@delta-infra/cli 1.0.97 → 1.0.99

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

@@ -1,129 +1,129 @@
-# LDM-BO 详细规则
-
-所有调用直接使用 `delta-cli science invoke`，不是本地 PDF2Dock runner。仅用于小分子 SMILES；
-抗体、CDRH3 或 AntBO 场景必须使用 AntBO 能力边界。
-provider、模型路径、Vina/ReaSyn/GPU/LLM 配置由服务端注入，不放入请求 JSON。
-
-## Health
-
-operation：`health`，无 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.
-
-`acquisition_values` 只能按业务响应原值报告。除非当前业务响应明确给出字段定义，否则
-不得把它描述为预测 Vina、预测 objective、不确定性、置信度、expected improvement，
-也不得自行判断“越大/越小越好”。服务未返回推荐理由时，明确写“服务未返回推荐
-理由”，不得根据分子骨架、杂原子或模型机制补写解释。
-
-## 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.
+# LDM-BO 详细规则
+
+所有调用直接使用 `delta-cli science invoke`，不是本地 PDF2Dock runner。仅用于小分子 SMILES；
+抗体、CDRH3 或 AntBO 场景必须使用 AntBO 能力边界。
+provider、模型路径、Vina/ReaSyn/GPU/LLM 配置由服务端注入，不放入请求 JSON。
+
+## Health
+
+operation：`health`，无 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.
+
+`acquisition_values` 只能按业务响应原值报告。除非当前业务响应明确给出字段定义，否则
+不得把它描述为预测 Vina、预测 objective、不确定性、置信度、expected improvement，
+也不得自行判断“越大/越小越好”。服务未返回推荐理由时，明确写“服务未返回推荐
+理由”，不得根据分子骨架、杂原子或模型机制补写解释。
+
+## 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/pubchem.md

@@ -1,126 +1,126 @@
-# PubChem 详细规则
-
-只能通过 `delta-cli science invoke` 调用。本文件中的业务响应位于 CLI 顶层 `data`；
-只按本文件说明读取字段，不得递归搜索。本文件中的 URL 只用于说明 endpoint schema，
-不授权直接 HTTP。普通名称基础查询只调用一次 `compound-summary`；多个名称
-只调用一次 `compound-batch-summary`，默认 body 仅包含 `identifiers` 和
-`namespace:"name"`，不得先调用 health/schema。
-
-结果直接从 `data` 投影。批量记录位于 `data.results[*]`，原始标签在 `input`，
-属性在嵌套 `properties`。SMILES 回退顺序固定为
-`CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`。
-PubChem `XLogP` 与 RDKit `MolLogP` 不得互换；not_found 不得用本地计算补值。
-
-Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
-
-## Health
-
-operation：`health`，无 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
-}
-```
+# PubChem 详细规则
+
+只能通过 `delta-cli science invoke` 调用。本文件中的业务响应位于 CLI 顶层 `data`；
+只按本文件说明读取字段，不得递归搜索。本文件中的 URL 只用于说明 endpoint schema，
+不授权直接 HTTP。普通名称基础查询只调用一次 `compound-summary`；多个名称
+只调用一次 `compound-batch-summary`，默认 body 仅包含 `identifiers` 和
+`namespace:"name"`，不得先调用 health/schema。
+
+结果直接从 `data` 投影。批量记录位于 `data.results[*]`，原始标签在 `input`，
+属性在嵌套 `properties`。SMILES 回退顺序固定为
+`CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`。
+PubChem `XLogP` 与 RDKit `MolLogP` 不得互换；not_found 不得用本地计算补值。
+
+Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
+
+## Health
+
+operation：`health`，无 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
+}
+```

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

@@ -1,68 +1,68 @@
-# pymatgen 详细规则
-
-所有调用直接使用 `delta-cli science invoke`。无机化学式、组成和式量优先使用 pymatgen，不用 PubChem
-或本地元素表替代。结构 operation 必须发送完整结构文本，不能发送本地文件路径；
-支持 `cif`、`poscar`、`json`、`cssr`、`xsf`，不接收 LAMMPS data/dump。
-
-## Health
-
-operation：`health`，无 body。
-
-## Composition Parse
-
-operation：`composition-parse`。
-
-```json
-{"formula": "LiFePO4", "format": "formula"}
-```
-
-Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
-`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
-`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
-`weight_fractions`, `error`.
-
-## Structure Parse / Summary
-
-operation：`structure-parse` 或 `structure-summary`。
-
-```json
-{"input": "<CIF text>", "format": "cif", "primitive": false}
-```
-
-Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-Summary fields include `formula`, `reduced_formula`, `chemical_system`,
-`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
-`species`.
-
-## Structure Convert
-
-operation：`structure-convert`。
-
-```json
-{
-  "input": "<CIF text>",
-  "input_format": "cif",
-  "output_format": "poscar",
-  "primitive": false
-}
-```
-
-Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-## Symmetry
-
-operation：`structure-symmetry`。
-
-```json
-{
-  "input": "<CIF text>",
-  "format": "cif",
-  "primitive": false,
-  "symprec": 0.01,
-  "angle_tolerance": 5.0
-}
-```
-
-Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
-`point_group_symbol`, `hall`, and `nsites`.
+# pymatgen 详细规则
+
+所有调用直接使用 `delta-cli science invoke`。无机化学式、组成和式量优先使用 pymatgen，不用 PubChem
+或本地元素表替代。结构 operation 必须发送完整结构文本，不能发送本地文件路径；
+支持 `cif`、`poscar`、`json`、`cssr`、`xsf`，不接收 LAMMPS data/dump。
+
+## Health
+
+operation：`health`，无 body。
+
+## Composition Parse
+
+operation：`composition-parse`。
+
+```json
+{"formula": "LiFePO4", "format": "formula"}
+```
+
+Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
+`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
+`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
+`weight_fractions`, `error`.
+
+## Structure Parse / Summary
+
+operation：`structure-parse` 或 `structure-summary`。
+
+```json
+{"input": "<CIF text>", "format": "cif", "primitive": false}
+```
+
+Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+Summary fields include `formula`, `reduced_formula`, `chemical_system`,
+`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
+`species`.
+
+## Structure Convert
+
+operation：`structure-convert`。
+
+```json
+{
+  "input": "<CIF text>",
+  "input_format": "cif",
+  "output_format": "poscar",
+  "primitive": false
+}
+```
+
+Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+## Symmetry
+
+operation：`structure-symmetry`。
+
+```json
+{
+  "input": "<CIF text>",
+  "format": "cif",
+  "primitive": false,
+  "symprec": 0.01,
+  "angle_tolerance": 5.0
+}
+```
+
+Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
+`point_group_symbol`, `hall`, and `nsites`.

package/skills/delta-science/references/{qe-dft.md → qe.md}

@@ -4,9 +4,9 @@ QE 用于通过 Chemistry Gateway 执行可追踪的异步 Quantum ESPRESSO 工
 Gateway/Science Server contract，不运行本地 `pw.x`，不调用内部 QE 容器，也不提交 shell
 命令、scheduler 脚本、`pseudo_dir`、`outdir` 或主机路径。
 
-本 reference 的服务路由标签为 `qe`，preflight 中对应的领域 skill 名为 `qe-dft`。
-实际 `tools.name` 与 `tool_endpoints.name` 必须逐字取自当前 CLI catalog。下列路径是 QE
-服务契约，不是可直接访问的 URL，也不是可以自动改写的 endpoint 别名。
+本 reference 对应 CLI 的真实工具为 `qe`。实际 `tools.name` 与 `tool_endpoints.name`
+必须逐字取自当前 CLI catalog。下列路径是 QE 服务契约，不是可直接访问的 URL，也不是
+可以自动改写的 endpoint 别名。
 
 ## 能力分组
 
@@ -21,7 +21,7 @@ Gateway/Science Server contract，不运行本地 `pw.x`，不调用内部 QE
 | `/chem/qe/v1/qe/jobs/{job_id}/events`、`steps`、`logs`、`artifacts` | 读取作业过程和结果 | 只读 |
 | `/chem/qe/v1/qe/jobs/{job_id}:cancel`、`:retry`、`:review` | 取消、重试和科学审核 | 远端变更 |
 
-选择新工具或新 operation 时，依次使用：
+选择新 operation 时，先使用：
 
 ```text
 delta-cli science list