@researai/deepscientist 1.5.16 → 1.6.0

package/src/skills/science/references/packages/starry.md

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+# starry stellar and exoplanet mapper
+
+## Catalog
+
+- Package id: `starry`
+- Domains: `astronomy_astrophysics`
+- Tags: `astronomy`, `exoplanets`, `stellar`, `lightcurve`, `mapping`, `sphericalharmonics`
+- Knowledge URL: https://github.com/skilled-scipkg/starry
+- Source archive URL: https://github.com/skilled-scipkg/starry/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/rodluger/starry
+- Homepage: https://starry.readthedocs.io
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+starry provides fast analytic models of stellar and exoplanet surface maps to generate and fit transit, eclipse, and phase light curves.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `starry`.
+
+## Package Check
+
+For Python-facing environments, start with an import/version check and then a
+minimal package-specific smoke test:
+
+```bash
+python - <<'PY'
+import importlib, json, pathlib
+package_id = 'starry'
+result = {"package_id": package_id, "import": "failed", "version": None, "smoke": "not_run"}
+try:
+    module = importlib.import_module(package_id.replace('-', '_').split('_jl')[0])
+    result["import"] = "passed"
+    result["version"] = getattr(module, "__version__", None)
+except Exception as exc:
+    result["error"] = repr(exc)
+pathlib.Path("validation/environment").mkdir(parents=True, exist_ok=True)
+pathlib.Path(f"validation/environment/{package_id}_doctor.json").write_text(json.dumps(result, indent=2), encoding="utf-8")
+PY
+```
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `starry` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/strawberryfields.md

@@ -0,0 +1,73 @@
+# Strawberry Fields Continuous-Variable Quantum Toolkit
+
+## Catalog
+
+- Package id: `strawberryfields`
+- Domains: `electromagnetics`
+- Tags: `quantum-computing`, `photonics`, `continuous-variable`, `quantum-optics`, `circuit-simulation`, `bosonic-systems`
+- Knowledge URL: https://github.com/skilled-scipkg/strawberryfields
+- Source archive URL: https://github.com/skilled-scipkg/strawberryfields/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/XanaduAI/strawberryfields
+- Homepage: https://xanadu.ai
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Strawberry Fields is a Python platform for designing, simulating, and optimizing continuous-variable photonic quantum circuits, including near-term algorithms and execution pathways for quantum optical hardware.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `strawberryfields`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/strawberryfields_doctor.json` before treating the
+runtime as usable.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `strawberryfields` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/su2.md

@@ -0,0 +1,80 @@
+# SU2 Open-Source CFD Suite
+
+## Catalog
+
+- Package id: `su2`
+- Domains: `computational_fluid_dynamics`
+- Tags: `cfd`, `aerodynamics`, `multiphysics`, `pde`, `optimization`, `simulation`
+- Knowledge URL: https://github.com/skilled-scipkg/SU2
+- Source archive URL: https://github.com/skilled-scipkg/SU2/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/su2code/SU2
+- Homepage: https://su2code.github.io
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+SU2 is an open-source C++ suite for computational fluid dynamics, multiphysics PDE simulation, and adjoint-driven aerodynamic shape optimization for engineering analysis and design.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `su2`.
+
+## Package Check
+
+For CLI/HPC-oriented environments, check the executable or loaded module before
+running any expensive job:
+
+```bash
+command -v su2 || true
+su2 --version || true
+```
+
+If the package is available only through environment modules, record the module
+state and the exact executable path in `validation/environment/su2_doctor.json`.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `su2` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/sunny-jl.md

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+# Sunny.jl Magnetic Materials Modeling
+
+## Catalog
+
+- Package id: `sunny-jl`
+- Domains: `computational_science`
+- Tags: `magnetism`, `spin-waves`, `spin-dynamics`, `quantum-materials`, `scattering`
+- Knowledge URL: https://github.com/skilled-scipkg/Sunny.jl
+- Source archive URL: https://github.com/skilled-scipkg/Sunny.jl/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/SunnySuite/Sunny.jl
+- Homepage: https://sunnysuite.github.io/Sunny.jl/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Sunny.jl models magnetic materials with symmetry-aware Hamiltonians, quantum spin excitations, finite-temperature spin dynamics, and fitting to neutron or X-ray scattering data.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `sunny-jl`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/sunny-jl_doctor.json` before treating the
+runtime as usable.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `sunny-jl` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/sw4.md

@@ -0,0 +1,73 @@
+# SW4 Seismic Waves Solver
+
+## Catalog
+
+- Package id: `sw4`
+- Domains: `computational_science`
+- Tags: `sw4`, `seismology`, `geophysics`, `seismic-modeling`, `elastic-waves`, `finite-difference`, `earthquake-simulation`
+- Knowledge URL: https://github.com/skilled-scipkg/sw4
+- Source archive URL: https://github.com/skilled-scipkg/sw4/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/geodynamics/sw4
+- Homepage: https://github.com/geodynamics/sw4
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+SW4 is a high-order solver for 3D seismic wave propagation with free-surface and absorbing boundaries, supporting point-force and moment-tensor earthquake source modeling.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `sw4`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/sw4_doctor.json` before treating the
+runtime as usable.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `sw4` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/swift.md

@@ -0,0 +1,88 @@
+# SWIFT Astrophysical Simulation Engine
+
+## Catalog
+
+- Package id: `swift`
+- Domains: `astronomy_astrophysics`, `computational_fluid_dynamics`, `workflow_provenance`, `robotics_physics`
+- Tags: `astrophysics`, `cosmology`, `hydrodynamics`, `sph`, `gravity`, `hpc`
+- Knowledge URL: https://github.com/skilled-scipkg/SWIFT
+- Source archive URL: https://github.com/skilled-scipkg/SWIFT/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/SWIFTSIM/SWIFT
+- Homepage: http://www.swiftsim.com
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+SWIFT is a high-performance astrophysics engine for cosmological particle simulations, combining gravity and smoothed particle hydrodynamics with fine-grained tasking across large HPC systems.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `swift`.
+
+## Package Check
+
+For Python-facing environments, start with an import/version check and then a
+minimal package-specific smoke test:
+
+```bash
+python - <<'PY'
+import importlib, json, pathlib
+package_id = 'swift'
+result = {"package_id": package_id, "import": "failed", "version": None, "smoke": "not_run"}
+try:
+    module = importlib.import_module(package_id.replace('-', '_').split('_jl')[0])
+    result["import"] = "passed"
+    result["version"] = getattr(module, "__version__", None)
+except Exception as exc:
+    result["error"] = repr(exc)
+pathlib.Path("validation/environment").mkdir(parents=True, exist_ok=True)
+pathlib.Path(f"validation/environment/{package_id}_doctor.json").write_text(json.dumps(result, indent=2), encoding="utf-8")
+PY
+```
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `swift` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/tdnegf.md

@@ -0,0 +1,73 @@
+# TDNEGF Hybrid Quantum Transport
+
+## Catalog
+
+- Package id: `tdnegf`
+- Domains: `computational_science`
+- Tags: `tdnegf`, `quantum-transport`, `nonequilibrium-greens-function`, `spintronics`, `open-quantum-systems`
+- Knowledge URL: https://github.com/skilled-scipkg/TDNEGF
+- Source archive URL: https://github.com/skilled-scipkg/TDNEGF/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/Jalil199/TDNEGF
+- Homepage: https://github.com/Jalil199/TDNEGF
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+TDNEGF-Hybrid provides one-time TDNEGF ODE simulation of open quantum devices, evolving reduced density matrices and auxiliary states to compute time-resolved charge and spin transport observables.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `tdnegf`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/tdnegf_doctor.json` before treating the
+runtime as usable.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `tdnegf` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.

package/src/skills/science/references/packages/tenpy.md

@@ -0,0 +1,73 @@
+# TeNPy Tensor Network Python
+
+## Catalog
+
+- Package id: `tenpy`
+- Domains: `computational_science`
+- Tags: `tensor-networks`, `quantum-many-body`, `dmrg`, `tebd`, `matrix-product-states`, `computational-physics`
+- Knowledge URL: https://github.com/skilled-scipkg/tenpy
+- Source archive URL: https://github.com/skilled-scipkg/tenpy/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/tenpy/tenpy
+- Homepage: https://github.com/tenpy/tenpy
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+TeNPy is a tensor-network simulation library for strongly correlated quantum many-body systems, with readable yet extensible implementations of DMRG, TEBD, and related matrix-product-state algorithms for physics research.
+
+## DeepScientist Runtime Rule
+
+This card is package knowledge and routing context only. It does not mean the
+solver, Python module, CLI binary, compiled backend, license server, dataset, or
+HPC module is installed in the active environment. Before computed work, use
+`bash_exec(...)` to perform an import, executable, version, and smoke-test check
+appropriate for `tenpy`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/tenpy_doctor.json` before treating the
+runtime as usable.
+
+Record the result with `artifact.science(...)` as `science.package_check`. Use
+`status="passed"` only when the environment can run at least a minimal smoke
+path. Use `status="failed"` or `status="blocked"` when the check explains why
+execution cannot proceed.
+
+Generated import or executable names are starting points. If `tenpy` uses
+a different Python module, CLI binary, environment module, container, or wrapper
+script, adjust the check before concluding the solver is unavailable.
+
+## Expected Science Nodes
+
+- `science.package_check` for import/executable/version/smoke-test evidence
+- `science.computational_run` for solver execution, simulation, fitting, or numerical computation
+- `science.dataset_analysis` when the task primarily analyzes existing data
+- `science.parameter_sweep` when varying parameters, inputs, models, or solver settings
+- `science.validation_result` for convergence, units, schema, controls, or correctness checks
+- `science.claim` only after evidence paths or related nodes support the claim
+
+## Evidence Path Conventions
+
+- `simulations/inputs/` for generated or selected solver inputs
+- `simulations/logs/` for stdout, stderr, scheduler logs, or solver logs
+- `simulations/outputs/` for structured run outputs
+- `analyses/scripts/`, `analyses/logs/`, and `analyses/outputs/` for dataset analysis
+- `validation/environment/` for package checks
+- `validation/runs/` for convergence, unit, schema, or correctness sidecars
+- `figures/` for derived visualizations
+
+## Validation Checklist
+
+- Record package version, executable path, backend, module state, or container image when relevant.
+- Preserve input files and parameters that define the scientific state.
+- Capture units, coordinate conventions, timestep/mesh/basis/model settings, seeds, and convergence criteria when applicable.
+- Validate output schema and important physical or statistical invariants before recording a computed claim.
+- Link claims to run, analysis, sweep, and validation nodes rather than relying on prose.
+
+## Common Pitfalls
+
+- Do not treat the package card or knowledge URL as runtime availability.
+- Do not weaken solver tolerances, physical models, dataset filters, or convergence criteria to make a run pass unless the change is explicitly part of the scientific question.
+- Do not call a value `computed` unless the corresponding run or analysis happened in the current quest and evidence paths are recorded.
+- Do not copy package knowledge-base material into the quest without preserving its source and license context.