py-scholar-agent 0.1.0__tar.gz

py_scholar_agent-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 zfy465914233
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

py_scholar_agent-0.1.0/MANIFEST.in

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+include .scholar.json
+include schemas/answer.schema.json
+recursive-include templates *
+recursive-include skills *
+recursive-include scholar_agent *

py_scholar_agent-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: py-scholar-agent
+Version: 0.1.0
+Summary: Knowledge flywheel MCP server + academic paper research pipeline for Claude Code and VS Code Copilot
+Author-email: Fangyi Zhou <zfy465914233@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/zfy465914233/scholar-agent
+Project-URL: Repository, https://github.com/zfy465914233/scholar-agent
+Project-URL: Issues, https://github.com/zfy465914233/scholar-agent/issues
+Project-URL: Changelog, https://github.com/zfy465914233/scholar-agent/blob/main/CHANGELOG.md
+Keywords: mcp,knowledge-management,arxiv,academic-research,obsidian
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Education
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jsonschema<5,>=4.23
+Requires-Dist: fastmcp>=2.0
+Requires-Dist: PyMuPDF>=1.24.0
+Requires-Dist: requests>=2.28
+Provides-Extra: academic
+Requires-Dist: PyYAML>=6.0; extra == "academic"
+Provides-Extra: embedding
+Requires-Dist: sentence-transformers>=3.0; extra == "embedding"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Requires-Dist: ruff>=0.8; extra == "dev"
+Requires-Dist: mypy>=1.10; extra == "dev"
+Requires-Dist: pre-commit>=3.7; extra == "dev"
+Provides-Extra: all
+Requires-Dist: scholar-agent[academic,embedding]; extra == "all"
+Dynamic: license-file
+
+<p align="center">
+  <img src="assets/banner.svg" alt="Scholar Agent" width="720" />
+</p>
+
+<p align="center">
+  <img src="https://img.shields.io/badge/python-3.10+-blue.svg" alt="Python 3.10+" />
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT" />
+  <img src="https://img.shields.io/badge/MCP-Ready-brightgreen.svg" alt="MCP Ready" />
+  <img src="https://img.shields.io/badge/tests-276%20passing-brightgreen.svg" alt="Tests" />
+  <img src="https://img.shields.io/pypi/v/scholar-agent?color=blue" alt="PyPI" />
+</p>
+
+<p align="center">
+  <a href="README.zh-CN.md">中文</a>
+</p>
+
+<p align="center">
+  <strong>AI that gets smarter in YOUR domain — every question compounds.</strong><br/>
+  Online research + local knowledge accumulation + MCP integration for Claude Code & VS Code Copilot.
+</p>
+
+---
+
+## Demo
+
+<p align="center">
+  <img src="assets/demo.gif" alt="Scholar Agent Demo" width="720" />
+</p>
+
+<p align="center"><sub>Ask → Research → Accumulate → Next question hits local cache instantly</sub></p>
+
+<p align="center">
+  <img src="assets/flywheel.svg" alt="Knowledge Flywheel" width="720" />
+</p>
+
+Each round compounds. Knowledge cards have full lifecycle management: **draft → reviewed → trusted → stale → deprecated**.
+
+---
+
+## Why Scholar Agent?
+
+| | ChatGPT / Claude | Obsidian + Plugins | Zotero | **Scholar Agent** |
+|---|---|---|---|---|
+| Domain knowledge accumulates | No — every chat starts fresh | Manual curation | Bibliography only | **Automatic — every query compounds** |
+| Structured research with citations | Sometimes | Manual | Partial | **Yes — structured synthesis + confidence scores** |
+| Academic paper pipeline | Limited | Via plugins | Yes | **Search → Score → Analyze → Extract → Recommend** |
+| Works offline | No | Yes | Partial | **Yes — local BM25 index, falls back gracefully** |
+| Human-readable knowledge base | Chat history | Markdown files | PDF library | **Obsidian-compatible Markdown + wiki-links** |
+| Integrates with your IDE | No | No | Partial | **MCP server for Claude Code, VS Code Copilot, OpenCode** |
+| Knowledge quality gates | None | None | None | **Lifecycle management + quality scoring + validation** |
+
+---
+
+## Quick Start
+
+### Install
+
+```bash
+pip install py-scholar-agent
+```
+
+Or from source:
+
+```bash
+git clone https://github.com/zfy465914233/scholar-agent.git
+cd scholar-agent
+pip install -e .
+```
+
+### Setup
+
+```bash
+scholar-agent init
+```
+
+One command creates data directories, writes config, and registers MCP with Claude Code. You're done.
+
+### Modes
+
+| Mode | Command | Data Location | Scope |
+|------|---------|---------------|-------|
+| **Global** (recommended) | `scholar-agent init` | `~/scholar/` | Every project |
+| **Project-Local** | `SCHOLAR_HOME=./scholar scholar-agent init` | `my-project/scholar/` | Current project only |
+| **Docker** | `docker run -v ~/scholar:/data scholar-agent serve-mcp` | Container volume | Isolated |
+
+---
+
+## What It Does
+
+### Knowledge Flywheel
+
+Ask a question → Scholar Agent researches (web + academic APIs) → synthesizes a structured answer with citations → saves as a knowledge card → indexes it with BM25. Next time a similar question comes up, it hits the local index first — **fast, accurate, and free**.
+
+### Academic Research Pipeline
+
+- **Paper Search** — arXiv, DBLP, Semantic Scholar. Filter by 10+ top conferences
+- **Smart Scoring** — 4-dimensional engine (relevance, recency, popularity, quality)
+- **Deep Analysis** — 20+ section Obsidian-style notes with AI-assisted completion
+- **Figure Extraction** — From arXiv source archives and PDFs
+- **Daily Recommendations** — Automated search, scoring, deduplication
+- **Paper → Knowledge Card** — Feed analyses back into the flywheel
+- **Keyword Auto-Linking** — `[[wiki-links]]` across all notes
+
+### MCP Tools
+
+**Core** (always available): `query_knowledge` · `save_research` · `list_knowledge` · `capture_answer` · `ingest_source` · `build_graph`
+
+**Academic** (set `SCHOLAR_ACADEMIC=1`): `search_papers` · `search_conf_papers` · `download_paper` · `analyze_paper` · `extract_paper_images` · `paper_to_card` · `daily_recommend` · `link_paper_keywords`
+
+---
+
+## CLI Reference
+
+| Command | Description |
+|---------|-------------|
+| `scholar-agent init` | One-command setup: data dirs + config + MCP registration |
+| `scholar-agent serve-mcp` | Start the MCP server |
+| `scholar-agent doctor` | Show environment and config diagnostics |
+| `scholar-agent config show` | Show resolved configuration |
+| `scholar-agent install claude --write` | Register MCP with Claude Code |
+| `scholar-agent install vscode --write` | Register MCP with VS Code Copilot |
+| `scholar-agent install opencode --write` | Register MCP with OpenCode |
+
+---
+
+## Configuration
+
+### Environment Variables
+
+| Variable | Required | Description |
+|----------|----------|-------------|
+| `SCHOLAR_ACADEMIC` | No | Set to `1` to enable academic tools |
+| `SCHOLAR_HOME` | No | Override data directory (default: `~/scholar/`) |
+| `S2_API_KEY` | No | Semantic Scholar API key ([get one free](https://api.semanticscholar.org/)) |
+| `LLM_API_KEY` | No | LLM API key for advanced synthesis pipeline |
+
+### Config File
+
+See [`.scholar.example.json`](.scholar.example.json) for a full example with comments. Key sections:
+
+- `knowledge_dir` — Knowledge cards directory
+- `index_path` — BM25 search index
+- `academic.research_interests` — Your domains, keywords, arXiv categories
+- `academic.scoring` — Paper scoring weights
+
+---
+
+## Recommended Workflow
+
+For best paper analysis quality:
+
+1. **Download**: `download_paper("2510.24701", title="Paper Title", domain="LLM")`
+2. **Extract images**: `extract_paper_images("2510.24701")`
+3. **Deep analysis**: `analyze_paper(paper_json)`
+
+> Downloading the PDF first enables full-text extraction, producing notes with specific data, formulas, and experimental results.
+
+---
+
+## Development
+
+```bash
+make dev       # Install with dev dependencies + pre-commit hooks
+make lint      # Run ruff + mypy
+make test      # Run test suite (276 tests, ~7s, fully offline)
+make coverage  # Run tests with coverage report
+make build     # Build distribution package
+make docker    # Build Docker image
+```
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed guidelines.
+
+## Features at a Glance
+
+- **Multi-perspective research** — 5 perspectives (academic, technical, applied, contrarian, historical)
+- **Obsidian compatible** — Markdown + YAML frontmatter + `[[wiki-links]]`
+- **Knowledge governance** — Validate frontmatter, detect orphans, find duplicates, manage lifecycle
+- **Provider fault tolerance** — Each source fails independently; graceful offline fallback
+- **Cross-platform** — macOS, Linux, Windows
+
+## License
+
+MIT — see [LICENSE](LICENSE).

py_scholar_agent-0.1.0/README.md

@@ -0,0 +1,183 @@
+<p align="center">
+  <img src="assets/banner.svg" alt="Scholar Agent" width="720" />
+</p>
+
+<p align="center">
+  <img src="https://img.shields.io/badge/python-3.10+-blue.svg" alt="Python 3.10+" />
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT" />
+  <img src="https://img.shields.io/badge/MCP-Ready-brightgreen.svg" alt="MCP Ready" />
+  <img src="https://img.shields.io/badge/tests-276%20passing-brightgreen.svg" alt="Tests" />
+  <img src="https://img.shields.io/pypi/v/scholar-agent?color=blue" alt="PyPI" />
+</p>
+
+<p align="center">
+  <a href="README.zh-CN.md">中文</a>
+</p>
+
+<p align="center">
+  <strong>AI that gets smarter in YOUR domain — every question compounds.</strong><br/>
+  Online research + local knowledge accumulation + MCP integration for Claude Code & VS Code Copilot.
+</p>
+
+---
+
+## Demo
+
+<p align="center">
+  <img src="assets/demo.gif" alt="Scholar Agent Demo" width="720" />
+</p>
+
+<p align="center"><sub>Ask → Research → Accumulate → Next question hits local cache instantly</sub></p>
+
+<p align="center">
+  <img src="assets/flywheel.svg" alt="Knowledge Flywheel" width="720" />
+</p>
+
+Each round compounds. Knowledge cards have full lifecycle management: **draft → reviewed → trusted → stale → deprecated**.
+
+---
+
+## Why Scholar Agent?
+
+| | ChatGPT / Claude | Obsidian + Plugins | Zotero | **Scholar Agent** |
+|---|---|---|---|---|
+| Domain knowledge accumulates | No — every chat starts fresh | Manual curation | Bibliography only | **Automatic — every query compounds** |
+| Structured research with citations | Sometimes | Manual | Partial | **Yes — structured synthesis + confidence scores** |
+| Academic paper pipeline | Limited | Via plugins | Yes | **Search → Score → Analyze → Extract → Recommend** |
+| Works offline | No | Yes | Partial | **Yes — local BM25 index, falls back gracefully** |
+| Human-readable knowledge base | Chat history | Markdown files | PDF library | **Obsidian-compatible Markdown + wiki-links** |
+| Integrates with your IDE | No | No | Partial | **MCP server for Claude Code, VS Code Copilot, OpenCode** |
+| Knowledge quality gates | None | None | None | **Lifecycle management + quality scoring + validation** |
+
+---
+
+## Quick Start
+
+### Install
+
+```bash
+pip install py-scholar-agent
+```
+
+Or from source:
+
+```bash
+git clone https://github.com/zfy465914233/scholar-agent.git
+cd scholar-agent
+pip install -e .
+```
+
+### Setup
+
+```bash
+scholar-agent init
+```
+
+One command creates data directories, writes config, and registers MCP with Claude Code. You're done.
+
+### Modes
+
+| Mode | Command | Data Location | Scope |
+|------|---------|---------------|-------|
+| **Global** (recommended) | `scholar-agent init` | `~/scholar/` | Every project |
+| **Project-Local** | `SCHOLAR_HOME=./scholar scholar-agent init` | `my-project/scholar/` | Current project only |
+| **Docker** | `docker run -v ~/scholar:/data scholar-agent serve-mcp` | Container volume | Isolated |
+
+---
+
+## What It Does
+
+### Knowledge Flywheel
+
+Ask a question → Scholar Agent researches (web + academic APIs) → synthesizes a structured answer with citations → saves as a knowledge card → indexes it with BM25. Next time a similar question comes up, it hits the local index first — **fast, accurate, and free**.
+
+### Academic Research Pipeline
+
+- **Paper Search** — arXiv, DBLP, Semantic Scholar. Filter by 10+ top conferences
+- **Smart Scoring** — 4-dimensional engine (relevance, recency, popularity, quality)
+- **Deep Analysis** — 20+ section Obsidian-style notes with AI-assisted completion
+- **Figure Extraction** — From arXiv source archives and PDFs
+- **Daily Recommendations** — Automated search, scoring, deduplication
+- **Paper → Knowledge Card** — Feed analyses back into the flywheel
+- **Keyword Auto-Linking** — `[[wiki-links]]` across all notes
+
+### MCP Tools
+
+**Core** (always available): `query_knowledge` · `save_research` · `list_knowledge` · `capture_answer` · `ingest_source` · `build_graph`
+
+**Academic** (set `SCHOLAR_ACADEMIC=1`): `search_papers` · `search_conf_papers` · `download_paper` · `analyze_paper` · `extract_paper_images` · `paper_to_card` · `daily_recommend` · `link_paper_keywords`
+
+---
+
+## CLI Reference
+
+| Command | Description |
+|---------|-------------|
+| `scholar-agent init` | One-command setup: data dirs + config + MCP registration |
+| `scholar-agent serve-mcp` | Start the MCP server |
+| `scholar-agent doctor` | Show environment and config diagnostics |
+| `scholar-agent config show` | Show resolved configuration |
+| `scholar-agent install claude --write` | Register MCP with Claude Code |
+| `scholar-agent install vscode --write` | Register MCP with VS Code Copilot |
+| `scholar-agent install opencode --write` | Register MCP with OpenCode |
+
+---
+
+## Configuration
+
+### Environment Variables
+
+| Variable | Required | Description |
+|----------|----------|-------------|
+| `SCHOLAR_ACADEMIC` | No | Set to `1` to enable academic tools |
+| `SCHOLAR_HOME` | No | Override data directory (default: `~/scholar/`) |
+| `S2_API_KEY` | No | Semantic Scholar API key ([get one free](https://api.semanticscholar.org/)) |
+| `LLM_API_KEY` | No | LLM API key for advanced synthesis pipeline |
+
+### Config File
+
+See [`.scholar.example.json`](.scholar.example.json) for a full example with comments. Key sections:
+
+- `knowledge_dir` — Knowledge cards directory
+- `index_path` — BM25 search index
+- `academic.research_interests` — Your domains, keywords, arXiv categories
+- `academic.scoring` — Paper scoring weights
+
+---
+
+## Recommended Workflow
+
+For best paper analysis quality:
+
+1. **Download**: `download_paper("2510.24701", title="Paper Title", domain="LLM")`
+2. **Extract images**: `extract_paper_images("2510.24701")`
+3. **Deep analysis**: `analyze_paper(paper_json)`
+
+> Downloading the PDF first enables full-text extraction, producing notes with specific data, formulas, and experimental results.
+
+---
+
+## Development
+
+```bash
+make dev       # Install with dev dependencies + pre-commit hooks
+make lint      # Run ruff + mypy
+make test      # Run test suite (276 tests, ~7s, fully offline)
+make coverage  # Run tests with coverage report
+make build     # Build distribution package
+make docker    # Build Docker image
+```
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed guidelines.
+
+## Features at a Glance
+
+- **Multi-perspective research** — 5 perspectives (academic, technical, applied, contrarian, historical)
+- **Obsidian compatible** — Markdown + YAML frontmatter + `[[wiki-links]]`
+- **Knowledge governance** — Validate frontmatter, detect orphans, find duplicates, manage lifecycle
+- **Provider fault tolerance** — Each source fails independently; graceful offline fallback
+- **Cross-platform** — macOS, Linux, Windows
+
+## License
+
+MIT — see [LICENSE](LICENSE).

py_scholar_agent-0.1.0/pyproject.toml

@@ -0,0 +1,122 @@
+[project]
+name = "py-scholar-agent"
+version = "0.1.0"
+description = "Knowledge flywheel MCP server + academic paper research pipeline for Claude Code and VS Code Copilot"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.10"
+authors = [
+    {name = "Fangyi Zhou", email = "zfy465914233@gmail.com"},
+]
+keywords = ["mcp", "knowledge-management", "arxiv", "academic-research", "obsidian"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Education",
+    "Typing :: Typed",
+]
+
+dependencies = [
+    "jsonschema>=4.23,<5",
+    "fastmcp>=2.0",
+    "PyMuPDF>=1.24.0",
+    "requests>=2.28",
+]
+
+[project.optional-dependencies]
+academic = [
+    "PyYAML>=6.0",
+]
+embedding = [
+    "sentence-transformers>=3.0",
+]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov>=5.0",
+    "ruff>=0.8",
+    "mypy>=1.10",
+    "pre-commit>=3.7",
+]
+all = [
+    "scholar-agent[academic,embedding]",
+]
+
+[project.scripts]
+scholar-agent = "scholar_agent.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/zfy465914233/scholar-agent"
+Repository = "https://github.com/zfy465914233/scholar-agent"
+Issues = "https://github.com/zfy465914233/scholar-agent/issues"
+Changelog = "https://github.com/zfy465914233/scholar-agent/blob/main/CHANGELOG.md"
+
+[build-system]
+requires = ["setuptools>=68.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["scholar_agent*"]
+
+[tool.setuptools.package-data]
+scholar_agent = ["schemas/**", "templates/**", "config_data/**", "skills/**", "validation/**"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--tb=short -q"
+
+[tool.ruff]
+target-version = "py310"
+line-length = 120
+src = ["src", "tests"]
+
+[tool.ruff.lint]
+select = [
+    "E",    # pycodestyle errors
+    "W",    # pycodestyle warnings
+    "F",    # pyflakes
+    "I",    # isort
+    "UP",   # pyupgrade
+    "B",    # flake8-bugbear
+    "SIM",  # flake8-simplify
+    "TCH",  # flake8-type-checking
+    "RUF",  # ruff-specific
+]
+ignore = [
+    "E501",   # line too long (handled by formatter)
+    "E402",   # module-level import not at top (common in scripts)
+    "RUF001", # ambiguous unicode character in string (Chinese content)
+    "RUF002", # ambiguous unicode character in docstring (Chinese content)
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["scholar_agent"]
+
+[tool.mypy]
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+check_untyped_defs = true
+no_implicit_optional = true
+warn_redundant_casts = true
+exclude = ["tests/", "scripts/"]
+
+[[tool.mypy.overrides]]
+module = ["fitz.*", "pymupdf.*", "fastmcp.*", "sentence_transformers.*"]
+ignore_missing_imports = true
+
+[tool.coverage.run]
+source = ["scholar_agent"]
+omit = ["tests/*"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+fail_under = 60

py_scholar_agent-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

py_scholar_agent-0.1.0/skills/paper-analysis/SKILL.md

@@ -0,0 +1,80 @@
+---
+name: paper-analysis
+description: "Deep analysis of a single paper: download PDF, extract figures, generate structured 20+ section note, fill LLM placeholders."
+allowed-tools: Bash
+---
+
+# Paper Analysis Skill
+
+Generate a comprehensive analysis note for a single paper.
+
+## Step 1: Download the paper
+
+```
+download_paper(paper_id="2510.24701", title="Paper Title", domain="LLM")
+```
+
+This caches the PDF locally under `paper-notes/<title>/`.
+
+## Step 2: Extract figures
+
+```
+extract_paper_images(paper_id="2510.24701")
+```
+
+Auto-detects the local PDF. Images go to `paper-notes/<title>/images/`.
+
+## Step 3: Generate the analysis note
+
+```
+analyze_paper(paper_json='{"title": "...", "authors": [...], "arxiv_id": "..."}', language="zh")
+```
+
+Returns:
+- `note_path`: path to the generated markdown note
+- `quality_check`: whether the note has unfilled placeholders
+- `pdf_text`: full text extracted from the PDF (if available)
+- `instructions`: if placeholders exist, instructions to fill them
+
+## Step 4: Fill placeholders
+
+The generated note contains `<!-- LLM: describe method -->` style placeholders. When `instructions` is non-null, you MUST fill all placeholders using the `pdf_text` field:
+
+### Filling rules
+
+1. Read the note at `note_path`.
+2. For each `<!-- LLM: ... -->` placeholder, replace it with substantive content drawn from `pdf_text`.
+3. Be specific: cite numbers, dataset names, architecture details, formula descriptions.
+4. Do NOT leave any placeholder unfilled.
+5. Write the complete filled note back using the Write tool.
+
+### Section guide
+
+| Section | What to write |
+|---------|---------------|
+| Core information | One-sentence contribution, key result, paper type |
+| Abstract translation | Translate or paraphrase the abstract with domain context |
+| Research background | What problem existed, why it matters |
+| Research questions | List the explicit or implicit questions the paper addresses |
+| Method overview | Architecture, algorithm, pipeline — with specifics |
+| Experimental results | Datasets, metrics, comparisons, ablation findings |
+| Deep analysis | Strengths, weaknesses, assumptions, limitations |
+| Comparison with related work | Position vs. prior art |
+| Technical roadmap | Where this fits in the broader research trajectory |
+| Future work | Open questions the paper raises |
+| Comprehensive evaluation | Your own 1-5 rating with justification |
+| My notes | Leave empty for user to fill |
+
+## Step 5: Convert to knowledge card (optional)
+
+```
+paper_to_card(paper_json='...', note_path='/path/to/note.md')
+```
+
+## Step 6: Link keywords (optional)
+
+```
+link_paper_keywords()
+```
+
+Scans all notes and auto-creates `[[wiki-links]]` for technical terms.