simjecture 0.1.0__tar.gz

simjecture-0.1.0/.env.example

@@ -0,0 +1,17 @@
+# Never commit an actual credential. Export these in the shell or use a local
+# untracked .env loader.
+DEEPSEEK_API_KEY=
+ACS_MODEL_PROVIDER=deepseek
+
+# Official DeepSeek defaults. Override only with model IDs exposed by the
+# selected provider.
+ACS_DEFAULT_MODEL=deepseek-v4-flash
+ACS_ESCALATION_MODEL=deepseek-v4-pro
+
+# Optional legacy OpenAI-compatible proxy route. Leave both unset for the
+# official provider above.
+CP_API_KEY=
+CP_API_BASE_URL=
+# The MVP automatically changes route after repeated empty or transient responses.
+# These are consecutive provider-failure bounds, not scientific turn limits.
+ACS_MODEL_TIMEOUT_SECONDS=300

simjecture-0.1.0/.gitattributes

@@ -0,0 +1,9 @@
+# Preserve autonomous run artifacts byte-for-byte, including model-authored
+# formatting. Generated figures likewise need not satisfy source whitespace
+# checks.
+demos/gray_scott_counterexample/record/** -whitespace
+demos/collisionless_gem_reconnection/record/** -whitespace
+docs/_static/demos/*.svg -whitespace
+
+*.npz binary
+*.png binary

simjecture-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,151 @@
+name: ci
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  documentation:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Install uv
+        run: python -m pip install uv
+      - name: Install documentation environment
+        run: uv sync --frozen --group docs
+      - name: Build documentation without warnings
+        run: uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html
+
+  deterministic-core:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Install sandbox runtime
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes bubblewrap
+          if sysctl kernel.unprivileged_userns_clone > /dev/null 2>&1; then
+            sudo sysctl -w kernel.unprivileged_userns_clone=1
+          fi
+          if sysctl kernel.apparmor_restrict_unprivileged_userns > /dev/null 2>&1; then
+            sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
+          fi
+          bwrap --unshare-all --die-with-parent \
+            --ro-bind /usr /usr \
+            --ro-bind /lib /lib \
+            --ro-bind /lib64 /lib64 \
+            /usr/bin/true
+      - name: Install uv
+        run: python -m pip install uv
+      - name: Install locked environment
+        run: uv sync --frozen --extra tui
+      - name: Lint
+        run: uv run ruff check .
+      - name: Test
+        run: uv run pytest --cov=conjecture_solver --cov-report=term-missing
+      - name: Reproduce planted benchmark
+        run: uv run simjecture benchmark kinetic-sufficiency --assert-falsified
+      - name: Reproduce independent PIC benchmark
+        run: uv run simjecture benchmark electrostatic-pic --assert-falsified
+      - name: Run recoverable planted campaign
+        run: uv run simjecture campaign planted --ledger /tmp/acs-ci.sqlite3 --output /tmp/acs-artifact
+      - name: Verify discovery package
+        run: uv run simjecture package verify /tmp/acs-artifact/discovery_package.json
+      - name: Run PIC discovery campaign
+        run: uv run simjecture campaign pic --ledger /tmp/acs-pic-ci.sqlite3 --output /tmp/acs-pic-artifact
+      - name: Verify PIC discovery package
+        run: uv run simjecture package verify /tmp/acs-pic-artifact/discovery_package.json
+      - name: Run blinded search and independent confirmation
+        run: >-
+          uv run simjecture search blinded --offline-ai-fixture
+          --ledger /tmp/acs-blinded-ci.sqlite3
+          --output /tmp/acs-blinded-artifact
+      - name: Run budgeted multi-action campaign
+        run: >-
+          uv run simjecture orchestrate blinded --offline-ai-fixture
+          --ledger /tmp/acs-multi-action-ci.sqlite3
+          --output /tmp/acs-multi-action-artifact
+      - name: Verify committed schemas
+        run: uv run simjecture schemas --output schemas --check
+      - name: Verify recorded autonomous demos
+        run: |
+          uv run python demos/gray_scott_counterexample/verify_record.py
+          uv run python demos/collisionless_gem_reconnection/verify_record.py
+
+  warpx-instrument:
+    runs-on: ubuntu-latest
+    timeout-minutes: 25
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+    steps:
+      - uses: actions/checkout@v7
+      - uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: environments/warpx-cpu.yml
+          environment-name: acs-warpx-cpu-26-07
+          cache-environment: true
+          init-shell: bash
+      - name: Install project tooling
+        run: |
+          python -m pip install uv
+          uv sync --frozen
+      - name: Verify the deployable WarpX CPU capability
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes bubblewrap
+          if sysctl kernel.unprivileged_userns_clone > /dev/null 2>&1; then
+            sudo sysctl -w kernel.unprivileged_userns_clone=1
+          fi
+          if sysctl kernel.apparmor_restrict_unprivileged_userns > /dev/null 2>&1; then
+            sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
+          fi
+          mkdir -p .runtime
+          ln -s "$CONDA_PREFIX" .runtime/warpx-cpu
+          uv run simjecture doctor --profile warpx-cpu
+      - name: Compile restricted reference and candidate PICMI inputs
+        run: >-
+          uv run python scripts/qualify_warpx.py
+          --python "$CONDA_PREFIX/bin/python"
+          --work-directory /tmp/acs-warpx-qualification
+          --output /tmp/acs-warpx-qualification.json
+      - name: Qualify openPMD diagnostics and physics on the fixed matrix
+        run: >-
+          uv run python scripts/qualify_warpx_physics.py
+          --warpx-python "$CONDA_PREFIX/bin/python"
+          --work-root /tmp/acs-warpx-physics-qualification
+          --output /tmp/acs-warpx-physics-qualification.json
+      - name: Run the durable analytic-to-qualified-WarpX campaign
+        run: >-
+          uv run python scripts/run_qualified_warpx_campaign.py
+          /tmp/acs-warpx-physics-qualification.json
+          --offline-ai-fixture
+          --warpx-python "$CONDA_PREFIX/bin/python"
+          --work-root /tmp/acs-warpx-confirmation
+          --ledger /tmp/acs-qualified-warpx-campaign.sqlite3
+          --output /tmp/acs-qualified-warpx-campaign
+      - name: Verify qualified WarpX campaign package
+        run: >-
+          uv run simjecture package verify
+          /tmp/acs-qualified-warpx-campaign/qualified_warpx_campaign_package.json
+      - uses: actions/upload-artifact@v7
+        with:
+          name: warpx-instrument-records
+          path: |
+            /tmp/acs-warpx-qualification.json
+            /tmp/acs-warpx-physics-qualification.json
+            /tmp/acs-warpx-physics-qualification_results.json
+            /tmp/acs-qualified-warpx-campaign.sqlite3
+            /tmp/acs-qualified-warpx-campaign/

simjecture-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,43 @@
+name: release
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  publish-pypi:
+    name: Publish Python distribution to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/simjecture
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Install build frontend
+        run: python -m pip install uv
+      - name: Require the release tag to match the package version
+        run: |
+          python - <<'PY'
+          import os
+          import tomllib
+
+          with open("pyproject.toml", "rb") as stream:
+              version = tomllib.load(stream)["project"]["version"]
+          tag = os.environ["GITHUB_REF_NAME"]
+          expected = f"v{version}"
+          if tag != expected:
+              raise SystemExit(f"release tag {tag!r} does not match {expected!r}")
+          PY
+      - name: Build source and wheel distributions
+        run: uv build
+      - name: Publish with PyPI Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@release/v1

simjecture-0.1.0/.gitignore

@@ -0,0 +1,19 @@
+.env
+.venv/
+.runtime/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+.hypothesis/
+.coverage
+htmlcov/
+docs/_build/
+build/
+dist/
+*.egg-info/
+*.sqlite3
+*.sqlite3-shm
+*.sqlite3-wal
+artifacts/
+data/

simjecture-0.1.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

simjecture-0.1.0/CHANGELOG.md

@@ -0,0 +1,57 @@
+# Changelog
+
+This project follows semantic versioning. Dates use ISO 8601.
+
+## 0.1.0 — 2026-08-15
+
+- Added a read-only MVP run monitor and headless `status` / `watch` commands.
+  A missing report is incomplete, not running. `watch` Ctrl-C stops the viewer
+  only.
+- Added an optional Textual dashboard (`uv sync --extra tui`) that attaches to
+  a run directory, launches through `--hypothesis-file`, and can cancel a
+  verified child process. Audit artifacts remain authoritative; no fabricated
+  scientific completion percentage is shown.
+- Added action-boundary pause/resume through `operator_input/control.json`,
+  headless `pause`/`resume`, and verified detach/reattach via supervisor
+  records. Pause does not use SIGSTOP and does not write a terminal report.
+- Made resume replay every structured MVP option, enforce one runner per output
+  directory, and preserve the cumulative wall-time envelope across sessions.
+  Automatic replay refuses external writable/configuration paths rather than
+  trusting paths supplied by an imported run artifact.
+- Bound attached-run controls to PID, process start time, exact command line,
+  and output directory. Stored hypothesis, instruction, and guided inputs are
+  contained and content-addressed; conflicting launches cannot overwrite them.
+- Rendered hypotheses, claims, logs, and artifacts as literal terminal text,
+  moved cancellation waits off the UI thread, and corrected long-watch,
+  historical-heartbeat, and terminal-finish projections.
+- Split the dashboard's flat claim list into a scientific hypothesis tree and
+  validation claims linked to the selected hypothesis. A complete audit-ledger
+  view remains available for every scientific, instrument, diagnostic, and
+  control claim.
+- Projected provider token usage from durable assistant transcript records.
+- Added the domain-neutral natural-language hypothesis sandbox.
+- Added prospective evidence contracts, claim-level provenance, commissioned
+  capability execution, and guarded claim closure.
+- Added durable model and simulator actions with restart and replay semantics.
+- Added an optional release-pinned WarpX CPU/CUDA capability and diagnostic
+  skill system.
+- Added analytic, electrostatic PIC, nonlinear Landau, reaction-diffusion, and
+  two-dimensional collisionless GEM evaluation records.
+- Added curated Sphinx/MyST documentation, citation metadata, release licensing,
+  contribution guidance, and private-first publication infrastructure.
+- Made JSON evidence validation treat equal finite integer and floating-point
+  values consistently while preserving Boolean type separation.
+- Bounded capability runtime-integrity scans to standard package metadata roots,
+  avoiding repeated whole-runtime filesystem walks.
+- Made sandboxed Python commands use the harness's locked interpreter and
+  read-only scientific package set, including NumPy, SciPy, Matplotlib, and
+  pandas, without exposing the host home or user site.
+- Added idempotent `install` profiles and a read-only, JSON-capable `doctor` for
+  the core scientific stack and release-pinned WarpX CPU/CUDA capabilities.
+- Added self-contained, integrity-checked Gray–Scott and collisionless GEM
+  records that can be inspected without an API key or simulator runtime.
+
+This release is an auditable research prototype of the evidence harness and
+recorded campaigns. It does not claim unrestricted scientific problem solving.
+Independently confirmed new results, and use of the same tooling in further
+simulation-gated fields, are the next step.

simjecture-0.1.0/CITATION.cff

@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite the exact software version and Git commit."
+title: "Simjecture"
+type: software
+version: 0.1.0
+date-released: 2026-08-15
+abstract: >-
+  An evidence-governed runtime for autonomous computational experimentation and
+  falsification over hypothesis trees.
+authors:
+  - family-names: Zhu
+    given-names: Bowen
+license: Apache-2.0
+repository-code: "https://github.com/tomzhu0225/simjecture"
+url: "https://github.com/tomzhu0225/simjecture"
+keywords:
+  - autonomous science
+  - computational physics
+  - evidence provenance
+  - hypothesis testing
+  - scientific agents

simjecture-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,36 @@
+# Contributing
+
+Contributions are welcome during the research-preview phase. Changes must keep
+the distinction between scientific reasoning and infrastructure authority
+explicit: agents may choose scientific details, while the harness controls
+permissions, provenance, resource limits, and evidence eligibility.
+
+## Development setup
+
+```bash
+uv sync --all-groups
+uv run ruff check .
+uv run pytest
+uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html
+```
+
+## Pull requests
+
+- Keep each change scoped and explain which observed failure or public contract
+  motivates it.
+- Add regression tests for harness behavior.
+- Do not commit credentials, local runtime installations, raw multi-gigabyte
+  simulation output, or unpublished third-party material.
+- Clearly label fixtures, commissioning output, discovery evidence, and held-out
+  confirmation evidence.
+- Do not strengthen a scientific conclusion beyond the evidence contract and
+  recorded numerical qualification.
+
+Generated schemas must remain synchronized:
+
+```bash
+uv run simjecture schemas --output schemas --check
+```
+
+By contributing, you agree that your contribution is licensed under the Apache
+License 2.0.

simjecture-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
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simjecture-0.1.0/NOTICE

@@ -0,0 +1,6 @@
+Simjecture
+Copyright 2026 Bowen Zhu
+
+This product includes software developed by Simjecture contributors.
+Third-party software and services retain their own
+copyrights and licenses; see THIRD_PARTY_NOTICES.md.