@delta-infra/cli 1.0.80 → 1.0.81

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

@@ -1,116 +1,116 @@
-# GSAS-II 详细规则
-
-所有调用只走统一 wrapper。模拟必须使用真实 CIF；精修必须使用真实 powder data、
-instrument parameters 和 phase CIF，任何失败不得用合成数据补齐。输入不是 CIF 时，
-先使用当前任务中成功的 pymatgen `structure-convert` 结果。
-
-## Health
-
-operation：`health`，无 body。
-
-Key response fields in `data`: `status`, `service`, `gsasii_available`,
-`metadata`, and `limits`.
-
-只有用户明确要求健康检查时才调用；不要在模拟或精修前自动增加 health。
-
-## 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.
-
-## 跨工具交接
-
-结构转换、衍射模拟和精修必须在本 Skill 内通过 wrapper 逐步完成：
-`pymatgen structure-convert -> gsasii powder-simulate/powder-refine`。下游只使用上一步
-成功 native 中的结构文本或 profile；不得执行本地脚本或直连服务。
+# GSAS-II 详细规则
+
+所有调用只走统一 wrapper。模拟必须使用真实 CIF；精修必须使用真实 powder data、
+instrument parameters 和 phase CIF，任何失败不得用合成数据补齐。输入不是 CIF 时，
+先使用当前任务中成功的 pymatgen `structure-convert` 结果。
+
+## Health
+
+operation：`health`，无 body。
+
+Key response fields in `data`: `status`, `service`, `gsasii_available`,
+`metadata`, and `limits`.
+
+只有用户明确要求健康检查时才调用；不要在模拟或精修前自动增加 health。
+
+## 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.
+
+## 跨工具交接
+
+结构转换、衍射模拟和精修必须在本 Skill 内通过 wrapper 逐步完成：
+`pymatgen structure-convert -> gsasii powder-simulate/powder-refine`。下游只使用上一步
+成功 native 中的结构文本或 profile；不得执行本地脚本或直连服务。

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

@@ -1,66 +1,66 @@
-# LAMMPS 详细规则
-
-所有调用只走统一 wrapper。LAMMPS 不从化学式、CIF 或 POSCAR 自动推断 data、原子
-类型、势函数与边界条件。成功执行不表示物理收敛或生产可用。
-
-## Health
-
-operation：`health`，无 body。
-
-Key response fields in `data`: `status`, `service`, `lammps_available`,
-`metadata`, and `limits`.
-
-只有用户明确要求健康检查时才调用；不要在模拟前自动增加 health。
-
-## 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.
-
-最终只复制当前 native 的 `last_thermo`、final step/temperature/total energy、
-warnings 和用户要求的输出文件摘要。禁止把总能量除以原子数、替换步数、换算单位或
-推测收敛性、稳定性。最小示例必须先调用 `lj-melt-example`，再把其
-`native["request"]` 原样交给 `run`；不得传 wrapper 外层 envelope。
+# LAMMPS 详细规则
+
+所有调用只走统一 wrapper。LAMMPS 不从化学式、CIF 或 POSCAR 自动推断 data、原子
+类型、势函数与边界条件。成功执行不表示物理收敛或生产可用。
+
+## Health
+
+operation：`health`，无 body。
+
+Key response fields in `data`: `status`, `service`, `lammps_available`,
+`metadata`, and `limits`.
+
+只有用户明确要求健康检查时才调用；不要在模拟前自动增加 health。
+
+## 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.
+
+最终只复制当前 native 的 `last_thermo`、final step/temperature/total energy、
+warnings 和用户要求的输出文件摘要。禁止把总能量除以原子数、替换步数、换算单位或
+推测收敛性、稳定性。最小示例必须先调用 `lj-melt-example`，再把其
+`native["request"]` 原样交给 `run`；不得传 wrapper 外层 envelope。

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

@@ -1,130 +1,130 @@
-# LDM-BO 详细规则
-
-所有调用只走统一 wrapper，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
-}
-```
-
+# LDM-BO 详细规则
+
+所有调用只走统一 wrapper，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 native response inside gateway `data`:
-
-```json
-{
-  "recommendations": ["CCC"],
-  "acquisition_values": [0.12],
-  "n_objectives": 1
-}
-```
-
+
+```json
+{
+  "recommendations": ["CCC"],
+  "acquisition_values": [0.12],
+  "n_objectives": 1
+}
+```
+
 LDM methods may include an `llm` diagnostics object.
 
 `acquisition_values` 只能按 native 原值报告。除非当前 native 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 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",
-    "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.
+
+## 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 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",
+    "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.