@delta-infra/cli 1.0.75 → 1.0.77

package/skills/lammps/references/endpoints.md

@@ -1,61 +1,61 @@
-# LAMMPS Endpoint Reference
-
-All paths are relative to `http://111.2.199.31:52317/api/v1`.
-
-## Health
-
-`GET /chem/lammps/health`
-
-Key response fields in `data`: `status`, `service`, `lammps_available`,
-`metadata`, and `limits`.
-
-Use this before long simulations. A healthy service should report
-`data.status == "ok"` and `data.lammps_available == true`.
-
-## Built-In Lennard-Jones Example
-
-`GET /chem/lammps/examples/lj-melt`
-
-Returns a complete `request` payload for `/chem/lammps/run`, plus workflow notes
-showing where pymatgen and GSAS-II fit around LAMMPS.
-
-## Run
-
-`POST /chem/lammps/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.
+# LAMMPS Endpoint Reference
+
+All paths are relative to `http://111.2.199.31:52317/api/v1`.
+
+## Health
+
+`GET /chem/lammps/health`
+
+Key response fields in `data`: `status`, `service`, `lammps_available`,
+`metadata`, and `limits`.
+
+Use this before long simulations. A healthy service should report
+`data.status == "ok"` and `data.lammps_available == true`.
+
+## Built-In Lennard-Jones Example
+
+`GET /chem/lammps/examples/lj-melt`
+
+Returns a complete `request` payload for `/chem/lammps/run`, plus workflow notes
+showing where pymatgen and GSAS-II fit around LAMMPS.
+
+## Run
+
+`POST /chem/lammps/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.

package/skills/ldm-bo/SKILL.md

@@ -1,30 +1,35 @@
----
-name: ldm-bo
-description: 当用户要求对小分子 SMILES 使用 LDM-BO/PDF2Dock、Vina+NN、ReaSyn，生成下一条小分子候选或运行分子 BO trajectory 时使用。不得用于抗体、CDRH3、AntBO 或 /biology/antbo 场景；这些场景必须路由 antbo-service。
----
-
-# 小分子 LDM-BO 服务
-
-## 强制规则
-
-- 只用 `python_repl` 执行 `$SKILLS_ROOT/delta-science/scripts/invoke.py`，
-  tool=`ldm-bo`；禁止 Bash、路径探测、字面 CLI、直接 HTTP 和本地 PDF2Dock。
-- `python_repl` 工具参数只能包含 `code`，禁止 `deps/dependencies/packages`。
-- 业务结果直接位于 `r["native"]`，禁止 `native.data`。
-- provider、模型路径、Vina/ReaSyn/GPU/LLM 配置由服务端注入，不放入请求 JSON。
-- 抗体/CDRH3 即使出现 “LDM” 也禁止调用本 Skill。
-
-## operation 选择
-
-- `health`：检查 PDF2Dock/Vina/ReaSyn/NN/LLM 等部署依赖，无 body。
-- `recommend`：`method`、小分子 `pool`、真实
-  `history:[{smiles,scores}]`、`batch_size`。
-- `trajectory`：保留连字符键 `seed-smiles`、`num-evaluations`、`batch-size`，以及
-  method、seed、objective；有界 smoke 使用 `bo-tanimoto` 和很小 evaluation 数。
-
-详细最小 payload 和 native 响应见 `references/endpoints.md`。缺 Vina、ReaSyn、模型或
-LLM 配置时原样报告后端错误，不切换方法或本地生成候选。
-
-通过 wrapper 调用一次并显式打印有界 native 投影；成功后立即
-`step_finish(status="done", summary=<同一 JSON>)`，失败则
-`step_finish(status="failed", summary=<原始错误短摘要>)`。禁止重试和后续工具。
+---
+name: ldm-bo
+description: 当用户要求对小分子 SMILES 使用 LDM-BO/PDF2Dock、Vina+NN、ReaSyn，生成下一条小分子候选或运行分子 BO trajectory 时使用。不得用于抗体、CDRH3、AntBO 或 /biology/antbo 场景；这些场景必须路由 antbo-service。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
+
+# 小分子 LDM-BO 服务
+
+## 强制规则
+
+- 只用 `python_repl` 执行 `$SKILLS_ROOT/delta-science/scripts/invoke.py`，
+  tool=`ldm-bo`；禁止 Bash、路径探测、字面 CLI、直接 HTTP 和本地 PDF2Dock。
+- `python_repl` 工具参数只能包含 `code`，禁止 `deps/dependencies/packages`。
+- 业务结果直接位于 `r["native"]`，禁止 `native.data`。
+- provider、模型路径、Vina/ReaSyn/GPU/LLM 配置由服务端注入，不放入请求 JSON。
+- 抗体/CDRH3 即使出现 “LDM” 也禁止调用本 Skill。
+
+## operation 选择
+
+- `health`：检查 PDF2Dock/Vina/ReaSyn/NN/LLM 等部署依赖，无 body。
+- `recommend`：`method`、小分子 `pool`、真实
+  `history:[{smiles,scores}]`、`batch_size`。
+- `trajectory`：保留连字符键 `seed-smiles`、`num-evaluations`、`batch-size`，以及
+  method、seed、objective；有界 smoke 使用 `bo-tanimoto` 和很小 evaluation 数。
+
+详细最小 payload 和 native 响应见 `references/endpoints.md`。缺 Vina、ReaSyn、模型或
+LLM 配置时原样报告后端错误，不切换方法或本地生成候选。
+
+通过 wrapper 调用一次并显式打印有界 native 投影；成功后立即
+`step_finish(status="done", summary=<同一 JSON>)`，失败则
+`step_finish(status="failed", summary=<原始错误短摘要>)`。禁止重试和后续工具。

package/skills/ldm-bo/agents/openai.yaml

@@ -1,4 +1,4 @@
-interface:
-  display_name: "LDM-BO ????"
-  short_description: "?? Delta CLI ????????????????"
-  default_prompt: "?? $ldm-bo ?????????????????"
+interface:
+  display_name: "LDM-BO 小分子优化"
+  short_description: "通过 Delta CLI 生成小分子候选或执行分子优化轨迹"
+  default_prompt: "使用 $ldm-bo 为这个小分子任务推荐下一条候选。"

package/skills/ldm-bo/references/endpoints.md

@@ -1,127 +1,127 @@
-# LDM-BO API Endpoint Reference
-
-All paths are relative to `http://111.2.199.31:52317/api/v1`.
-
-This reference is for using the exposed HTTP API. It is not a local PDF2Dock
-runner.
-
-## Health
-
-`GET /chem/ldm-bo/health`
-
-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
-
-`POST /chem/ldm-bo/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 native response inside gateway `data`:
-
-```json
-{
-  "recommendations": ["CCC"],
-  "acquisition_values": [0.12],
-  "n_objectives": 1
-}
-```
-
-LDM methods may include an `llm` diagnostics object.
-
-## Full Trajectory
-
-`POST /chem/ldm-bo/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 native response inside gateway `data`:
-
-```json
-{
-  "config": {},
-  "history": [],
-  "summary": {}
-}
-```
-
-LDM methods may include `llm_trajectory`.
-
-## Error Handling
-
-The service maps native `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",
-    "service_url": "http://ldm-bo-service:8895",
-    "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 wrapper intentionally preserves user payloads and lets `bo_api` own native
-defaults and schema behavior.
+# LDM-BO API Endpoint Reference
+
+All paths are relative to `http://111.2.199.31:52317/api/v1`.
+
+This reference is for using the exposed HTTP API. It is not a local PDF2Dock
+runner.
+
+## Health
+
+`GET /chem/ldm-bo/health`
+
+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
+
+`POST /chem/ldm-bo/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 native response inside gateway `data`:
+
+```json
+{
+  "recommendations": ["CCC"],
+  "acquisition_values": [0.12],
+  "n_objectives": 1
+}
+```
+
+LDM methods may include an `llm` diagnostics object.
+
+## Full Trajectory
+
+`POST /chem/ldm-bo/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 native response inside gateway `data`:
+
+```json
+{
+  "config": {},
+  "history": [],
+  "summary": {}
+}
+```
+
+LDM methods may include `llm_trajectory`.
+
+## Error Handling
+
+The service maps native `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",
+    "service_url": "http://ldm-bo-service:8895",
+    "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 wrapper intentionally preserves user payloads and lets `bo_api` own native
+defaults and schema behavior.

package/skills/manifest.json

@@ -1,17 +1,17 @@
-{
-  "skills": [
-    "delta-sandbox",
-    "delta-shared",
-    "delta-science",
-    "pubchem",
-    "rdkit",
-    "pymatgen",
-    "gsasii",
-    "lammps",
-    "delta-bo",
-    "ldm-bo",
-    "synbo-service",
-    "antbo-service",
-    "antbo-ldm-guard"
-  ]
-}
+{
+  "skills": [
+    "delta-sandbox",
+    "delta-shared",
+    "delta-science",
+    "pubchem",
+    "rdkit",
+    "pymatgen",
+    "gsasii",
+    "lammps",
+    "delta-bo",
+    "ldm-bo",
+    "synbo-service",
+    "antbo-service",
+    "antbo-ldm-guard"
+  ]
+}