# Scholar MCP [](https://github.com/pvliesdonk/scholar-mcp/actions/workflows/ci.yml) [](https://codecov.io/gh/pvliesdonk/scholar-mcp) [](https://repowise.dev/repo/pvliesdonk/scholar-mcp) [](https://repowise.dev/repo/pvliesdonk/scholar-mcp) [](https://pypi.org/project/pvliesdonk-scholar-mcp/) [](https://pypi.org/project/pvliesdonk-scholar-mcp/) [](LICENSE) [](https://github.com/pvliesdonk/scholar-mcp/pkgs/container/scholar-mcp) [](https://pvliesdonk.github.io/scholar-mcp/) [](https://pvliesdonk.github.io/scholar-mcp/latest/llms.txt) [](https://github.com/pvliesdonk/fastmcp-server-template) Scholarly papers, patents, books, standards and PDF conversion **[Documentation](https://pvliesdonk.github.io/scholar-mcp/)** | **[Config wizard](https://pvliesdonk.github.io/scholar-mcp/latest/configuration-generator/)** | **[PyPI](https://pypi.org/project/pvliesdonk-scholar-mcp/)** | **[Docker](https://github.com/pvliesdonk/scholar-mcp/pkgs/container/scholar-mcp)** ## Features 29 tools, organised by scholarly source type. ### Source domains - **Papers**: full-text search with year/venue/field/citation filters; single-paper lookup by DOI, S2 ID, arXiv ID, ACM ID, or PubMed ID; author profile and name search; forward citations, backward references, BFS graph traversal, shortest-path bridge discovery; recommendations from positive/negative examples; BibTeX/CSL-JSON/RIS citation generation with OpenAlex venue enrichment. - **Patents**: search across 100+ patent offices via EPO OPS with CPC/applicant/inventor/jurisdiction filters; bibliographic, claims, description, family, legal, and citations sections; NPL-to-paper resolution via Semantic Scholar and paper-to-patent citation discovery. EPO credentials are optional; other domains work without them. - **Books**: Open Library search by title/author/keywords, no API key required; lookup by ISBN-10/13 or by Open Library work/edition ID; subject-based recommendations sorted by popularity; Google Books excerpts and preview links; WorldCat permalinks for library discovery; cover image caching. Papers with an ISBN in `externalIds` are automatically enriched with publisher, edition, cover URL, and subject data from Open Library. - **Standards**: identifier resolution, search, and metadata retrieval for NIST, IETF, W3C, and ETSI standards, with optional full-text fetch and Markdown conversion via docling. Tier 2 ISO, IEC, IEEE, Common Criteria (CC), and CEN/CENELEC metadata (including ISO/IEC/IEEE joint standards and the CC ↔ ISO/IEC 15408 cross-link) is synced locally via `sync-standards`. ISO, IEC, IEEE have a live-fetch fallback for unsynced identifiers; CC and CEN have no live API and require a sync first. Citations matching standards patterns (RFC, ISO, NIST SP, IEEE, EN, CC) are automatically enriched with structured `standard_metadata` including identifier, title, body, status, and full-text URL when available (see [docs/guides/standards.md](docs/guides/standards.md)). ### Cross-cutting - **Enrichment pipeline**: phased enrichment from multiple sources: OpenAlex (OA status, affiliations, funders, concepts), CrossRef (publisher, page ranges, container titles), Google Books (preview links, excerpts), and Open Library (book metadata). Runs automatically on paper and book results. - **PDF conversion**: download open-access PDFs and convert to Markdown via [docling-serve](https://github.com/DS4SD/docling-serve), with optional VLM enrichment for formulas and figures; automatic fallback to ArXiv, PubMed Central, and Unpaywall when Semantic Scholar has no OA link; direct URL download for PDFs found elsewhere. - **Intelligent caching**: SQLite-backed cache with per-table TTLs (30 days for papers/authors, 7 days for citations/references) and identifier aliasing. - **Authentication**: bearer token, OIDC (OAuth 2.1), or both simultaneously (multi-auth). - **Multi-transport**: stdio (Claude Desktop), HTTP (streamable-http), and SSE transports. - **Linux packages**: `.deb` and `.rpm` packages with systemd service and security hardening. ### Coverage by domain Per-domain depth is uneven. Papers currently have the richest tool surface (citation graph, recommendations, cross-referencing to all three other domains); standards are the leanest. That reflects public data availability, not a value hierarchy: writing a paper typically needs all four source types for citations and prior art. Parity work is tracked in [GitHub issues](https://github.com/pvliesdonk/scholar-mcp/issues) and [milestones](https://github.com/pvliesdonk/scholar-mcp/milestones); the roadmap shows intent, not a completeness commitment. ## What you can do with it With this server mounted in an MCP client (Claude, etc.), you can: - **Survey a field**: "Find the 20 most-cited papers on graph neural networks from 2020 to 2024 and draft a literature review outline." Composes `search_papers` + `get_citations` + `enrich_paper`. - **Trace a citation path**: "What's the shortest citation path from 'Attention is All You Need' to 'RLHF for dialogue agents'?" Uses `find_bridge_papers` + `get_citation_graph`. - **Cross-reference prior art**: "For this patent family, list academic papers it cites and any books or standards that show up in the description." Composes `get_patent` + `batch_resolve` + standards/book enrichment. - **Generate a bibliography**: "Emit BibTeX for these 30 DOIs with OpenAlex venue data." Uses `generate_citations`. - **Look up a standard**: "What's the latest status of RFC 9000, and fetch the Markdown full text." Uses `resolve_standard_identifier` + `get_standard`. ## Installation ### From PyPI ```bash pip install pvliesdonk-scholar-mcp ``` If you add optional extras via the `PROJECT-EXTRAS-START` / `PROJECT-EXTRAS-END` sentinels in `pyproject.toml`, document them below: - **`[all]`**: every production feature in one extra; the Linux packages and the Claude Desktop bundle install it. - **`[debug]`**: adds the remote debugger (`debugpy`); see [Remote debugging](docs/deployment/docker.md#remote-debugging). The base package already carries FastMCP through `fastmcp-pvl-core`, so `pip install pvliesdonk-scholar-mcp` is enough to run `scholar-mcp serve`. The older `[mcp]` extra is kept so existing install commands keep working; it adds nothing beyond the base package. ### From source ```bash git clone https://github.com/pvliesdonk/scholar-mcp.git cd scholar-mcp uv sync --all-extras --all-groups ``` ### Docker ```bash docker pull ghcr.io/pvliesdonk/scholar-mcp:latest ``` To run the newest merged code instead of the newest release, use the rolling `edge` tag. It is rebuilt on every merge to `main` and carries no version identity. See [Image tags](docs/deployment/docker.md#image-tags) for the full tag list. ```bash docker pull ghcr.io/pvliesdonk/scholar-mcp:edge ``` A `compose.yml` ships at the repo root and runs as-is: copy `.env.example` to `.env`, then `docker compose up -d`. It publishes port 8000 on the host and assumes no reverse proxy; [Docker Compose](docs/deployment/docker.md#docker-compose) covers the configuration split, the domain sentinel blocks, and a Traefik overlay. To attach a remote Python debugger (development only; the protocol is unauthenticated), see [Remote debugging](docs/deployment/docker.md#remote-debugging). ### Linux packages (.deb / .rpm) Download `.deb` or `.rpm` packages from the [GitHub Releases](https://github.com/pvliesdonk/scholar-mcp/releases) page. Both install a hardened systemd unit; env configuration is sourced from `/etc/scholar-mcp/env` (copy from the shipped `/etc/scholar-mcp/env.example`). ### Claude Desktop (.mcpb bundle) Download the `.mcpb` bundle from the [GitHub Releases](https://github.com/pvliesdonk/scholar-mcp/releases) page and double-click to install, or run: ```bash mcpb install scholar-mcp-.mcpb ``` Claude Desktop prompts for required env vars via a GUI wizard, with no manual JSON editing needed. For manual Claude Desktop configuration and setup options, see [Claude Desktop deployment](docs/deployment/claude-desktop.md). ## Release channels Artifacts ship on three channels. Each row lists exactly what that channel publishes. | Channel | Version identity | Artifacts | |---|---|---| | `edge` (rolling) | None; the commit is the identity | Docker image `:edge` rebuilt on every merge to `main`; `.mcpb` bundle as the `mcpb-bundle-edge` workflow artifact; Claude Code plugin `.zip` as the `plugin-zip-edge` artifact; rolling `unstable` docs version. It leaves no git tag, GitHub release, or PyPI entry behind. | | Pre-release | `vX.Y.Z-rc.N`, computed and reviewed in its release pull request | PyPI (as the pre-release `X.Y.ZrcN`); GitHub release with wheels, `sdist`, `.deb`/`.rpm` packages, `.mcpb` bundle, plugin `.zip`, and SBOM attached; Docker image under its immutable `vX.Y.Z-rc.N` tag plus the ordering-aware rolling `rc` tag. Skips the plugin marketplace, the MCP registry, and the docs deploy. | | Stable | `vX.Y.Z` | Everything: PyPI, Docker (version tag plus ordering-aware `latest` / `vX` / `vX.Y`), `.deb`/`.rpm`, GitHub release assets (wheels, `sdist`, `.mcpb` bundle, plugin `.zip`, SBOM), plugin marketplace and MCP registry entries (when the release is the newest stable), versioned docs with an ordering-aware `latest` alias. | Pre-releases reach PyPI so that a candidate's `.mcpb` bundle installs: the bundle points at PyPI rather than carrying the code. Ordinary installers never see them, because a PEP 440 resolver skips pre-releases unless the requirement pins one or you pass `--pre`. Ask for a candidate by name with `pip install pvliesdonk-scholar-mcp==X.Y.ZrcN`. PyPI spells it in the PEP 440 canonical form, while tags use SemVer. Rolling pointers are ordering-aware, so a patch release cut from an old `release/X.Y` branch never moves `latest`-style tags back to older content, and a candidate for an already-released version never moves `rc`. See [Release process](docs/deployment/release-process.md) for the full model. ## Quick start ```bash scholar-mcp serve # stdio transport scholar-mcp serve --transport http --port 8000 # streamable HTTP ``` For library usage (embedding the domain logic without the MCP transport), import from the `scholar_mcp` package directly. See the project's domain modules under `src/scholar_mcp/` for entry points. ### Server info The server registers a built-in `get_server_info` tool (via `fastmcp_pvl_core.register_server_info_tool`) so operators can confirm the deployed version with a single MCP call. The default response carries `server_name`, `server_version`, and `core_version`. Servers that talk to a remote upstream wire upstream version reporting inside the `DOMAIN-UPSTREAM-START` / `DOMAIN-UPSTREAM-END` sentinel in `src/scholar_mcp/server.py`; see [`tool-registration`](.agents/skills/tool-registration/SKILL.md#server-info-tool-get_server_info) for the wiring pattern. ### Health The server serves `/health` (liveness, a static `200`) and `/health/ready` (readiness, `503` when a backing store or a domain check fails) outside the MCP mount and outside auth, via `fastmcp_pvl_core.register_health_routes`. `compose.yml` probes the first. Domain readiness checks go in the `health_checks` dict in `src/scholar_mcp/server.py`; see [Docker deployment](docs/deployment/docker.md#health) for the routes, the mount-path rule, and `SCHOLAR_MCP_HEALTH_DETAIL`. ## Configuration The most common environment variables, shared across all `fastmcp-pvl-core`-based services: | Variable | Default | Description | |---|---|---| | `SCHOLAR_MCP_KV_STORE_URL` | `file:///data/state` | Persistent-state backend URL shared by every pvl-core subsystem that needs state. `memory://` is in-process and lost on restart; `file:///path` persists on one server; `redis://`, `dynamodb://` and `mongodb://` each need their matching extra. When unset, defaults to `file:///data/state` (the volume family Docker images mount), or to `memory://` (with a warning) on a host where that directory is not usable. | | `FASTMCP_LOG_LEVEL` | `INFO` | Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG. | | `FASTMCP_ENABLE_RICH_LOGGING` | `true` | Rich color output for a terminal; false gives one plain or JSON line per record. Off in the container image and the systemd unit, since neither is a terminal and Rich wraps a structured record at its 80-column fallback. | This table and the one under [Domain configuration](#domain-configuration) are curated subsets. The complete generated reference, with every variable the server reads, is the [configuration reference](docs/configuration.md); `.env.example` lists the same surface in copy-paste form. ## Authentication Callers authenticate via a bearer token or OIDC (mutually exclusive). See the [Authentication guide](docs/guides/authentication.md) for setup, mapped multi-subject tokens, OIDC, and troubleshooting. ## Post-scaffold checklist After `copier copy` and `gh repo create --push`: 1. **Fill in the DOMAIN blocks** (every section marked with a `DOMAIN` sentinel comment) in this README and in `AGENTS.md`. The `GENERATED-ENV-TABLE-*` regions are not DOMAIN blocks; the config generator owns them and rewrites them on every run. 2. Configure GitHub secrets (see below). 3. Install dev + docs tooling: `uv sync --all-extras --all-groups`. 4. Install pre-commit hooks: `uv run pre-commit install`. 5. Run the gate locally: `uv run pytest -x -q && uv run ruff check --fix . && uv run ruff format . && uv run mypy src/ tests/`. 6. Push the first commit. CI should be green. ## GitHub secrets CI workflows reference two required repository secrets and one optional Claude token. Configure them via **Settings → Secrets and variables → Actions** or with `gh secret set`: | Secret | Used by | How to generate | |---|---|---| | `RELEASE_TOKEN` | `release-prepare.yml`, `release.yml`, `copier-update.yml`, `renovate.yml`, `bootstrap.yml` | Fine-grained PAT at with `contents: write`, `pull_requests: write`, and `administration: write` (bootstrap applies the repository rulesets + auto-merge). Must belong to a repository admin: the shipped rulesets grant bypass to the admin role, and the release tag + GitHub release that knope creates after a release pull request merges rely on it (pull requests the token opens also need it so their CI runs). Scoped to this repo. | | `CODECOV_TOKEN` | `ci.yml` | : sign in with GitHub and add the repo. The upload token is on its settings page. | | `CLAUDE_CODE_OAUTH_TOKEN` | `claude.yml` | Optional. Run `claude setup-token` locally and configure this only for `@claude` or opted-in automatic review. | ```bash gh secret set RELEASE_TOKEN gh secret set CODECOV_TOKEN # Optional: enables @claude and opted-in automatic review. gh secret set CLAUDE_CODE_OAUTH_TOKEN ``` > Dependency updates are handled by **Renovate** (`renovate.yml`), which reuses > `RELEASE_TOKEN`. It maintains `uv.lock` and auto-merges patch/minor bumps once > the `CI Success` check is green; `bootstrap.yml` enables auto-merge and applies > the repository rulesets (`.github/rulesets/`) on first push. See > [Repository Protection](docs/deployment/repository-protection.md) for the > per-branch posture and bypass model. GitHub Actions are updated in the copier > template and arrive via `copier update`, not per-repo. `GITHUB_TOKEN` is auto-provided; no action needed. ## Local development The PR gate (matches CI): ```bash uv run pytest -x -q # tests uv run ruff check --fix . && uv run ruff format . # lint + format uv run mypy src/ tests/ # type-check ``` Pre-commit runs a subset of the gate on each commit; see `.pre-commit-config.yaml` for details, or [`AGENTS.md`](AGENTS.md) for the full Hard PR Acceptance Gates. ## Troubleshooting ### Moving a scaffolded project `uv sync` creates `.venv/bin/*` scripts with absolute shebangs pointing at the venv Python. If you move the repo after scaffolding (`mv /old/path /new/path`), `uv run pytest` fails with `ModuleNotFoundError: No module named 'fastmcp'` because the stale shebang resolves to a different interpreter than the venv's site-packages. **Fix:** ```bash rm -rf .venv uv sync --all-extras --all-groups ``` `uv run python -m pytest` also works as a one-shot workaround (bypasses the stale entry-script shim). ### `uv.lock` refresh after `copier update` When `copier update` introduces new dependencies (such as a new extra added to `pyproject.toml.jinja`), the CI install step runs `uv sync --locked`, which fails against a stale lockfile. Run `uv lock` locally and commit the refreshed `uv.lock` alongside accepting the copier-update PR. CI installs with `--locked` (and the review workflow with `--frozen`) so no job ever rewrites `uv.lock` in its own workspace: a job that re-locks hides the drift it just repaired, and a dirty workspace breaks any later `git checkout` in the same job. Lockfile drift then shows up as a red install step with a clear message, not as a silent mutation. ## Contributing `CONTRIBUTING.md` holds the rules for issues and pull requests, and where a fix belongs: `fastmcp-pvl-core` for library code, the template for template-owned files, this repository for anything inside its `DOMAIN-*` / `CONFIG-*` / `PROJECT-*` blocks. `AGENTS.md` carries the conventions and gates; the skills under `.agents/skills/` carry the task procedures, among them `code-review` (local self-review before a pull request), `writing-release-notes` (release notes), `applying-template-updates` (the weekly template update pull request) and `authoring-issues-prs` (filing). The release procedure is in [docs/deployment/release-process.md](docs/deployment/release-process.md); the template update procedure in [docs/deployment/template-updates.md](docs/deployment/template-updates.md). ## Links - [Documentation](https://pvliesdonk.github.io/scholar-mcp/) - [llms.txt](https://pvliesdonk.github.io/scholar-mcp/latest/llms.txt) - [FastMCP](https://gofastmcp.com) - [fastmcp-pvl-core](https://pypi.org/project/fastmcp-pvl-core/) ## Domain configuration The variables this project features as its entry points (domain variables use the `SCHOLAR_MCP_` prefix): | Variable | Default | Required | Description | |---|---|---|---| | `SCHOLAR_MCP_READ_ONLY` | `true` | No | When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them. | | `SCHOLAR_MCP_S2_API_KEY` | (none) | No | Semantic Scholar API key. Optional but strongly recommended: unauthenticated requests are limited to ~1 req/s. Request one at https://www.semanticscholar.org/product/api#api-key-form. | | `SCHOLAR_MCP_DOCLING_URL` | (none) | No | Base URL of a running docling-serve instance for PDF conversion (such as http://localhost:5001). When unset, PDF conversion tools return an error. | | `SCHOLAR_MCP_CACHE_DIR` | `/data/scholar-mcp` | No | Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/). | | `SCHOLAR_MCP_CONTACT_EMAIL` | (none) | No | Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source. | This is a curated subset: a field appears here when its `tags` metadata includes `readme`. Every domain variable is documented in the [configuration reference](docs/configuration.md), grouped the same way the config wizard presents them. Domain-config fields are composed inside `src/scholar_mcp/config.py` between the `CONFIG-FIELDS-START` / `CONFIG-FIELDS-END` sentinels; env reads go through `fastmcp_pvl_core.env(_ENV_PREFIX, "SUFFIX", default)` so naming stays consistent, and field invariants go in `__post_init__` between the `CONFIG-VALIDATE-START` / `CONFIG-VALIDATE-END` sentinels. Each field's `metadata` `help`, `tags`, and `wizard` group generate the reference tables directly, so keep them accurate and complete. ## Key design decisions - **Library-first, MCP-optional.** The core domain logic (S2/EPO/Open Library/standards clients, enrichment pipeline, cache) is importable without FastMCP; the MCP server is a thin async wrapper. Enables reuse in scripts, notebooks, and other servers. - **Sync domain code, async MCP layer.** Backend clients are synchronous; MCP tools call them via `asyncio.to_thread()`. Simpler client code, explicit offloading at the transport boundary. - **SQLite cache with per-table TTLs and identifier aliases.** Papers / authors last 30 days, citations / references 7 days. DOI ↔ S2 ID ↔ arXiv ID aliasing survives across cache clears so repeated enrichment hits the same row. - **Read-only by default.** Write-tagged tools (PDF download/convert, patent PDF) are hidden unless `SCHOLAR_MCP_READ_ONLY=false`. Safer default for first-run. - **Slow work becomes a background job.** Every tool whose work can run long runs through the `fastmcp-pvl-core` jobs layer, whether the slow part is a docling conversion, an EPO throttle being waited out, or a graph walk making one request per node. A call that beats `SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S` returns its result directly; a slower one returns a handle to poll with `get_job_result`. No tool decides in advance whether to go background, so a cache hit needs no special case. - **EPO throttling is waited out, not queued.** The traffic light is consulted before every request and cached for a minute, so a retry sooner than that would re-read the cache rather than ask again. Each backoff outlasts the cache; an exhausted daily quota is reported immediately instead, since it will not clear today. - **Tier 2 standards sync out-of-band.** ISO/IEC/IEEE/CC/CEN catalogues come from community Relaton dumps via `scholar-mcp sync-standards`, not live at runtime, which avoids paywalled-HTML scraping and keeps tool calls fast.