@cyanheads/pubmed-mcp-server 2.7.8 → 2.7.9

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 (5) hide show
  1. package/AGENTS.md +7 -2
  2. package/CLAUDE.md +7 -2
  3. package/README.md +5 -5
  4. package/package.json +5 -4
  5. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,8 +1,8 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.7.8
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.16`
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+ **Version:** 2.7.9
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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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.
@@ -269,8 +269,10 @@ Available skills:
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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  | `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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  | `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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+ | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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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-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
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  | `api-config` | AppConfig, parseConfig, env vars |
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  | `api-context` | Context interface, logger, state, progress |
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  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
@@ -283,6 +285,8 @@ Available skills:
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  | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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  | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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+ **Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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+
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  When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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  ---
@@ -303,6 +307,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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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 release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |
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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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package/CLAUDE.md CHANGED
@@ -1,8 +1,8 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.7.8
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.16`
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+ **Version:** 2.7.9
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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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.
@@ -269,8 +269,10 @@ Available skills:
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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  | `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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  | `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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+ | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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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-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
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  | `api-config` | AppConfig, parseConfig, env vars |
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  | `api-context` | Context interface, logger, state, progress |
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  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
@@ -283,6 +285,8 @@ Available skills:
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  | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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  | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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+ **Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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+
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  When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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  ---
@@ -303,6 +307,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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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 release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |
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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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package/README.md CHANGED
@@ -9,7 +9,7 @@
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- [![Version](https://img.shields.io/badge/Version-2.7.8-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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+ [![Version](https://img.shields.io/badge/Version-2.7.9-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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@@ -204,7 +204,7 @@ A public instance is available at `https://pubmed.caseyjhand.com/mcp` — no ins
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  ```json
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  {
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  "mcpServers": {
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- "pubmed": {
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+ "pubmed-mcp-server": {
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  "type": "streamable-http",
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  "url": "https://pubmed.caseyjhand.com/mcp"
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  }
@@ -219,7 +219,7 @@ Add the following to your MCP client configuration file.
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  ```json
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  {
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  "mcpServers": {
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- "pubmed": {
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+ "pubmed-mcp-server": {
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  "type": "stdio",
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  "command": "bunx",
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  "args": ["@cyanheads/pubmed-mcp-server@latest"],
@@ -238,7 +238,7 @@ Or with npx (no Bun required):
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  ```json
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  {
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  "mcpServers": {
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- "pubmed": {
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+ "pubmed-mcp-server": {
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  "type": "stdio",
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  "command": "npx",
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  "args": ["-y", "@cyanheads/pubmed-mcp-server@latest"],
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  ```json
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  {
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  "mcpServers": {
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- "pubmed": {
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+ "pubmed-mcp-server": {
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  "type": "stdio",
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  "command": "docker",
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  "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubmed-mcp-server:latest"]
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@cyanheads/pubmed-mcp-server",
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- "version": "2.7.8",
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+ "version": "2.7.9",
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  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
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  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
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  "type": "module",
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  "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubmed-mcp-server.mcpb",
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  "changelog:build": "bun run scripts/build-changelog.ts",
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  "changelog:check": "bun run scripts/build-changelog.ts --check",
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+ "release:github": "bun run scripts/release-github.ts",
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  "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
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  "start:stdio": "MCP_TRANSPORT_TYPE=stdio bun ./dist/index.js",
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  "start:http": "MCP_TRANSPORT_TYPE=http bun ./dist/index.js"
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  "access": "public"
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  },
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  "dependencies": {
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- "@cyanheads/mcp-ts-core": "^0.9.16",
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+ "@cyanheads/mcp-ts-core": "^0.9.21",
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  "defuddle": "^0.18.1",
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  "fast-xml-parser": "^5.8.0",
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  "linkedom": "^0.18.12",
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  "@biomejs/biome": "^2.4.16",
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  "@types/node": "^25.9.1",
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  "@types/sanitize-html": "^2.16.1",
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- "@vitest/coverage-istanbul": "^4.1.7",
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+ "@vitest/coverage-istanbul": "^4.1.8",
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  "depcheck": "^1.4.7",
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  "fast-check": "^4.8.0",
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  "ignore": "^7.0.5",
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  "tsc-alias": "^1.8.17",
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  "typescript": "^6.0.3",
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- "vitest": "^4.1.7"
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+ "vitest": "^4.1.8"
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  }
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  }
package/server.json CHANGED
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  "url": "https://github.com/cyanheads/pubmed-mcp-server",
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  "source": "github"
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  },
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- "version": "2.7.8",
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+ "version": "2.7.9",
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  "remotes": [
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  {
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  "type": "streamable-http",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.7.8",
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+ "version": "2.7.9",
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  "packageArguments": [
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  "type": "positional",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.7.8",
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+ "version": "2.7.9",
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  "packageArguments": [
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  {
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  "type": "positional",