simjecture 0.3.1__tar.gz → 0.4.0__tar.gz

{simjecture-0.3.1 → simjecture-0.4.0}/.github/workflows/ci.yml

@@ -50,7 +50,16 @@ jobs:
       - name: Install uv
         run: python -m pip install uv
       - name: Install locked environment
-        run: uv sync --frozen --extra tui
+        run: uv sync --frozen --extra tui --extra dsh
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "22.23.1"
+          cache: npm
+          cache-dependency-path: integrations/dsh/package-lock.json
+      - name: Install pinned DSH test runtime
+        run: npm ci --prefix integrations/dsh
+      - name: Test DSH adapter and real MCP profile
+        run: SIMJECTURE_MCP_EXECUTABLE="$PWD/.venv/bin/simjecture-mcp" npm test --prefix integrations/dsh
       - name: Lint
         run: uv run ruff check .
       - name: Test
@@ -83,6 +92,7 @@ jobs:
         run: |
           uv run python demos/gray_scott_counterexample/verify_record.py
           uv run python demos/collisionless_gem_reconnection/verify_record.py
+          uv run python demos/agent_roles_validation/verify_record.py
 
   warpx-instrument:
     runs-on: ubuntu-latest

{simjecture-0.3.1 → simjecture-0.4.0}/.github/workflows/release.yml

@@ -40,7 +40,16 @@ jobs:
             --ro-bind /lib64 /lib64 \
             /usr/bin/true
       - name: Install locked test environment
-        run: uv sync --frozen --extra tui
+        run: uv sync --frozen --extra tui --extra dsh
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "22.23.1"
+          cache: npm
+          cache-dependency-path: integrations/dsh/package-lock.json
+      - name: Install pinned DSH test runtime
+        run: npm ci --prefix integrations/dsh
+      - name: Test DSH adapter and real MCP profile
+        run: SIMJECTURE_MCP_EXECUTABLE="$PWD/.venv/bin/simjecture-mcp" npm test --prefix integrations/dsh
       - name: Lint release source
         run: uv run ruff check .
       - name: Test release source

{simjecture-0.3.1 → simjecture-0.4.0}/.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 .ruff_cache/
 .hypothesis/
 .coverage
+.coverage.*
 htmlcov/
 docs/_build/
 build/
@@ -16,5 +17,9 @@ dist/
 *.sqlite3-shm
 *.sqlite3-wal
 artifacts/
+!demos/agent_roles_validation/record/workspace/artifacts/
+!demos/agent_roles_validation/record/workspace/artifacts/*.json
 data/
 .private/
+
+integrations/dsh/node_modules/

{simjecture-0.3.1 → simjecture-0.4.0}/CHANGELOG.md

@@ -4,6 +4,47 @@ This project follows semantic versioning. Dates use ISO 8601.
 
 ## Unreleased
 
+## 0.4.0 — 2026-09-20
+
+- Updated the bundled DSH integration to the tested `0.1.5-rc.2` runtime,
+  including current session, tool-call, prompt and structured-output APIs.
+  The Python release and DSH bundle now share version `0.4.0`.
+- Enabled native web search, page retrieval, shell, filesystem, skills,
+  workflows and configured plugins for research agents. Scientific calls retain
+  role restrictions; independent judges retain their frozen-case isolation.
+- Separated the native research workspace from authoritative campaign files.
+  Upgrades start a fresh `.research-v1` conversation, reconcile existing kernel
+  state, and preserve older conversations. Built-in DSH file/shell policies
+  protect records; arbitrary installed plugins remain trusted process code.
+- Added `read_workspace_image` for bounded PNG, JPEG and WebP image inspection
+  through MCP, with dimensions and content hashes. Inspection is not evidence
+  acceptance and requires a vision-capable model.
+- Extended the Simote scientific tool catalog for image reads. Matching Simote
+  changes add AGY workers and judges; Simote remains a separate optional app.
+- Added real-runtime DSH tests for role isolation, context pruning, V2/V3 log
+  migration, durable-job recovery and complete CLI/MCP pause/resume behavior.
+- Verified native search, fetch, file writing and image inspection with real
+  DeepSeek API calls on non-simulation research tasks.
+- Added a Linux launch bundle containing the wheel, source distribution,
+  matching DSH profile, setup/launch scripts and SHA-256 checksums.
+
+## 0.3.2 — 2026-09-09
+
+- Added `simjecture-call`, a one-shot JSON transport for trusted supervisors,
+  including Simote's SSH bridge, with sandbox readiness probing and durable
+  campaign recovery.
+- Added persistent, claim-scoped scientific role assignments with tool filters,
+  operation budgets, idempotent retries, session tracking, and validated handoffs.
+  Independent adjudication continues to use the existing evidence and claim gates.
+- Documented the optional Simote campaign workspace and Codex/Grok role workflow.
+- Included a hashed audit extract and offline verifier for a live Codex/Grok
+  integration campaign. This validates the transport and scientific role workflow
+  on a finite Euler error-bound claim; it is not a new scientific discovery.
+- Bundled built-in capability descriptors in wheels and discover them alongside
+  packaged skills, so installed deployments can use the same resource catalog.
+- Clarified the distinction between authored Python source and upstream
+  observation data when declaring experiment inputs.
+
 ## 0.3.1 — 2026-08-30
 
 - Added equation-of-state capabilities for atoMEC, Singularity-EOS, and M-ANEOS, with a shared `eos` skill that records each code's model limits.

{simjecture-0.3.1 → simjecture-0.4.0}/CITATION.cff

@@ -2,8 +2,8 @@ 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: 0.3.1
-date-released: 2026-08-30
+version: 0.4.0
+date-released: 2026-09-20
 abstract: >-
   An evidence-governed runtime for autonomous computational experimentation and
   falsification over hypothesis trees.

{simjecture-0.3.1 → simjecture-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: simjecture
-Version: 0.3.1
+Version: 0.4.0
 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
@@ -24,6 +24,7 @@ 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: pillow<13,>=10
 Requires-Dist: pydantic<3,>=2.9
 Requires-Dist: scipy<2,>=1.12
 Provides-Extra: dsh
@@ -49,7 +50,7 @@ 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 0.3 extends the infrastructure with a
+> **Research preview:** version 0.4 extends the infrastructure with a
 > license-safe FLASH resistive-MHD capability and an explicitly bounded
 > island-coalescence audit. It does not claim to solve arbitrary
 > scientific prose, establish truth about nature from one simulator, or replace
@@ -289,11 +290,11 @@ the human-first projection.
 
 ## DeepSeek Harness integration
 
-The v0.2.2 integration moves the model-facing research loop to DeepSeek Harness
+The v0.4.0 integration moves the model-facing research loop to DeepSeek Harness
 without moving scientific authority out of Simjecture. DSH owns the provider,
 conversation, retry policy, compaction, and resumable session. A native MCP
-boundary implements 22 typed endpoints. A compact persistent Lead Scientist
-sees seven coordination tools and delegates claim work to fresh, scoped
+boundary implements 23 typed endpoints. A compact persistent Lead Scientist
+sees eight scientific coordination/inspection tools plus native research tools and delegates claim work to fresh, scoped
 Falsifier/Experimenter, Blocker Resolver, and Repair Scientist sessions. A separate fresh,
 tool-free Judge reviews surviving claims. The Python campaign kernel continues to own hypotheses,
 evidence contracts, commissioning, skills, simulation capabilities, sandboxing,
@@ -326,6 +327,12 @@ process state or charging stopped-process downtime.
 
 ## Core safeguards
 
+Codex and Grok CLI agents can also work on a shared campaign through Simote's
+claim-scoped role tasks. See [Simote agent roles](docs/how-to/simote-agent-roles.md)
+for assignment, independent judging, and restart recovery.
+The [completed live Codex/Grok validation](demos/agent_roles_validation/) includes
+a hashed audit extract and an offline numerical verifier.
+
 - 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.

{simjecture-0.3.1 → simjecture-0.4.0}/README.md

@@ -13,7 +13,7 @@ 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 0.3 extends the infrastructure with a
+> **Research preview:** version 0.4 extends the infrastructure with a
 > license-safe FLASH resistive-MHD capability and an explicitly bounded
 > island-coalescence audit. It does not claim to solve arbitrary
 > scientific prose, establish truth about nature from one simulator, or replace
@@ -253,11 +253,11 @@ the human-first projection.
 
 ## DeepSeek Harness integration
 
-The v0.2.2 integration moves the model-facing research loop to DeepSeek Harness
+The v0.4.0 integration moves the model-facing research loop to DeepSeek Harness
 without moving scientific authority out of Simjecture. DSH owns the provider,
 conversation, retry policy, compaction, and resumable session. A native MCP
-boundary implements 22 typed endpoints. A compact persistent Lead Scientist
-sees seven coordination tools and delegates claim work to fresh, scoped
+boundary implements 23 typed endpoints. A compact persistent Lead Scientist
+sees eight scientific coordination/inspection tools plus native research tools and delegates claim work to fresh, scoped
 Falsifier/Experimenter, Blocker Resolver, and Repair Scientist sessions. A separate fresh,
 tool-free Judge reviews surviving claims. The Python campaign kernel continues to own hypotheses,
 evidence contracts, commissioning, skills, simulation capabilities, sandboxing,
@@ -290,6 +290,12 @@ process state or charging stopped-process downtime.
 
 ## Core safeguards
 
+Codex and Grok CLI agents can also work on a shared campaign through Simote's
+claim-scoped role tasks. See [Simote agent roles](docs/how-to/simote-agent-roles.md)
+for assignment, independent judging, and restart recovery.
+The [completed live Codex/Grok validation](demos/agent_roles_validation/) includes
+a hashed audit extract and an offline numerical verifier.
+
 - 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.

simjecture-0.4.0/demos/agent_roles_validation/README.md

@@ -0,0 +1,44 @@
+# Live Codex/Grok role validation
+
+This is an actual subscription-CLI integration run, using Simote's Codex and
+Grok drivers, its role-filtered MCP tools, a real loopback SSH connection, and
+Simjecture's Bubblewrap execution/evidence kernel. No model or scientific
+execution was mocked. It deliberately tests a simple false claim, not a new
+scientific discovery.
+
+- Grok falsified the original 0.001 error bound for ten binary64 Euler steps.
+- A fresh Codex Repair Scientist changed only the bound to 0.02 and registered
+  a prospective contract without running an experiment.
+- A fresh Grok Falsifier generated new evidence. An intentionally dropped
+  contract-registration response was recovered by retrying identical arguments
+  and the same operation ID; the durable result did not change.
+- A fresh, tool-free Codex judge accepted the evidence for the repaired finite
+  claim. Simjecture then finalized the record with all five claims closed.
+
+The supervisor was reopened between phases, and the first Falsifier's session
+was also resumed during integration debugging. Failed commissioning controls
+remain in the record alongside their corrected successors. The worker models
+were Grok 4.6 and GPT-6 Astra, using Grok CLI 1.0.13 and Codex CLI 0.153.4.
+
+The original binary64 reference subtraction reports an error of
+0.01920100107144218. The refined enclosure against mathematical exp(-1) is
+[0.019201001071442167, 0.01920100107144217]. Both reject 0.001 and lie below
+0.02. The verifier independently checks the refined interval at 80-digit
+precision:
+
+```bash
+python3 demos/agent_roles_validation/verify_record.py
+```
+
+The configured GPU containers denied Bubblewrap namespaces. Their attempted
+runs remained non-evidence; successful validation used the local Linux CPU
+through SSH instead. Campaign creation now probes this prerequisite first.
+
+`record/` is an explicit audit extract with agent-authored programs, numerical
+artifacts, provenance, claims, and the final report. It omits provider logs,
+native session cursors, worker authentication material, and runtime resource
+caches, and is not a resumable backup. `sha256.json` binds the extract's files.
+The original finalizer report is preserved byte-for-byte; its elapsed time
+describes finalization, not the full external CLI workflow.
+The opt-in reproduction scripts live in the sibling Simote checkout under
+`scripts/live-scientific-campaign.ts` and `scripts/export-scientific-validation.py`.

simjecture-0.4.0/demos/agent_roles_validation/record/artifact_provenance.json

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