simjecture 0.2.2__tar.gz → 0.3.1__tar.gz

{simjecture-0.2.2 → simjecture-0.3.1}/.gitignore

@@ -17,3 +17,4 @@ dist/
 *.sqlite3-wal
 artifacts/
 data/
+.private/

{simjecture-0.2.2 → simjecture-0.3.1}/CHANGELOG.md

@@ -4,6 +4,26 @@ This project follows semantic versioning. Dates use ISO 8601.
 
 ## Unreleased
 
+## 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.
+- Added sealed directory inputs in execution sandbox with recursive deterministic manifest hashing and read-only container mounting.
+- Clarified child claim evidence lineage and stale scientific execution binding protections.
+- Added a FLASH 2D Resistive-MHD island-coalescence demonstration with figures
+  generated from the guided HDF5 anchor, a real Web UI capture, and an
+  explicitly labelled campaign audit. The root interval is falsified; the
+  repair branch remains open because its evidence lineage did not close.
+- Added the `flash-demo` optional dependency for HDF5-backed figure
+  regeneration.
+- Enhanced Web UI test suite with proxy isolation.
+
 ## 0.2.2 — 2026-08-24
 
 - Fixed a process-lifecycle race where the supervisor that launched a short

{simjecture-0.2.2 → simjecture-0.3.1}/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: 0.2.2
-date-released: 2026-08-24
+version: 0.3.1
+date-released: 2026-08-30
 abstract: >-
   An evidence-governed runtime for autonomous computational experimentation and
   falsification over hypothesis trees.

{simjecture-0.2.2 → simjecture-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: simjecture
-Version: 0.2.2
+Version: 0.3.1
 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
@@ -28,6 +28,8 @@ Requires-Dist: pydantic<3,>=2.9
 Requires-Dist: scipy<2,>=1.12
 Provides-Extra: dsh
 Requires-Dist: mcp<3,>=2; extra == 'dsh'
+Provides-Extra: flash-demo
+Requires-Dist: h5py<4,>=3.10; extra == 'flash-demo'
 Provides-Extra: tui
 Requires-Dist: textual<9,>=2.0; extra == 'tui'
 Description-Content-Type: text/markdown
@@ -47,16 +49,18 @@ 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
+> **Research preview:** version 0.3 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
 > 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.
+that have a sharp question and a checkable instrument. The 0.3 preview records
+both the origin domain and that generalization, and adds a fluid-MHD campaign
+whose unresolved repair state is preserved rather than hidden.
 
 ## The core idea: AI low-hanging fruit
 
@@ -288,9 +292,9 @@ the human-first projection.
 The v0.2.2 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 21 typed endpoints. A compact persistent Lead Scientist
-sees six coordination tools and delegates claim work to fresh, scoped
-Falsifier/Experimenter and Repair Scientist sessions. A separate fresh,
+boundary implements 22 typed endpoints. A compact persistent Lead Scientist
+sees seven coordination 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,
 provenance, and guarded claim closure. Existing WarpX CPU/CUDA capabilities use
@@ -341,6 +345,7 @@ process state or charging stopped-process downtime.
 | 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 |
+| [FLASH resistive-MHD island-coalescence audit](demos/resistive_mhd_island_coalescence/) | Root interval falsified; repair branch open | Actual guided FLASH fields, bounded root counterexample, and an honest unresolved child state |
 
 Run 0004 produced a finite-sample point-estimate falsification of its operational
 child claim, while its three-seed uncertainty interval still crossed the proposed
@@ -348,7 +353,7 @@ 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
+The 0.3 preview 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
@@ -356,8 +361,10 @@ origin domain and beyond.
 
 ## Recorded autonomous demos
 
-The repository includes two inspectable release demonstrations rather than only
-descriptions of past runs.
+The repository includes three inspectable release demonstrations rather than
+only descriptions of past runs. Gray–Scott and GEM are portable recorded
+campaigns; the FLASH demo is an operator-dependent anchor plus a clearly
+labelled audit extract because its repair branch did not close.
 
 ### Gray–Scott finite-domain counterexample
 
@@ -394,6 +401,24 @@ summaries, hash-addressed provenance for 482 original artifacts, and
 representative final fields. See
 [`demos/collisionless_gem_reconnection/`](demos/collisionless_gem_reconnection/).
 
+### FLASH resistive-MHD island-coalescence audit
+
+The FLASH demo starts from one natural-language Sweet–Parker-like scaling
+hypothesis. Its actual guided anchor produces the HDF5 field states and
+reconnection diagnostics used in the figures. A local six-hour autonomous
+campaign falsified the specified root exponent interval (`p = -0.406453`,
+95% CI `[-0.423266, -0.389641]`), then ran out of budget while a repaired
+child remained open. The high-resolution child output and analyzer lineage did
+not satisfy the final closure-eligibility rules, so the repository does not
+call that branch verified.
+
+![FLASH island-coalescence anchor](demos/resistive_mhd_island_coalescence/figures/island_coalescence_evolution.png)
+
+See [`demos/resistive_mhd_island_coalescence/`](demos/resistive_mhd_island_coalescence/)
+for the exact hypothesis, guided commissioning manifest, audit extract,
+actual web capture, limitations, and figure-generation script. FLASH itself is
+operator-supplied and is not redistributed.
+
 Every campaign also exposes the built-in
 [`scientific-markdown`](skills/scientific-markdown/SKILL.md) skill. It gives the
 agent a common notation for equations, code identifiers, contracts, evidence
@@ -422,6 +447,29 @@ 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-0.2.2 → simjecture-0.3.1}/README.md

@@ -13,16 +13,18 @@ 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
+> **Research preview:** version 0.3 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
 > 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.
+that have a sharp question and a checkable instrument. The 0.3 preview records
+both the origin domain and that generalization, and adds a fluid-MHD campaign
+whose unresolved repair state is preserved rather than hidden.
 
 ## The core idea: AI low-hanging fruit
 
@@ -254,9 +256,9 @@ the human-first projection.
 The v0.2.2 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 21 typed endpoints. A compact persistent Lead Scientist
-sees six coordination tools and delegates claim work to fresh, scoped
-Falsifier/Experimenter and Repair Scientist sessions. A separate fresh,
+boundary implements 22 typed endpoints. A compact persistent Lead Scientist
+sees seven coordination 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,
 provenance, and guarded claim closure. Existing WarpX CPU/CUDA capabilities use
@@ -307,6 +309,7 @@ process state or charging stopped-process downtime.
 | 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 |
+| [FLASH resistive-MHD island-coalescence audit](demos/resistive_mhd_island_coalescence/) | Root interval falsified; repair branch open | Actual guided FLASH fields, bounded root counterexample, and an honest unresolved child state |
 
 Run 0004 produced a finite-sample point-estimate falsification of its operational
 child claim, while its three-seed uncertainty interval still crossed the proposed
@@ -314,7 +317,7 @@ 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
+The 0.3 preview 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
@@ -322,8 +325,10 @@ origin domain and beyond.
 
 ## Recorded autonomous demos
 
-The repository includes two inspectable release demonstrations rather than only
-descriptions of past runs.
+The repository includes three inspectable release demonstrations rather than
+only descriptions of past runs. Gray–Scott and GEM are portable recorded
+campaigns; the FLASH demo is an operator-dependent anchor plus a clearly
+labelled audit extract because its repair branch did not close.
 
 ### Gray–Scott finite-domain counterexample
 
@@ -360,6 +365,24 @@ summaries, hash-addressed provenance for 482 original artifacts, and
 representative final fields. See
 [`demos/collisionless_gem_reconnection/`](demos/collisionless_gem_reconnection/).
 
+### FLASH resistive-MHD island-coalescence audit
+
+The FLASH demo starts from one natural-language Sweet–Parker-like scaling
+hypothesis. Its actual guided anchor produces the HDF5 field states and
+reconnection diagnostics used in the figures. A local six-hour autonomous
+campaign falsified the specified root exponent interval (`p = -0.406453`,
+95% CI `[-0.423266, -0.389641]`), then ran out of budget while a repaired
+child remained open. The high-resolution child output and analyzer lineage did
+not satisfy the final closure-eligibility rules, so the repository does not
+call that branch verified.
+
+![FLASH island-coalescence anchor](demos/resistive_mhd_island_coalescence/figures/island_coalescence_evolution.png)
+
+See [`demos/resistive_mhd_island_coalescence/`](demos/resistive_mhd_island_coalescence/)
+for the exact hypothesis, guided commissioning manifest, audit extract,
+actual web capture, limitations, and figure-generation script. FLASH itself is
+operator-supplied and is not redistributed.
+
 Every campaign also exposes the built-in
 [`scientific-markdown`](skills/scientific-markdown/SKILL.md) skill. It gives the
 agent a common notation for equations, code identifiers, contracts, evidence
@@ -388,6 +411,29 @@ 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-0.3.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,31 @@
+# Third-party notices
+
+Simjecture depends on separately distributed open-source
+packages, including HTTPX, NumPy, Pydantic, and SciPy. Their licenses are
+reported by the installed Python distributions and are not replaced by this
+repository's Apache-2.0 license.
+
+WarpX is an optional external simulation capability. The repository contains
+integration guidance and independently authored launch and diagnostic code; it
+does not relicense WarpX, its binaries, or its dependencies. Consult the WarpX
+distribution for its license and required notices.
+
+FLASH is an optional, separately obtained simulation capability. FLASH is not
+distributed by this repository. Its upstream terms restrict redistribution and
+describe separate commercial-use requirements. Operators must obtain FLASH
+from the [official code-request page](https://flash.rochester.edu/site/flashcode/coderequest.html),
+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
+information supplied by their generators.

simjecture-0.3.1/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-0.3.1/capabilities/flash-island-coalescence-resistive-mhd-4.8.json

@@ -0,0 +1,42 @@
+{
+  "environment": {
+    "FLASH_EXECUTABLE": "/opt/acs-capabilities/flash-island-coalescence-resistive-mhd-4.8/bin/flash4",
+    "FLASH_MPI_LAUNCHER": "/usr/bin/orterun",
+    "FLASH_MPI_RANKS": "4",
+    "FLASH_PREFLIGHT_PARFILE": "/opt/acs-capabilities/flash-island-coalescence-resistive-mhd-4.8/share/preflight/flash.par",
+    "OMPI_MCA_btl": "self,vader",
+    "OMPI_MCA_pml": "ob1",
+    "OMP_NUM_THREADS": "1",
+    "PYTHONDONTWRITEBYTECODE": "1",
+    "PYTHONPATH": "/opt/acs-capabilities/flash-island-coalescence-resistive-mhd-4.8/lib/python3.12/site-packages"
+  },
+  "executable": "bin/flash-python",
+  "identity_files": [
+    "bin/flash4",
+    "share/build-record.json",
+    "share/preflight/flash.par"
+  ],
+  "manifest": {
+    "description": "Operator-supplied FLASH 4.8 MPI/HDF5 runtime compiled for a 2D compressible resistive-MHD island-coalescence application",
+    "executable_kind": "python-flash-application-mpi-hdf5",
+    "name": "flash-island-coalescence-resistive-mhd-4.8",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.environment_valid",
+      "checks.executable_present",
+      "checks.mpi_launcher_present",
+      "checks.parameter_file_present",
+      "checks.parameter_file_copied",
+      "checks.process_completed",
+      "checks.return_code_zero",
+      "checks.hdf5_output_created",
+      "checks.hdf5_output_readable"
+    ],
+    "preflight_resource": "examples/runtime_smoke.py",
+    "preflight_result": "flash_mhd_capability_smoke.json",
+    "schema_version": "0.1.0",
+    "skill": "flash-mhd",
+    "version": "4.8.local.1"
+  },
+  "runtime_root": "../.runtime/flash-island-coalescence-resistive-mhd-4.8"
+}

simjecture-0.3.1/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-0.3.1/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-0.3.1/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-0.2.2 → simjecture-0.3.1}/demos/README.md

@@ -1,9 +1,11 @@
 # Demonstrations
 
 Release demonstrations are recorded scientific runs, not hand-written examples
-that merely exercise an API. A recorded demo should include the exact natural-
+that merely exercise an API. Portable recorded runs include the exact natural-
 language input, durable claim ledger, transcript, final report, generated
 programs, numerical outputs, provenance, and figures made from those outputs.
+Operator-dependent demos state clearly which inputs are local and which claims
+remain unresolved.
 
 ## Recorded autonomous runs
 
@@ -12,7 +14,13 @@ programs, numerical outputs, provenance, and figures made from those outputs.
   campaign instruction, the agent authored a reaction-diffusion solver and
   found a finite-domain counterexample in 23.8 minutes.
 - [`collisionless_gem_reconnection/`](collisionless_gem_reconnection/) is the
-  primary plasma demo. From a validated non-evidentiary GEM starting instrument,
+  primary kinetic plasma demo. From a validated non-evidentiary GEM starting instrument,
   the agent designed and executed a held-out 12-run CUDA ensemble, falsified its
   operational child under a frozen rule, and correctly left the population root
   open.
+- [`resistive_mhd_island_coalescence/`](resistive_mhd_island_coalescence/) is the
+  fluid-plasma MHD demo. It bundles an operator-validated, non-evidentiary
+  FLASH anchor and an audit extract from a six-hour autonomous campaign. The
+  campaign falsified the specified root interval ($p \approx -0.406$), while
+  its repair branch remains explicitly open because the final analyzer lineage
+  was not closure-eligible.

simjecture-0.3.1/demos/resistive_mhd_island_coalescence/.gitignore

@@ -0,0 +1 @@
+guided/anchor_run/