setup · diff

git:20251217.e27dd0a to git:20261011.673710b

27 added, 9 removed. Audit A to A.

---

name: setup

- description: This skill should be used when user encounters "paper-search MCP error", "Docker not found", "Docker not running", "paper search not working", or needs help configuring paper search integration.

+ description: This skill should be used when the user asks to "set up paper search", reports "paper-search command not found", wants to "replace paper search MCP", or needs help with paper search credentials.

---

- # Paper Search Tools Setup

+ # Set up Paper Search CLI

- Run `/paper-search-tools:setup` to configure Paper Search MCP.

+ Use [fcakyon/paper-search-cli](https://github.com/fcakyon/paper-search-cli) for paper searches, DOI lookup, PDF downloads, and text extraction. It requires uv and Python 3.10+; Docker and an MCP server are unnecessary.

- ## Quick Fixes

+ 1. Run `uv --version`. If missing, follow the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/).

+ 2. Install the CLI:

- - **Docker not found** - Install Docker (see setup command)

- - **Docker not running** - Start Docker Desktop

- - **Connection failed** - Restart Claude Code after Docker starts

+ ```bash

+ uv tool install 'git+https://github.com/fcakyon/paper-search-cli'

+ ```

- ## Don't Need Paper Search?

+ 3. Run `paper-search --help` and `paper-search sources`. If the command is not on PATH, run `uv tool update-shell` and open a new shell.

+ 4. Check a public source:

- Disable via `/mcp` command to prevent errors.

+ ```bash

+ paper-search search 'object detection' -s crossref -n 3

+ ```

+ Inspect the JSON `errors` field before declaring the search successful. An empty result or a provider error does not confirm working access.

+ For updates, run `uv tool upgrade paper-search-cli`.

+ ## Credentials

+ Use the CLI's [.env.example](https://github.com/fcakyon/paper-search-cli/blob/main/.env.example) for provider keys. Its current configuration path is `~/.config/paper-search-mcp/.env`; the legacy path and `PAPER_SEARCH_MCP_*` names remain supported. Do not print secret values.

+ IEEE, Scopus, and Web of Science need credentials. Scopus and Web of Science require explicit source selection. Unpaywall needs an email. Metadata access does not guarantee access to a PDF.

+ ## Migrate from the MCP plugin

+ This plugin no longer registers the Docker MCP server. Reload the updated plugin to discard its old registration. If the user separately configured a `paper-search` MCP entry, identify that entry and remove it only when requested; preserve other servers. Run CLI commands directly without waiting for an MCP connection.