@cyanheads/pubmed-mcp-server 2.7.1 → 2.7.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (10) hide show
  1. package/CLAUDE.md +16 -4
  2. package/README.md +11 -2
  3. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  4. package/dist/services/europe-pmc/europe-pmc-service.js +1 -0
  5. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  6. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  7. package/dist/services/ncbi/response-handler.js +8 -6
  8. package/dist/services/ncbi/response-handler.js.map +1 -1
  9. package/package.json +11 -6
  10. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -2,7 +2,7 @@
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  **Server:** @cyanheads/pubmed-mcp-server
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  **Version:** 2.6.12
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.1`
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.4`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -262,7 +262,7 @@ Available skills:
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  | `devcheck` | Lint, format, typecheck, audit |
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  | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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  | `maintenance` | Investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest` |
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- | `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR |
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+ | `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR / `.mcpb` bundle on GitHub Releases |
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  | `api-auth` | Auth modes, scopes, JWT/OAuth |
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  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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  | `api-config` | AppConfig, parseConfig, env vars |
@@ -288,19 +288,31 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run build` | Compile TypeScript |
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  | `bun run rebuild` | Clean + build |
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  | `bun run clean` | Remove build artifacts |
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- | `bun run devcheck` | Lint + format + typecheck + security |
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+ | `bun run devcheck` | Lint + format + typecheck + security + packaging alignment |
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+ | `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — `bun update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
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  | `bun run tree` | Generate directory structure doc |
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  | `bun run format` | Auto-fix formatting |
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  | `bun run test` | Run tests |
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  | `bun run lint:mcp` | Validate MCP definitions against spec |
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+ | `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
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+ | `bun run list-skills` | List skills in `skills/` with name + description |
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+ | `bun run bundle` | Build and pack as `dist/pubmed-mcp-server.mcpb` for one-click Claude Desktop install |
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  | `bun run start:stdio` | Production mode (stdio) |
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  | `bun run start:http` | Production mode (HTTP) |
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  ---
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+ ## Bundling
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+
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+ `bun run bundle` produces `dist/pubmed-mcp-server.mcpb` for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
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+ **Adding an env var requires both files**: `server.json` stdio `environmentVariables[]` (registry discovery) and `manifest.json` `mcp_config.env` (bundle install UX, plus `user_config` if user-prompted). `bun run lint:packaging` (run by `devcheck`) verifies the env var names align.
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+ ---
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+
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  ## Publishing
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- Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, and GHCR, halting on the first failure. For reference, the underlying commands are:
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+ Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, GHCR, and attaches the `.mcpb` bundle to the GitHub Release, halting on the first failure. For reference, the underlying commands are:
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  ```bash
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  bun publish --access public
package/README.md CHANGED
@@ -7,9 +7,17 @@
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.7.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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- [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-2.7.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ </div>
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+ <div align="center">
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+ [![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubmed-mcp-server/releases/latest/download/pubmed-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubmed-mcp-server&config=eyJjb21tYW5kIjoibnB4IC15IEBjeWFuaGVhZHMvcHVibWVkLW1jcC1zZXJ2ZXIifQ%3D%3D) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubmed-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fpubmed-mcp-server%22%5D%7D)
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+ [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  </div>
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@@ -296,6 +304,7 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
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  | `MCP_PUBLIC_URL` | Public origin override for TLS-terminating reverse-proxy deployments (landing page, Server Card, RFC 9728 metadata). | none |
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  | `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |
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  | `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |
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+ | `MCP_GC_PRESSURE_INTERVAL_MS` | Opt-in Bun-only forced-GC pressure loop (ms). Drains the per-request `McpServer`/`McpSessionTransport` cycle under sustained low-traffic HTTP. Recommended starting point if heap growth is observed: `60000`. | `0` (disabled) |
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  | `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
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  | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
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  | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2BpB;;;;;;;GAOG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;gBAG1B,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM;IAmBrC;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC;IAkF3E;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC;IAkBnC;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS;IAgCnD;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
package/dist/services/europe-pmc/europe-pmc-service.js CHANGED
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  */
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  import { internalError, JsonRpcErrorCode, McpError, serializationError, validationError, } from '@cyanheads/mcp-ts-core/errors';
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  import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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+ // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
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  import { XMLParser, XMLValidator } from 'fast-xml-parser';
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  import { getServerConfig } from '../../config/server-config.js';
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  import { recoveryFor } from '../../services/error-contracts.js';
package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
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+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -7,13 +7,15 @@
7
7
  import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
8
8
  import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
9
9
  /**
10
- * fast-xml-parser is pinned to `~5.7.3` in package.json. 5.8.0 deprecates
11
- * `XMLValidator` in favor of a new sibling package `fast-xml-validator`
12
- * (published days before the deprecation, 0 dependents, by the same author).
13
- * 5.8.0 carries no security fix or feature we need, so we stay on 5.7.x until
14
- * `fast-xml-validator` has time in the wild. Re-evaluate during a future
15
- * `maintenance` pass — if `bun update --latest` bumps this, restore the pin.
10
+ * fast-xml-parser 5.8.0 marks the in-tree `XMLValidator` as `@deprecated` in
11
+ * favor of the new sibling package `fast-xml-validator`. The export still
12
+ * works; we stay on it until the sibling has real adoption (was 17 days old
13
+ * with 1 star at 5.8.0 release). Both call sites strip `<!DOCTYPE ...>`
14
+ * before `XMLValidator.validate`, so the tightened DOCTYPE entity validation
15
+ * 5.8.0 adds via `xml-naming` cannot reach us. Revisit when the sibling
16
+ * matures.
16
17
  */
18
+ // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
17
19
  import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
18
20
  import { recoveryFor } from '../../services/error-contracts.js';
19
21
  /**
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.7.1",
3
+ "version": "2.7.3",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
@@ -18,7 +18,11 @@
18
18
  "tree": "bun run scripts/tree.ts",
19
19
  "format": "biome check --write --unsafe",
20
20
  "test": "bunx vitest run",
21
+ "audit:refresh": "rm -f bun.lock && bun install && bun audit",
22
+ "list-skills": "bun run scripts/list-skills.ts",
21
23
  "lint:mcp": "bun run scripts/lint-mcp.ts",
24
+ "lint:packaging": "bun run scripts/lint-packaging.ts",
25
+ "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubmed-mcp-server.mcpb",
22
26
  "changelog:build": "bun run scripts/build-changelog.ts",
23
27
  "changelog:check": "bun run scripts/build-changelog.ts --check",
24
28
  "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
@@ -72,24 +76,25 @@
72
76
  "access": "public"
73
77
  },
74
78
  "dependencies": {
75
- "@cyanheads/mcp-ts-core": "^0.9.1",
79
+ "@cyanheads/mcp-ts-core": "^0.9.4",
76
80
  "defuddle": "^0.18.1",
77
- "fast-xml-parser": "~5.7.3",
81
+ "fast-xml-parser": "^5.8.0",
78
82
  "linkedom": "^0.18.12",
79
83
  "pino-pretty": "^13.1.3",
80
84
  "sanitize-html": "^2.17.4",
81
- "unpdf": "^1.6.2"
85
+ "unpdf": "^1.6.2",
86
+ "zod": "^4.4.3"
82
87
  },
83
88
  "devDependencies": {
84
89
  "@biomejs/biome": "^2.4.15",
85
90
  "@types/node": "^25.9.1",
86
91
  "@types/sanitize-html": "^2.16.1",
87
- "@vitest/coverage-istanbul": "^4.1.6",
92
+ "@vitest/coverage-istanbul": "^4.1.7",
88
93
  "depcheck": "^1.4.7",
89
94
  "fast-check": "^4.8.0",
90
95
  "ignore": "^7.0.5",
91
96
  "tsc-alias": "^1.8.17",
92
97
  "typescript": "^6.0.3",
93
- "vitest": "^4.1.6"
98
+ "vitest": "^4.1.7"
94
99
  }
95
100
  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.7.1",
9
+ "version": "2.7.3",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.7.1",
22
+ "version": "2.7.3",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -66,7 +66,7 @@
66
66
  "registryBaseUrl": "https://registry.npmjs.org",
67
67
  "identifier": "@cyanheads/pubmed-mcp-server",
68
68
  "runtimeHint": "bun",
69
- "version": "2.7.1",
69
+ "version": "2.7.3",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",