@delta-infra/cli 1.0.73 → 1.0.75

package/scripts/run.js

@@ -1,65 +1,65 @@
-#!/usr/bin/env node
-// Copyright (c) 2026 Delta Infra Authors
-// SPDX-License-Identifier: MIT
-
-const { execFileSync } = require("child_process");
-const fs = require("fs");
-const path = require("path");
-
-const ext = process.platform === "win32" ? ".exe" : "";
-const bin = path.join(__dirname, "..", "bin", "delta-cli" + ext);
-
-// On Windows, a crashed self-update may have left the binary renamed to .old.
-const oldBin = bin + ".old";
-function restoreOldBinary() {
-  try {
-    if (fs.existsSync(bin)) {
-      fs.rmSync(bin, { force: true });
-    }
-    fs.renameSync(oldBin, bin);
-    return true;
-  } catch { return false; }
-}
-
-if (process.platform === "win32" && fs.existsSync(oldBin)) {
-  if (!fs.existsSync(bin)) {
-    restoreOldBinary();
-  } else {
-    try {
-      execFileSync(bin, ["--version"], { stdio: "ignore", timeout: 10000 });
-      try { fs.rmSync(oldBin, { force: true }); } catch {}
-    } catch {
-      restoreOldBinary();
-    }
-  }
-}
-
-const args = process.argv.slice(2);
-
-// Intercept install/uninstall — run wizard, bypass native binary
-if (args[0] === "install" || args[0] === "uninstall") {
-  require("./install-wizard.js");
-} else {
-  // Auto-download binary if missing (e.g. npx skipped postinstall)
-  if (!fs.existsSync(bin)) {
-    try {
-      execFileSync(process.execPath, [path.join(__dirname, "install.js")], {
-        stdio: "inherit",
-        env: { ...process.env, DELTA_CLI_RUN: "true", DELTA_CLI_VERSION: process.env.DELTA_CLI_VERSION || "" },
-      });
-    } catch {
-      console.error(
-        `\nFailed to auto-install delta-cli binary.\n` +
-        `To fix, run the install script manually:\n` +
-        `  node "${path.join(__dirname, "install.js")}"\n`
-      );
-      process.exit(1);
-    }
-  }
-
-  try {
-    execFileSync(bin, args, { stdio: "inherit" });
-  } catch (e) {
-    process.exit(e.status || 1);
-  }
-}
+#!/usr/bin/env node
+// Copyright (c) 2026 Delta Infra Authors
+// SPDX-License-Identifier: MIT
+
+const { execFileSync } = require("child_process");
+const fs = require("fs");
+const path = require("path");
+
+const ext = process.platform === "win32" ? ".exe" : "";
+const bin = path.join(__dirname, "..", "bin", "delta-cli" + ext);
+
+// On Windows, a crashed self-update may have left the binary renamed to .old.
+const oldBin = bin + ".old";
+function restoreOldBinary() {
+  try {
+    if (fs.existsSync(bin)) {
+      fs.rmSync(bin, { force: true });
+    }
+    fs.renameSync(oldBin, bin);
+    return true;
+  } catch { return false; }
+}
+
+if (process.platform === "win32" && fs.existsSync(oldBin)) {
+  if (!fs.existsSync(bin)) {
+    restoreOldBinary();
+  } else {
+    try {
+      execFileSync(bin, ["--version"], { stdio: "ignore", timeout: 10000 });
+      try { fs.rmSync(oldBin, { force: true }); } catch {}
+    } catch {
+      restoreOldBinary();
+    }
+  }
+}
+
+const args = process.argv.slice(2);
+
+// Intercept install/uninstall — run wizard, bypass native binary
+if (args[0] === "install" || args[0] === "uninstall") {
+  require("./install-wizard.js");
+} else {
+  // Auto-download binary if missing (e.g. npx skipped postinstall)
+  if (!fs.existsSync(bin)) {
+    try {
+      execFileSync(process.execPath, [path.join(__dirname, "install.js")], {
+        stdio: "inherit",
+        env: { ...process.env, DELTA_CLI_RUN: "true", DELTA_CLI_VERSION: process.env.DELTA_CLI_VERSION || "" },
+      });
+    } catch {
+      console.error(
+        `\nFailed to auto-install delta-cli binary.\n` +
+        `To fix, run the install script manually:\n` +
+        `  node "${path.join(__dirname, "install.js")}"\n`
+      );
+      process.exit(1);
+    }
+  }
+
+  try {
+    execFileSync(bin, args, { stdio: "inherit" });
+  } catch (e) {
+    process.exit(e.status || 1);
+  }
+}

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

@@ -0,0 +1,54 @@
+---
+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。
+---
+
+# AntBO LDM 能力边界
+
+本 Skill 没有可执行的 Science operation，也没有 wrapper、endpoint 或 payload 示例。
+为了兼容 Kimi 对“无 artifact 的 step_finish”误判为 loop，先生成一个只记录能力边界的
+本地证据文件；这不是 Science 调用，也不发送远端请求。
+
+第一次工具调用必须是 `python_repl`，工具参数只能包含 `code`，执行以下等价逻辑：
+
+```python
+import json, os
+from pathlib import Path
+
+result = {
+    "supported": False,
+    "tool": "antbo",
+    "operation": "ldm-suggest",
+    "remote_request_sent": False,
+    "reason": "当前 Delta CLI catalog 未暴露 antbo LDM suggest operation",
+}
+output_path = Path(os.environ["WORKSPACE_ROOT"]) / "antbo_ldm_unsupported.json"
+output_path.write_text(json.dumps(result, ensure_ascii=False, indent=2), encoding="utf-8")
+print(str(output_path))
+```
+
+随后调用且只调用一次：
+
+```text
+step_finish(
+  status="done",
+  summary="当前 Delta CLI catalog 未暴露 antbo LDM suggest operation；未发送远端请求。",
+  output_ref=<刚生成的 antbo_ldm_unsupported.json 绝对路径>
+)
+```
+
+必须逐字使用上述 summary 和真实 output_ref。调用后立即结束，不输出其他文字，不调用
+任何工具。外层若核验，只能原子 `read_file(output_ref)` 一次，禁止其他操作。
+
+禁止行为：
+
+- 除上述一次本地文件写入外，禁止其他 `python_repl`；禁止 Bash、health、catalog、
+  filesystem、目录 read/list、ask_user；
+- 禁止创建 history JSON，禁止先要求用户提供序列或评分；
+- 禁止调用 `antbo-service`、`ldm-bo` 或通用子代理；
+- 禁止生成、转换、评价或声称返回候选 CDRH3；
+- 禁止把 AntBO health 公布的公司内部 endpoint 当成 Delta CLI operation。
+
+公司服务能力与 Delta CLI catalog 是两层能力。当前 Memento 只能通过 CLI catalog
+调用 `antbo` 的 `health/run-default-job/run/log/jobs/stop`；因此 AntBO LDM 请求必须在
+本 Skill 内以固定能力边界答复结束。

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

@@ -0,0 +1,4 @@
+interface:
+  display_name: "AntBO LDM ????"
+  short_description: "????? Delta CLI ??? AntBO LDM ????"
+  default_prompt: "?? $antbo-ldm-guard ???? AntBO LDM ?????? Delta CLI ???"

package/skills/antbo-service/SKILL.md

@@ -0,0 +1,74 @@
+---
+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。
+---
+
+# AntBO 服务
+
+## 路由排除
+
+AntBO/CDRH3 LDM、suggest、下一条候选序列请求不进入本 Skill，必须由
+`antbo-ldm-guard` 处理。不得先调用本 Skill 的 health。
+
+## 路由与能力边界
+
+当前 Delta CLI catalog 暴露：
+
+- `health`：健康检查，只读。
+- `run-default-job`：启动默认后台任务，有副作用。
+- `run`：自定义同步任务，有副作用且可能长时间运行。
+- `log`：读取日志，只读。
+- `jobs`：列出当前容器登记的活动任务，只读。
+- `stop`：停止任务，有副作用。
+
+当前没有 `ldm/suggest`、`ldm/initialize` 或 `ldm/evaluate`。这些请求严格执行最上方
+终止分支；health 返回的公司内部 endpoint 不能覆盖 CLI catalog。
+
+## 强制执行规则
+
+1. 实时 Science 调用的第一个执行工具只能是 `python_repl`。
+   `python_repl` 工具参数只能包含 `code`，禁止 `deps/dependencies/packages`。
+2. 只通过 `os.environ["SKILLS_ROOT"]` 定位
+   `delta-science/scripts/invoke.py`，使用 `subprocess.run(..., shell=False)`。
+3. 禁止 Bash、`list_dir`、`read_file`、`which`、`where`、`ls`、wrapper/环境检查，
+   禁止执行字面命令 `CLI`、`cli` 或 `delta-cli`。
+4. 禁止 `curl`、`requests`、`httpx`、浏览器、网关直连和本地 AntBO。
+5. 业务结果直接位于 `result["native"]`；禁止读取 `native.data`。
+6. 每个 operation 的场景、最小参数和投影必须按
+   `references/operations.md`，不得猜相近 endpoint。
+
+## 唯一 wrapper 模板
+
+```python
+import json, os, subprocess, sys
+wrapper = os.path.join(os.environ["SKILLS_ROOT"], "delta-science", "scripts", "invoke.py")
+argv = [sys.executable, wrapper, "--tool", "antbo", "--endpoint", endpoint]
+if data is not None:
+    argv += ["--data-json", json.dumps(data)]
+if params is not None:
+    argv += ["--params-json", json.dumps(params)]
+p = subprocess.run(argv, capture_output=True, text=True, shell=False)
+if p.returncode != 0:
+    raise RuntimeError(p.stderr or p.stdout)
+r = json.loads(p.stdout)
+if r.get("ok") is not True or r.get("transport") != "delta-cli":
+    raise RuntimeError(r)
+n = r["native"]
+print(json.dumps({"transport": r["transport"], "endpoint": r["endpoint"], "native": n}, ensure_ascii=False))
+```
+
+执行前只按 `references/operations.md` 设置 `endpoint`、`data`、`params`。成功后将
+结果投影为用户要求的最小字段，不打印完整日志或 envelope。
+
+## 副作用与完成回执
+
+- `run-default-job`、`run`、`stop` 只有用户明确授权时才能执行。
+- 变更操作结果未知、超时或断连时禁止重试；客户端失败不表示远程操作未发生。
+- 只有同一次 `run-default-job` native 同时含 `started=true`、非空 `pid` 以及
+  `log_name` 或 `log_path` 时，才能说任务已启动。
+- `run` 仅用于用户明确提供并授权的受限脚本/config/antigen 路径，不生成任意路径。
+- `stop` 优先使用用户确认的 PID；不得在多任务不明确时无参数停止。
+
+成功后立即调用 `step_finish(status="done", summary=<有界结果 JSON>)` 恰好一次；
+失败时调用 `step_finish(status="failed", summary=<原始错误短摘要>)`。调用后不得输出
+自由文本或使用其他工具。

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

@@ -0,0 +1,4 @@
+interface:
+  display_name: "AntBO ????"
+  short_description: "?? Delta CLI ???????? AntBO ??????"
+  default_prompt: "?? $antbo-service ??????? AntBO ???????"

package/skills/antbo-service/references/operations.md

@@ -0,0 +1,45 @@
+# AntBO operation 契约
+
+在 `SKILL.md` 的 wrapper 模板中设置 `endpoint`、`data`、`params`。业务结果直接位于
+`r["native"]`。标为“变更”的 operation 只有用户明确授权时才能执行，且不得重试。
+
+## health（只读）
+
+- 情景：检查远程 AntBO 环境是否可用。
+- 代码：`endpoint="health"; data=None; params=None`
+- 投影：status、antbo_available、metadata、limits、warnings。
+
+## run-default-job（变更）
+
+- 情景：用户明确要求启动标准后台续跑任务。
+- 代码：`endpoint="run-default-job"; data=None; params={"log_name":"antbo_<唯一时间戳>.log","append":False,"timeout_seconds":86400}`
+- 投影：started、pid、log_name/log_path、timeout_seconds；未知结果禁止重试。
+
+## run（重型变更）
+
+- 情景：用户明确给出受限 AntBO 脚本、配置、抗原文件并要求同步执行。
+- 代码：`endpoint="run"; data={"script_path":"./bo/main.py","config_path":"./bo/config.yaml","n_trials":1,"seed":42,"antigens_file":"<项目根内路径>","extra_args":[],"timeout_seconds":86400,"cuda_visible_devices":"0","conda_env":"DGM","log_name":"antbo_custom.log","append":False}; params=None`
+- 投影：ok、returncode、timed_out、log_path、日志截断状态；不在最终答复展开完整日志。
+
+## log（只读）
+
+- 情景：用户提供已知 log_name 并要求查看尾部日志。
+- 代码：`endpoint="log"; data=None; params={"log_name":"antbo_run.log"}`
+- 投影：log_name、log、log_truncated；长日志只给有界尾部摘要。
+
+## jobs（只读）
+
+- 情景：查看当前 service 容器登记的活动作业。
+- 代码：`endpoint="jobs"; data=None; params=None`
+- 投影：jobs 中 pid、running、returncode、log_name、log_path。
+
+## stop（变更）
+
+- 情景：用户明确要求停止已确认 PID 的任务。
+- 代码：`endpoint="stop"; data=None; params={"pid":12345}`
+- 投影：stopped、pid、message；不得盲目重试或在多任务时无参数调用。
+
+## 当前不支持：AntBO LDM
+
+`ldm/suggest`、`ldm/initialize`、`ldm/evaluate` 不在 CLI catalog。不得调用工具或
+切换到分子 `ldm-bo`，以 Skill 规定的固定能力边界答复结束步骤。

package/skills/delta-bo/SKILL.md

@@ -0,0 +1,31 @@
+---
+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。
+---
+
+# Delta-BO 服务
+
+## 强制规则
+
+- 只用 `python_repl` 执行 `$SKILLS_ROOT/delta-science/scripts/invoke.py`，
+  tool=`delta-bo`；禁止 Bash、路径探测、字面 CLI、直接 HTTP 和本地 BO。
+- `python_repl` 工具参数只能包含 `code`，禁止 `deps/dependencies/packages`。
+- 业务结果直接在 `r["native"]`，禁止 `native.data`。
+- 当前 catalog 只有 `commands`（无 body）与 `generate`（JSON body）。旧文档中的
+  session/space/objective/policy/suggest/observe/loop 等不是当前 CLI operation，
+  不得执行或猜 endpoint。
+
+## generate 最小规则
+
+- 没有真实历史，或历史少于 5 条且用户未明确要求 BO：用
+  `algorithm:"random-search"`，给有界 `params`、`num_suggestions` 和 seed。
+- 有真实历史且明确要求 BO：使用 `objectives`、object-form
+  `histories.decisions/observations`，必要时才加入 model/acquisition/solver。
+- 参数类型仅 `numeric`、`integer`、`categorical`；不得编造观测或最优结果。
+- 只报告 native 的 suggestions、metadata、warnings、diversity；空建议或失败不得用
+  本地 GP/UCB/随机数替代。
+
+最小 payload 见 `references/endpoints.md` 的 Stateless Generate。通过 wrapper 一次
+调用、校验并显式打印有界 JSON，然后立即
+`step_finish(status="done", summary=<同一 JSON>)`；失败则 `status="failed"`。
+调用后不得输出自由文本或使用其他工具。

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

@@ -0,0 +1,4 @@
+interface:
+  display_name: "Delta-BO ????"
+  short_description: "?? Delta CLI ???????????????"
+  default_prompt: "?? $delta-bo ??????????????????"

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

@@ -0,0 +1,263 @@
+# Delta-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 demo runner.
+
+## Health And Command Discovery
+
+`GET /chem/delta-bo/health`
+
+`GET /chem/delta-bo/commands`
+
+`/commands` returns the native route list exposed by the deployed service.
+
+For a formatted catalog with gateway URLs against the deployed service, run the
+bundled skill-local script (no local `delta_bo` package required):
+
+```bash
+python3 scripts/remote_list_eng_cmds.py --format markdown
+python3 scripts/remote_list_eng_cmds.py --format json
+```
+
+For complete local route metadata including parameters, the offline equivalent
+`list_eng_cmds.py` (requires a Delta-BO dev environment with dependencies
+installed, not bundled) walks the same command registry used by the service
+dispatcher and is the source of truth for possible native API usage.
+
+## Stateless Generate
+
+`POST /chem/delta-bo/generate`
+
+Random search:
+
+```json
+{
+  "params": [{"name": "x", "type": "numeric", "low": 0.0, "high": 1.0}],
+  "num_suggestions": 3,
+  "algorithm": "random-search",
+  "seed": 42
+}
+```
+
+BO with history:
+
+```json
+{
+  "params": [
+    {"name": "temperature", "type": "numeric", "low": 20.0, "high": 120.0},
+    {"name": "catalyst", "type": "categorical", "choices": ["A", "B", "C"]}
+  ],
+  "objectives": [{"name": "yield", "minimize": false}],
+  "num_suggestions": 2,
+  "algorithm": "bo",
+  "model": {"name": "gp", "min_samples": 2, "train_steps": 50},
+  "acq_target": {"name": "ucb", "beta": 2.0},
+  "solver": {"name": "ga", "pop_size": 40, "n_gen": 10},
+  "histories": {
+    "decisions": [[40.0, "A"], [80.0, "B"], [100.0, "C"]],
+    "observations": [0.42, 0.61, 0.53]
+  },
+  "seed": 7
+}
+```
+
+Parameter types: `numeric`, `integer`, `categorical`.
+
+Histories may also use object-form rows, which are safer for agents:
+
+```json
+{
+  "histories": {
+    "decisions": [
+      {"temperature": 40.0, "catalyst": "A"},
+      {"temperature": 80.0, "catalyst": "B"}
+    ],
+    "observations": [
+      {"yield": 0.42},
+      {"yield": 0.61}
+    ]
+  }
+}
+```
+
+Optional diversity controls:
+
+```json
+{
+  "diversity": {
+    "deduplicate": true,
+    "min_numeric_distance": {"temperature": 5.0},
+    "prefer_unique_categories": true
+  },
+  "constraints": [
+    {"type": "unique_batch"},
+    {"type": "avoid_seen_decisions"},
+    {
+      "type": "max_temperature_for_category",
+      "category_param": "solvent",
+      "temperature_param": "temperature",
+      "category": "dichloromethane",
+      "max": 40
+    }
+  ]
+}
+```
+
+Response fields include:
+
+```json
+{
+  "suggestions": [[{"name": "temperature", "value": 72.0}]],
+  "suggestion_metadata": [
+    {
+      "acquisition_value": null,
+      "nearest_history": {
+        "decision": [{"name": "temperature", "value": 80.0}],
+        "distance": 0.08
+      },
+      "rationale": "exploitation"
+    }
+  ],
+  "warnings": [
+    "Only 3 observations supplied; GP fit may be weak. Consider random-search or more initial points."
+  ],
+  "generated_candidate_count": 15,
+  "diversity": {
+    "requested": true,
+    "deduplicated": true,
+    "duplicates_removed": 2
+  }
+}
+```
+
+## Native Stateful Command API
+
+Gateway path pattern:
+
+```text
+POST /chem/delta-bo/v1/{command_path}
+```
+
+Native route `/v1/session/new` maps to gateway route:
+
+```text
+/api/v1/chem/delta-bo/v1/session/new
+```
+
+Minimal random-search session:
+
+```bash
+curl -s "$DBO/v1/session/new" \
+  -H "Content-Type: application/json" \
+  -d '{"name":"api_session"}'
+
+curl -s "$DBO/v1/space" \
+  -H "Content-Type: application/json" \
+  -d '{"decision_expression":"Joint({\"x\": Num(-5, 10), \"y\": Num(0, 15)})"}'
+
+curl -s "$DBO/v1/objective" \
+  -H "Content-Type: application/json" \
+  -d '{"source":"objectives/branin_simple.py","minimize":true}'
+
+curl -s "$DBO/v1/policy/random-search" \
+  -H "Content-Type: application/json" \
+  -d '{"policy_id":"random_init","replace":true}'
+
+curl -s "$DBO/v1/suggest" \
+  -H "Content-Type: application/json" \
+  -d '{"num":3,"policy_id":"random_init"}'
+```
+
+Common native commands:
+
+```text
+session/new
+session/save
+space
+objective
+policy/random-search
+policy/bo
+policy/bo.model/gp
+policy/bo.target/ucb
+policy/bo.target/ei
+policy/bo.solver/ga
+policy/flags
+suggest
+observe
+loop
+status
+best
+plot/best-so-far
+```
+
+Use `GET /chem/delta-bo/commands` for the deployed list; run the bundled
+`scripts/remote_list_eng_cmds.py --format markdown/json` for a formatted catalog
+against the deployed service, or the offline `list_eng_cmds.py` (local Delta-BO
+dev environment, not bundled) for full parameter schemas.
+
+## Native BO Policy Setup
+
+A typical stateful BO configuration is:
+
+```bash
+curl -s "$DBO/v1/policy/bo" \
+  -H "Content-Type: application/json" \
+  -d '{"replace":true}'
+
+curl -s "$DBO/v1/policy/bo.model/gp" \
+  -H "Content-Type: application/json" \
+  -d '{"train_steps":50,"min_samples":2}'
+
+curl -s "$DBO/v1/policy/bo.target/ucb" \
+  -H "Content-Type: application/json" \
+  -d '{"beta":2.0}'
+
+curl -s "$DBO/v1/policy/bo.solver/ga" \
+  -H "Content-Type: application/json" \
+  -d '{"pop_size":40,"n_gen":10}'
+```
+
+For random initialization policy creation:
+
+```bash
+curl -s "$DBO/v1/policy/random-search" \
+  -H "Content-Type: application/json" \
+  -d '{"policy_id":"random_init","replace":true}'
+```
+
+Then run an optimization loop:
+
+```bash
+curl -s "$DBO/v1/loop" \
+  -H "Content-Type: application/json" \
+  -d '{"iterations":5,"batch_size":1,"policy_id":"main","timeout":300}'
+```
+
+Response shape is nested:
+
+```json
+{
+  "code": 0,
+  "message": "success",
+  "data": {
+    "ok": true,
+    "result": {
+      "data": {},
+      "summary": "...",
+      "meta": {"command_path": "/v1/..."}
+    }
+  }
+}
+```
+
+## Retry Safety
+
+Setup/configuration requests such as `space`, `objective`, `policy/bo`, and
+`policy/random-search` can be repeated with the same payload. Use
+`{"replace": true}` for policy creation so repeated setup calls remain
+idempotent.
+
+Do not blindly retry state-changing optimization commands such as `loop`,
+`suggest`, `observe`, `session/new`, or `session/save`, because a retry may
+advance or duplicate remote experiment state.