@delta-infra/cli 1.1.16 → 1.1.18
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +27 -9
- package/checksums.txt +5 -5
- package/package.json +1 -1
- package/skills/delta-sandbox/SKILL.md +278 -276
- package/skills/delta-sandbox/agents/openai.yaml +3 -3
- package/skills/delta-sandbox/references/commands.md +45 -45
- package/skills/delta-sandbox/references/lifecycle.md +61 -61
- package/skills/delta-sandbox/references/recipes.md +66 -66
- package/skills/delta-science/AGENTS.md +2 -2
- package/skills/delta-science/SKILL.md +181 -139
- package/skills/delta-science/agents/openai.yaml +2 -2
- package/skills/delta-science/references/antbo.md +52 -47
- package/skills/delta-science/references/delta-bo.md +22 -19
- package/skills/delta-science/references/gsasii.md +14 -12
- package/skills/delta-science/references/lammps.md +13 -11
- package/skills/delta-science/references/ldm-bo.md +14 -11
- package/skills/delta-science/references/materials-design.md +80 -68
- package/skills/delta-science/references/pubchem.md +18 -16
- package/skills/delta-science/references/pymatgen.md +10 -9
- package/skills/delta-science/references/qe.md +72 -63
- package/skills/delta-science/references/rdkit.md +22 -19
- package/skills/delta-science/references/strbo.md +44 -36
- package/skills/delta-science/references/synbo.md +30 -27
- package/skills/delta-science/references/xrd.md +197 -186
- package/skills/delta-shared/SKILL.md +60 -58
- package/skills/delta-shared/agents/openai.yaml +3 -3
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# Delta-BO
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# Delta-BO reference
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`commands`
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Make all online calls with `delta-cli science invoke`; the tool is always `delta-bo`. The current
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CLI catalogue exposes only `commands` and `generate`. Do not infer operations from old HTTP
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documentation or call the stateful command API directly.
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## commands
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Use case: The user asks which Delta-BO commands are supported by the current deployment.
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```text
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delta-cli science invoke --tool delta-bo --endpoint commands
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```
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No request body. Report only the command list in the current business response; do not fill it in from historical documentation.
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## generate
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Use case: Generate random-search or Bayesian-optimisation suggestions for numeric, integer or categorical experimental variables.
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When there is no real history, or fewer than five historical observations and the user has not explicitly requested BO, use bounded random search:
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```json
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```
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When real history is available and the user explicitly requests BO, you may use:
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```json
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```
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Supported parameter types are `numeric`, `integer` and `categorical`. Prefer object-form history
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to avoid ambiguity about the order of array columns. Do not invent observations, objective values
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or purported optima.
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Optional deduplication and constraints:
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```json
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}
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```
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`generated_candidate_count`
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Report only fields actually present in the business response: `suggestions`,
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`suggestion_metadata`, `warnings`, `generated_candidate_count` and `diversity`. Do not replace
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empty suggestions or a failure with local GP, UCB or random-number results.
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##
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## Known legacy capabilities that are not exposed
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The old service included stateful commands such as session, space, objective, policy, suggest,
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observe, loop, status and best, but they are not current Delta CLI operations. This Skill records
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only that capability boundary: it includes no URL or curl examples and does not run those
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operations. To extend the interface, first expose the operation and request schema through Science
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Server, then update this reference.
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# GSAS-II
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# GSAS-II reference
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instrument parameters
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Make all calls with `delta-cli science invoke`. Simulation requires a real CIF; refinement
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requires real powder data, instrument parameters and phase CIFs. Never fill in a failed result
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with synthetic data. If the input is not a CIF, first use a successful pymatgen
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`structure-convert` result from the current task.
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## Health
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Operation: `health`; no request body.
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Key response fields in `data`: `status`, `service`, `gsasii_available`,
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`metadata`, and `limits`.
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Call this only when the user explicitly asks for a health check; do not add a health call automatically before simulation or refinement.
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## Powder Simulation
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Operation: `powder-simulate`.
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```json
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## Powder Refinement
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Operation: `powder-refine`.
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- Refinement may return `valid: false` with partial phase/profile information
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if GSAS-II constructed the project but a refinement step failed.
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##
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## Cross-tool hand-off
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`pymatgen structure-convert -> gsasii powder-simulate/powder-refine
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Complete structure conversion, diffraction simulation and refinement step by step through the
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CLI within this Skill: `pymatgen structure-convert -> gsasii powder-simulate/powder-refine`.
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Use downstream only the structure text or profile from the preceding successful business response;
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do not run local scripts or call the service directly.
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# LAMMPS
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# LAMMPS reference
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Make all calls with `delta-cli science invoke`. LAMMPS does not infer data files, atom types,
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potentials or boundary conditions from a formula, CIF or POSCAR. Successful execution does not
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establish physical convergence or production readiness.
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## Health
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Operation: `health`; no request body.
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Key response fields in `data`: `status`, `service`, `lammps_available`,
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`metadata`, and `limits`.
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Call this only when the user explicitly asks for a health check; do not add a health call automatically before simulation.
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## Built-In Lennard-Jones Example
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Operation: `lj-melt-example`.
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Returns a complete `request` payload for the `run` operation, plus workflow notes
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showing where pymatgen and GSAS-II fit around LAMMPS.
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## Run
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Operation: `run`.
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warnings, and a summary of output files requested by the user from the current business response.
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convergence or stability. For the minimal example, call `lj-melt-example` first, then pass its
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`request` from the current business response to `run` unchanged; do not pass the outer CLI envelope.
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# LDM-BO
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# LDM-BO reference
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provider
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for small-molecule SMILES only. Use the AntBO capability boundary for antibody, CDRH3 or AntBO
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tasks. The server injects the provider, model paths and Vina/ReaSyn/GPU/LLM settings; do not put
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interpreter, `bo_api.py`, Vina binary, ReaSyn repo/interpreter/checkpoints, NN
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objective, uncertainty, confidence or expected improvement, and do not infer whether higher or
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lower is better. If the service provides no recommendation rationale, state “The service returned
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no recommendation rationale”; do not add an explanation based on molecular scaffolds, heteroatoms
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or model mechanisms.
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## Full Trajectory
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# Materials Design reference
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Materials Design
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Materials Design builds surrogate models from experimental or computational materials tables,
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validates models, defines feasible candidate spaces, and ranks candidates with uncertainty
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estimates. Recommendations are hypotheses to validate, not confirmed materials, synthesis routes
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or experimental results.
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`tools.name` and `tool_endpoints.name`. The Gateway paths below describe the service contract;
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## Service boundary
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| Service path | Purpose | Result boundary |
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| `/chem/materials-design/health` | Gateway
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| `/chem/materials-design/v1/capabilities` |
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| `/chem/materials-design/health` | Gateway-to-service readiness check | `status`, dependency availability, limits |
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| `/chem/materials-design/v1/capabilities` | Input formats, models, validation modes and limits | Capability catalogue |
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| `/chem/materials-design/v1/jobs` | Upload training/candidate tables and create an asynchronous job | `202`, `job_id`, status and links |
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| `/chem/materials-design/v1/jobs/{job_id}` | Read job status | `status`, `result_status`, result, warnings |
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| `/chem/materials-design/v1/jobs/{job_id}/cancel` | Request cancellation | Cancellation request/final state |
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| `/chem/materials-design/v1/jobs/{job_id}/artifacts` | List artifacts | name, size, media_type, SHA-256 |
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| `/chem/materials-design/v1/jobs/{job_id}/artifacts/{path}` | Download one artifact | Raw report/JSON/CSV/figure bytes |
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```text
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--params '{"job_id":"mdjob_...","artifact_path":"report.html"}' --output report.html
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catalogue, or the catalogue does not return enough request-schema detail, stop and report that it
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is not exposed. Do not guess endpoint names, bodies or compatibility aliases.
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## CLI
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## CLI capability boundaries
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`science file download
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multipart data. Do not disguise a local path or base64 as a file field. Artifact downloads are
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also raw bytes: save and verify them with `science file download`, and do not treat them as
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ordinary JSON results. Do not call `materials-design-service:8900` or connect directly to the
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preflight Gateway.
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## Inputs and configuration
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Before modelling, confirm:
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- `feature_columns
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- identifier
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- `feature_columns`, `controllable_columns`, `target_column` or `objectives`;
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- identifier, metadata, leakage, post-measurement and group/time columns, and their units;
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- objective direction, feasibility constraints, candidate table or candidate-generation rules;
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- missing values, duplicate samples, measurement conditions, data sources and validation split strategy.
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Core fields for a single-objective configuration:
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```json
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{
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}
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```
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`allow_extrapolation
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For multiple objectives, use `objectives: [{"target_column": "...", "direction": "maximize|minimize"}]`
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and explicit Pareto/EHVI settings. Prefer the user's `candidate_file`. If the service generates
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candidates from observed ranges, explicitly preserve steps, hard constraints, composition
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closure, `max_candidates` and `allow_extrapolation`. Do not optimise identifier, post-measurement
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or leakage columns, or out-of-domain points without authorisation. Do not extrapolate arbitrarily
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to fill the candidate count.
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## Results handling
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Assess job `status` and `result_status` separately:
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- `status`: `pending`, `running`, `completed`, `failed` or `cancelled`;
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- `result_status`: `complete`, `exploratory`, `readiness_only` or `failed`.
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`202` means only that the service accepted or queued the job; it does not mean model training is
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complete. `completed` does not mean the ranking is reliable. Say that the data and validation
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support candidate ranking only when `result_status` is `complete`. Treat `exploratory` only as a
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learning hypothesis; for `readiness_only`, read the readiness information and request missing
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inputs; report `failed` as returned. Always preserve the returned validation, ranking, warnings
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and error.
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Keep predictions distinct from observations and cross-validation predictions. At minimum, report
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data coverage, the split, model comparisons, uncertainty calibration, candidate feasibility,
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in-domain/out-of-domain status, EI/PI/UCB or Pareto settings, and the plan for experimental
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validation. Do not present model variance as experimental error or candidate predictions as
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measured values.
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## Artifacts and errors
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Read artifacts only when the user asks for them or the workflow requires them. Verify downloaded
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content against the `size`, `media_type` and SHA-256 returned by the listing; do not infer formats
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from filenames. The service may produce `report.html`, `result.json`,
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`data_dictionary.json`, `model_comparison.csv`, OOF/residual/calibration files,
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`search_space.json`, `candidate_predictions.csv`, `shortlist.csv`, `recommendation_views.csv`,
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+
`pareto_front.csv` and `figures/*`.
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+
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Common terminal conditions include configuration/file-format errors, a missing target or
|
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candidate space, upload/row/candidate-count limits being exceeded, an unready backend, or a
|
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+
missing job or artifact. Do not retry blindly after a submission timeout or disconnection: a
|
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|
+
multipart upload may already have created a job, so first check whether a `job_id` was returned.
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+
Do not replace a failure or empty recommendation with local regression, GP, random numbers or a
|
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+
manual ranking.
|
|
@@ -1,25 +1,27 @@
|
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1
|
-
# PubChem
|
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1
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+
# PubChem reference
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2
2
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3
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7
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-
`
|
|
3
|
+
Call this tool only through `delta-cli science invoke`. Business responses are in the top-level
|
|
4
|
+
CLI `data`; read only the fields described here and do not search recursively. URLs in this file
|
|
5
|
+
explain the endpoint schema and do not authorise direct HTTP access. For a basic lookup by a
|
|
6
|
+
single common name, call `compound-summary` once. For multiple names, call
|
|
7
|
+
`compound-batch-summary` once with a default body containing only `identifiers` and
|
|
8
|
+
`namespace:"name"`; do not call health or schema first.
|
|
8
9
|
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
`CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES
|
|
12
|
-
|
|
10
|
+
Project results directly from `data`. Batch records are in `data.results[*]`, the original label
|
|
11
|
+
is in `input`, and properties are nested under `properties`. Use this fixed SMILES fallback
|
|
12
|
+
order: `CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`. Do not treat PubChem
|
|
13
|
+
`XLogP` and RDKit `MolLogP` as interchangeable; do not fill a `not_found` result with local
|
|
14
|
+
calculations.
|
|
13
15
|
|
|
14
16
|
Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
|
|
15
17
|
|
|
16
18
|
## Health
|
|
17
19
|
|
|
18
|
-
|
|
20
|
+
Operation: `health`; no request body.
|
|
19
21
|
|
|
20
22
|
## Resolve CIDs
|
|
21
23
|
|
|
22
|
-
|
|
24
|
+
Operation: `compound-resolve-cids`.
|
|
23
25
|
|
|
24
26
|
```json
|
|
25
27
|
{"identifier": "aspirin", "namespace": "name", "max_records": 20}
|
|
@@ -29,7 +31,7 @@ operation:`compound-resolve-cids`。
|
|
|
29
31
|
|
|
30
32
|
## Properties
|
|
31
33
|
|
|
32
|
-
|
|
34
|
+
Operation: `compound-properties`.
|
|
33
35
|
|
|
34
36
|
```json
|
|
35
37
|
{
|
|
@@ -49,7 +51,7 @@ Allowed properties include `MolecularFormula`, `MolecularWeight`,
|
|
|
49
51
|
|
|
50
52
|
## Synonyms
|
|
51
53
|
|
|
52
|
-
|
|
54
|
+
Operation: `compound-synonyms`.
|
|
53
55
|
|
|
54
56
|
```json
|
|
55
57
|
{"identifier": "2244", "namespace": "cid", "max_synonyms": 50}
|
|
@@ -59,7 +61,7 @@ operation:`compound-synonyms`。
|
|
|
59
61
|
|
|
60
62
|
## Summary
|
|
61
63
|
|
|
62
|
-
|
|
64
|
+
Operation: `compound-summary`.
|
|
63
65
|
|
|
64
66
|
```json
|
|
65
67
|
{
|
|
@@ -80,7 +82,7 @@ an equivalent key such as `ConnectivitySMILES`.
|
|
|
80
82
|
|
|
81
83
|
## Batch Summary
|
|
82
84
|
|
|
83
|
-
|
|
85
|
+
Operation: `compound-batch-summary`.
|
|
84
86
|
|
|
85
87
|
```json
|
|
86
88
|
{
|
|
@@ -1,16 +1,17 @@
|
|
|
1
|
-
# pymatgen
|
|
1
|
+
# pymatgen reference
|
|
2
2
|
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
3
|
+
Make all calls with `delta-cli science invoke`. Prefer pymatgen for inorganic formulae,
|
|
4
|
+
composition and formula weight; do not use PubChem or a local element table as a substitute.
|
|
5
|
+
Structure operations require the complete structure text, not a local file path. Supported formats
|
|
6
|
+
are `cif`, `poscar`, `json`, `cssr` and `xsf`; LAMMPS data and dump files are not accepted.
|
|
6
7
|
|
|
7
8
|
## Health
|
|
8
9
|
|
|
9
|
-
|
|
10
|
+
Operation: `health`; no request body.
|
|
10
11
|
|
|
11
12
|
## Composition Parse
|
|
12
13
|
|
|
13
|
-
|
|
14
|
+
Operation: `composition-parse`.
|
|
14
15
|
|
|
15
16
|
```json
|
|
16
17
|
{"formula": "LiFePO4", "format": "formula"}
|
|
@@ -23,7 +24,7 @@ Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
|
|
|
23
24
|
|
|
24
25
|
## Structure Parse / Summary
|
|
25
26
|
|
|
26
|
-
|
|
27
|
+
Operation: `structure-parse` or `structure-summary`.
|
|
27
28
|
|
|
28
29
|
```json
|
|
29
30
|
{"input": "<CIF text>", "format": "cif", "primitive": false}
|
|
@@ -37,7 +38,7 @@ Summary fields include `formula`, `reduced_formula`, `chemical_system`,
|
|
|
37
38
|
|
|
38
39
|
## Structure Convert
|
|
39
40
|
|
|
40
|
-
|
|
41
|
+
Operation: `structure-convert`.
|
|
41
42
|
|
|
42
43
|
```json
|
|
43
44
|
{
|
|
@@ -52,7 +53,7 @@ Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
|
|
|
52
53
|
|
|
53
54
|
## Symmetry
|
|
54
55
|
|
|
55
|
-
|
|
56
|
+
Operation: `structure-symmetry`.
|
|
56
57
|
|
|
57
58
|
```json
|
|
58
59
|
{
|