@delta-infra/cli 1.0.98 → 1.1.0

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())

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

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