@delta-agentcloud/cli 0.0.0-stage → 1.1.20

package/skills/delta-science/references/delta-bo.md

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+# Delta-BO reference
+
+Make all online calls with `delta-cli science invoke`; the tool is always `delta-bo`. The current
+CLI catalogue exposes only `commands` and `generate`. Do not infer operations from old HTTP
+documentation or call the stateful command API directly.
+
+## commands
+
+Use case: The user asks which Delta-BO commands are supported by the current deployment.
+
+```text
+delta-cli science invoke --tool delta-bo --endpoint commands
+```
+
+No request body. Report only the command list in the current business response; do not fill it in from historical documentation.
+
+## generate
+
+Use case: Generate random-search or Bayesian-optimisation suggestions for numeric, integer or categorical experimental variables.
+
+When there is no real history, or fewer than five historical observations and the user has not explicitly requested BO, use bounded random search:
+
+```json
+{
+  "params": [
+    {"name": "x", "type": "numeric", "low": 0.0, "high": 1.0}
+  ],
+  "num_suggestions": 3,
+  "algorithm": "random-search",
+  "seed": 42
+}
+```
+
+When real history is available and the user explicitly requests BO, you may use:
+
+```json
+{
+  "params": [
+    {"name": "temperature", "type": "numeric", "low": 20.0, "high": 120.0},
+    {"name": "catalyst", "type": "categorical", "choices": ["A", "B", "C"]}
+  ],
+  "objectives": [{"name": "yield", "minimize": false}],
+  "num_suggestions": 2,
+  "algorithm": "bo",
+  "model": {"name": "gp", "min_samples": 2, "train_steps": 50},
+  "acq_target": {"name": "ucb", "beta": 2.0},
+  "solver": {"name": "ga", "pop_size": 40, "n_gen": 10},
+  "histories": {
+    "decisions": [
+      {"temperature": 40.0, "catalyst": "A"},
+      {"temperature": 80.0, "catalyst": "B"}
+    ],
+    "observations": [
+      {"yield": 0.42},
+      {"yield": 0.61}
+    ]
+  },
+  "seed": 7
+}
+```
+
+Supported parameter types are `numeric`, `integer` and `categorical`. Prefer object-form history
+to avoid ambiguity about the order of array columns. Do not invent observations, objective values
+or purported optima.
+
+Optional deduplication and constraints:
+
+```json
+{
+  "diversity": {
+    "deduplicate": true,
+    "min_numeric_distance": {"temperature": 5.0},
+    "prefer_unique_categories": true
+  },
+  "constraints": [
+    {"type": "unique_batch"},
+    {"type": "avoid_seen_decisions"}
+  ]
+}
+```
+
+Report only fields actually present in the business response: `suggestions`,
+`suggestion_metadata`, `warnings`, `generated_candidate_count` and `diversity`. Do not replace
+empty suggestions or a failure with local GP, UCB or random-number results.
+
+## Known legacy capabilities that are not exposed
+
+The old service included stateful commands such as session, space, objective, policy, suggest,
+observe, loop, status and best, but they are not current Delta CLI operations. This Skill records
+only that capability boundary: it includes no URL or curl examples and does not run those
+operations. To extend the interface, first expose the operation and request schema through Science
+Server, then update this reference.

package/skills/delta-science/references/gsasii.md

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+# GSAS-II reference
+
+Make all calls with `delta-cli science invoke`. Simulation requires a real CIF; refinement
+requires real powder data, instrument parameters and phase CIFs. Never fill in a failed result
+with synthetic data. If the input is not a CIF, first use a successful pymatgen
+`structure-convert` result from the current task.
+
+## Health
+
+Operation: `health`; no request body.
+
+Key response fields in `data`: `status`, `service`, `gsasii_available`,
+`metadata`, and `limits`.
+
+Call this only when the user explicitly asks for a health check; do not add a health call automatically before simulation or refinement.
+
+## Powder Simulation
+
+Operation: `powder-simulate`.
+
+```json
+{
+  "cif": "<CIF text>",
+  "phase_name": "phase",
+  "instrument_parameters": "<GSAS-II instrument parameter text>",
+  "histogram_name": "simulation",
+  "t_min": 10.0,
+  "t_max": 80.0,
+  "t_step": 0.02,
+  "include_profile": true,
+  "max_profile_points": 1000,
+  "include_reflections": true,
+  "max_reflections": 1000,
+  "return_refined_cif": false,
+  "return_project": false
+}
+```
+
+Use either `t_step` or `n_points`, not both. Optional fields include
+`wavelength`, `radiation`, `scale`, `include_profile`, `max_profile_points`,
+`include_reflections`, `max_reflections`, `return_refined_cif`, and
+`return_project`.
+
+The response includes `profile` points with `x`, `y_calc`, optional background,
+bounded `reflections` with hkl/d-spacing/2theta where available, and metadata.
+If `return_project` is true, `project_base64` contains the GSAS-II `.gpx`
+project. If `return_refined_cif` is true, `refined_cif` contains exported CIF
+text for pymatgen handoff when GSAS-II supports export for the phase.
+
+Notes:
+
+- `cif` should be valid CIF text. If the input is POSCAR/JSON/CSSR/XSF, use
+  pymatgen `structure-convert` first with `output_format: "cif"`.
+- `instrument_parameters` should be GSAS-II instrument parameter text such as
+  `INST_XRY.PRM` when instrument-specific simulation is needed.
+- For quick simulation only, `instrument_parameters` may be omitted. The service
+  then generates a simple CW X-ray instrument model from `wavelength` or
+  `radiation` (`CuKa` by default; also supports aliases such as `MoKa`, `CoKa`,
+  `CrKa`, and explicit numeric wavelength).
+- Refinement still requires real `instrument_parameters`.
+- `max_profile_points` controls response sampling. Use small values for smoke
+  tests and larger values for profile comparison.
+- Older deployed gateway images may require `max_profile_points >= 10`.
+
+## Powder Refinement
+
+Operation: `powder-refine`.
+
+```json
+{
+  "powder_data": "<two-column or three-column powder data text>",
+  "powder_format": "xy",
+  "instrument_parameters": "<GSAS-II instrument parameter text>",
+  "phases": [
+    {"name": "phase", "cif": "<CIF text>"}
+  ],
+  "refinement_mode": "rietveld",
+  "refinement_steps": [],
+  "max_cycles": 3,
+  "histogram_name": "powder",
+  "include_profile": true,
+  "max_profile_points": 1000,
+  "include_reflections": true,
+  "max_reflections": 1000,
+  "return_refined_cif": false,
+  "return_project": false
+}
+```
+
+Supported `powder_format` values: `xy`, `xye`, `fxye`, `gsas`, and `csv`.
+
+`refinement_mode: "rietveld"` is currently implemented. `pawley` and `lebail`
+return a clear not-implemented response until the service wires the
+mode-specific GSAS-II setup.
+
+The response includes fit `residuals` when available, phase summaries, sampled
+profile points, bounded `reflections`, warnings, optional `refined_cif`, and
+the optional `.gpx` project.
+
+Notes:
+
+- Use `xy` for simple whitespace-delimited `x y` rows, `xye` for `x y esd`,
+  `csv` for numeric comma-separated rows, or `gsas`/`fxye` for GSAS-like powder
+  formats.
+- `max_cycles: 0` is useful for project-construction smoke tests. Increase it
+  only when the powder data, phase model, instrument file, and refinement steps
+  are realistic.
+- `refinement_steps` is passed to `G2Project.do_refinements`. Keep recipes
+  incremental and inspect `warnings`, `residuals`, and `lst` output.
+- Refinement may return `valid: false` with partial phase/profile information
+  if GSAS-II constructed the project but a refinement step failed.
+
+## Cross-tool hand-off
+
+Complete structure conversion, diffraction simulation and refinement step by step through the
+CLI within this Skill: `pymatgen structure-convert -> gsasii powder-simulate/powder-refine`.
+Use downstream only the structure text or profile from the preceding successful business response;
+do not run local scripts or call the service directly.

package/skills/delta-science/references/lammps.md

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+# LAMMPS reference
+
+Make all calls with `delta-cli science invoke`. LAMMPS does not infer data files, atom types,
+potentials or boundary conditions from a formula, CIF or POSCAR. Successful execution does not
+establish physical convergence or production readiness.
+
+## Health
+
+Operation: `health`; no request body.
+
+Key response fields in `data`: `status`, `service`, `lammps_available`,
+`metadata`, and `limits`.
+
+Call this only when the user explicitly asks for a health check; do not add a health call automatically before simulation.
+
+## Built-In Lennard-Jones Example
+
+Operation: `lj-melt-example`.
+
+Returns a complete `request` payload for the `run` operation, plus workflow notes
+showing where pymatgen and GSAS-II fit around LAMMPS.
+
+## Run
+
+Operation: `run`.
+
+```json
+{
+  "input_script": "<LAMMPS input script>",
+  "files": [
+    {"path": "system.data", "content": "<LAMMPS data file text>", "encoding": "text"}
+  ],
+  "timeout_seconds": 30,
+  "max_thermo_rows": 1000,
+  "log_tail_lines": 200,
+  "output_files": ["dump.lammpstrj", "final.data"],
+  "include_log": true,
+  "include_stdout": false,
+  "include_stderr": false
+}
+```
+
+`files` are written into a fresh job working directory before LAMMPS starts.
+`encoding` can be `text` or `base64`.
+
+The response includes parsed thermo rows, the final thermo row, atom count when
+detectable, log tail, warnings, and requested output files. Text output files
+return `content`; binary output files return `content_base64`.
+
+Notes:
+
+- Use relative file paths only.
+- The service rejects unsafe commands such as `shell`, `python`, `plugin`, and
+  `jump` by default.
+- `include <relative-file>` is allowed when the included file is supplied in
+  `files`; absolute paths, parent-directory traversal, URLs, and `jump` loops
+  are rejected.
+- Dump/data products are returned as raw requested output files, not structured
+  parsed atom-frame objects.
+- The gateway is synchronous; keep interactive runs short.
+- Force-field choice is caller responsibility. The service executes explicit
+  LAMMPS input and does not infer potentials from formulas or structures.
+
+In the final reply, include only `last_thermo`, the final step/temperature/total energy,
+warnings, and a summary of output files requested by the user from the current business response.
+Do not divide total energy by the atom count, substitute steps, convert units, or infer
+convergence or stability. For the minimal example, call `lj-melt-example` first, then pass its
+`request` from the current business response to `run` unchanged; do not pass the outer CLI envelope.

package/skills/delta-science/references/ldm-bo.md

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+# LDM-BO reference
+
+Make all calls with `delta-cli science invoke`; do not use the local PDF2Dock runner. This tool is
+for small-molecule SMILES only. Use the AntBO capability boundary for antibody, CDRH3 or AntBO
+tasks. The server injects the provider, model paths and Vina/ReaSyn/GPU/LLM settings; do not put
+them in the request JSON.
+
+## Health
+
+Operation: `health`; no request body.
+
+The response reports whether the adapter can see the mounted PDF2Dock
+interpreter, `bo_api.py`, Vina binary, ReaSyn repo/interpreter/checkpoints, NN
+model files, cache directory, GPU settings, and LLM configuration. Missing LLM
+settings degrade health because LDM methods need them.
+
+## One-Step Recommend
+
+Operation: `recommend`.
+
+Wraps `bo_api.recommend_next_smiles`.
+
+Typical payload:
+
+```json
+{
+  "method": "bo-tanimoto",
+  "pool": ["CCO", "CCN", "CCC"],
+  "history": [
+    {"smiles": "CCO", "scores": [-7.1]},
+    {"smiles": "CCN", "scores": [-6.8]}
+  ],
+  "batch_size": 1
+}
+```
+
+Typical business response inside the documented gateway `data`:
+
+```json
+{
+  "recommendations": ["CCC"],
+  "acquisition_values": [0.12],
+  "n_objectives": 1
+}
+```
+
+LDM methods may include an `llm` diagnostics object.
+
+Report `acquisition_values` exactly as returned in the business response. Unless the current
+business response explicitly defines the field, do not describe it as predicted Vina, a predicted
+objective, uncertainty, confidence or expected improvement, and do not infer whether higher or
+lower is better. If the service provides no recommendation rationale, state “The service returned
+no recommendation rationale”; do not add an explanation based on molecular scaffolds, heteroatoms
+or model mechanisms.
+
+## Full Trajectory
+
+Operation: `trajectory`.
+
+Wraps `bo_api.run_search_trajectory`.
+
+Small smoke payload:
+
+```json
+{
+  "method": "bo-tanimoto",
+  "seed": 42,
+  "seed-smiles": "CCO,CCN,CCC",
+  "num-evaluations": 4,
+  "batch-size": 1,
+  "objective": "vina+nn"
+}
+```
+
+Typical business response inside the documented gateway `data`:
+
+```json
+{
+  "config": {},
+  "history": [],
+  "summary": {}
+}
+```
+
+LDM methods may include `llm_trajectory`.
+
+## Error Handling
+
+The service maps `bo_api` error JSON to an upstream failure. The gateway
+returns a standard error envelope:
+
+```json
+{
+  "code": 1,
+  "message": "AutoDock Vina executable not found...",
+  "data": {
+    "endpoint": "/v1/trajectory",
+    "ldm_bo_response": {
+      "error": "...",
+      "error_type": "ValueError",
+      "traceback": "Traceback ..."
+    }
+  }
+}
+```
+
+Common causes are missing Vina, missing ReaSyn, wrong Python interpreter, CUDA
+device mismatch, missing LLM credentials for LDM methods, or an unwritable Vina
+cache directory.
+
+## Provider Settings
+
+Do not send provider settings in request JSON. The adapter reads these from
+deployment config and passes them as Python kwargs to `bo_api`:
+
+```text
+vina_bin
+vina_cache_dir
+vina_max_workers
+gp_device
+reasyn_repo
+reasyn_python_bin
+reasyn_model_path
+reasyn_devices
+nn_model_path
+nn_metadata_path
+llm_model
+llm_base_url
+llm_api_key
+```
+
+The CLI forwards the user payload; `bo_api` owns business defaults and schema behavior.

package/skills/delta-science/references/materials-design.md

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+# Materials Design reference
+
+Materials Design builds surrogate models from experimental or computational materials tables,
+validates models, defines feasible candidate spaces, and ranks candidates with uncertainty
+estimates. Recommendations are hypotheses to validate, not confirmed materials, synthesis routes
+or experimental results.
+
+The routing label for this reference is `materials-design`. Use the current output of
+`delta-cli science list` and `delta-cli science endpoints list <tool>` as the authority for
+`tools.name` and `tool_endpoints.name`. The Gateway paths below describe the service contract;
+they are not URLs to construct or access directly.
+
+## Service boundary
+
+The service provides the following capabilities:
+
+| Service path | Purpose | Result boundary |
+| --- | --- | --- |
+| `/chem/materials-design/health` | Gateway-to-service readiness check | `status`, dependency availability, limits |
+| `/chem/materials-design/v1/capabilities` | Input formats, models, validation modes and limits | Capability catalogue |
+| `/chem/materials-design/v1/jobs` | Upload training/candidate tables and create an asynchronous job | `202`, `job_id`, status and links |
+| `/chem/materials-design/v1/jobs/{job_id}` | Read job status | `status`, `result_status`, result, warnings |
+| `/chem/materials-design/v1/jobs/{job_id}/cancel` | Request cancellation | Cancellation request/final state |
+| `/chem/materials-design/v1/jobs/{job_id}/artifacts` | List artifacts | name, size, media_type, SHA-256 |
+| `/chem/materials-design/v1/jobs/{job_id}/artifacts/{path}` | Download one artifact | Raw report/JSON/CSV/figure bytes |
+
+Route all JSON/query calls through:
+
+```text
+delta-cli science invoke --tool TOOL --endpoint ENDPOINT --data JSON
+```
+
+Submit training tables through the controlled file adapter:
+
+```text
+delta-cli science file invoke --tool materials-design --endpoint job-submit \
+  --file train.xlsx --candidate-file candidates.xlsx --data CONFIG_JSON
+delta-cli science task submit --tool materials-design --operation job-status \
+  --input '{"job_id":"mdjob_..."}' --wait
+delta-cli science file download --tool materials-design --endpoint artifact-download \
+  --params '{"job_id":"mdjob_...","artifact_path":"report.html"}' --output report.html
+```
+
+Use `--params JSON` only for read-only query operations. If a new tool is absent from the
+catalogue, or the catalogue does not return enough request-schema detail, stop and report that it
+is not exposed. Do not guess endpoint names, bodies or compatibility aliases.
+
+## CLI capability boundaries
+
+The raw service request for `POST /v1/jobs` is `multipart/form-data` and contains at least:
+
+```text
+file=<training table>
+candidate_file=<optional candidate table>
+config=<serialized JSON object>
+```
+
+`science invoke` accepts only a JSON object body and JSON query parameters; it cannot express
+multipart data. Do not disguise a local path or base64 as a file field. Artifact downloads are
+also raw bytes: save and verify them with `science file download`, and do not treat them as
+ordinary JSON results. Do not call `materials-design-service:8900` or connect directly to the
+preflight Gateway.
+
+## Inputs and configuration
+
+Before modelling, confirm:
+
+- `feature_columns`, `controllable_columns`, `target_column` or `objectives`;
+- identifier, metadata, leakage, post-measurement and group/time columns, and their units;
+- objective direction, feasibility constraints, candidate table or candidate-generation rules;
+- missing values, duplicate samples, measurement conditions, data sources and validation split strategy.
+
+Core fields for a single-objective configuration:
+
+```json
+{
+  "feature_columns": ["Bi", "In", "Ti"],
+  "controllable_columns": ["Bi", "In", "Ti"],
+  "identifier_columns": ["sample_id"],
+  "target_column": "T",
+  "target_direction": "maximize",
+  "validation": {"strategy": "kfold", "n_splits": 5},
+  "model_names": ["ExtraTrees", "GPR", "Ridge"],
+  "random_state": 42,
+  "recommendation_count": 10
+}
+```
+
+For multiple objectives, use `objectives: [{"target_column": "...", "direction": "maximize|minimize"}]`
+and explicit Pareto/EHVI settings. Prefer the user's `candidate_file`. If the service generates
+candidates from observed ranges, explicitly preserve steps, hard constraints, composition
+closure, `max_candidates` and `allow_extrapolation`. Do not optimise identifier, post-measurement
+or leakage columns, or out-of-domain points without authorisation. Do not extrapolate arbitrarily
+to fill the candidate count.
+
+## Results handling
+
+Assess job `status` and `result_status` separately:
+
+- `status`: `pending`, `running`, `completed`, `failed` or `cancelled`;
+- `result_status`: `complete`, `exploratory`, `readiness_only` or `failed`.
+
+`202` means only that the service accepted or queued the job; it does not mean model training is
+complete. `completed` does not mean the ranking is reliable. Say that the data and validation
+support candidate ranking only when `result_status` is `complete`. Treat `exploratory` only as a
+learning hypothesis; for `readiness_only`, read the readiness information and request missing
+inputs; report `failed` as returned. Always preserve the returned validation, ranking, warnings
+and error.
+
+Keep predictions distinct from observations and cross-validation predictions. At minimum, report
+data coverage, the split, model comparisons, uncertainty calibration, candidate feasibility,
+in-domain/out-of-domain status, EI/PI/UCB or Pareto settings, and the plan for experimental
+validation. Do not present model variance as experimental error or candidate predictions as
+measured values.
+
+## Artifacts and errors
+
+Read artifacts only when the user asks for them or the workflow requires them. Verify downloaded
+content against the `size`, `media_type` and SHA-256 returned by the listing; do not infer formats
+from filenames. The service may produce `report.html`, `result.json`,
+`data_dictionary.json`, `model_comparison.csv`, OOF/residual/calibration files,
+`search_space.json`, `candidate_predictions.csv`, `shortlist.csv`, `recommendation_views.csv`,
+`pareto_front.csv` and `figures/*`.
+
+Common terminal conditions include configuration/file-format errors, a missing target or
+candidate space, upload/row/candidate-count limits being exceeded, an unready backend, or a
+missing job or artifact. Do not retry blindly after a submission timeout or disconnection: a
+multipart upload may already have created a job, so first check whether a `job_id` was returned.
+Do not replace a failure or empty recommendation with local regression, GP, random numbers or a
+manual ranking.

package/skills/delta-science/references/pubchem.md

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+# PubChem reference
+
+Call this tool only through `delta-cli science invoke`. Business responses are in the top-level
+CLI `data`; read only the fields described here and do not search recursively. URLs in this file
+explain the endpoint schema and do not authorise direct HTTP access. For a basic lookup by a
+single common name, call `compound-summary` once. For multiple names, call
+`compound-batch-summary` once with a default body containing only `identifiers` and
+`namespace:"name"`; do not call health or schema first.
+
+Project results directly from `data`. Batch records are in `data.results[*]`, the original label
+is in `input`, and properties are nested under `properties`. Use this fixed SMILES fallback
+order: `CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`. Do not treat PubChem
+`XLogP` and RDKit `MolLogP` as interchangeable; do not fill a `not_found` result with local
+calculations.
+
+Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
+
+## Health
+
+Operation: `health`; no request body.
+
+## Resolve CIDs
+
+Operation: `compound-resolve-cids`.
+
+```json
+{"identifier": "aspirin", "namespace": "name", "max_records": 20}
+```
+
+`max_records`: 1-100.
+
+## Properties
+
+Operation: `compound-properties`.
+
+```json
+{
+  "identifier": "2244",
+  "namespace": "cid",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"]
+}
+```
+
+Allowed properties include `MolecularFormula`, `MolecularWeight`,
+`CanonicalSMILES`, `IsomericSMILES`, `SMILES`, `ConnectivitySMILES`,
+`IUPACName`, `InChI`, `InChIKey`, `XLogP`, `TPSA`, `HBondDonorCount`,
+`HBondAcceptorCount`, `RotatableBondCount`, `ExactMass`, `MonoisotopicMass`,
+`Charge`, `HeavyAtomCount`, `Complexity`, `CovalentUnitCount`,
+`DefinedAtomStereoCount`, `UndefinedAtomStereoCount`, `DefinedBondStereoCount`,
+`UndefinedBondStereoCount`, and `IsotopeAtomCount`.
+
+## Synonyms
+
+Operation: `compound-synonyms`.
+
+```json
+{"identifier": "2244", "namespace": "cid", "max_synonyms": 50}
+```
+
+`max_synonyms`: 1-500.
+
+## Summary
+
+Operation: `compound-summary`.
+
+```json
+{
+  "identifier": "aspirin",
+  "namespace": "name",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"],
+  "synonym_limit": 20
+}
+```
+
+`synonym_limit`: 0-100. Use this endpoint for general compound lookup because
+it resolves CID, selected properties, and synonyms in one call.
+
+Response fields include `valid`, `cid`, `properties`, `properties_raw`,
+`aliases`, `synonyms`, and `metadata`. Numeric properties are coerced to JSON
+numbers when possible. Requested SMILES aliases are filled when PubChem returns
+an equivalent key such as `ConnectivitySMILES`.
+
+## Batch Summary
+
+Operation: `compound-batch-summary`.
+
+```json
+{
+  "identifiers": ["aspirin", "ibuprofen", "caffeine"],
+  "namespace": "name",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "XLogP", "TPSA"],
+  "synonym_limit": 5
+}
+```
+
+Limits: 1-100 identifiers. The response preserves input order and includes
+per-item errors:
+
+```json
+{
+  "valid": false,
+  "namespace": "name",
+  "properties_requested": ["CanonicalSMILES"],
+  "results": [
+    {
+      "input": "aspirin",
+      "valid": true,
+      "cid": 2244,
+      "properties": {
+        "CanonicalSMILES": "CC(=O)Oc1ccccc1C(=O)O",
+        "ConnectivitySMILES": "CC(=O)Oc1ccccc1C(=O)O",
+        "_aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
+        "properties_raw": {}
+      },
+      "properties_raw": {},
+      "aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
+      "synonyms": []
+    },
+    {
+      "input": "bad-name",
+      "valid": false,
+      "error": "not found"
+    }
+  ],
+  "count": 2,
+  "failed_count": 1
+}
+```