json
+phaseprobe check --example predator-prey
+phaseprobe scan --example logistic --fail-on-finding
+```
+
+Exit codes are stable: `0` completed, `1` declared policy or explicit `--fail-on-finding`, `2` invalid input/configuration, `3` numerical failure, and `4` internal PhaseProbe defect.
+
+## Included deterministic examples
+
+| example | command | positive evidence | negative control | direct technical source |
+| --- | --- | --- | --- | --- |
+| Logistic map | `phaseprobe scan --example logistic` | Finite-time period-2 to period-4 classification bracket | `--example logistic-negative` stays period-2 over its declared range | [May, 1976](https://www.nature.com/articles/261459a0) |
+| Lorenz system | `phaseprobe perturb --example lorenz` | Small initial separation exceeds the declared finite-time trajectory-distance threshold | Short window plus unreachable threshold reports no finding | [Lorenz, 1963](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml) |
+| Predator–prey | `phaseprobe check --example predator-prey` | Refined RK4 step preserves the analytic first integral within tolerance | Coarse step fails the invariant-drift policy | [Lotka, 1920](https://doi.org/10.1073/pnas.6.7.410) |
+| Genetic toggle | `phaseprobe perturb --example toggle` | Bounded initial-state perturbation reaches the opposite dominant state | Smaller declared range stays in the baseline basin | [Gardner, Cantor & Collins, 2000](https://www.nature.com/articles/35002131) |
+
+Each configuration records the seed, fixed integration/iteration settings, tolerances, burn-in, observation window, classification rule, refinement rule, invalid-state policy, and trace cap. See [examples/README.md](examples/README.md) for equations and interpretation.
+
+### Measured reference run
+
+On 2026-08-01 with CPython 3.12.13 on Windows, the instrumented logistic quick-start scan completed in 10.114 seconds with a 34.81 MiB peak process-tree working set. All eight positive/negative example commands completed in 12.238 seconds. The final 38-test suite with branch coverage completed in 64.86 seconds at 87.92% coverage. These are observations from one local run, not cross-machine performance claims; the generated transcript is in [assets/demo-session.txt](assets/demo-session.txt).
+
+## Evidence artifacts
+
+Every execution is bounded under `.phaseprobe/runs/<run-id>/`:
+
+```text
+run.json       complete versioned evidence
+findings.json  compact finding or negative result
+replay.json    schema-versioned integrity-protected fixture
+trace.jsonl    capped baseline/changed retained points
+report.html    self-contained offline report
+manifest.json  sizes and SHA-256 hashes
+```
+
+Model names used for generated test paths are sanitized. The generated source comes from a fixed template; configuration strings never become executable Python.
+
+## What PhaseProbe adds—and what it does not
+
+| existing category | established strength | PhaseProbe’s narrower job |
+| --- | --- | --- |
+| Solvers such as SciPy | Integrate differential equations with mature numerical methods | Consume an adapter’s trajectories and preserve a discovered qualitative boundary as test evidence |
+| Property-based testing such as Hypothesis | Generate and shrink broad input domains | Search declared simulation dimensions with model-specific observables and classes |
+| Bifurcation/attractor tools such as AUTO, PyDSTool, and Attractors.jl | Deep continuation, bifurcation, attractor, and basin analysis | Lightweight black-box numerical brackets plus replay and pytest materialization |
+| Sensitivity tools such as SALib | Quantify input contributions to output variation | Find a reproducible qualitative predicate change |
+| Simulation environments such as Mesa, NetLogo, cadCAD, and Golly | Build, run, and explore models | Test adapters without becoming another simulation environment |
+
+The evidence-backed audit is in [PRIOR_ART.md](PRIOR_ART.md).
+
+## Adapter interfaces
+
+Adapters implement a small typed protocol:
+
+```python
+class ModelAdapter(Protocol):
+    name: str
+    identity: str
+    dimensions: tuple[str, ...]
+
+    def initial_state(self, config, seed): ...
+    def step(self, state, parameters, dt): ...
+    def observe(self, state): ...
+    def classify(self, trace, tolerances): ...
+    def invariants(self, trace, parameters, tolerances): ...
+```
+
+The explicit serializable state tuple makes bounded perturbation, invalid-value detection, trace hashing, and replay straightforward. See [ARCHITECTURE.md](ARCHITECTURE.md) for extension guidance.
+
+Whole-trajectory solvers use the optional protocol instead of a fake step loop:
+
+```python
+class TrajectoryAdapter(Protocol):
+    name: str
+    identity: str
+    dimensions: tuple[str, ...]
+    replay_mode: Literal["exact", "tolerance"]
+
+    def initial_state(self, config, seed): ...
+    def simulate(self, initial_state, parameters, config, seed): ...
+    def observe(self, trace): ...
+    def classify(self, trace, tolerances): ...
+    def invariants(self, trace, parameters, tolerances): ...
+    def configuration(self): ...
+```
+
+`SolveIVPAdapter` records the explicit identity plus a digest of serializable numerical settings.
+It never serializes or claims to securely hash arbitrary callable source.
+
+## Scientific scope
+
+PhaseProbe uses these terms deliberately:
+
+- finite-time trajectory divergence: measured separation over the recorded window;
+- sensitive-dependence evidence: repeatable finite-time divergence under a declared small perturbation, not by itself a proof of chaos;
+- numerical instability: behavior attributable to the numerical method or step size;
+- invariant violation: a declared conservation or boundedness rule failed;
+- qualitative regime change: the adapter’s declared classifier changed;
+- bifurcation evidence: a numerical class-change bracket, not an exact bifurcation point;
+- invalid integration: NaN, infinity, overflow, state-shape mismatch, or hard bound breach;
+- solver failure: the step method could not advance a valid state.
+
+The Lorenz examples report `finite-time divergence rate`; they do not compute or claim a Lyapunov exponent. Adaptive SciPy replay is tolerance-based, never exact deterministic replay. “Smallest” always means smallest found within the declared bounded search. Read [SCIENTIFIC_METHODS.md](SCIENTIFIC_METHODS.md) and [LIMITATIONS.md](LIMITATIONS.md).
+
+## Development
+
+```bash
+python -m pip install -e ".[dev]"
+python -m pip install -e ".[dev,scipy]"  # include optional adapter tests
+python -m ruff format --check .
+python -m ruff check .
+python -m mypy src tests
+python -m pytest --cov=phaseprobe
+python -m build
+python scripts/check_links.py
+python scripts/hygiene.py
+```
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) and the concrete good-first-issue templates in `.github/ISSUE_TEMPLATE/`.
+
+## License and citation
+
+Apache-2.0. Copyright 2026 Ali. Citation metadata is in [CITATION.cff](CITATION.cff).

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phaseprobe-0.2.0.dist-info/entry_points.txt

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+[console_scripts]
+phaseprobe = phaseprobe.cli:main

phaseprobe-0.2.0.dist-info/licenses/LICENSE

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+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      direction or management of such entity, whether by contract or
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+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
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+      including but not limited to software source code, documentation
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+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
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