crossref-local 0.3.1__tar.gz → 0.5.0__tar.gz

crossref_local-0.5.0/.env.example

@@ -0,0 +1,57 @@
+# CrossRef Local Configuration
+# Copy this file to .env and customize as needed
+
+# =============================================================================
+# LOCAL MODE - Direct database access
+# =============================================================================
+
+# Path to CrossRef SQLite database (optional - auto-detected if not set)
+# CROSSREF_LOCAL_DB=/path/to/crossref.db
+
+# =============================================================================
+# DEVELOPMENT / DEBUGGING
+# =============================================================================
+
+# Enable debug mode for verbose logging
+# CROSSREF_LOCAL_DEBUG_MODE=1
+
+# Cache directory (default: ~/.cache/crossref-local)
+# CROSSREF_LOCAL_CACHE_DIR=/path/to/cache
+
+# =============================================================================
+# REMOTE MODE - HTTP API access (via SSH tunnel or direct connection)
+# =============================================================================
+
+# Force remote mode (set to "remote" or "local")
+# CROSSREF_LOCAL_MODE=remote
+
+# API URL for remote mode (default: http://localhost:31291)
+# CROSSREF_LOCAL_API_URL=http://localhost:31291
+
+# Server host/port (for run-server-http)
+# CROSSREF_LOCAL_HOST=0.0.0.0
+# CROSSREF_LOCAL_PORT=31291
+
+# =============================================================================
+# SCITEX INTEGRATION (takes priority over CROSSREF_LOCAL_* variables)
+# =============================================================================
+# Port scheme: 3129X (31290: scitex-cloud, 31291: crossref, 31292: openalex)
+#
+# SCITEX_SCHOLAR_CROSSREF_DB=/path/to/crossref.db
+# SCITEX_SCHOLAR_CROSSREF_MODE=remote
+# SCITEX_SCHOLAR_CROSSREF_HOST=0.0.0.0
+# SCITEX_SCHOLAR_CROSSREF_PORT=31291
+
+# =============================================================================
+# TYPICAL SSH TUNNEL SETUP
+# =============================================================================
+# 1. Create SSH tunnel to your database server:
+#    ssh -L 31291:127.0.0.1:31291 your-nas-server
+#
+# 2. Set environment variables:
+#    export CROSSREF_LOCAL_MODE=remote
+#    export CROSSREF_LOCAL_API_URL=http://localhost:31291
+#
+# 3. Or use CLI flags:
+#    crossref-local --http search "machine learning"
+#    crossref-local --api-url http://localhost:31291 search "query"

{crossref_local-0.3.1 → crossref_local-0.5.0}/.github/workflows/test.yml

@@ -30,11 +30,18 @@ jobs:
         run: |
           python scripts/create_test_db.py --rows 500
 
-      - name: Run tests
+      - name: Run tests with coverage
         run: |
-          pytest tests/ -v --tb=short
+          pytest tests/ -v --tb=short --cov=crossref_local --cov-report=term-missing --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false
 
       - name: Test CLI
         run: |
           crossref-local --help
-          crossref-local info || true
+          crossref-local status || true

{crossref_local-0.3.1 → crossref_local-0.5.0}/.gitignore

@@ -132,6 +132,7 @@ data/*
 **/*.ppt
 **/*.pptx
 **/*.txt
+!docs/sphinx/requirements.txt
 **/*.log
 **/*.db
 **/*.sqlite
@@ -681,3 +682,4 @@ GITIGNORED/
 tests/fixtures/*.db
 tests/fixtures/*.json
 _.venv/
+.coverage

crossref_local-0.5.0/.readthedocs.yaml

@@ -0,0 +1,31 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/sphinx" directory with Sphinx
+sphinx:
+  configuration: docs/sphinx/conf.py
+  fail_on_warning: false
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  - epub
+
+# Python configuration
+python:
+  install:
+    # Install package with all optional dependencies
+    - method: pip
+      path: .
+      extra_requirements:
+        - all
+    # Install sphinx documentation requirements
+    - requirements: docs/sphinx/requirements.txt

{crossref_local-0.3.1 → crossref_local-0.5.0}/CHANGELOG.md

@@ -5,6 +5,45 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2026-01-24
+
+### Added
+- **Collections API** - HTTP endpoints for paper collections (`/collections/*`)
+  - CRUD operations: list, create, query, delete
+  - Download as JSON, CSV, BibTeX, or DOIs
+  - Statistics endpoint for collection analytics
+- **Citation HTTP endpoints** - RESTful citation access
+  - `GET /citations/{doi}/citing` - Papers citing this DOI
+  - `GET /citations/{doi}/cited` - Papers cited by this DOI
+  - `GET /citations/{doi}/count` - Citation count
+  - `GET /citations/{doi}/network` - Citation network graph
+- **Multi-tenant support** - X-User-ID header for collection scoping
+- **Security hardening**
+  - Path traversal protection via name sanitization
+  - Input validation with field whitelist (14 allowed fields)
+  - Size limits: MAX_LIMIT=10000, MAX_DOIS=1000
+- Shell completion command (`crossref-local completion bash/zsh/fish/install/status`)
+- Paper cache module for efficient collection management
+- MCP subcommand group (`crossref-local mcp {start,doctor,installation,list-tools}`)
+- `--help-recursive` option for complete CLI help
+- Remote deployment docs with systemd and Docker examples
+- Automated MCP server installation via Makefile
+- RemoteClient collection methods mixin
+
+### Changed
+- Default port changed from 8333 to 31291 (SCITEX convention)
+- Server refactored into modular package (`server/`)
+- Reorganized CLI commands for better clarity
+- Improved MCP tools alignment with CLI commands
+- SCITEX environment variables supported with fallback chain
+- Examples renamed to follow numbered convention (04_mcp_demo)
+- Updated .env.example with all environment variables
+
+### Fixed
+- Remote client `get_many` batch response includes citation_count
+- CI workflow now includes pytest-cov for coverage reporting
+- Circular import between cache.py and cache_export.py
+
 ## [0.3.1] - 2026-01-14
 
 ### Added

{crossref_local-0.3.1 → crossref_local-0.5.0}/Makefile

@@ -7,7 +7,8 @@
 #   make status    - Show database status
 
 .PHONY: help install dev test status db-info db-schema db-indices fts-build fts-status \
-        citations-status citations-rebuild check clean nfs-setup nfs-status nfs-stop
+        citations-status citations-rebuild check clean nfs-setup nfs-status nfs-stop \
+        mcp-install mcp-uninstall mcp-status mcp-start mcp-stop mcp-restart mcp-logs
 
 # Paths
 PROJECT_ROOT := $(shell pwd)
@@ -136,36 +137,7 @@ help: ## Show this help
 ##@ Status & Information
 
 status: ## Show overall system status (run this first!)
-	@echo "╔════════════════════════════════════════════════════════════╗"
-	@echo "║           CROSSREF LOCAL - STATUS                         ║"
-	@echo "╚════════════════════════════════════════════════════════════╝"
-	@echo ""
-	@echo "=== Database ==="
-	@if [ -f "$(DB_PATH)" ]; then \
-		echo "  ✓ Database exists: $(DB_PATH)"; \
-		echo "  Size: $$(du -h "$(DB_PATH)" | cut -f1)"; \
-	else \
-		echo "  ✗ Database NOT FOUND: $(DB_PATH)"; \
-		echo "    Hint: Check data symlink or run 'make download'"; \
-	fi
-	@echo ""
-	@echo "=== NFS Server ==="
-	@$(SCRIPTS)/nfs/check.sh
-	@echo ""
-	@echo "=== Running Processes ==="
-	@ps aux | grep -E "(rebuild_citations|build_fts|sqlite3)" | grep -v grep | head -5 || echo "  No database processes running"
-	@echo ""
-	@echo "=== Screen Sessions ==="
-	@screen -ls 2>/dev/null | grep -E "(citations|fts|rebuild)" || echo "  No relevant screen sessions"
-	@echo ""
-	@echo "=== Quick Stats ==="
-	@if [ -f "$(DB_PATH)" ]; then \
-		echo "  Works:     $$(sqlite3 "$(DB_PATH)" "SELECT stat FROM sqlite_stat1 WHERE tbl='works' LIMIT 1;" 2>/dev/null | cut -d' ' -f1 || echo '?')"; \
-		echo "  Citations: $$(sqlite3 "$(DB_PATH)" "SELECT MAX(rowid) FROM citations;" 2>/dev/null || echo '?')"; \
-	fi
-	@echo ""
-	@echo "For detailed database info: make db-info"
-	@echo "For NFS details: make nfs-status"
+	@$(SCRIPTS)/status.sh
 
 db-info: ## Show database tables, indices, and row counts
 	@$(SCRIPTS)/database/99_db_info.sh
@@ -257,6 +229,32 @@ create-missing-indices: ## Create any missing indices
 maintain-indices: ## Analyze and optimize indices
 	@$(SCRIPTS)/database/99_maintain_indexes.sh
 
+##@ MCP Server (Remote Access)
+
+mcp-install: ## Install MCP server as systemd service
+	@$(SCRIPTS)/deployment/mcp/install.sh $(if $(DB),--db $(DB),) $(if $(PORT),--port $(PORT),)
+
+mcp-uninstall: ## Remove MCP systemd service
+	@$(SCRIPTS)/deployment/mcp/install.sh --uninstall
+
+mcp-status: ## Show MCP server status
+	@$(SCRIPTS)/deployment/mcp/status.sh
+
+mcp-start: ## Start MCP server
+	@sudo systemctl start crossref-mcp
+	@echo "✓ MCP server started"
+
+mcp-stop: ## Stop MCP server
+	@sudo systemctl stop crossref-mcp
+	@echo "✓ MCP server stopped"
+
+mcp-restart: ## Restart MCP server
+	@sudo systemctl restart crossref-mcp
+	@echo "✓ MCP server restarted"
+
+mcp-logs: ## Show MCP server logs (live)
+	@journalctl -u crossref-mcp -f
+
 ##@ NFS Server
 
 nfs-setup: ## Setup NFS server to share database (requires .env with SUDO_PASSWORD)

{crossref_local-0.3.1 → crossref_local-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: crossref-local
-Version: 0.3.1
+Version: 0.5.0
 Summary: Local CrossRef database with 167M+ works and full-text search
 Project-URL: Homepage, https://github.com/ywatanabe1989/crossref_local
 Project-URL: Repository, https://github.com/ywatanabe1989/crossref_local
@@ -18,6 +18,7 @@ Classifier: Topic :: Database
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 Requires-Dist: click>=8.0
+Requires-Dist: rich>=13.0
 Provides-Extra: all
 Requires-Dist: fastapi>=0.100; extra == 'all'
 Requires-Dist: fastmcp>=0.4; extra == 'all'
@@ -43,11 +44,20 @@ Requires-Dist: networkx>=3.0; extra == 'viz'
 Requires-Dist: pyvis>=0.3; extra == 'viz'
 Description-Content-Type: text/markdown
 
+<!-- ---
+!-- Timestamp: 2026-01-16 19:15:51
+!-- Author: ywatanabe
+!-- File: /home/ywatanabe/proj/crossref-local/README.md
+!-- --- -->
+
 # CrossRef Local
 
 Local CrossRef database with 167M+ scholarly works, full-text search, and impact factor calculation.
 
+[![PyPI version](https://badge.fury.io/py/crossref-local.svg)](https://badge.fury.io/py/crossref-local)
+[![Documentation](https://readthedocs.org/projects/crossref-local/badge/?version=latest)](https://crossref-local.readthedocs.io/en/latest/)
 [![Tests](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml/badge.svg)](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml)
+[![Coverage](https://codecov.io/gh/ywatanabe1989/crossref-local/branch/main/graph/badge.svg)](https://codecov.io/gh/ywatanabe1989/crossref-local)
 [![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 
@@ -55,6 +65,22 @@ Local CrossRef database with 167M+ scholarly works, full-text search, and impact
   <img src="examples/readme_figure.png" alt="CrossRef Local Demo" width="800"/>
 </p>
 
+<details>
+<summary><strong>MCP Demo Video</strong></summary>
+
+<p align="center">
+  <a href="https://scitex.ai/media/videos/crossref-local-v0.3.1-demo.mp4">
+    <img src="examples/demo_mcp_out/crossref-local-v0.3.1-demo-thumbnail_6m55s.png" alt="Demo Video Thumbnail" width="600"/>
+  </a>
+</p>
+
+Live demonstration of MCP server integration with Claude Code for `epilepsy seizure prediction` literature review:
+- Full-text search on title, abstracts, and keywords across 167M papers (22ms response)
+
+📄 [Full demo documentation](examples/demo_mcp.org) | 📊 [Generated diagrams](examples/demo_mcp_out/)
+
+</details>
+
 <details>
 <summary><strong>Why CrossRef Local?</strong></summary>
 
@@ -135,9 +161,8 @@ async def main():
 
 ```bash
 crossref-local search "CRISPR genome editing" -n 5
-crossref-local get 10.1038/nature12373
-crossref-local impact-factor Nature -y 2023  # IF: 54.067
-crossref-local info  # Database stats
+crossref-local search-by-doi 10.1038/nature12373
+crossref-local status  # Configuration and database stats
 ```
 
 With abstracts (`-a` flag):
@@ -160,53 +185,68 @@ Found 4 matches in 128.4ms
 
 Start the FastAPI server:
 ```bash
-crossref-local api --host 0.0.0.0 --port 3333
+crossref-local relay --host 0.0.0.0 --port 31291
 ```
 
 Endpoints:
 ```bash
 # Search works (FTS5)
-curl "http://localhost:3333/works?q=CRISPR&limit=10"
+curl "http://localhost:31291/works?q=CRISPR&limit=10"
 
 # Get by DOI
-curl "http://localhost:3333/works/10.1038/nature12373"
+curl "http://localhost:31291/works/10.1038/nature12373"
 
 # Batch DOI lookup
-curl -X POST "http://localhost:3333/works/batch" \
+curl -X POST "http://localhost:31291/works/batch" \
   -H "Content-Type: application/json" \
   -d '{"dois": ["10.1038/nature12373", "10.1126/science.aax0758"]}'
 
+# Citation endpoints
+curl "http://localhost:31291/citations/10.1038/nature12373/citing"
+curl "http://localhost:31291/citations/10.1038/nature12373/cited"
+curl "http://localhost:31291/citations/10.1038/nature12373/count"
+
+# Collection endpoints
+curl "http://localhost:31291/collections"
+curl -X POST "http://localhost:31291/collections" \
+  -H "Content-Type: application/json" \
+  -d '{"name": "my_papers", "query": "CRISPR", "limit": 100}'
+curl "http://localhost:31291/collections/my_papers/download?format=bibtex"
+
 # Database info
-curl "http://localhost:3333/info"
+curl "http://localhost:31291/info"
 ```
 
-Remote access via SSH tunnel:
+HTTP mode (connect to running server):
 ```bash
-# On local machine
-ssh -L 3333:127.0.0.1:3333 nas
+# On local machine (if server is remote)
+ssh -L 31291:127.0.0.1:31291 your-server
 
 # Python client
-from crossref_local import configure_remote
-configure_remote("http://localhost:3333")
+from crossref_local import configure_http
+configure_http("http://localhost:31291")
+
+# Or via CLI
+crossref-local --http search "CRISPR"
 ```
 
 </details>
 
 <details>
-<summary><strong>MCP Server (Claude Desktop)</strong></summary>
+<summary><strong>MCP Server</strong></summary>
 
-Run as MCP server for Claude Desktop integration:
+Run as MCP (Model Context Protocol) server:
 ```bash
-crossref-local serve
+crossref-local mcp start
 ```
 
-Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
+Local MCP client configuration:
 ```json
 {
   "mcpServers": {
     "crossref-local": {
       "command": "crossref-local",
-      "args": ["serve"],
+      "args": ["mcp", "start"],
       "env": {
         "CROSSREF_LOCAL_DB": "/path/to/crossref.db"
       }
@@ -215,12 +255,36 @@ Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
 }
 ```
 
+Remote MCP via HTTP (recommended):
+```bash
+# On server: start persistent MCP server
+crossref-local mcp start -t http --host 0.0.0.0 --port 8082
+```
+```json
+{
+  "mcpServers": {
+    "crossref-remote": {
+      "url": "http://your-server:8082/mcp"
+    }
+  }
+}
+```
+
+Diagnose setup:
+```bash
+crossref-local mcp doctor        # Check dependencies and database
+crossref-local mcp list-tools    # Show available MCP tools
+crossref-local mcp installation  # Show client config examples
+```
+
+See [docs/remote-deployment.md](docs/remote-deployment.md) for systemd and Docker setup.
+
 Available tools:
-- `search_works` - Full-text search across 167M+ papers
-- `get_work` - Get paper by DOI
-- `count_works` - Count matching papers
-- `database_info` - Database statistics
-- `calculate_impact_factor` - Journal impact factor
+- `search` - Full-text search across 167M+ papers
+- `search_by_doi` - Get paper by DOI
+- `enrich_dois` - Add citation counts and references to DOIs
+- `status` - Database statistics
+- `cache_*` - Paper collection management
 
 </details>
 

{crossref_local-0.3.1 → crossref_local-0.5.0}/README.md

@@ -1,8 +1,17 @@
+<!-- ---
+!-- Timestamp: 2026-01-16 19:15:51
+!-- Author: ywatanabe
+!-- File: /home/ywatanabe/proj/crossref-local/README.md
+!-- --- -->
+
 # CrossRef Local
 
 Local CrossRef database with 167M+ scholarly works, full-text search, and impact factor calculation.
 
+[![PyPI version](https://badge.fury.io/py/crossref-local.svg)](https://badge.fury.io/py/crossref-local)
+[![Documentation](https://readthedocs.org/projects/crossref-local/badge/?version=latest)](https://crossref-local.readthedocs.io/en/latest/)
 [![Tests](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml/badge.svg)](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml)
+[![Coverage](https://codecov.io/gh/ywatanabe1989/crossref-local/branch/main/graph/badge.svg)](https://codecov.io/gh/ywatanabe1989/crossref-local)
 [![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 
@@ -10,6 +19,22 @@ Local CrossRef database with 167M+ scholarly works, full-text search, and impact
   <img src="examples/readme_figure.png" alt="CrossRef Local Demo" width="800"/>
 </p>
 
+<details>
+<summary><strong>MCP Demo Video</strong></summary>
+
+<p align="center">
+  <a href="https://scitex.ai/media/videos/crossref-local-v0.3.1-demo.mp4">
+    <img src="examples/demo_mcp_out/crossref-local-v0.3.1-demo-thumbnail_6m55s.png" alt="Demo Video Thumbnail" width="600"/>
+  </a>
+</p>
+
+Live demonstration of MCP server integration with Claude Code for `epilepsy seizure prediction` literature review:
+- Full-text search on title, abstracts, and keywords across 167M papers (22ms response)
+
+📄 [Full demo documentation](examples/demo_mcp.org) | 📊 [Generated diagrams](examples/demo_mcp_out/)
+
+</details>
+
 <details>
 <summary><strong>Why CrossRef Local?</strong></summary>
 
@@ -90,9 +115,8 @@ async def main():
 
 ```bash
 crossref-local search "CRISPR genome editing" -n 5
-crossref-local get 10.1038/nature12373
-crossref-local impact-factor Nature -y 2023  # IF: 54.067
-crossref-local info  # Database stats
+crossref-local search-by-doi 10.1038/nature12373
+crossref-local status  # Configuration and database stats
 ```
 
 With abstracts (`-a` flag):
@@ -115,53 +139,68 @@ Found 4 matches in 128.4ms
 
 Start the FastAPI server:
 ```bash
-crossref-local api --host 0.0.0.0 --port 3333
+crossref-local relay --host 0.0.0.0 --port 31291
 ```
 
 Endpoints:
 ```bash
 # Search works (FTS5)
-curl "http://localhost:3333/works?q=CRISPR&limit=10"
+curl "http://localhost:31291/works?q=CRISPR&limit=10"
 
 # Get by DOI
-curl "http://localhost:3333/works/10.1038/nature12373"
+curl "http://localhost:31291/works/10.1038/nature12373"
 
 # Batch DOI lookup
-curl -X POST "http://localhost:3333/works/batch" \
+curl -X POST "http://localhost:31291/works/batch" \
   -H "Content-Type: application/json" \
   -d '{"dois": ["10.1038/nature12373", "10.1126/science.aax0758"]}'
 
+# Citation endpoints
+curl "http://localhost:31291/citations/10.1038/nature12373/citing"
+curl "http://localhost:31291/citations/10.1038/nature12373/cited"
+curl "http://localhost:31291/citations/10.1038/nature12373/count"
+
+# Collection endpoints
+curl "http://localhost:31291/collections"
+curl -X POST "http://localhost:31291/collections" \
+  -H "Content-Type: application/json" \
+  -d '{"name": "my_papers", "query": "CRISPR", "limit": 100}'
+curl "http://localhost:31291/collections/my_papers/download?format=bibtex"
+
 # Database info
-curl "http://localhost:3333/info"
+curl "http://localhost:31291/info"
 ```
 
-Remote access via SSH tunnel:
+HTTP mode (connect to running server):
 ```bash
-# On local machine
-ssh -L 3333:127.0.0.1:3333 nas
+# On local machine (if server is remote)
+ssh -L 31291:127.0.0.1:31291 your-server
 
 # Python client
-from crossref_local import configure_remote
-configure_remote("http://localhost:3333")
+from crossref_local import configure_http
+configure_http("http://localhost:31291")
+
+# Or via CLI
+crossref-local --http search "CRISPR"
 ```
 
 </details>
 
 <details>
-<summary><strong>MCP Server (Claude Desktop)</strong></summary>
+<summary><strong>MCP Server</strong></summary>
 
-Run as MCP server for Claude Desktop integration:
+Run as MCP (Model Context Protocol) server:
 ```bash
-crossref-local serve
+crossref-local mcp start
 ```
 
-Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
+Local MCP client configuration:
 ```json
 {
   "mcpServers": {
     "crossref-local": {
       "command": "crossref-local",
-      "args": ["serve"],
+      "args": ["mcp", "start"],
       "env": {
         "CROSSREF_LOCAL_DB": "/path/to/crossref.db"
       }
@@ -170,12 +209,36 @@ Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
 }
 ```
 
+Remote MCP via HTTP (recommended):
+```bash
+# On server: start persistent MCP server
+crossref-local mcp start -t http --host 0.0.0.0 --port 8082
+```
+```json
+{
+  "mcpServers": {
+    "crossref-remote": {
+      "url": "http://your-server:8082/mcp"
+    }
+  }
+}
+```
+
+Diagnose setup:
+```bash
+crossref-local mcp doctor        # Check dependencies and database
+crossref-local mcp list-tools    # Show available MCP tools
+crossref-local mcp installation  # Show client config examples
+```
+
+See [docs/remote-deployment.md](docs/remote-deployment.md) for systemd and Docker setup.
+
 Available tools:
-- `search_works` - Full-text search across 167M+ papers
-- `get_work` - Get paper by DOI
-- `count_works` - Count matching papers
-- `database_info` - Database statistics
-- `calculate_impact_factor` - Journal impact factor
+- `search` - Full-text search across 167M+ papers
+- `search_by_doi` - Get paper by DOI
+- `enrich_dois` - Add citation counts and references to DOIs
+- `status` - Database statistics
+- `cache_*` - Paper collection management
 
 </details>