pubmed-stream 0.4.3

Added

• A listing in the official MCP Registry, which other MCP directories copy: server.json describes the server as the PyPI package run with uvx and the argument mcp, with the optional NCBI_API_KEY and NCBI_EMAIL, and the README carries the hidden line mcp-name: io.github.melhzy/pubmed-stream by which the registry checks that the PyPI package belongs to it. The release steps in the README end with mcp-publisher publish, and the tests keep server.json's versions and name in step with the package.

• The MCP server reports progress. When the assistant asks for it, download, fetch_abstracts and build_knowledge_graph send MCP progress notifications while they run: the articles downloaded so far, the abstracts fetched, and the search, key paper or build the knowledge graph is at. search_and_download, fetch_abstracts and create_kg take a progress callback, called with (done, total, message), for the same.

Fixed

• On Windows, the console window that a desktop app's start opens for the MCP server no longer stays on screen: the server hides it as soon as it runs, so it only flashes. A desktop app such as Claude's or ChatGPT's has no console, so Windows gives the server a new one, where a terminal's server shares the terminal's console; the window is hidden only when every process attached to the console is uv, a launcher or Python, so a terminal is never touched (hide_own_console).
• Cowork can start the plugin's server. The Claude Code manifest gives the NCBI API key option an empty default: Cowork ignores an MCP server that references an option without one, and never asks for values, where Claude Code asks at install. The README, the plugin's README and tutorial 7 say how the Claude desktop app reaches pubmed-stream: its Code tab has the plugin installed from the terminal; Cowork needs the plugin on the claude.ai account, added from Customize > Plugins with melhzy/pubmed-stream as a marketplace; chat cannot start a program on the computer. init counts a plugin synced from the account, which Claude Code loads with no settings entry, so it writes no second server for the folder. The Codex CLI calls the skill as $pubmed-stream:literature-search, as the docs now say.

Changed

• PyPI describes pubmed-stream as what it now is, literature searches in PubMed and PubMed Central for researchers and their AI assistants, with an MCP server and a plugin for Claude Code and Codex, and its keywords and classifiers add MCP, the assistants, Ollama and artificial intelligence, so searches for them find it.

• The MCP server's instructions, which every assistant receives on connecting, cover all nine tools and the order to use them in, ask for each search to be reported with its count, and say to prefer pubmed-stream's tools to other PubMed tools the assistant may have, since pubmed-stream saves every article it reads; AGENTS.md and the plugin's skill say the same.

• The plugin has a README of its own, as Anthropic's plugin directory requires, saying what it runs, sends and saves. The README and tutorial 7 say what to type to call pubmed-stream in Claude Code, the Codex app and the Codex CLI, that Claude's chat cannot use it, what to do when the plugin's first start takes too long, and what to do when Claude Code reaches for Anthropic's own PubMed connector instead.

• The plugin's Codex settings moved from .mcp.json to .codex-plugin/mcp.json and give the server 60 seconds to start and 600 per call, instead of Codex's 10 and 60: the first start downloads pubmed-stream, and a large download or a knowledge graph takes minutes. Claude Code reads the server from .claude-plugin/plugin.json, as before.

• The README, tutorial 7 and the assistant's instructions explain how pubmed-stream connects to Claude Code and Codex: the MCP server is part of the Python library, started as pubmed-stream mcp, and the plugin, init and claude mcp add or codex mcp add only tell the assistant how to start it. The README has a new title, a section on the three ways to connect with the nine tools listed, and installs the Codex plugin from the terminal with codex plugin add pubmed-stream@pubmed-stream. When the tools are missing, AGENTS.md and the plugin's skill tell the assistant what to ask the researcher to run, and pubmed-stream mcp --help lists all nine tools and the three ways. Tutorial 7 adds MCP to its list of tools, explains the connection in section 3, shows how to update, list and remove the plugin, describes what the plugin contains, and troubleshoots either way of connecting; the glossary has entries for plugin, skill and uv, and its MCP entry links to the renamed section; the setup, troubleshooting and Obsidian guides and the tutorials index name the plugin beside init.

Upgrade: pip install --upgrade pubmed-stream