@delta-infra/cli 1.0.79 → 1.0.81

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

@@ -1,263 +0,0 @@
-# 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.

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

@@ -1,48 +0,0 @@
-# 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/references/operation-contracts.md

@@ -1,137 +0,0 @@
-# Delta Science operation 最小契约
-
-本文只记录当前 CLI catalog 已暴露的 9 个 tools、42 个 operations。选择 operation 后
-只读取对应小节。代码示例均在同一个 `python_repl` 中先定义以下函数；禁止 Bash、
-目录探测、直接 HTTP 和字面 CLI 命令。
-
-调用 `python_repl` 时工具参数必须严格为 `{"code":"..."}`；禁止添加 `deps`、
-`dependencies`、`packages` 或任何其他字段。
-
-```python
-import json, os, subprocess, sys
-
-wrapper = os.path.join(os.environ["SKILLS_ROOT"], "delta-science", "scripts", "invoke.py")
-
-def invoke(tool, endpoint, data=None, params=None):
-    argv = [sys.executable, wrapper, "--tool", tool, "--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)
-    return r["native"]
-```
-
-每个代码示例只调用一次。将返回值投影成用户要求的有界 JSON 并显式 `print`，然后
-调用 `step_finish(status="done", summary=<同一 JSON>)` 恰好一次。失败则
-`step_finish(status="failed", summary=<原始错误短摘要>)`，禁止重试或改走其他链路。
-
-## PubChem（tool=`pubchem`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “PubChem 服务现在能用吗？” | `n=invoke("pubchem","health")` | status、availability、metadata、limits、warnings |
-| `compound-resolve-cids` | “把 aspirin 解析成 CID。” | `n=invoke("pubchem","compound-resolve-cids",data={"identifier":"aspirin","namespace":"name","max_records":20})` | identifier、valid、cids、error |
-| `compound-properties` | “查 aspirin 的分子式和分子量。” | `n=invoke("pubchem","compound-properties",data={"identifier":"aspirin","namespace":"name","properties":["MolecularFormula","MolecularWeight"]})` | cid、valid、properties、aliases、error |
-| `compound-synonyms` | “列出 aspirin 的前 5 个同义词。” | `n=invoke("pubchem","compound-synonyms",data={"identifier":"aspirin","namespace":"name","max_synonyms":5})` | cid、valid、synonyms、error |
-| `compound-summary` | “查阿司匹林的基础身份信息。” | `n=invoke("pubchem","compound-summary",data={"identifier":"aspirin","namespace":"name"})` | valid、cid、properties 中用户要求的键 |
-| `compound-batch-summary` | “一次比较 aspirin 和 caffeine 的基础属性。” | `n=invoke("pubchem","compound-batch-summary",data={"identifiers":["aspirin","caffeine"],"namespace":"name"})` | results[*].input、valid/error、properties |
-
-## RDKit（tool=`rdkit`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “RDKit 服务可用吗？” | `n=invoke("rdkit","health")` | status、availability、metadata、limits、warnings |
-| `parse` | “这个 SMILES 合法吗？” | `n=invoke("rdkit","parse",data={"input":"CCO","format":"smiles","sanitize":True})` | valid、canonical_smiles、formula、inchi_key、warnings/error |
-| `descriptors` | “计算乙醇的基础 RDKit 描述符。” | `n=invoke("rdkit","descriptors",data={"smiles":"CCO","descriptor_set":"basic","sanitize":True})` | valid、descriptors、warnings/error |
-| `batch-descriptors` | “批量算几个 SMILES 的描述符。” | `n=invoke("rdkit","batch-descriptors",data={"smiles":["CCO","c1ccccc1"],"descriptor_set":"basic","sanitize":True})` | results 中输入、valid、descriptors、error |
-| `batch-parse-describe` | “校验阿司匹林并给基础描述符。” | `n=invoke("rdkit","batch-parse-describe",data={"molecules":[{"id":"aspirin","smiles":"CC(=O)OC1=CC=CC=C1C(=O)O"}],"descriptor_set":"basic","sanitize":True})` | results[*].id、valid、canonical_smiles、descriptors、warnings/error |
-| `render` | “画一张乙醇结构图。” | `n=invoke("rdkit","render",data={"smiles":"CCO","image_format":"png","width":500,"height":400})` | 指定图像字段；PNG 解码后验证 magic bytes |
-| `fingerprint` | “生成乙醇 Morgan 指纹。” | `n=invoke("rdkit","fingerprint",data={"smiles":"CCO","radius":2,"n_bits":2048})` | valid、fingerprint_metadata、on_bits、warnings/error |
-| `similarity` | “比较乙醇和乙胺的结构相似度。” | `n=invoke("rdkit","similarity",data={"query_smiles":"CCO","target_smiles":"CCN","radius":2,"n_bits":2048})` | similarity、metric、fingerprint metadata |
-| `similarity-matrix` | “比较一组分子的两两相似度。” | `n=invoke("rdkit","similarity-matrix",data={"molecules":[{"id":"a","smiles":"CCO"},{"id":"b","smiles":"CCN"}],"fingerprint":{"type":"morgan","radius":2,"n_bits":2048},"sanitize":True})` | matrix、ranked_pairs[{a,b,similarity}] |
-| `substructure` | “筛出含羧酸子结构的分子。” | `n=invoke("rdkit","substructure",data={"query_smarts":"C(=O)O","target_smiles":["CC(=O)O","CCO"]})` | query 与每个目标的 match/matches、valid/error |
-
-## pymatgen（tool=`pymatgen`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “pymatgen 服务是否正常？” | `n=invoke("pymatgen","health")` | status、availability、metadata、limits、warnings |
-| `composition-parse` | “解析 LiFePO4 的组成和式量。” | `n=invoke("pymatgen","composition-parse",data={"formula":"LiFePO4","format":"formula"})` | valid、formula、reduced_formula、chemical_system、weight、element_amounts |
-| `structure-parse` | “校验这段 CIF 能否解析。” | `n=invoke("pymatgen","structure-parse",data={"input":cif_text,"format":"cif","primitive":False})` | valid、formula、nsites、lattice、warnings/error |
-| `structure-summary` | “总结这段 CIF 的结构信息。” | `n=invoke("pymatgen","structure-summary",data={"input":cif_text,"format":"cif","primitive":False})` | formula、reduced_formula、density、volume、lattice、species |
-| `structure-convert` | “把 CIF 转成 POSCAR。” | `n=invoke("pymatgen","structure-convert",data={"input":cif_text,"input_format":"cif","output_format":"poscar","primitive":False})` | valid、output_format、转换后的结构文本、warnings/error |
-| `structure-symmetry` | “分析这段 CIF 的空间群。” | `n=invoke("pymatgen","structure-symmetry",data={"input":cif_text,"format":"cif","primitive":False,"symprec":0.01,"angle_tolerance":5.0})` | space_group_symbol/number、crystal_system、point_group_symbol、hall、nsites |
-
-## GSAS-II（tool=`gsasii`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “GSAS-II 服务能做衍射计算吗？” | `n=invoke("gsasii","health")` | status、gsasii_available、metadata、limits、warnings |
-| `powder-simulate` | “用这个 CIF 模拟 Cu Kα 粉末衍射。” | `n=invoke("gsasii","powder-simulate",data={"cif":cif_text,"phase_name":"phase","radiation":"CuKa","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})` | valid、profile、reflections、metadata、warnings |
-| `powder-refine` | “用真实粉末数据和仪器文件做 Rietveld 精修。” | `n=invoke("gsasii","powder-refine",data={"powder_data":powder_text,"powder_format":"xy","instrument_parameters":instrument_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})` | valid、residuals、phase summaries、profile、reflections、warnings |
-
-## LAMMPS（tool=`lammps`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “LAMMPS 服务可用吗？” | `n=invoke("lammps","health")` | status、lammps_available、metadata、limits、warnings |
-| `lj-melt-example` | “给我跑部署自带的最小 LJ 示例做检查。” | `n=invoke("lammps","lj-melt-example")` | 示例说明与精确 `request`；此调用本身不执行模拟 |
-| `run` | “执行刚才返回的最小 LJ 请求。” | `example=invoke("lammps","lj-melt-example"); n=invoke("lammps","run",data=example["request"])` | valid、last_thermo、thermo rows、warnings、请求的输出文件；此场景固定两次依赖调用 |
-
-`run` 也可接收用户明确提供的 `input_script`、相对路径 files、timeout 和有界输出配置；
-不得从化学式猜力场。长任务需明确授权，失败后不得重试。
-
-## Delta-BO（tool=`delta-bo`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `commands` | “当前 Delta-BO 支持哪些命令？” | `n=invoke("delta-bo","commands")` | 当前部署返回的命令列表，不从旧文档补充 |
-| `generate` | “在 0 到 1 之间给两个随机初始实验点。” | `n=invoke("delta-bo","generate",data={"params":[{"name":"x","type":"numeric","low":0.0,"high":1.0}],"num_suggestions":2,"algorithm":"random-search","seed":42})` | suggestions、suggestion_metadata、warnings、diversity |
-
-有历史观测且用户明确要求 BO 时，`generate` 可加入 objectives、object-form histories、
-model/acquisition/solver；历史少于 5 条默认 random-search，不编造观测。
-
-## LDM-BO（tool=`ldm-bo`）
-
-只用于小分子 SMILES/PDF2Dock，不用于抗体、CDRH3 或 AntBO。
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “分子 LDM-BO 服务可用吗？” | `n=invoke("ldm-bo","health")` | availability、Vina/ReaSyn/模型/LLM 配置状态、warnings |
-| `recommend` | “从候选池给下一条小分子 SMILES。” | `n=invoke("ldm-bo","recommend",data={"method":"bo-tanimoto","pool":["CCO","CCN","CCC"],"history":[{"smiles":"CCO","scores":[-7.1]},{"smiles":"CCN","scores":[-6.8]}],"batch_size":1})` | recommendations、acquisition_values、n_objectives、llm diagnostics |
-| `trajectory` | “跑一个有界的小分子 BO 轨迹。” | `n=invoke("ldm-bo","trajectory",data={"method":"bo-tanimoto","seed":42,"seed-smiles":"CCO,CCN,CCC","num-evaluations":4,"batch-size":1,"objective":"vina+nn"})` | config、history、summary、llm_trajectory；保留连字符字段 |
-
-## SynBO（tool=`synbo`）
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “SynBO 服务当前可用吗？” | `n=invoke("synbo","health")` | status、synbo_available、metadata、limits、runtime、warnings |
-| `initialize` | “没有实验历史，先选三组反应条件。” | `n=invoke("synbo","initialize",data={"condition_dict":{"catalyst":["Pd(OAc)2","Pd(PPh3)4"],"solvent":["THF","Toluene"],"base":["K2CO3","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})` | recommendations/initial conditions、warnings、metadata |
-| `optimize` | “根据真实历史收率推荐下一批条件。” | `n=invoke("synbo","optimize",data={"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","device":"cpu","random_seed":42})` | recommendations、model/acquisition metadata、warnings；失败/空结果不得本地替代 |
-
-## AntBO（tool=`antbo`）
-
-抗体/CDRH3 场景即使出现 “LDM” 也必须路由到 AntBO，不得改用分子 LDM-BO。
-
-| operation | 人类情景 | 最小代码 | native 投影 |
-| --- | --- | --- | --- |
-| `health` | “AntBO 环境可用吗？” | `n=invoke("antbo","health")` | status、antbo_available、metadata、limits、warnings |
-| `run-default-job` | “启动标准 AntBO 后台任务。” | `n=invoke("antbo","run-default-job",params={"log_name":"antbo_<唯一时间戳>.log","append":False,"timeout_seconds":86400})` | started、pid、log_name/log_path、timeout_seconds |
-| `run` | “用明确的受限配置同步跑一次 AntBO。” | `n=invoke("antbo","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})` | ok、returncode、timed_out、log_path、log_truncated |
-| `log` | “查看 antbo_run.log 的尾部。” | `n=invoke("antbo","log",params={"log_name":"antbo_run.log"})` | log_name、log、log_truncated |
-| `jobs` | “查看当前活动 AntBO 作业。” | `n=invoke("antbo","jobs")` | jobs[*].pid/running/returncode/log_name/log_path |
-| `stop` | “停止 PID 12345。” | `n=invoke("antbo","stop",params={"pid":12345})` | stopped、pid、message |
-
-`run-default-job`、`run`、`stop` 是远程变更，必须有用户明确授权，未知结果不得重试。
-AntBO `ldm/suggest`、`ldm/initialize`、`ldm/evaluate` 当前不在 catalog：不调用工具，
-固定报告“未暴露该 operation；未发送远端请求”。
-
-注意：AntBO `health` 可能公布公司服务内部的 `ldm_suggest` 等 endpoint，但它们并不
-因此成为 Delta CLI operation；禁止调用不存在的 `antbo/catalog`，也禁止根据 health
-为 Memento 推导新的 endpoint。

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

@@ -1,112 +0,0 @@
-# 服务与参数参考
-
-只读取当前所选服务对应的部分。下文中的 endpoint 是 Delta CLI catalog 名称，不是 URL 路径。
-
-## PubChem
-
-Tool：`pubchem`。
-
-- 普通名称查询：`compound-summary`，data 为 `{"identifier":"caffeine","namespace":"name"}`。
-- 批量查询：`compound-batch-summary`。模糊的多分子比较必须严格使用 `{"identifiers":["aspirin","caffeine"],"namespace":"name"}`。
-- 批量查询不要添加 `properties` 或 `synonym_limit`，尤其不能把 `CID` 放进 `properties`。
-- 其他 operation：`compound-resolve-cids`、`compound-properties`、`compound-synonyms`。
-
-单个 `compound-summary` 的业务字段直接位于 wrapper 的 `native` 顶层：读取
-`native.valid`、`native.cid`、`native.properties` 和 `native.synonyms`；不存在
-`native.data` 这一层。
-
-模糊问题优先使用 summary。按 `CanonicalSMILES`、`ConnectivitySMILES`、`SMILES`、`IsomericSMILES` 的顺序提取 SMILES。PubChem 返回的 `MolecularWeight`、`XLogP` 和 `TPSA` 必须保留为 PubChem 数据。
-
-批量 native 输出为 `{"results":[...]}`。每条记录用 `input` 保存原始标签，化合物字段位于嵌套的 `properties`；记录不是平铺结构，集合键也不是 `compounds`。
-
-## RDKit
-
-Tool：`rdkit`。
-
-- `parse`：`{"input":"CCO","format":"smiles"}`
-- `descriptors`：`{"smiles":"CCO","descriptor_set":"basic","sanitize":true}`
-- `batch-parse-describe`：`{"molecules":[{"id":"ethanol","smiles":"CCO"}],"descriptor_set":"basic","sanitize":true}`
-- `render`：`{"smiles":"CCO","image_format":"png","width":500,"height":400}`
-- `similarity`：使用 `query_smiles` 和 `target_smiles`
-- `similarity-matrix`：使用 `molecules:[{id,smiles}]`
-- `substructure`：使用 `query_smarts` 和 `target_smiles`
-
-`batch-parse-describe` 使用 `molecules`，不能用 `inputs`；分子字段使用 `smiles`，不能用 `input`。fingerprint 选项是对象，不是布尔值。PubChem `XLogP` 与 RDKit `MolLogP` 使用不同模型。
-
-`similarity-matrix` 的 `ranked_pairs` 每项是
-`{"a": <输入 id>, "b": <输入 id>, "similarity": <数值>}`。不要读取
-`i`、`j` 或 `score`。
-
-## pymatgen
-
-Tool：`pymatgen`。
-
-- 化学式：`composition-parse`，data 为 `{"formula":"LiFePO4","format":"formula"}`
-- 结构 operation：`structure-parse`、`structure-summary`、`structure-convert`、`structure-symmetry`
-
-结构调用必须发送完整结构文本，不能发送本地文件路径。支持 CIF、POSCAR、JSON、CSSR 和 XSF。不要把 LAMMPS data/dump 文件交给 pymatgen。
-
-对无机化学式/式量，只报告当前 native 的 `formula`、`reduced_formula`、
-`chemical_system`、`weight` 与元素组成。PubChem 未收录时保留 `not_found`，
-不要编造 CID 或用本地计算补值。
-
-## GSAS-II
-
-Tool：`gsasii`；operation 为 `powder-simulate` 和 `powder-refine`。
-
-模拟需要完整 `cif` 文本。字段必须使用 `phase_name`、`include_profile`、`include_reflections`、`t_min`、`t_max` 和 `t_step`。
-
-精修需要真实的 `powder_data`、`instrument_parameters` 和 `phases:[{name,cif}]`。依赖模拟结果时，只能从成功调用的 native `profile[*].x` 和 `profile[*].y_calc` 构造粉末数据。
-
-## LAMMPS
-
-Tool：`lammps`。
-
-- 只读有界示例：`lj-melt-example`，无参数
-- 执行：`run`，参数必须是示例返回的精确 native `request`，或用户明确授权的 `input_script`/files
-
-绝不能把 CLI 外层信封传给 `run`，只能传 `native["request"]`。LAMMPS 不会自动推断力场。交互式运行必须保持有界。
-
-最小示例最终数值从当前 native `last_thermo` 读取；逐字保留 `Step`、`Temp`
-和 `TotEng`，不要除以原子数、换算单位或推测收敛性。
-
-## Delta-BO
-
-Tool：`delta-bo`。
-
-- 命令目录：`commands`，无参数
-- 无状态建议：`generate`，例如 `{"params":[{"name":"x","type":"numeric","low":0,"high":1}],"num_suggestions":2,"algorithm":"random-search","seed":42}`
-
-观测少于五条时，除非用户明确要求 BO，否则优先使用 `random-search`。有状态 native session 命令属于变更操作，不能盲目重试。
-
-## LDM-BO
-
-Tool：`ldm-bo`；operation 为 `recommend` 和 `trajectory`。
-
-有界测试使用 `bo-tanimoto`。`recommend` 接受 `method`、`pool`、`history:[{smiles,scores}]` 和 `batch_size`。`trajectory` 必须保留 native 连字符字段：`seed-smiles`、`num-evaluations` 和 `batch-size`。
-
-## SynBO
-
-Tool：`synbo`；operation 为 `initialize` 和 `optimize`。
-
-二者都使用 `condition_dict`、`opt_metrics` 和 `batch_size`。`optimize` 还要求数值型 `previous_results`，且每条记录必须包含全部条件和指标。有界 CPU 测试使用 `accuracy:"tiny"` 和 `device:"cpu"`，并串行执行。
-
-有真实 `previous_results` 的优化请求使用一次 `optimize`；每行必须包含全部条件列和
-数值指标。失败、超时或空 recommendations 时如实报告，禁止本地替代优化。
-
-## AntBO
-
-Tool：`antbo`。
-
-当前 CLI catalog 暴露 `health`、`run-default-job`、`run`、`log`、`jobs` 和
-`stop`；准确参数见 `operation-contracts.md`。没有 `ldm/suggest`、
-`ldm/initialize`、`ldm/evaluate`。遇到 AntBO/CDRH3 的这些 LDM 请求时不要调用工具、
-不要改用小分子 LDM-BO、不要探测目录或直连 HTTP；明确回复“当前 Delta CLI catalog
-未暴露该 operation；未发送远端请求”。
-
-启动作业只能根据同一次 native 的 `started`、`pid` 和 `log_name`/`log_path`
-报告；任一字段缺失时标记为未验证，不要重复提交或编造作业信息。
-
-`health`、`log`、`jobs` 是只读调用。`run-default-job`、`run`、`stop` 会改变远端状态；
-`run-default-job` 的 `log_name`、`append`、`timeout_seconds` 使用 `--params-json`。
-没有用户明确授权时不得启动或停止；未知结果不得重试。

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

@@ -1,69 +0,0 @@
-"""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",
-    },
-}