simjecture 0.3.0__tar.gz → 0.3.2__tar.gz

{simjecture-0.3.0 → simjecture-0.3.2}/.github/workflows/ci.yml

@@ -83,6 +83,7 @@ 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-0.3.0 → simjecture-0.3.2}/.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 .ruff_cache/
 .hypothesis/
 .coverage
+.coverage.*
 htmlcov/
 docs/_build/
 build/
@@ -16,4 +17,7 @@ dist/
 *.sqlite3-shm
 *.sqlite3-wal
 artifacts/
+!demos/agent_roles_validation/record/workspace/artifacts/
+!demos/agent_roles_validation/record/workspace/artifacts/*.json
 data/
+.private/

{simjecture-0.3.0 → simjecture-0.3.2}/CHANGELOG.md

@@ -4,6 +4,30 @@ This project follows semantic versioning. Dates use ISO 8601.
 
 ## Unreleased
 
+## 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.
+- Added an Optab opacity-table capability and `opacity` skill. Optab is documented as an abundance-consuming table generator, not an EOS solver.
+- Added `simjecture install` bootstraps for the EOS and opacity profiles, matching the WarpX CPU provisioning path.
+- FLASH install accepts an operator-owned `--repository` Git remote. Simjecture never ships a FLASH URL; a Git-ignored overlay can store local setup defaults.
+
 ## 0.3.0 — 2026-08-27
 
 - Added FLASH 4.8 2D compressible resistive-MHD application capability, commissioning protocol, and rank/timing calibrations.

{simjecture-0.3.0 → simjecture-0.3.2}/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: 0.3.0
-date-released: 2026-08-27
+version: 0.3.2
+date-released: 2026-09-09
 abstract: >-
   An evidence-governed runtime for autonomous computational experimentation and
   falsification over hypothesis trees.

{simjecture-0.3.0 → simjecture-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: simjecture
-Version: 0.3.0
+Version: 0.3.2
 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
@@ -326,6 +326,12 @@ 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.
@@ -447,6 +453,29 @@ 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).
 
+## Optional EOS and opacity capabilities
+
+Equation-of-state and opacity-table generators are optional instruments, not
+architectural dependencies. The installer clones and builds pinned upstream
+revisions into Git-ignored runtimes, then runs a non-evidentiary health probe:
+
+```bash
+uv run simjecture install atomec
+uv run simjecture install singularity-eos
+uv run simjecture install m-aneos
+uv run simjecture install optab
+```
+
+Repeating a command against a healthy runtime performs no installation. Use
+`--dry-run` to inspect the bootstrap command and `--repair` to replace an
+installer-managed prefix. The `eos` and `opacity` skills describe each code's
+interface and validity limits; they do not choose a material or scientific
+claim. An EOS evaluation is not an opacity table, and Optab consumes an
+external abundance table rather than solving an equation of state.
+
+See [`skills/eos/SKILL.md`](skills/eos/SKILL.md) and
+[`skills/opacity/SKILL.md`](skills/opacity/SKILL.md).
+
 ## Documentation
 
 The curated documentation uses Sphinx, MyST Markdown, and the PyData Sphinx

{simjecture-0.3.0 → simjecture-0.3.2}/README.md

@@ -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.
@@ -411,6 +417,29 @@ 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).
 
+## Optional EOS and opacity capabilities
+
+Equation-of-state and opacity-table generators are optional instruments, not
+architectural dependencies. The installer clones and builds pinned upstream
+revisions into Git-ignored runtimes, then runs a non-evidentiary health probe:
+
+```bash
+uv run simjecture install atomec
+uv run simjecture install singularity-eos
+uv run simjecture install m-aneos
+uv run simjecture install optab
+```
+
+Repeating a command against a healthy runtime performs no installation. Use
+`--dry-run` to inspect the bootstrap command and `--repair` to replace an
+installer-managed prefix. The `eos` and `opacity` skills describe each code's
+interface and validity limits; they do not choose a material or scientific
+claim. An EOS evaluation is not an opacity table, and Optab consumes an
+external abundance table rather than solving an equation of state.
+
+See [`skills/eos/SKILL.md`](skills/eos/SKILL.md) and
+[`skills/opacity/SKILL.md`](skills/opacity/SKILL.md).
+
 ## Documentation
 
 The curated documentation uses Sphinx, MyST Markdown, and the PyData Sphinx

{simjecture-0.3.0 → simjecture-0.3.2}/THIRD_PARTY_NOTICES.md

@@ -18,6 +18,13 @@ review the current license, and keep acquired source, modified source, and built
 binaries outside this source distribution. Simjecture's `flash-mhd` skill and
 capability metadata do not relicense FLASH.
 
+Optional equation-of-state and opacity packages (atoMEC, Singularity-EOS,
+M-ANEOS, and Optab) are obtained under their upstream licenses. The
+operator-triggered installer may clone and build pinned revisions into a
+Git-ignored runtime; this repository still does not relicense those packages or
+commit their source, binaries, or atomic databases. Consult each upstream
+distribution for its license and required notices.
+
 Model providers, literature services, and externally supplied guided
 commissioning packages are services or inputs rather than sublicensed parts of
 this source distribution. Run artifacts must retain the provenance and license

simjecture-0.3.2/capabilities/atomec-1.4.0.json

@@ -0,0 +1,28 @@
+{
+  "environment": {
+    "MPLBACKEND": "Agg",
+    "OMP_NUM_THREADS": "1",
+    "PYTHONDONTWRITEBYTECODE": "1"
+  },
+  "executable": "bin/python",
+  "identity_files": [
+    "share/build-record.json"
+  ],
+  "manifest": {
+    "description": "Operator-supplied atoMEC 1.4 finite-temperature Kohn-Sham average-atom runtime",
+    "executable_kind": "python-atomec",
+    "name": "atomec-1.4.0",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.import_succeeded",
+      "checks.energy_finite",
+      "checks.mean_ionization_in_range"
+    ],
+    "preflight_resource": "examples/atomec_runtime_smoke.py",
+    "preflight_result": "atomec_capability_smoke.json",
+    "schema_version": "0.1.0",
+    "skill": "eos",
+    "version": "1.4.0"
+  },
+  "runtime_root": "../.runtime/atomec-1.4.0"
+}

simjecture-0.3.2/capabilities/m-aneos-1.0.json

@@ -0,0 +1,34 @@
+{
+  "environment": {
+    "MANEOS_PREFLIGHT_INPUT": "/opt/acs-capabilities/m-aneos-1.0/share/preflight/ANEOS.INPUT",
+    "MANEOS_QUERY": "/opt/acs-capabilities/m-aneos-1.0/bin/maneos-query",
+    "PYTHONDONTWRITEBYTECODE": "1"
+  },
+  "executable": "bin/python",
+  "identity_files": [
+    "bin/maneos-query",
+    "share/build-record.json",
+    "share/preflight/ANEOS.INPUT"
+  ],
+  "manifest": {
+    "description": "Operator-supplied M-ANEOS 1.0 total-material analytic EOS query runtime",
+    "executable_kind": "python-maneos-query",
+    "name": "m-aneos-1.0",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.environment_valid",
+      "checks.executable_present",
+      "checks.input_present",
+      "checks.input_copied",
+      "checks.process_completed",
+      "checks.return_code_zero",
+      "checks.pressure_finite"
+    ],
+    "preflight_resource": "examples/maneos_runtime_smoke.py",
+    "preflight_result": "maneos_capability_smoke.json",
+    "schema_version": "0.1.0",
+    "skill": "eos",
+    "version": "1.0"
+  },
+  "runtime_root": "../.runtime/m-aneos-1.0"
+}

simjecture-0.3.2/capabilities/optab-1.3.1.json

@@ -0,0 +1,41 @@
+{
+  "environment": {
+    "OMPI_MCA_btl": "self,vader",
+    "OMPI_MCA_pml": "ob1",
+    "OMP_NUM_THREADS": "1",
+    "OPTAB_EXECUTABLE": "/opt/acs-capabilities/optab-1.3.1/bin/optab",
+    "OPTAB_MPI_LAUNCHER": "/opt/acs-capabilities/optab-1.3.1/bin/mpi-launcher",
+    "OPTAB_MPI_RANKS": "1",
+    "OPTAB_PREFLIGHT_INPUT": "/opt/acs-capabilities/optab-1.3.1/share/preflight",
+    "PYTHONDONTWRITEBYTECODE": "1"
+  },
+  "executable": "bin/python",
+  "identity_files": [
+    "bin/optab",
+    "bin/mpi-launcher",
+    "share/build-record.json"
+  ],
+  "manifest": {
+    "description": "Operator-supplied Optab 1.3 MPI/HDF5 opacity-table generator",
+    "executable_kind": "python-optab-mpi-hdf5",
+    "name": "optab-1.3.1",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.environment_valid",
+      "checks.executable_present",
+      "checks.mpi_launcher_present",
+      "checks.input_present",
+      "checks.input_copied",
+      "checks.process_completed",
+      "checks.return_code_zero",
+      "checks.hdf5_output_created",
+      "checks.hdf5_output_readable"
+    ],
+    "preflight_resource": "examples/optab_runtime_smoke.py",
+    "preflight_result": "optab_capability_smoke.json",
+    "schema_version": "0.1.0",
+    "skill": "opacity",
+    "version": "1.3.1"
+  },
+  "runtime_root": "../.runtime/optab-1.3.1"
+}

simjecture-0.3.2/capabilities/singularity-eos-1.12.1.json

@@ -0,0 +1,29 @@
+{
+  "environment": {
+    "PYTHONDONTWRITEBYTECODE": "1",
+    "SINGULARITY_EOS_QUERY": "/opt/acs-capabilities/singularity-eos-1.12.1/bin/eos-query"
+  },
+  "executable": "bin/python",
+  "identity_files": [
+    "bin/eos-query",
+    "share/build-record.json"
+  ],
+  "manifest": {
+    "description": "Operator-supplied Singularity-EOS 1.12 query runtime for named analytic closures",
+    "executable_kind": "python-singularity-eos-query",
+    "name": "singularity-eos-1.12.1",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.environment_valid",
+      "checks.evaluation_completed",
+      "checks.pressure_finite",
+      "checks.ideal_gas_pressure_matches_formula"
+    ],
+    "preflight_resource": "examples/singularity_runtime_smoke.py",
+    "preflight_result": "singularity_eos_capability_smoke.json",
+    "schema_version": "0.1.0",
+    "skill": "eos",
+    "version": "1.12.1"
+  },
+  "runtime_root": "../.runtime/singularity-eos-1.12.1"
+}

simjecture-0.3.2/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-0.3.2/demos/agent_roles_validation/record/artifact_provenance.json

@@ -0,0 +1,295 @@
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