simjecture 0.1.0__py3-none-any.whl

simjecture-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: simjecture
+Version: 0.1.0
+Summary: Evidence-governed autonomous experimentation and falsification for computational science
+Project-URL: Homepage, https://github.com/tomzhu0225/simjecture
+Project-URL: Documentation, https://github.com/tomzhu0225/simjecture/tree/main/docs
+Project-URL: Repository, https://github.com/tomzhu0225/simjecture
+Project-URL: Issues, https://github.com/tomzhu0225/simjecture/issues
+Author: Bowen Zhu
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: autonomous science,computational physics,falsification,hypothesis testing,scientific agents,simulation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: httpx<1,>=0.27
+Requires-Dist: matplotlib<4,>=3.8
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pandas<4,>=2.2
+Requires-Dist: pydantic<3,>=2.9
+Requires-Dist: scipy<2,>=1.12
+Provides-Extra: tui
+Requires-Dist: textual<9,>=2.0; extra == 'tui'
+Description-Content-Type: text/markdown
+
+# Simjecture
+
+**Hypothesize. Simulate. Falsify.**
+
+Simjecture is an evidence-governed autonomous experimentation and falsification
+system for computational science. It tackles long-horizon problems inside a
+human-defined problem contract where finding a useful law or counterexample
+requires a difficult search, but a proposed result can be checked much more
+cheaply. The model grows and tests a tree-like graph of competing hypotheses,
+writes its own experiments and diagnostics, and searches deliberately for the
+simplest result that survives independent verification. The harness controls
+what may count as evidence.
+
+> **Research preview:** version 0.1 validates the infrastructure and records real
+> autonomous simulation campaigns. It does not claim to solve arbitrary
+> scientific prose, establish truth about nature from one simulator, or replace
+> independent scientific review.
+
+The project began as an autonomous conjecture-solving harness for computational
+plasma physics. The same claim ledger, sandbox, commissioning rules, and
+capability framework are now ready to extend to other simulation-gated fields
+that have a sharp question and a checkable instrument. Version 0.1 records
+both the origin domain and that generalization.
+
+## The core idea: AI low-hanging fruit
+
+Scientific problems are not uniformly difficult. A candidate may be buried in
+a vast space of mechanisms, representations, and parameter regimes, while the
+decisive properties of that candidate are comparatively inexpensive to test.
+This **discovery–verification asymmetry** is a difficulty inversion: a problem
+that is high-hanging for human intuition may be low-hanging for a machine that
+can sustain search, write code, change representation, and reject failed ideas
+without fatigue.
+
+An **AI low-hanging-fruit problem** is therefore not a trivial problem. It is a
+scientifically valuable problem with a favorable machine difficulty profile:
+
+- a sharply defined question and evidence standard;
+- a large but structured space that benefits from persistent search;
+- a compact possible answer, such as a matched counterexample, scaling law,
+  phase boundary, missing variable, or impossibility statement; and
+- an affordable path to checking that answer without trusting model prose.
+
+The project tries to exploit this structure in computational science, where
+verification is graded, stochastic, model-dependent, and numerically fallible.
+A simulator producing a plausible figure is not a verifier; admissibility,
+convergence, uncertainty, independent diagnostics, and fresh confirmation all
+matter.
+
+## Search a hypothesis tree, not just a parameter grid
+
+The human supplies an immutable root proposition and the scientific boundaries.
+The agent owns the route through a changing frontier of daughter hypotheses:
+competing explanations, measurable predictions, discriminating tests,
+instrument checks, specializations, and repairs. Although “hypothesis tree” is
+the intuitive picture, the durable structure is a typed graph because one node
+may depend on or test several others.
+
+```text
+root proposition
+├── alternative explanation A
+├── alternative explanation B
+├── predicted signature / discriminating test
+├── instrument and numerical validity claims
+└── repaired or narrower proposition after a failure
+```
+
+Each experiment should remove uncertainty from this graph, not merely add
+another point to a scan. A failed diagnostic challenges the instrument rather
+than the physics. A valid counterexample may reject a parent hypothesis, but it
+only *motivates* a repaired daughter; that daughter needs new evidence of its
+own. Falsified branches remain useful recorded knowledge rather than being
+rewritten into a success story.
+
+## Counterexamples are first-class outputs
+
+The default scientific posture is destructive: ask what cheapest valid
+calculation could break the active claim. Useful witnesses include two matched
+cases with different outcomes, a bound or invariance violation, a monotonicity
+reversal, a threshold crossing, or a path-dependence pair. A candidate witness
+has asymmetric leverage: one verified witness can reject a universal
+sufficiency or bound claim even when confirming that claim everywhere would be
+impossible. It must still pass numerical and physical validity gates, survive
+fresh held-out tests, and face deliberate attempts to explain it away or
+falsify the resulting law.
+
+The primary output is therefore not generated prose. It is an independently
+inspectable **discovery package**: the hypothesis graph, compact discovery
+object, exact commands, source hashes, simulator outputs, diagnostics,
+uncertainty and validation results, failed alternatives, falsification attempts,
+and scoped claim dispositions. An honest bounded null result is also acceptable.
+
+## How the search works
+
+```text
+human-defined question + root hypothesis + evidence standard
+                              │
+                              ▼
+             search the typed hypothesis frontier
+                              │
+                              ▼
+             choose a discriminating intervention
+                              │
+                              ▼
+       agent-authored experiment, diagnostic, or simulation
+                              │
+                              ▼
+       commissioning + physical and numerical validity gates
+                    │                         │
+              invalid run                 valid evidence
+                    │                         │
+         recorded non-evidence      support / counterexample /
+         and instrument repair            unresolved result
+                    │                         │
+                    └──────────┬──────────────┘
+                               ▼
+                    update the hypothesis graph
+                               │
+                               ▼
+             fresh confirmation + adversarial attack
+                               │
+                               ▼
+                  verifiable discovery package
+```
+
+The agent owns scientific choices within the supplied scope; the harness owns
+evidence eligibility. It does not hard-code a plasma model, diagnostic sequence,
+or daughter-hypothesis tree, even though plasma was the first domain. It does
+require prospective evidence contracts, commissioned instruments, immutable
+provenance, and guarded claim closure so that a persuasive explanation cannot
+substitute for a valid result.
+
+## Explore a completed run — no API key required
+
+The fastest way to see Simjecture is to replay the recorded Gray–Scott campaign.
+It is a real 23.8-minute autonomous run, preserved with its hypothesis tree,
+transcript, agent-written programs, numerical evidence, and provenance. Replay
+is read-only: it makes no model calls and starts no simulations.
+
+```bash
+git clone https://github.com/tomzhu0225/simjecture.git
+cd simjecture
+uv sync --frozen --extra tui
+uv run python demos/gray_scott_counterexample/verify_record.py
+uv run simjecture tui demos/gray_scott_counterexample/record
+```
+
+Inside the dashboard, select hypotheses to inspect their linked evidence and
+validation claims; press `v` for the complete typed audit ledger. For a
+non-interactive summary instead, run:
+
+```bash
+uv run simjecture status demos/gray_scott_counterexample/record
+```
+
+The dashboard is a human-readable projection. The files in the recorded run
+remain the authoritative scientific record.
+
+## Quick start
+
+Requirements:
+
+- Linux with Python 3.11 or newer
+- [uv](https://docs.astral.sh/uv/)
+- Bubblewrap (`bwrap`) for the isolated natural-language MVP
+- an API key for an enabled model provider
+
+```bash
+git clone https://github.com/tomzhu0225/simjecture.git
+cd simjecture
+uv sync --frozen
+uv run simjecture install core
+
+export DEEPSEEK_API_KEY='your-process-local-key'
+uv run simjecture mvp \
+  --hypothesis "A charged particle's magnetic moment is conserved when the magnetic field varies slowly across its gyro-orbit." \
+  --output artifacts/magnetic-mirror-mvp
+```
+
+`conjecture-solver` and `acs` remain compatibility aliases. The internal Python
+package remains `conjecture_solver`, preserving the implementation namespace
+used by existing capabilities and integrations. Never place a real provider key
+in a tracked file, prompt, run workspace, or command transcript.
+
+An operator may add an instrument preference without changing the root
+hypothesis:
+
+```bash
+uv run simjecture mvp \
+  --hypothesis-file hypothesis.txt \
+  --instruction "Use the installed WarpX capability." \
+  --output artifacts/campaign
+```
+
+For expensive problems, `--guided-commission` can provide a known-runnable,
+operator-validated starting program. Guided files remain non-evidentiary until
+the agent prospectively contracts and executes fresh evidence.
+
+Inspect a durable run without starting another campaign. These commands do not
+require the optional terminal extra and do not invent a scientific completion
+percentage:
+
+```bash
+uv run simjecture status artifacts/magnetic-mirror-mvp
+uv run simjecture watch artifacts/magnetic-mirror-mvp
+```
+
+A missing `mvp_report.json` is reported as incomplete, not as running. Ctrl-C
+on `watch` stops the viewer only. `pause` requests a stop at the next action
+boundary; `resume` repeats a self-contained stored launch contract without
+resetting its cumulative wall-time budget. External writable or configuration
+paths require the operator to repeat the reviewed original command.
+
+The optional dashboard is a projection of the same artifacts:
+
+```bash
+uv sync --extra tui
+uv run simjecture tui
+uv run simjecture tui artifacts/magnetic-mirror-mvp
+```
+
+Its primary view separates the scientific hypothesis tree from instrument,
+diagnostic, and control claims attached to the selected hypothesis. Press `v`
+for the complete typed audit ledger; no claim or provenance record is hidden by
+the human-first projection.
+
+## Core safeguards
+
+- Network-isolated writable agent workspace with no provider credentials.
+- Typed, single-action model protocol and bounded tool outputs.
+- Prospective evidence contracts with machine-checkable JSON assertions.
+- Workbench artifacts permanently separated from evidence-stage artifacts.
+- Source- and command-bound capability commissioning.
+- Exact artifact provenance, hashes, seeds, runtimes, and claim linkage.
+- Durable transcripts, crash recovery, replay, cancellation, and idempotency.
+- Numerical failure remains non-evidence.
+- Immutable root-claim and guarded scientific closure semantics.
+- Soft startup literature search when public retrieval is available.
+
+## Current evidence
+
+| Evaluation | Status | What it establishes |
+|---|---|---|
+| Matched-moment kinetic sufficiency | Qualified planted counterexample | End-to-end analytic, independent PIC, and WarpX verification in the plasma origin domain |
+| Magnetic mirror and nonlinear Landau MVPs | Completed plasma research runs | Natural-language operation on origin-domain problems |
+| Gray–Scott MVP | Completed research run | Same harness on a non-plasma, agent-authored instrument |
+| [Collisionless GEM held-out campaign 0004](demos/collisionless_gem_reconnection/) | 12 fresh CUDA runs completed | Guided autonomous commissioning, execution, analysis, and guarded claim handling |
+
+Run 0004 produced a finite-sample point-estimate falsification of its operational
+child claim, while its three-seed uncertainty interval still crossed the proposed
+population threshold. The immutable root remained open. This is documented as a
+real autonomous run and an example of why machine provenance does not remove the
+need for independent scientific audit.
+
+Version 0.1 ships that harness. The next step is to use it: apply the same
+claim ledger, sandbox, commissioning rules, and capability framework to more
+simulation-gated problems, and hunt independently confirmed new results — a
+compact law, a matched counterexample, or a scoped impossibility — in the
+origin domain and beyond.
+
+## Recorded autonomous demos
+
+The repository includes two inspectable release demonstrations rather than only
+descriptions of past runs.
+
+### Gray–Scott finite-domain counterexample
+
+Starting from a natural-language Gray–Scott hypothesis and no campaign
+instruction, the agent rejected an unsuitable installed capability, authored
+its own numerical instrument, proposed and tested a daughter hypothesis, and
+found a finite-domain counterexample in 23.8 minutes.
+
+![Gray–Scott counterexample: recorded numerical evidence](docs/_static/demos/gray-scott-result.png)
+
+The package contains the exact input, complete transcript, portable hypothesis
+ledger, prospective evidence contracts, final report, source and command
+provenance, all agent-written programs, numerical arrays, integrity checker,
+and a read-only TUI replay. See
+[`demos/gray_scott_counterexample/`](demos/gray_scott_counterexample/).
+
+### Collisionless GEM reconnection ensemble
+
+Starting from a validated, explicitly non-evidentiary GEM CUDA instrument, the
+agent designed a held-out confirmation campaign, commissioned its simulator and
+analyzer, and executed 12 fresh fully kinetic simulations across three paired
+seeds, two temperature ratios, and two particle counts. Each run used a
+256×128 grid, four kinetic populations, 4,623 explicit steps, and 26 openPMD
+field states.
+
+![Recorded collisionless GEM ensemble](docs/_static/demos/gem-ensemble-result.png)
+
+The 16-PPC endpoint ratio was `1.0122`, with a paired-bootstrap 95% interval of
+`[0.8232, 1.4374]`, against a proposed threshold of `1.25`. The frozen
+finite-sample rule falsified the operational daughter, while the population
+root remained open because the three-seed interval crossed the threshold. The
+package preserves the exact autonomous transcript and claim ledger, all 12 run
+summaries, hash-addressed provenance for 482 original artifacts, and
+representative final fields. See
+[`demos/collisionless_gem_reconnection/`](demos/collisionless_gem_reconnection/).
+
+## Optional WarpX capability
+
+WarpX is the first simulation skill and executable capability, not an
+architectural dependency. The versioned skill covers PICMI interfaces, explicit
+and implicit time integration, openPMD diagnostics, numerical risks, CPU/GPU
+deployment, and resource scaling. Local runtime installations remain ignored by
+Git and are mounted read-only into the sandbox.
+
+Install and verify the release-pinned CPU capability with:
+
+```bash
+uv run simjecture install warpx-cpu
+uv run simjecture doctor --profile warpx-cpu
+```
+
+CUDA remains an explicit hardware-specific profile whose audited WarpX source
+checkout must be supplied by the operator. The installer validates its pinned
+revision before invoking the existing build and openPMD probe.
+
+See [`skills/warpx/SKILL.md`](skills/warpx/SKILL.md) and the deployment reference
+in [`skills/warpx/references/local-cuda-deployment.md`](skills/warpx/references/local-cuda-deployment.md).
+
+## Documentation
+
+The curated documentation uses Sphinx, MyST Markdown, and the PyData Sphinx
+Theme.
+
+```bash
+uv sync --group docs
+uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html
+```
+
+Start with [`docs/index.md`](docs/index.md). The accompanying manuscript is
+maintained separately until its archival release.
+
+## Development
+
+```bash
+uv sync --all-groups --extra tui
+uv run ruff check .
+uv run pytest
+uv run simjecture schemas --output schemas --check
+```
+
+See [CONTRIBUTING.md](CONTRIBUTING.md), [SECURITY.md](SECURITY.md), and
+[THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
+
+## Repository map
+
+```text
+src/conjecture_solver/   core models, ledgers, orchestration, sandbox, and CLI
+skills/                  versioned model-readable scientific capabilities
+capabilities/            installed executable capability manifests
+demos/                   bounded demonstrations and operator examples
+schemas/                 committed public JSON Schemas
+scripts/                 qualification, deployment, audit, and maintenance tools
+tests/                   deterministic and integration regression coverage
+docs/                    curated documentation
+```
+
+## Citation and license
+
+Citation metadata is provided in [CITATION.cff](CITATION.cff). Until the
+accompanying paper receives an archival identifier, cite the exact software
+version and Git commit used for a result.
+
+Copyright 2026 Bowen Zhu and contributors. Licensed under the
+[Apache License 2.0](LICENSE).

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simjecture-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any

simjecture-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+acs = conjecture_solver.cli:main
+conjecture-solver = conjecture_solver.cli:main
+simjecture = conjecture_solver.cli:main