@researai/deepscientist 1.5.17 → 1.6.0

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

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+# Astropy Astronomy Core Library
+
+## Catalog
+
+- Package id: `astropy`
+- Domains: `astronomy_astrophysics`, `workflow_provenance`
+- Tags: `astronomy`, `astrophysics`, `fits`, `coordinates`, `cosmology`, `units`
+- Knowledge URL: https://github.com/skilled-scipkg/astropy
+- Source archive URL: https://github.com/skilled-scipkg/astropy/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/astropy/astropy
+- Homepage: https://www.astropy.org
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Astropy is the core Python library for astronomy, covering units, coordinates, time handling, FITS files, WCS, tables, and cosmology workflows.
+
+## 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 `astropy`.
+
+## 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 = 'astropy'
+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 `astropy` 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/astroquery.md

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+# Astroquery Astronomical Data Access
+
+## Catalog
+
+- Package id: `astroquery`
+- Domains: `astronomy_astrophysics`
+- Tags: `astronomy`, `astroinformatics`, `catalog-query`, `archive-access`, `observational-data`, `astropy-affiliated`
+- Knowledge URL: https://github.com/skilled-scipkg/astroquery
+- Source archive URL: https://github.com/skilled-scipkg/astroquery/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/astropy/astroquery
+- Homepage: http://astroquery.readthedocs.org/en/latest/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Astroquery provides a unified Python interface for querying online astronomical catalogs, mission archives, and object databases through service-specific modules and standardized query methods.
+
+## 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 `astroquery`.
+
+## 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 = 'astroquery'
+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 `astroquery` 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/atomate2.md

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+# Atomate2 Materials Workflow Library
+
+## Catalog
+
+- Package id: `atomate2`
+- Domains: `quantum_chemistry`, `materials_science`, `workflow_provenance`
+- Tags: `materials-science`, `workflow-automation`, `high-throughput`, `dft`, `vasp`, `computational-materials`
+- Knowledge URL: https://github.com/skilled-scipkg/atomate2
+- Source archive URL: https://github.com/skilled-scipkg/atomate2/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/materialsproject/atomate2
+- Homepage: https://materialsproject.github.io/atomate2/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Atomate2 provides composable high-throughput computational materials science workflows for running and managing VASP and related calculations of electronic, vibrational, and defect properties at scale.
+
+## 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 `atomate2`.
+
+## Package Check
+
+For CLI/HPC-oriented environments, check the executable or loaded module before
+running any expensive job:
+
+```bash
+command -v atomate2 || true
+atomate2 --version || true
+```
+
+If the package is available only through environment modules, record the module
+state and the exact executable path in `validation/environment/atomate2_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 `atomate2` 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/atomsmltr.md

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+# atomSmltr Laser Cooling and Trapping Simulator
+
+## Catalog
+
+- Package id: `atomsmltr`
+- Domains: `computational_science`
+- Tags: `atomic-physics`, `laser-cooling`, `cold-atoms`, `magneto-optical-trap`, `numerical-simulation`
+- Knowledge URL: https://github.com/skilled-scipkg/atomSmltr
+- Source archive URL: https://github.com/skilled-scipkg/atomSmltr/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/adareau/atomSmltr
+- Homepage: https://atomsmltr.readthedocs.io/en/latest/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+atomSmltr is a modular Python toolkit for simulating laser-cooled atoms in custom laser and magnetic field geometries with trajectory integration.
+
+## 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 `atomsmltr`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/atomsmltr_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 `atomsmltr` 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/awkward.md

@@ -0,0 +1,73 @@
+# Awkward Array
+
+## Catalog
+
+- Package id: `awkward`
+- Domains: `high_energy_physics`
+- Tags: `awkward`, `ragged-arrays`, `jagged-data`, `columnar-analysis`, `scikit-hep`
+- Knowledge URL: https://github.com/skilled-scipkg/awkward
+- Source archive URL: https://github.com/skilled-scipkg/awkward/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/scikit-hep/awkward
+- Homepage: https://awkward-array.org
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Awkward Array enables NumPy-like, compiled operations on deeply nested, variable-length, and record-rich scientific data, making jagged JSON-like event structures fast and practical to analyze.
+
+## 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 `awkward`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/awkward_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 `awkward` 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/batman.md

@@ -0,0 +1,88 @@
+# BATMAN Exoplanet Transit Light-Curve Modeler
+
+## Catalog
+
+- Package id: `batman`
+- Domains: `astronomy_astrophysics`
+- Tags: `astronomy`, `exoplanets`, `transit-light-curves`, `photometry`, `time-series`
+- Knowledge URL: https://github.com/skilled-scipkg/batman
+- Source archive URL: https://github.com/skilled-scipkg/batman/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/lkreidberg/batman
+- Homepage: http://lkreidberg.github.io/batman
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+BATMAN is a Python package for very fast computation of exoplanet transit light curves, supporting multiple limb-darkening laws for fitting and simulating planetary transit photometry.
+
+## 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 `batman`.
+
+## 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 = 'batman'
+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 `batman` 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/biopython.md

@@ -0,0 +1,88 @@
+# Biopython
+
+## Catalog
+
+- Package id: `biopython`
+- Domains: `bioinformatics`
+- Tags: `bioinformatics`, `computational-biology`, `molecular-biology`, `sequence-analysis`, `genomics`
+- Knowledge URL: https://github.com/skilled-scipkg/biopython
+- Source archive URL: https://github.com/skilled-scipkg/biopython/archive/refs/heads/master.zip
+- Upstream project URL: https://github.com/biopython/biopython
+- Homepage: http://biopython.org/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Biopython provides Python tools for bioinformatics and computational molecular biology, covering biological sequence parsing, alignments, phylogenetics, and interfaces to common genomics and proteomics data sources.
+
+## 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 `biopython`.
+
+## 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 = 'biopython'
+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 `biopython` 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/bloqade.md

@@ -0,0 +1,73 @@
+# Bloqade Neutral Atom Quantum SDK
+
+## Catalog
+
+- Package id: `bloqade`
+- Domains: `workflow_provenance`
+- Tags: `quantum-computing`, `neutral-atoms`, `rydberg`, `quantum-sdk`, `edsl`, `quera`
+- Knowledge URL: https://github.com/skilled-scipkg/bloqade
+- Source archive URL: https://github.com/skilled-scipkg/bloqade/archive/refs/heads/main.zip
+- Upstream project URL: https://github.com/QuEraComputing/bloqade
+- Homepage: https://bloqade.quera.com/latest/
+- Catalog source: FermiLink skilled-scipkg, commit `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## When To Consider
+
+Bloqade is QuEra's Python SDK and eDSL suite for programming, compiling, and simulating neutral-atom quantum computing workflows on Rydberg-atom hardware and related backends.
+
+## 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 `bloqade`.
+
+## Package Check
+
+Use a package-specific import, executable, or module check and save the result
+under `validation/environment/bloqade_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 `bloqade` 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.