@delta-infra/cli 1.0.75 → 1.0.76

package/README.md

@@ -288,21 +288,37 @@ delta-cli 内置 AI Agent 操作手册（Skills），帮助 Claude Code 等 AI
 # 安装仓库中的全部 Skills
 npx skills add delta-infra/delta-infra-cli -y -g
 
-# 也可以只安装某个 Skill，例如 Science 总控
-npx skills add delta-infra/delta-infra-cli -s delta-science
+# 也可以只安装某个具名服务 Skill，例如 PubChem
+npx skills add delta-infra/delta-infra-cli -s pubchem
 ```
 
 Skill 文件位于 `skills/` 目录：
 - `delta-shared/` — 全局通用规则（认证、配置、错误处理）
 - `delta-sandbox/` — Sandbox 操作指南（生命周期、命令路由）
-- `delta-science/` — Science 总控、跨服务编排、统一 Delta CLI wrapper
+- `delta-science/` — 具名 Science Skill 共用的编排参考与 Delta CLI wrapper
 - `pubchem/`、`rdkit/`、`pymatgen/` — 化合物与材料基础计算
 - `gsasii/`、`lammps/` — 衍射和分子动力学
 - `delta-bo/`、`ldm-bo/`、`synbo-service/` — 科学优化流程
 - `antbo-service/`、`antbo-ldm-guard/` — AntBO 作业与未暴露 LDM 请求保护
 
-一键安装、升级和卸载会同步上述完整集合；具名服务 Skill 负责参数契约，
-`delta-science` 负责从简短的人类科研请求中选择服务并组织数据交接。
+一键安装、升级和卸载会同步上述完整集合。Memento 等宿主在规划阶段直接选择具名
+服务 Skill；`delta-science` 只提供共享调用契约和跨步骤数据交接规则，不直接承接
+普通用户步骤。Science Skill 仅暴露 `read_file`、`python_repl` 和 `step_finish` 等
+完成任务所需的最小工具集合。
+
+### 添加 Science tool 或 operation
+
+`skills/science-tools.json` 是规范 tool、operation、legacy endpoint、Skill 清单和 npm
+打包目录的唯一配置源。修改后运行：
+
+```bash
+node scripts/generate-science-catalog.js
+node scripts/generate-science-catalog.js --check
+```
+
+生成器会同步 Go catalog、Python wrapper 映射、`skills/manifest.json`、npm `files`
+清单及 catalog 参考文档。给现有服务增加 operation 时不需要创建新 Skill；只有新增
+具有独立用户意图和参数契约的服务时，才新增一个服务级 Skill 目录。
 
 ## 开发
 
@@ -388,7 +404,7 @@ make release
 ```bash
 export GH_TOKEN=<your-github-pat>
 export NPM_TOKEN=<your-npm-token>
-./release.sh v1.0.75
+./release.sh v1.0.76
 ```
 
 脚本执行步骤：
@@ -396,7 +412,7 @@ export NPM_TOKEN=<your-npm-token>
 2. 使用 Docker + `make release` 交叉编译 5 个平台二进制文件。
 3. 在 `bin/` 目录生成 `.tar.gz` / `.zip` 归档。
 4. 通过 `.ci/publish-github-release.js` 创建 GitHub Release 并上传资产。
-5. 同步 `package.json` 与 `scripts/install.js` 到公开仓库 `yzailab/delta-infra-cli`。
+5. 同步 npm 脚本、README 与全部 Skills 到公开仓库 `yzailab/delta-infra-cli`。
 6. 执行 `npm publish --access public` 发布 `@delta-infra/cli`。
 
 需要提前安装 `gh` CLI、Node.js/npm，并配置 `GH_TOKEN` 与 `NPM_TOKEN`。CI 流程可参考 `.gitlab-ci.yml`。

package/checksums.txt

@@ -1,5 +1,5 @@
-b70320aa2f2a5cff600a4f9b10240e586650efc157bc455e6edfcd76e57354af *delta-cli-darwin-amd64.tar.gz
-9a6821279d9e61115e9a4444bcdad2db29a524f75e6d3ecc694e903dc09bbe65 *delta-cli-darwin-arm64.tar.gz
-ba142ae01ab832a0b950ba88e27fdf92d06483021d43ea9c1932966434f3dab1 *delta-cli-linux-amd64.tar.gz
-46df3385a51d36affbbeb984fb26f1cb38762a7957f03c70cddf951dee7bedf6 *delta-cli-linux-arm64.tar.gz
-14279afab95f712f706ee19061cffe88786fb7a2202764c05f7680f0779873d2 *delta-cli-windows-amd64.zip
+ef1d8380dc3490bfc6a20a0d9d375a7fa4296b6f6054b0476f7c230ca4f1928c  delta-cli-darwin-amd64.tar.gz
+a7cdcb28ada4df83bb2c9e58635b97fd10af526e9cbb71a35e5536ff72a4b7fd  delta-cli-darwin-arm64.tar.gz
+e0002c8e7416d8ee3c5a5676edbcaaaa4b04364b308bb7158b3970e6600b8926  delta-cli-linux-amd64.tar.gz
+23739e55285ae3080a707a9d12c27460a6ca57def2cb48c9ce7d227443e560e3  delta-cli-linux-arm64.tar.gz
+166f5ff32925daca82cf8ae76bf59a00014238d22a1aa3defb81d587103dc951  delta-cli-windows-amd64.zip

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@delta-infra/cli",
-  "version": "1.0.75",
+  "version": "1.0.76",
   "description": "Delta Infra CLI for sandbox compute and science tools.",
   "bin": {
     "delta-cli": "scripts/run.js"
@@ -14,6 +14,7 @@
     "scripts/install-wizard.js",
     "scripts/run.js",
     "skills/manifest.json",
+    "skills/science-tools.json",
     "skills/delta-sandbox/",
     "skills/delta-shared/",
     "skills/delta-science/",

package/skills/antbo-ldm-guard/SKILL.md

@@ -1,7 +1,11 @@
 ---
-name: antbo-ldm-guard
-description: 任何同时涉及 AntBO/抗体/CDRH3 与 LDM/suggest/下一条候选序列的请求都必须优先于所有其他 AntBO Skill 立即使用本 Skill，即使历史序列或评分尚未提供。当前 Delta CLI catalog 未暴露 AntBO LDM initialize/evaluate/suggest；唯一正确结果是说明未发送远端请求，禁止询问数据、建文件、调用 health/Science/filesystem 或改用小分子 LDM-BO。
----
+name: antbo-ldm-guard
+description: 任何同时涉及 AntBO/抗体/CDRH3 与 LDM/suggest/下一条候选序列的请求都必须优先于所有其他 AntBO Skill 立即使用本 Skill，即使历史序列或评分尚未提供。当前 Delta CLI catalog 未暴露 AntBO LDM initialize/evaluate/suggest；唯一正确结果是说明未发送远端请求，禁止询问数据、建文件、调用 health/Science/filesystem 或改用小分子 LDM-BO。
+metadata:
+  allowed-tools:
+    - python_repl
+    - step_finish
+---
 
 # AntBO LDM 能力边界
 

package/skills/antbo-ldm-guard/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "AntBO LDM ????"
-  short_description: "????? Delta CLI ??? AntBO LDM ????"
-  default_prompt: "?? $antbo-ldm-guard ???? AntBO LDM ?????? Delta CLI ???"
+  display_name: "AntBO LDM 能力边界"
+  short_description: "识别当前 CLI 未暴露的 AntBO LDM 候选请求并安全终止"
+  default_prompt: "使用 $antbo-ldm-guard 判断这项 AntBO LDM 请求是否可执行。"

package/skills/antbo-service/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: antbo-service
-description: 当用户明确要求检查 AntBO 服务健康状态、启动默认或自定义 AntBO 作业、读取 AntBO 日志、列出活动作业或停止指定作业时使用。当前 Delta CLI operation 为 health、run-default-job、run、log、jobs、stop。
----
+name: antbo-service
+description: 当用户明确要求检查 AntBO 服务健康状态、启动默认或自定义 AntBO 作业、读取 AntBO 日志、列出活动作业或停止指定作业时使用。当前 Delta CLI operation 为 health、run-default-job、run、log、jobs、stop。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # AntBO 服务
 

package/skills/antbo-service/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "AntBO ????"
-  short_description: "?? Delta CLI ???????? AntBO ??????"
-  default_prompt: "?? $antbo-service ??????? AntBO ???????"
+  display_name: "AntBO 抗体优化服务"
+  short_description: "通过 Delta CLI 启动、查询或停止 AntBO 优化作业"
+  default_prompt: "使用 $antbo-service 执行这项 AntBO 作业管理任务。"

package/skills/delta-bo/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: delta-bo
-description: 当用户需要列出当前 Delta-BO 命令，或针对数值、整数、分类实验变量生成随机搜索/贝叶斯优化建议时使用。当前 Delta CLI catalog 只暴露 commands 与 generate；不得通过 Skill 猜测或直连旧的 stateful command API。
----
+name: delta-bo
+description: 当用户需要列出当前 Delta-BO 命令，或针对数值、整数、分类实验变量生成随机搜索/贝叶斯优化建议时使用。当前 Delta CLI catalog 只暴露 commands 与 generate；不得通过 Skill 猜测或直连旧的 stateful command API。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # Delta-BO 服务
 

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

@@ -1,4 +1,4 @@
 interface:
-  display_name: "Delta-BO ????"
-  short_description: "?? Delta CLI ???????????????"
-  default_prompt: "?? $delta-bo ??????????????????"
+  display_name: "Delta-BO 实验优化"
+  short_description: "通过 Delta CLI 为数值、整数和分类变量生成实验建议"
+  default_prompt: "使用 $delta-bo 根据变量空间生成下一批实验建议。"

package/skills/delta-sandbox/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "Delta Sandbox ????"
-  short_description: "?? Delta CLI ???????????????????"
-  default_prompt: "?? $delta-sandbox ???????????????"
+  display_name: "Delta Sandbox 工作站"
+  short_description: "通过 Delta CLI 安全创建、运行并销毁隔离计算工作站"
+  default_prompt: "使用 $delta-sandbox 在隔离工作站中完成这项计算并返回结果。"

package/skills/delta-science/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: delta-science
-description: "用于所有涉及化合物、材料、衍射、分子动力学、贝叶斯优化、反应条件或抗体优化的 Science 任务，包括简短、模糊的人类请求。每个实时操作必须选择具名 Science service Skill，并由 python_repl 执行本 Skill 的 invoke.py 走 Delta CLI；禁止通用子代理、Bash、目录探测、直接 HTTP、字面 CLI 命令和 native.data。AntBO/CDRH3 LDM 请求先判断 catalog，不得先问数据或派发 filesystem。"
----
+name: delta-science
+description: "Delta Science 的内部共享运行时与跨服务编排参考。不要把普通用户步骤直接路由到本 Skill；规划器必须按科学目标选择 pubchem、rdkit、pymatgen、gsasii、lammps、delta-bo、ldm-bo、synbo-service、antbo-service 或 antbo-ldm-guard，并把跨服务任务拆成具名 Skill 步骤。"
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # Delta Science
 

package/skills/delta-science/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "Delta Science ????"
-  short_description: "?? Delta CLI ?????????? Science ????"
-  default_prompt: "?? $delta-science ?? Delta CLI ?????????"
+  display_name: "Delta Science 公共运行时"
+  short_description: "为具名 Science Skill 提供共享 CLI 调用和交接契约"
+  default_prompt: "使用 $delta-science 规划跨服务 Science 流程并拆分为具名 Skill 步骤。"

package/skills/delta-science/references/generated-catalog.md

@@ -0,0 +1,48 @@
+# Science catalog（自动生成）
+
+本文件由 `skills/science-tools.json` 生成；不要手工修改。规范名称供 CLI/Skill 使用，legacy 名称仅用于兼容已部署的 `/science_tool` catalog。
+
+| 规范 tool | Skill | 类别 | operation | legacy endpoint |
+| --- | --- | --- | --- | --- |
+| pubchem | pubchem | molecule-information | health | chem_pubchem_health |
+| pubchem | pubchem | molecule-information | compound-resolve-cids | chem_pubchem_compound_resolve-cids |
+| pubchem | pubchem | molecule-information | compound-properties | chem_pubchem_compound_properties |
+| pubchem | pubchem | molecule-information | compound-synonyms | chem_pubchem_compound_synonyms |
+| pubchem | pubchem | molecule-information | compound-summary | chem_pubchem_compound_summary |
+| pubchem | pubchem | molecule-information | compound-batch-summary | chem_pubchem_compound_batch-summary |
+| rdkit | rdkit | cheminformatics | health | chem_rdkit_health |
+| rdkit | rdkit | cheminformatics | parse | chem_rdkit_parse |
+| rdkit | rdkit | cheminformatics | descriptors | chem_rdkit_descriptors |
+| rdkit | rdkit | cheminformatics | batch-descriptors | chem_rdkit_batch-descriptors |
+| rdkit | rdkit | cheminformatics | batch-parse-describe | chem_rdkit_batch-parse-describe |
+| rdkit | rdkit | cheminformatics | render | chem_rdkit_render |
+| rdkit | rdkit | cheminformatics | fingerprint | chem_rdkit_fingerprint |
+| rdkit | rdkit | cheminformatics | similarity | chem_rdkit_similarity |
+| rdkit | rdkit | cheminformatics | similarity-matrix | chem_rdkit_similarity-matrix |
+| rdkit | rdkit | cheminformatics | substructure | chem_rdkit_substructure |
+| pymatgen | pymatgen | materials-informatics | health | chem_pymatgen_health |
+| pymatgen | pymatgen | materials-informatics | composition-parse | chem_pymatgen_composition_parse |
+| pymatgen | pymatgen | materials-informatics | structure-parse | chem_pymatgen_structure_parse |
+| pymatgen | pymatgen | materials-informatics | structure-summary | chem_pymatgen_structure_summary |
+| pymatgen | pymatgen | materials-informatics | structure-convert | chem_pymatgen_structure_convert |
+| pymatgen | pymatgen | materials-informatics | structure-symmetry | chem_pymatgen_structure_symmetry |
+| gsasii | gsasii | diffraction | health | chem_gsasii_health |
+| gsasii | gsasii | diffraction | powder-simulate | chem_gsasii_powder_simulate |
+| gsasii | gsasii | diffraction | powder-refine | chem_gsasii_powder_refine |
+| lammps | lammps | molecular-dynamics | health | chem_lammps_health |
+| lammps | lammps | molecular-dynamics | lj-melt-example | chem_lammps_examples_lj-melt |
+| lammps | lammps | molecular-dynamics | run | chem_lammps_run |
+| delta-bo | delta-bo | optimization | commands | chem_delta-bo_commands |
+| delta-bo | delta-bo | optimization | generate | chem_delta-bo_generate |
+| ldm-bo | ldm-bo | molecule-optimization | health | chem_ldm-bo_health |
+| ldm-bo | ldm-bo | molecule-optimization | recommend | chem_ldm-bo_recommend |
+| ldm-bo | ldm-bo | molecule-optimization | trajectory | chem_ldm-bo_trajectory |
+| synbo | synbo-service | reaction-optimization | health | chem_synbo_health |
+| synbo | synbo-service | reaction-optimization | initialize | chem_synbo_initialize |
+| synbo | synbo-service | reaction-optimization | optimize | chem_synbo_optimize |
+| antbo | antbo-service | antibody-optimization | health | biology_antbo_health |
+| antbo | antbo-service | antibody-optimization | run-default-job | biology_antbo_run_default_job |
+| antbo | antbo-service | antibody-optimization | run | biology_antbo_run |
+| antbo | antbo-service | antibody-optimization | log | biology_antbo_log |
+| antbo | antbo-service | antibody-optimization | jobs | biology_antbo_jobs |
+| antbo | antbo-service | antibody-optimization | stop | biology_antbo_stop |

package/skills/delta-science/scripts/generated_catalog.py

@@ -0,0 +1,69 @@
+"""Generated Science catalog aliases. Do not edit by hand."""
+
+LEGACY_TOOL_ALIASES = {
+    "synbo": "synbo-service",
+    "antbo": "antbo-service",
+}
+
+LEGACY_ENDPOINTS = {
+    "pubchem": {
+        "health": "chem_pubchem_health",
+        "compound-resolve-cids": "chem_pubchem_compound_resolve-cids",
+        "compound-properties": "chem_pubchem_compound_properties",
+        "compound-synonyms": "chem_pubchem_compound_synonyms",
+        "compound-summary": "chem_pubchem_compound_summary",
+        "compound-batch-summary": "chem_pubchem_compound_batch-summary",
+    },
+    "rdkit": {
+        "health": "chem_rdkit_health",
+        "parse": "chem_rdkit_parse",
+        "descriptors": "chem_rdkit_descriptors",
+        "batch-descriptors": "chem_rdkit_batch-descriptors",
+        "batch-parse-describe": "chem_rdkit_batch-parse-describe",
+        "render": "chem_rdkit_render",
+        "fingerprint": "chem_rdkit_fingerprint",
+        "similarity": "chem_rdkit_similarity",
+        "similarity-matrix": "chem_rdkit_similarity-matrix",
+        "substructure": "chem_rdkit_substructure",
+    },
+    "pymatgen": {
+        "health": "chem_pymatgen_health",
+        "composition-parse": "chem_pymatgen_composition_parse",
+        "structure-parse": "chem_pymatgen_structure_parse",
+        "structure-summary": "chem_pymatgen_structure_summary",
+        "structure-convert": "chem_pymatgen_structure_convert",
+        "structure-symmetry": "chem_pymatgen_structure_symmetry",
+    },
+    "gsasii": {
+        "health": "chem_gsasii_health",
+        "powder-simulate": "chem_gsasii_powder_simulate",
+        "powder-refine": "chem_gsasii_powder_refine",
+    },
+    "lammps": {
+        "health": "chem_lammps_health",
+        "lj-melt-example": "chem_lammps_examples_lj-melt",
+        "run": "chem_lammps_run",
+    },
+    "delta-bo": {
+        "commands": "chem_delta-bo_commands",
+        "generate": "chem_delta-bo_generate",
+    },
+    "ldm-bo": {
+        "health": "chem_ldm-bo_health",
+        "recommend": "chem_ldm-bo_recommend",
+        "trajectory": "chem_ldm-bo_trajectory",
+    },
+    "synbo": {
+        "health": "chem_synbo_health",
+        "initialize": "chem_synbo_initialize",
+        "optimize": "chem_synbo_optimize",
+    },
+    "antbo": {
+        "health": "biology_antbo_health",
+        "run-default-job": "biology_antbo_run_default_job",
+        "run": "biology_antbo_run",
+        "log": "biology_antbo_log",
+        "jobs": "biology_antbo_jobs",
+        "stop": "biology_antbo_stop",
+    },
+}

package/skills/delta-science/scripts/invoke.py

@@ -12,78 +12,12 @@ import subprocess
 import sys
 import time
 from typing import Any
-from urllib.parse import urlsplit
-
-
-SKILL_DIR = Path(__file__).resolve().parents[1]
-
-LEGACY_TOOL_ALIASES = {
-    "antbo": "antbo-service",
-    "synbo": "synbo-service",
-}
-
-LEGACY_ENDPOINTS = {
-    "pubchem": {
-        "health": "chem_pubchem_health",
-        "compound-resolve-cids": "chem_pubchem_compound_resolve-cids",
-        "compound-properties": "chem_pubchem_compound_properties",
-        "compound-synonyms": "chem_pubchem_compound_synonyms",
-        "compound-summary": "chem_pubchem_compound_summary",
-        "compound-batch-summary": "chem_pubchem_compound_batch-summary",
-    },
-    "rdkit": {
-        "health": "chem_rdkit_health",
-        "parse": "chem_rdkit_parse",
-        "descriptors": "chem_rdkit_descriptors",
-        "batch-descriptors": "chem_rdkit_batch-descriptors",
-        "batch-parse-describe": "chem_rdkit_batch-parse-describe",
-        "render": "chem_rdkit_render",
-        "fingerprint": "chem_rdkit_fingerprint",
-        "similarity": "chem_rdkit_similarity",
-        "similarity-matrix": "chem_rdkit_similarity-matrix",
-        "substructure": "chem_rdkit_substructure",
-    },
-    "pymatgen": {
-        "health": "chem_pymatgen_health",
-        "composition-parse": "chem_pymatgen_composition_parse",
-        "structure-parse": "chem_pymatgen_structure_parse",
-        "structure-summary": "chem_pymatgen_structure_summary",
-        "structure-convert": "chem_pymatgen_structure_convert",
-        "structure-symmetry": "chem_pymatgen_structure_symmetry",
-    },
-    "gsasii": {
-        "health": "chem_gsasii_health",
-        "powder-simulate": "chem_gsasii_powder_simulate",
-        "powder-refine": "chem_gsasii_powder_refine",
-    },
-    "lammps": {
-        "health": "chem_lammps_health",
-        "lj-melt-example": "chem_lammps_examples_lj-melt",
-        "run": "chem_lammps_run",
-    },
-    "delta-bo": {
-        "commands": "chem_delta-bo_commands",
-        "generate": "chem_delta-bo_generate",
-    },
-    "ldm-bo": {
-        "health": "chem_ldm-bo_health",
-        "recommend": "chem_ldm-bo_recommend",
-        "trajectory": "chem_ldm-bo_trajectory",
-    },
-    "synbo": {
-        "health": "chem_synbo_health",
-        "initialize": "chem_synbo_initialize",
-        "optimize": "chem_synbo_optimize",
-    },
-    "antbo": {
-        "health": "biology_antbo_health",
-        "run-default-job": "biology_antbo_run_default_job",
-        "run": "biology_antbo_run",
-        "log": "biology_antbo_log",
-        "jobs": "biology_antbo_jobs",
-        "stop": "biology_antbo_stop",
-    },
-}
+from urllib.parse import urlsplit
+
+from generated_catalog import LEGACY_ENDPOINTS, LEGACY_TOOL_ALIASES
+
+
+SKILL_DIR = Path(__file__).resolve().parents[1]
 
 
 def _json_object(raw: str | None, flag: str) -> dict[str, Any] | None:

package/skills/delta-shared/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "Delta CLI ?????"
-  short_description: "?? Delta CLI ??????????????????"
-  default_prompt: "?? $delta-shared ???? Delta CLI ????????"
+  display_name: "Delta CLI 共享规则"
+  short_description: "处理 Delta CLI 的配置、认证、错误与安全边界"
+  default_prompt: "使用 $delta-shared 检查并处理 Delta CLI 的配置或认证问题。"

package/skills/gsasii/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: gsasii
-description: 当用户要求使用真实 CIF 模拟粉末 XRD/中子衍射，或使用真实粉末数据、仪器参数与相模型执行 GSAS-II Rietveld 精修时使用。所有实时请求只走 Delta CLI wrapper；禁止伪造 CIF、粉末数据或仪器文件。
----
+name: gsasii
+description: 当用户要求使用真实 CIF 模拟粉末 XRD/中子衍射，或使用真实粉末数据、仪器参数与相模型执行 GSAS-II Rietveld 精修时使用。所有实时请求只走 Delta CLI wrapper；禁止伪造 CIF、粉末数据或仪器文件。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # GSAS-II 服务
 

package/skills/gsasii/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "GSAS-II ????"
-  short_description: "?? Delta CLI ???????????????"
-  default_prompt: "?? $gsasii ??????????????"
+  display_name: "GSAS-II 衍射分析"
+  short_description: "通过 Delta CLI 进行粉末衍射模拟或 Rietveld 精修"
+  default_prompt: "使用 $gsasii 完成这项粉末衍射模拟或精修任务。"

package/skills/lammps/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: lammps
-description: 当用户要求检查 LAMMPS 服务、运行部署自带的有界 LJ melt 示例，或使用明确的 LAMMPS input/data/force-field 配置执行分子动力学、最小化并读取 thermo/log/dump/data 输出时使用。所有实时调用只走 Delta CLI；成功执行不代表物理收敛或生产可用。
----
+name: lammps
+description: 当用户要求检查 LAMMPS 服务、运行部署自带的有界 LJ melt 示例，或使用明确的 LAMMPS input/data/force-field 配置执行分子动力学、最小化并读取 thermo/log/dump/data 输出时使用。所有实时调用只走 Delta CLI；成功执行不代表物理收敛或生产可用。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # LAMMPS 服务
 

package/skills/lammps/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "LAMMPS ?????"
-  short_description: "?? Delta CLI ?????????????????"
-  default_prompt: "?? $lammps ???????????????????"
+  display_name: "LAMMPS 分子动力学"
+  short_description: "通过 Delta CLI 运行有界分子动力学和能量最小化"
+  default_prompt: "使用 $lammps 运行这项分子动力学任务并报告关键结果。"

package/skills/ldm-bo/SKILL.md

@@ -1,7 +1,12 @@
 ---
-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。
----
+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
 

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

@@ -1,4 +1,4 @@
 interface:
-  display_name: "LDM-BO ????"
-  short_description: "?? Delta CLI ????????????????"
-  default_prompt: "?? $ldm-bo ?????????????????"
+  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/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"
+  ]
+}

package/skills/pubchem/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: pubchem
-description: 当用户给出化学品、分子、药物名称并询问 CID、同义词、分子式、分子量、SMILES、InChI、IUPAC 名、XLogP、TPSA 或供受体数量时使用；也用于在 RDKit 前批量把名称解析为 SMILES。所有实时请求只走 Delta CLI wrapper，并以当前 WORKSPACE_ROOT 下的有界 JSON 作为权威交接产物。
----
+name: pubchem
+description: 当用户给出化学品、分子、药物名称并询问 CID、同义词、分子式、分子量、SMILES、InChI、IUPAC 名、XLogP、TPSA 或供受体数量时使用；也用于在 RDKit 前批量把名称解析为 SMILES。所有实时请求只走 Delta CLI wrapper，并以当前 WORKSPACE_ROOT 下的有界 JSON 作为权威交接产物。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # PubChem 服务
 

package/skills/pubchem/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "PubChem ?????"
-  short_description: "?? Delta CLI ????????????????"
-  default_prompt: "?? $pubchem ????????????????"
+  display_name: "PubChem 化合物查询"
+  short_description: "通过 Delta CLI 查询化合物身份、结构与公共性质"
+  default_prompt: "使用 $pubchem 查询这个化合物的基础身份和分子性质。"

package/skills/pymatgen/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: pymatgen
-description: 当用户需要解析材料化学式与组成、计算式量、解析或总结 CIF/POSCAR/JSON/CSSR/XSF 晶体结构、转换结构格式或分析空间群和对称性时使用。所有实时请求只走 Delta CLI wrapper；无机化学式优先使用本 Skill，不用 PubChem 或本地元素表替代。
----
+name: pymatgen
+description: 当用户需要解析材料化学式与组成、计算式量、解析或总结 CIF/POSCAR/JSON/CSSR/XSF 晶体结构、转换结构格式或分析空间群和对称性时使用。所有实时请求只走 Delta CLI wrapper；无机化学式优先使用本 Skill，不用 PubChem 或本地元素表替代。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # pymatgen 服务
 

package/skills/pymatgen/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "pymatgen ????"
-  short_description: "?? Delta CLI ???????????????"
-  default_prompt: "?? $pymatgen ??????????????"
+  display_name: "pymatgen 材料分析"
+  short_description: "通过 Delta CLI 解析材料组成、晶体结构和空间群"
+  default_prompt: "使用 $pymatgen 分析这个材料的组成或晶体结构。"

package/skills/rdkit/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: rdkit
-description: 当用户需要通过已部署的 Delta Science 服务校验或规范化 SMILES/InChI、计算 RDKit 描述符、指纹、相似度、渲染或子结构筛选时使用。所有实时请求只能由 python_repl 直接执行 delta-science Skill 的 invoke.py；禁止 Bash、目录探测、直接 HTTP、本地 RDKit 和 native.data 路径。
----
+name: rdkit
+description: 当用户需要通过已部署的 Delta Science 服务校验或规范化 SMILES/InChI、计算 RDKit 描述符、指纹、相似度、渲染或子结构筛选时使用。所有实时请求只能由 python_repl 直接执行 delta-science Skill 的 invoke.py；禁止 Bash、目录探测、直接 HTTP、本地 RDKit 和 native.data 路径。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # RDKit 服务
 

package/skills/rdkit/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "RDKit ?????"
-  short_description: "?? Delta CLI ?????????????????"
-  default_prompt: "?? $rdkit ???????????????????"
+  display_name: "RDKit 化学信息学"
+  short_description: "通过 Delta CLI 解析分子并计算描述符、相似度和子结构"
+  default_prompt: "使用 $rdkit 校验这些分子并完成所需的结构计算。"

package/skills/science-tools.json

@@ -0,0 +1,127 @@
+{
+  "schema_version": 1,
+  "base_skills": [
+    "delta-sandbox",
+    "delta-shared",
+    "delta-science"
+  ],
+  "tools": [
+    {
+      "name": "pubchem",
+      "skill": "pubchem",
+      "legacy_tool": "pubchem",
+      "category": "molecule-information",
+      "operations": {
+        "health": "chem_pubchem_health",
+        "compound-resolve-cids": "chem_pubchem_compound_resolve-cids",
+        "compound-properties": "chem_pubchem_compound_properties",
+        "compound-synonyms": "chem_pubchem_compound_synonyms",
+        "compound-summary": "chem_pubchem_compound_summary",
+        "compound-batch-summary": "chem_pubchem_compound_batch-summary"
+      }
+    },
+    {
+      "name": "rdkit",
+      "skill": "rdkit",
+      "legacy_tool": "rdkit",
+      "category": "cheminformatics",
+      "operations": {
+        "health": "chem_rdkit_health",
+        "parse": "chem_rdkit_parse",
+        "descriptors": "chem_rdkit_descriptors",
+        "batch-descriptors": "chem_rdkit_batch-descriptors",
+        "batch-parse-describe": "chem_rdkit_batch-parse-describe",
+        "render": "chem_rdkit_render",
+        "fingerprint": "chem_rdkit_fingerprint",
+        "similarity": "chem_rdkit_similarity",
+        "similarity-matrix": "chem_rdkit_similarity-matrix",
+        "substructure": "chem_rdkit_substructure"
+      }
+    },
+    {
+      "name": "pymatgen",
+      "skill": "pymatgen",
+      "legacy_tool": "pymatgen",
+      "category": "materials-informatics",
+      "operations": {
+        "health": "chem_pymatgen_health",
+        "composition-parse": "chem_pymatgen_composition_parse",
+        "structure-parse": "chem_pymatgen_structure_parse",
+        "structure-summary": "chem_pymatgen_structure_summary",
+        "structure-convert": "chem_pymatgen_structure_convert",
+        "structure-symmetry": "chem_pymatgen_structure_symmetry"
+      }
+    },
+    {
+      "name": "gsasii",
+      "skill": "gsasii",
+      "legacy_tool": "gsasii",
+      "category": "diffraction",
+      "operations": {
+        "health": "chem_gsasii_health",
+        "powder-simulate": "chem_gsasii_powder_simulate",
+        "powder-refine": "chem_gsasii_powder_refine"
+      }
+    },
+    {
+      "name": "lammps",
+      "skill": "lammps",
+      "legacy_tool": "lammps",
+      "category": "molecular-dynamics",
+      "operations": {
+        "health": "chem_lammps_health",
+        "lj-melt-example": "chem_lammps_examples_lj-melt",
+        "run": "chem_lammps_run"
+      }
+    },
+    {
+      "name": "delta-bo",
+      "skill": "delta-bo",
+      "legacy_tool": "delta-bo",
+      "category": "optimization",
+      "operations": {
+        "commands": "chem_delta-bo_commands",
+        "generate": "chem_delta-bo_generate"
+      }
+    },
+    {
+      "name": "ldm-bo",
+      "skill": "ldm-bo",
+      "legacy_tool": "ldm-bo",
+      "category": "molecule-optimization",
+      "operations": {
+        "health": "chem_ldm-bo_health",
+        "recommend": "chem_ldm-bo_recommend",
+        "trajectory": "chem_ldm-bo_trajectory"
+      }
+    },
+    {
+      "name": "synbo",
+      "skill": "synbo-service",
+      "legacy_tool": "synbo-service",
+      "category": "reaction-optimization",
+      "operations": {
+        "health": "chem_synbo_health",
+        "initialize": "chem_synbo_initialize",
+        "optimize": "chem_synbo_optimize"
+      }
+    },
+    {
+      "name": "antbo",
+      "skill": "antbo-service",
+      "legacy_tool": "antbo-service",
+      "category": "antibody-optimization",
+      "operations": {
+        "health": "biology_antbo_health",
+        "run-default-job": "biology_antbo_run_default_job",
+        "run": "biology_antbo_run",
+        "log": "biology_antbo_log",
+        "jobs": "biology_antbo_jobs",
+        "stop": "biology_antbo_stop"
+      }
+    }
+  ],
+  "extra_skills": [
+    "antbo-ldm-guard"
+  ]
+}

package/skills/synbo-service/SKILL.md

@@ -1,7 +1,12 @@
 ---
-name: synbo-service
-description: 当用户需要对分类反应条件空间做初始采样，或基于真实历史反应结果使用 SynBO 推荐下一批催化剂、溶剂、碱等条件时使用。支持 health、initialize、optimize；所有调用只走 Delta CLI，重型 optimize 串行执行且超时不自动重试。
----
+name: synbo-service
+description: 当用户需要对分类反应条件空间做初始采样，或基于真实历史反应结果使用 SynBO 推荐下一批催化剂、溶剂、碱等条件时使用。支持 health、initialize、optimize；所有调用只走 Delta CLI，重型 optimize 串行执行且超时不自动重试。
+metadata:
+  allowed-tools:
+    - read_file
+    - python_repl
+    - step_finish
+---
 
 # SynBO 服务
 

package/skills/synbo-service/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "SynBO ??????"
-  short_description: "?? Delta CLI ????????????????"
-  default_prompt: "?? $synbo-service ??????????????????"
+  display_name: "SynBO 反应条件优化"
+  short_description: "通过 Delta CLI 初始化或优化分类反应条件空间"
+  default_prompt: "使用 $synbo-service 根据历史结果推荐下一批反应条件。"