@delta-infra/cli 1.1.19 → 1.1.21

package/scripts/run.js

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

package/skills/delta-protein/AGENTS.md

@@ -1,73 +1,73 @@
-# skills/delta-protein — Protein Analysis Skill Package
-
-**Parent:** `../AGENTS.md`
-
-## OVERVIEW
-
-Single public `delta-protein` skill: the unified entry point for Huada protein and
-bioinformatics online analysis tools (mutation prediction, structure prediction, MSA,
-protein design, docking, pocket/active-site analysis, conservation/InterPro,
-enzyme kinetics, solubility/pH prediction, and PubMed/PubChem/UniProt/PISA/PLIP
-lookup). It is host-neutral and routed exclusively through the Delta CLI
-(`science invoke`) to the Science Server's `huada_protein_tools` tool. Per-endpoint
-operation contracts live in `references/` and are loaded on demand; there are no
-separate planner-visible per-tool skills and no workflow endpoints.
-
-## STRUCTURE
-
-```
-delta-protein/
-├── SKILL.md                 # single entry point: routing, CLI-only execution, safety red lines
-├── agents/
-│   └── openai.yaml          # host agent registration
-└── references/
-    └── <endpoint>.md        # one registered endpoint's operation contract
-                             #  (39 endpoints under tool `huada_protein_tools`)
-```
-
-## DATA SOURCE
-
-- Tool/endpoint identity and request fields come from the live Catalog
-  (`delta-cli science list`, `delta-cli science endpoints list <tool>`) plus the
-  authoritative parameter registry in
-  `agent/protein_common/tool_registry/definitions.py` of the `delta-search-backend`
-  project (per-tool `params`, `required_groups`, `default_params`, `timeout`).
-- Response envelope is the Huada contract `{"status","message","tool_type",
-  "resultjson","download_url"}`; per-tool `resultjson` keys are derived from the
-  tool implementations, not invented.
-- Each registered endpoint is a single tool call. Multi-step card workflows
-  (cards/*.json) are NOT registered as endpoints and are not documented here; an
-  agent may chain single endpoints in sequence when the task requires it.
-
-## CONVENTIONS
-
-- JSON/query operations go through `delta-cli science invoke --tool huada_protein_tools --endpoint <name>`; binary artifacts from `download_url` go through `delta-cli science file download`
-- Endpoint names are exact server contracts, read from the Catalog — never invent fields/enums from memory
-- Success is reported only when the subprocess exit is 0 AND top-level JSON `ok` is `true`; `data` holds the service response
-- `references/` contains only registered real endpoints; routing and tool selection belong in `SKILL.md`
-- Host-neutral: `delta-cli` is the sole service boundary; no host-specific tool/env dependencies
-- Discover newly-deployed endpoints via `delta-cli science endpoints list huada_protein_tools`
-
-## MAINTENANCE
-
-- `scripts/gen_references.py` regenerates the `## Output Projection` and
-  `## Output Template` sections in every reference from
-  `scripts/output_metadata.json` (single source of truth for field projection /
-  presentation form / downstream reuse / provenance marker). Stdlib only, idempotent.
-- Workflow: update `output_metadata.json` → run
-  `python scripts/gen_references.py` → run `python scripts/gen_references.py --check`.
-  `--check` fails loudly on missing sections, drifting titles, broken SKILL links or
-  references not covered by metadata.
-- `output_metadata.json` `provenance` is `tested` (verified by a real `delta-cli`
-  invocation) or `derived` (from ToolSpec descriptions / agent templates, marked
-  "pending live calibration"). Newly verified endpoints should be flipped to `tested`.
-- After changing references/SKILL, resync the opencode install dir:
-  `python scripts/gen_references.py --sync "%USERPROFILE%\.config\opencode\skills\delta-protein"`.
-
-## ANTI-PATTERNS
-
-- Do not call `curl`/`requests`/`httpx`/browser/PowerShell web directly against any Huada or Gateway URL
-- Do not bypass delta-cli or attach local MCP tool servers directly
-- Do not fabricate protein sequences, structures, activity data, or algorithm results, and do not pass local-library results off as Science results
-- Do not create extra JSON/CSV/report/image artifacts unless the user explicitly asks
+# skills/delta-protein — Protein Analysis Skill Package
+
+**Parent:** `../AGENTS.md`
+
+## OVERVIEW
+
+Single public `delta-protein` skill: the unified entry point for Huada protein and
+bioinformatics online analysis tools (mutation prediction, structure prediction, MSA,
+protein design, docking, pocket/active-site analysis, conservation/InterPro,
+enzyme kinetics, solubility/pH prediction, and PubMed/PubChem/UniProt/PISA/PLIP
+lookup). It is host-neutral and routed exclusively through the Delta CLI
+(`science invoke`) to the Science Server's `huada_protein_tools` tool. Per-endpoint
+operation contracts live in `references/` and are loaded on demand; there are no
+separate planner-visible per-tool skills and no workflow endpoints.
+
+## STRUCTURE
+
+```
+delta-protein/
+├── SKILL.md                 # single entry point: routing, CLI-only execution, safety red lines
+├── agents/
+│   └── openai.yaml          # host agent registration
+└── references/
+    └── <endpoint>.md        # one registered endpoint's operation contract
+                             #  (39 endpoints under tool `huada_protein_tools`)
+```
+
+## DATA SOURCE
+
+- Tool/endpoint identity and request fields come from the live Catalog
+  (`delta-cli science list`, `delta-cli science endpoints list <tool>`) plus the
+  authoritative parameter registry in
+  `agent/protein_common/tool_registry/definitions.py` of the `delta-search-backend`
+  project (per-tool `params`, `required_groups`, `default_params`, `timeout`).
+- Response envelope is the Huada contract `{"status","message","tool_type",
+  "resultjson","download_url"}`; per-tool `resultjson` keys are derived from the
+  tool implementations, not invented.
+- Each registered endpoint is a single tool call. Multi-step card workflows
+  (cards/*.json) are NOT registered as endpoints and are not documented here; an
+  agent may chain single endpoints in sequence when the task requires it.
+
+## CONVENTIONS
+
+- JSON/query operations go through `delta-cli science invoke --tool huada_protein_tools --endpoint <name>`; binary artifacts from `download_url` go through `delta-cli science file download`
+- Endpoint names are exact server contracts, read from the Catalog — never invent fields/enums from memory
+- Success is reported only when the subprocess exit is 0 AND top-level JSON `ok` is `true`; `data` holds the service response
+- `references/` contains only registered real endpoints; routing and tool selection belong in `SKILL.md`
+- Host-neutral: `delta-cli` is the sole service boundary; no host-specific tool/env dependencies
+- Discover newly-deployed endpoints via `delta-cli science endpoints list huada_protein_tools`
+
+## MAINTENANCE
+
+- `scripts/gen_references.py` regenerates the `## Output Projection` and
+  `## Output Template` sections in every reference from
+  `scripts/output_metadata.json` (single source of truth for field projection /
+  presentation form / downstream reuse / provenance marker). Stdlib only, idempotent.
+- Workflow: update `output_metadata.json` → run
+  `python scripts/gen_references.py` → run `python scripts/gen_references.py --check`.
+  `--check` fails loudly on missing sections, drifting titles, broken SKILL links or
+  references not covered by metadata.
+- `output_metadata.json` `provenance` is `tested` (verified by a real `delta-cli`
+  invocation) or `derived` (from ToolSpec descriptions / agent templates, marked
+  "pending live calibration"). Newly verified endpoints should be flipped to `tested`.
+- After changing references/SKILL, resync the opencode install dir:
+  `python scripts/gen_references.py --sync "%USERPROFILE%\.config\opencode\skills\delta-protein"`.
+
+## ANTI-PATTERNS
+
+- Do not call `curl`/`requests`/`httpx`/browser/PowerShell web directly against any Huada or Gateway URL
+- Do not bypass delta-cli or attach local MCP tool servers directly
+- Do not fabricate protein sequences, structures, activity data, or algorithm results, and do not pass local-library results off as Science results
+- Do not create extra JSON/CSV/report/image artifacts unless the user explicitly asks
 - Do not break relative links between SKILL.md and `references/`