@delta-infra/cli 1.1.1 → 1.1.3

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

@@ -1,198 +1,198 @@
-# SynBO operation 参考
-
-所有在线调用都通过 `delta-cli science invoke`，服务地址来自 CLI 的标准
-`base_url` 派生配置（`{base_url}/science_tool`）。这里的路径只说明业务 operation，不得据此直连 HTTP。
-
-用户说“优化反应条件”“推荐下一批实验”“偶联反应怎么继续做”，或给出溶剂、温度、
-催化剂、碱、配体和历史得率时，即使没有提到 SynBO、BO、CLI 或字段名也使用本节。
-每个用户任务最多一次 SynBO 业务调用；成功后立即结束，validation、502、504、
-timeout、断连或空 recommendations 均不得换参数、换模型或重试。
-
-## Health
-
-operation：`health`，无 body。
-
-Reports SynBO import status, Torch/CUDA runtime availability, service limits,
-default device, and visible CUDA devices.
-
-Important fields inside gateway `data`:
-
-```json
-{
-  "status": "ok",
-  "synbo_available": true,
-  "metadata": {
-    "service": "synbo-service",
-    "engine": "synbo",
-    "version": "0.1.0",
-    "synbo_version": "0.1.0",
-    "default_device": "cpu",
-    "cuda_visible_devices": ""
-  },
-  "limits": {
-    "max_batch_size": 128,
-    "max_reaction_space_size": 200000,
-    "max_previous_rows": 10000
-  },
-  "runtime": {
-    "torch_available": true,
-    "cuda_available": false,
-    "cuda_device_count": 0,
-    "cuda_device_names": []
-  },
-  "warnings": []
-}
-```
-
-## Initialize
-
-operation：`initialize`。
-
-Use for initial condition sampling when no measured previous results exist.
-
-Request body:
-
-```json
-{
-  "condition_dict": {
-    "catalyst": ["Pd(OAc)2", "Pd(PPh3)4", "Pd2(dba)3"],
-    "solvent": ["THF", "Dioxane", "Toluene"],
-    "base": ["K2CO3", "NaOEt", "DBU"]
-  },
-  "opt_metrics": ["yield"],
-  "opt_metric_settings": [
-    {"opt_direct": "max", "opt_range": [0, 100], "metric_weight": 1.0}
-  ],
-  "batch_size": 3,
-  "sampling_method": "random",
-  "desc_normalize": "minmax",
-  "random_seed": 42
-}
-```
-
-Supported `sampling_method` values: `sobol`, `random`, `lhs`, `kmeans`.
-
-## Optimize
-
-operation：`optimize`。
-
-Use after measured experiment rows are available. Each previous row must contain
-all condition columns and all objective metric columns.
-
-Request body:
-
-```json
-{
-  "condition_dict": {
-    "catalyst": ["Pd(OAc)2", "Pd(PPh3)4", "Pd2(dba)3"],
-    "solvent": ["THF", "Dioxane", "Toluene"],
-    "base": ["K2CO3", "NaOEt", "DBU"]
-  },
-  "opt_metrics": ["yield"],
-  "previous_results": [
-    {"batch": 0, "catalyst": "Pd(OAc)2", "solvent": "THF", "base": "K2CO3", "yield": 42.0},
-    {"batch": 0, "catalyst": "Pd(PPh3)4", "solvent": "Dioxane", "base": "NaOEt", "yield": 55.0},
-    {"batch": 0, "catalyst": "Pd2(dba)3", "solvent": "Toluene", "base": "DBU", "yield": 63.0}
-  ],
-  "batch_size": 2,
-  "accuracy": "tiny",
-  "surrogate_model": "RF",
-  "acq_func": "UCB",
-  "device": "cpu",
-  "random_seed": 42
-}
-```
-
-### 数值条件必须先离散化
-
-SynBO 的 `condition_dict` 只接受显式列表，不接受连续范围对象。对于“温度
-40–100°C、催化剂用量 0.5–2.0%”并已有 60/70/80/90°C 与
-0.5/1.0/1.5/2.0% 历史值的任务，使用：
-
-```json
-{
-  "condition_dict": {
-    "solvent": ["ethanol", "acetonitrile", "DMSO"],
-    "temperature_C": ["40", "60", "70", "80", "90", "100"],
-    "catalyst_loading_pct": ["0.5", "1.0", "1.5", "2.0"]
-  },
-  "opt_metrics": ["yield"],
-  "previous_results": [
-    {
-      "batch": 0,
-      "solvent": "ethanol",
-      "temperature_C": "60",
-      "catalyst_loading_pct": "1.0",
-      "yield": 55.0
-    }
-  ],
-  "batch_size": 3,
-  "accuracy": "tiny",
-  "surrogate_model": "RF",
-  "acq_func": "UCB",
-  "device": "cpu",
-  "random_seed": 42
-}
-```
-
-约束：
-
-- 每个条件值统一为字符串，objective metric 保持数值。
-- 每条 `previous_results` 中的条件值必须出现在对应 `condition_dict` 列表中。
-- 连续范围的离散网格必须包含用户上下界和全部历史观测值；最终答案必须说明实际网格。
-- 将条件值显式序列化为字符串，并确保每条历史记录只使用 `condition_dict` 中列出的值。
-  如需小数据 CPU 设置，显式传递 `accuracy:"tiny"`、`surrogate_model:"RF"`、
-  `acq_func:"UCB"` 和 `device:"cpu"`；不得假定客户端会补充默认值。
-
-Useful optional fields:
-
-- `accuracy`: `tiny`, `low`, `medium`, `high`, or `ultra`.
-- `acq_func`: `EHVI`, `UCB`, `ParEGO`, or `NEI`.
-- `surrogate_model`: `GP`, `RF`, `BNN`, or `BayesianLinear`.
-- `device`: `cpu`, `auto`, `cuda`, or `cuda:0`.
-- `cuda_visible_devices`: request-level CUDA visibility hint. Use only when the
-  user explicitly asks for it and `/health` indicates a CUDA-capable runtime.
-- `constraints`: map condition type to prohibited values.
-
-## Descriptors
-
-If omitted, SynBO uses generated OneHot descriptors. To provide descriptors:
-
-```json
-{
-  "descriptors": {
-    "solvent": [
-      {"name": "THF", "polarity": 0.207, "boiling_point_C": 66.0},
-      {"name": "Toluene", "polarity": 0.099, "boiling_point_C": 110.6}
-    ]
-  },
-  "descriptor_index_col": "name"
-}
-```
-
-`descriptors` must contain exactly the same keys as `condition_dict`. Descriptor
-rows must include the configured index column and numeric descriptor columns.
-
-## Error Handling
-
-Gateway errors have the standard envelope:
-
-```json
-{
-  "code": 1,
-  "message": "SynBO service returned HTTP 400",
-  "data": {
-    "endpoint": "/synbo/optimize",
-    "synbo_response": {
-      "detail": "previous_results is missing metric columns: ['yield']"
-    }
-  }
-}
-```
-
-常见原因包括条件空间过大、条件值重复、历史条件值不在 condition_dict 中、
-descriptor 非数值、历史行缺列、metric 非数值，以及无 GPU 时请求 CUDA。
-
-服务端有独立于客户端的单次请求时限。GP、EHVI、高 accuracy 或共享资源繁忙可能导致
-timeout。普通用户任务中不得自动换参数重试；应报告“未产生推荐”，保留本次错误，
-由用户决定是否另起一次明确的回归测试。
+# SynBO operation 参考
+
+所有在线调用都通过 `delta-cli science invoke`，服务地址来自 CLI 的标准
+`base_url` 派生配置（`{base_url}/science_tool`）。这里的路径只说明业务 operation，不得据此直连 HTTP。
+
+用户说“优化反应条件”“推荐下一批实验”“偶联反应怎么继续做”，或给出溶剂、温度、
+催化剂、碱、配体和历史得率时，即使没有提到 SynBO、BO、CLI 或字段名也使用本节。
+每个用户任务最多一次 SynBO 业务调用；成功后立即结束，validation、502、504、
+timeout、断连或空 recommendations 均不得换参数、换模型或重试。
+
+## Health
+
+operation：`health`，无 body。
+
+Reports SynBO import status, Torch/CUDA runtime availability, service limits,
+default device, and visible CUDA devices.
+
+Important fields inside gateway `data`:
+
+```json
+{
+  "status": "ok",
+  "synbo_available": true,
+  "metadata": {
+    "service": "synbo-service",
+    "engine": "synbo",
+    "version": "0.1.0",
+    "synbo_version": "0.1.0",
+    "default_device": "cpu",
+    "cuda_visible_devices": ""
+  },
+  "limits": {
+    "max_batch_size": 128,
+    "max_reaction_space_size": 200000,
+    "max_previous_rows": 10000
+  },
+  "runtime": {
+    "torch_available": true,
+    "cuda_available": false,
+    "cuda_device_count": 0,
+    "cuda_device_names": []
+  },
+  "warnings": []
+}
+```
+
+## Initialize
+
+operation：`initialize`。
+
+Use for initial condition sampling when no measured previous results exist.
+
+Request body:
+
+```json
+{
+  "condition_dict": {
+    "catalyst": ["Pd(OAc)2", "Pd(PPh3)4", "Pd2(dba)3"],
+    "solvent": ["THF", "Dioxane", "Toluene"],
+    "base": ["K2CO3", "NaOEt", "DBU"]
+  },
+  "opt_metrics": ["yield"],
+  "opt_metric_settings": [
+    {"opt_direct": "max", "opt_range": [0, 100], "metric_weight": 1.0}
+  ],
+  "batch_size": 3,
+  "sampling_method": "random",
+  "desc_normalize": "minmax",
+  "random_seed": 42
+}
+```
+
+Supported `sampling_method` values: `sobol`, `random`, `lhs`, `kmeans`.
+
+## Optimize
+
+operation：`optimize`。
+
+Use after measured experiment rows are available. Each previous row must contain
+all condition columns and all objective metric columns.
+
+Request body:
+
+```json
+{
+  "condition_dict": {
+    "catalyst": ["Pd(OAc)2", "Pd(PPh3)4", "Pd2(dba)3"],
+    "solvent": ["THF", "Dioxane", "Toluene"],
+    "base": ["K2CO3", "NaOEt", "DBU"]
+  },
+  "opt_metrics": ["yield"],
+  "previous_results": [
+    {"batch": 0, "catalyst": "Pd(OAc)2", "solvent": "THF", "base": "K2CO3", "yield": 42.0},
+    {"batch": 0, "catalyst": "Pd(PPh3)4", "solvent": "Dioxane", "base": "NaOEt", "yield": 55.0},
+    {"batch": 0, "catalyst": "Pd2(dba)3", "solvent": "Toluene", "base": "DBU", "yield": 63.0}
+  ],
+  "batch_size": 2,
+  "accuracy": "tiny",
+  "surrogate_model": "RF",
+  "acq_func": "UCB",
+  "device": "cpu",
+  "random_seed": 42
+}
+```
+
+### 数值条件必须先离散化
+
+SynBO 的 `condition_dict` 只接受显式列表，不接受连续范围对象。对于“温度
+40–100°C、催化剂用量 0.5–2.0%”并已有 60/70/80/90°C 与
+0.5/1.0/1.5/2.0% 历史值的任务，使用：
+
+```json
+{
+  "condition_dict": {
+    "solvent": ["ethanol", "acetonitrile", "DMSO"],
+    "temperature_C": ["40", "60", "70", "80", "90", "100"],
+    "catalyst_loading_pct": ["0.5", "1.0", "1.5", "2.0"]
+  },
+  "opt_metrics": ["yield"],
+  "previous_results": [
+    {
+      "batch": 0,
+      "solvent": "ethanol",
+      "temperature_C": "60",
+      "catalyst_loading_pct": "1.0",
+      "yield": 55.0
+    }
+  ],
+  "batch_size": 3,
+  "accuracy": "tiny",
+  "surrogate_model": "RF",
+  "acq_func": "UCB",
+  "device": "cpu",
+  "random_seed": 42
+}
+```
+
+约束：
+
+- 每个条件值统一为字符串，objective metric 保持数值。
+- 每条 `previous_results` 中的条件值必须出现在对应 `condition_dict` 列表中。
+- 连续范围的离散网格必须包含用户上下界和全部历史观测值；最终答案必须说明实际网格。
+- 将条件值显式序列化为字符串，并确保每条历史记录只使用 `condition_dict` 中列出的值。
+  如需小数据 CPU 设置，显式传递 `accuracy:"tiny"`、`surrogate_model:"RF"`、
+  `acq_func:"UCB"` 和 `device:"cpu"`；不得假定客户端会补充默认值。
+
+Useful optional fields:
+
+- `accuracy`: `tiny`, `low`, `medium`, `high`, or `ultra`.
+- `acq_func`: `EHVI`, `UCB`, `ParEGO`, or `NEI`.
+- `surrogate_model`: `GP`, `RF`, `BNN`, or `BayesianLinear`.
+- `device`: `cpu`, `auto`, `cuda`, or `cuda:0`.
+- `cuda_visible_devices`: request-level CUDA visibility hint. Use only when the
+  user explicitly asks for it and `/health` indicates a CUDA-capable runtime.
+- `constraints`: map condition type to prohibited values.
+
+## Descriptors
+
+If omitted, SynBO uses generated OneHot descriptors. To provide descriptors:
+
+```json
+{
+  "descriptors": {
+    "solvent": [
+      {"name": "THF", "polarity": 0.207, "boiling_point_C": 66.0},
+      {"name": "Toluene", "polarity": 0.099, "boiling_point_C": 110.6}
+    ]
+  },
+  "descriptor_index_col": "name"
+}
+```
+
+`descriptors` must contain exactly the same keys as `condition_dict`. Descriptor
+rows must include the configured index column and numeric descriptor columns.
+
+## Error Handling
+
+Gateway errors have the standard envelope:
+
+```json
+{
+  "code": 1,
+  "message": "SynBO service returned HTTP 400",
+  "data": {
+    "endpoint": "/synbo/optimize",
+    "synbo_response": {
+      "detail": "previous_results is missing metric columns: ['yield']"
+    }
+  }
+}
+```
+
+常见原因包括条件空间过大、条件值重复、历史条件值不在 condition_dict 中、
+descriptor 非数值、历史行缺列、metric 非数值，以及无 GPU 时请求 CUDA。
+
+服务端有独立于客户端的单次请求时限。GP、EHVI、高 accuracy 或共享资源繁忙可能导致
+timeout。普通用户任务中不得自动换参数重试；应报告“未产生推荐”，保留本次错误，
+由用户决定是否另起一次明确的回归测试。

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

@@ -1,92 +1,92 @@
-#!/usr/bin/env python3
-"""Read the authoritative Delta Science catalog through delta-cli."""
-
-from __future__ import annotations
-
-import argparse
-import json
-import os
-import subprocess
-import sys
-import time
-
-from invoke import _parse_cli_error, _resolve_cli, _runtime_config
-
-
-def _parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(description=__doc__)
-    action = parser.add_mutually_exclusive_group(required=True)
-    action.add_argument("--tools", action="store_true")
-    action.add_argument("--endpoints", metavar="TOOL")
-    parser.add_argument("--cli")
-    parser.add_argument("--science-base-url")
-    parser.add_argument("--timeout", type=float, default=30.0)
-    return parser
-
-
-def main() -> int:
-    args = _parser().parse_args()
-    started = time.perf_counter()
-    kind = "tools" if args.tools else "endpoints"
-    try:
-        runtime = _runtime_config()
-        cli = _resolve_cli(args.cli, runtime)
-        env = os.environ.copy()
-        base_url = args.science_base_url or runtime.get("science_base_url")
-        if base_url:
-            env["DELTA_INFRA_SCIENCE_BASE_URL"] = str(base_url)
-
-        command = [cli, "science", "list"]
-        if args.endpoints:
-            command = [cli, "science", "endpoints", "list", args.endpoints]
-        completed = subprocess.run(
-            command,
-            capture_output=True,
-            text=True,
-            encoding="utf-8",
-            errors="replace",
-            env=env,
-            timeout=args.timeout,
-            check=False,
-        )
-        if completed.returncode != 0:
-            error_type, detail = _parse_cli_error(completed)
-            raise RuntimeError(f"{error_type}: {detail}")
-        root = json.loads(completed.stdout)
-        if not isinstance(root, dict) or root.get("ok") is not True:
-            raise RuntimeError(json.dumps(root, ensure_ascii=False))
-        if "data" not in root:
-            raise RuntimeError("CLI success envelope is missing data")
-        print(json.dumps({
-            "ok": True,
-            "transport": "delta-cli",
-            "catalog": kind,
-            "tool": args.endpoints,
-            "elapsed_seconds": round(time.perf_counter() - started, 3),
-            "native": root["data"],
-        }, ensure_ascii=False))
-        return 0
-    except subprocess.TimeoutExpired:
-        error_type = "timeout"
-        error = f"timeout after {args.timeout}s"
-    except (OSError, ValueError, json.JSONDecodeError) as exc:
-        error_type = "catalog"
-        error = str(exc)
-    except RuntimeError as exc:
-        error_type = "cli"
-        error = str(exc)
-
-    print(json.dumps({
-        "ok": False,
-        "transport": "delta-cli",
-        "catalog": kind,
-        "tool": args.endpoints,
-        "error_type": error_type,
-        "elapsed_seconds": round(time.perf_counter() - started, 3),
-        "error": error[:2000],
-    }, ensure_ascii=False))
-    return 1
-
-
-if __name__ == "__main__":
-    sys.exit(main())
+#!/usr/bin/env python3
+"""Read the authoritative Delta Science catalog through delta-cli."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+import subprocess
+import sys
+import time
+
+from invoke import _parse_cli_error, _resolve_cli, _runtime_config
+
+
+def _parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=__doc__)
+    action = parser.add_mutually_exclusive_group(required=True)
+    action.add_argument("--tools", action="store_true")
+    action.add_argument("--endpoints", metavar="TOOL")
+    parser.add_argument("--cli")
+    parser.add_argument("--science-base-url")
+    parser.add_argument("--timeout", type=float, default=30.0)
+    return parser
+
+
+def main() -> int:
+    args = _parser().parse_args()
+    started = time.perf_counter()
+    kind = "tools" if args.tools else "endpoints"
+    try:
+        runtime = _runtime_config()
+        cli = _resolve_cli(args.cli, runtime)
+        env = os.environ.copy()
+        base_url = args.science_base_url or runtime.get("science_base_url")
+        if base_url:
+            env["DELTA_INFRA_SCIENCE_BASE_URL"] = str(base_url)
+
+        command = [cli, "science", "list"]
+        if args.endpoints:
+            command = [cli, "science", "endpoints", "list", args.endpoints]
+        completed = subprocess.run(
+            command,
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            errors="replace",
+            env=env,
+            timeout=args.timeout,
+            check=False,
+        )
+        if completed.returncode != 0:
+            error_type, detail = _parse_cli_error(completed)
+            raise RuntimeError(f"{error_type}: {detail}")
+        root = json.loads(completed.stdout)
+        if not isinstance(root, dict) or root.get("ok") is not True:
+            raise RuntimeError(json.dumps(root, ensure_ascii=False))
+        if "data" not in root:
+            raise RuntimeError("CLI success envelope is missing data")
+        print(json.dumps({
+            "ok": True,
+            "transport": "delta-cli",
+            "catalog": kind,
+            "tool": args.endpoints,
+            "elapsed_seconds": round(time.perf_counter() - started, 3),
+            "native": root["data"],
+        }, ensure_ascii=False))
+        return 0
+    except subprocess.TimeoutExpired:
+        error_type = "timeout"
+        error = f"timeout after {args.timeout}s"
+    except (OSError, ValueError, json.JSONDecodeError) as exc:
+        error_type = "catalog"
+        error = str(exc)
+    except RuntimeError as exc:
+        error_type = "cli"
+        error = str(exc)
+
+    print(json.dumps({
+        "ok": False,
+        "transport": "delta-cli",
+        "catalog": kind,
+        "tool": args.endpoints,
+        "error_type": error_type,
+        "elapsed_seconds": round(time.perf_counter() - started, 3),
+        "error": error[:2000],
+    }, ensure_ascii=False))
+    return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())