scientific-writer 2.0.0__py3-none-any.whl → 2.0.1__py3-none-any.whl

scientific_writer/__init__.py

@@ -29,7 +29,7 @@ Example:
 from .api import generate_paper
 from .models import ProgressUpdate, PaperResult, PaperMetadata, PaperFiles
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 __author__ = "Scientific Writer Contributors"
 __license__ = "MIT"
 

scientific_writer-2.0.1.dist-info/METADATA

@@ -0,0 +1,268 @@
+Metadata-Version: 2.4
+Name: scientific-writer
+Version: 2.0.1
+Summary: AI-powered scientific writing with programmatic API and CLI - powered by Claude Sonnet 4.5 and the Claude Agents SDK
+License: MIT
+License-File: LICENSE
+Requires-Python: <=3.12,>=3.10
+Requires-Dist: claude-agent-sdk>=0.1.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: requests>=2.31.0
+Description-Content-Type: text/markdown
+
+# Claude Scientific Writer
+
+[![PyPI version](https://badge.fury.io/py/scientific-writer.svg)](https://badge.fury.io/py/scientific-writer)
+[![Total Downloads](https://static.pepy.tech/badge/scientific-writer)](https://pepy.tech/project/scientific-writer)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+A Python package and CLI for generating publication-ready scientific papers, reports, posters, grant proposals, and more academic documents with Claude Sonnet 4.5. Features real-time research lookup, intelligent paper detection, and comprehensive document conversion. Version 2.0 adds a fully typed, programmatic API while keeping the CLI 100% backward compatible.
+
+**✨ What's New in v2.0+**
+- Programmatic Python API with async support
+- Research lookup with Perplexity Sonar Pro
+- Intelligent paper detection (auto-resume editing)
+- Grant proposal generation (NSF, NIH, DOE, DARPA)
+- Research posters with LaTeX
+- Scientific schematics (CONSORT, circuits, pathways)
+- Document conversion (15+ formats with MarkItDown)
+- ScholarEval peer review framework
+
+## Quick Start
+
+### Prerequisites
+- Python 3.10-3.12
+- ANTHROPIC_API_KEY (required), OPENROUTER_API_KEY (optional for research lookup)
+
+### Install
+
+#### Option 1: Install from PyPI (Recommended)
+```bash
+pip install scientific-writer
+```
+
+#### Option 2: Install from source with uv
+```bash
+git clone https://github.com/yourusername/claude-scientific-writer.git
+cd claude-scientific-writer
+uv sync
+```
+
+### Configure API keys
+```bash
+# .env file (recommended)
+echo "ANTHROPIC_API_KEY=your_key" > .env
+echo "OPENROUTER_API_KEY=your_openrouter_key" >> .env
+# or export in your shell
+export ANTHROPIC_API_KEY='your_key'
+```
+
+### Use the CLI
+```bash
+# If installed via pip
+scientific-writer
+
+# If installed from source with uv
+uv run scientific-writer
+```
+
+### Use the Python API
+```python
+import asyncio
+from scientific_writer import generate_paper
+
+async def main():
+    async for update in generate_paper("Create a Nature paper on CRISPR gene editing"):
+        if update["type"] == "progress":
+            print(f"[{update['percentage']}%] {update['message']}")
+        else:
+            print(f"PDF: {update['files']['pdf_final']}")
+
+asyncio.run(main())
+```
+
+## Features
+
+### 📝 Document Generation
+- **Scientific papers** with IMRaD structure (Nature, Science, NeurIPS, etc.)
+- **Research posters** using LaTeX (beamerposter, tikzposter, baposter)
+- **Grant proposals** (NSF, NIH, DOE, DARPA) with agency-specific formatting
+- **Literature reviews** with systematic citation management
+- **Scientific schematics** (CONSORT diagrams, circuit diagrams, biological pathways)
+
+### 🤖 AI-Powered Capabilities
+- **Real-time research lookup** using Perplexity Sonar Pro (via OpenRouter)
+- **Intelligent paper detection** - automatically identifies references to existing papers
+- **Peer review feedback** with quantitative ScholarEval framework (8-dimension scoring)
+- **Iterative editing** with context-aware revision suggestions
+
+### 🔧 Developer-Friendly
+- **Programmatic API** - Full async Python API with type hints
+- **CLI interface** - Interactive command-line tool with progress tracking
+- **Progress streaming** - Real-time updates during generation
+- **Comprehensive results** - JSON output with metadata, file paths, citations
+
+### 📦 Data & File Integration
+- **Automatic data handling** - Drop files in `data/`, auto-sorted to `figures/` or `data/`
+- **Document conversion** - PDF, DOCX, PPTX, XLSX to Markdown with MarkItDown
+- **Bibliography management** - Automatic BibTeX generation and citation formatting
+- **Figure integration** - Images automatically referenced and organized
+
+## Typical Workflow
+
+### CLI Usage
+1. Place figures and data in `data/` at the project root (images → `figures/`, files → `data/` automatically)
+2. Run `scientific-writer` and describe what you want
+3. Follow progress updates; outputs saved to `paper_outputs/<timestamp>_<topic>/`
+
+```bash
+# Start a new paper
+> Create a Nature paper on CRISPR gene editing with 5 key references
+
+# Continue editing (automatically detected)
+> Add a methods section about the experimental setup
+
+# Reference existing paper by topic
+> Find the acoustics paper and add a conclusion section
+
+# Generate a grant proposal
+> Write an NSF proposal for quantum computing research
+
+# Create a research poster
+> Generate a conference poster from my paper
+```
+
+### API Usage
+```python
+import asyncio
+from scientific_writer import generate_paper
+
+async def main():
+    async for update in generate_paper(
+        query="Create a NeurIPS paper on transformers",
+        data_files=["results.csv", "figure.png"],
+        output_dir="./my_papers"
+    ):
+        if update["type"] == "progress":
+            print(f"[{update['percentage']}%] {update['message']}")
+        else:
+            print(f"✓ PDF: {update['files']['pdf_final']}")
+
+asyncio.run(main())
+```
+
+## Quick Reference
+
+### Common Commands
+
+| Task | Command Example |
+|------|----------------|
+| **Scientific Paper** | `> Create a Nature paper on CRISPR gene editing` |
+| **Grant Proposal** | `> Write an NSF proposal for quantum computing research` |
+| **Research Poster** | `> Generate a conference poster from my paper` |
+| **Literature Review** | `> Create a literature review on machine learning in healthcare` |
+| **Peer Review** | `> Evaluate this paper using the ScholarEval framework` |
+| **Continue Editing** | `> Add a methods section` (automatically continues current paper) |
+| **Find Existing Paper** | `> Find the acoustics paper and add a conclusion` |
+| **New Paper** | `> new paper on climate change` (explicitly start fresh) |
+
+### Research Lookup Examples
+
+```bash
+# Recent research (auto-triggers research lookup)
+> Create a paper on recent advances in quantum computing (2024)
+
+# Fact verification
+> What are the current success rates for CAR-T therapy?
+
+# Literature search
+> Find 10 recent papers on transformer architectures from 2023-2024
+```
+
+### Document Types
+
+| Type | Example |
+|------|---------|
+| **Papers** | Nature, Science, NeurIPS, ICML, IEEE, ACM |
+| **Grants** | NSF, NIH R01/R21/K, DOE, DARPA |
+| **Posters** | Conference posters (A0, A1, custom sizes) |
+| **Reviews** | Systematic literature reviews |
+| **Schematics** | CONSORT diagrams, circuits, biological pathways |
+
+### File Handling
+
+```bash
+# 1. Drop files in data/ folder
+cp results.csv ~/Documents/claude-scientific-writer/data/
+cp figure.png ~/Documents/claude-scientific-writer/data/
+
+# 2. Files are auto-sorted:
+#    Images (png, jpg, svg) → figures/
+#    Data (csv, json, txt) → data/
+
+# 3. Reference in paper
+> Create a paper analyzing the experimental results in results.csv
+```
+
+### API Quick Start
+
+```python
+import asyncio
+from scientific_writer import generate_paper
+
+# Simple usage
+async for update in generate_paper("Create a Nature paper on CRISPR"):
+    if update["type"] == "result":
+        print(f"PDF: {update['files']['pdf_final']}")
+
+# With data files
+async for update in generate_paper(
+    query="Analyze experimental results",
+    data_files=["results.csv", "figure.png"],
+    output_dir="./papers"
+):
+    if update["type"] == "progress":
+        print(f"[{update['percentage']}%] {update['message']}")
+```
+
+## Documentation
+
+### User Guides
+- [📖 Complete Features Guide](docs/FEATURES.md) - Comprehensive overview of all capabilities
+- [🔧 API Reference](docs/API.md) - Full programmatic API documentation
+- [🎯 Skills Overview](docs/SKILLS.md) - All available skills and tools
+- [🐛 Troubleshooting](docs/TROUBLESHOOTING.md) - Common issues and solutions
+
+### Developer Resources
+- [💻 Development Guide](docs/DEVELOPMENT.md) - Contributing and development setup
+- [📦 Releasing Guide](docs/RELEASING.md) - Versioning and publishing
+- [📋 Release Notes](CHANGELOG.md) - Version history and updates
+- [🤖 System Instructions](CLAUDE.md) - Agent instructions (advanced)
+
+## Versioning and Publishing (short)
+Use `uv` and the helper scripts:
+- Bump version (keeps pyproject + __init__ in sync): `uv run scripts/bump_version.py [patch|minor|major]`
+- Build and publish: `uv run scripts/publish.py` (or `--bump patch|minor|major`)
+See [docs/RELEASING.md](docs/RELEASING.md) for prerequisites, dry runs, tagging, and verification.
+
+## Migration (v1.x -> v2.0)
+- CLI remains unchanged (scientific-writer).
+- New programmatic API: from scientific_writer import generate_paper.
+- Legacy single-file script is replaced by a proper package; no action needed for CLI users.
+
+## License
+MIT - see LICENSE.
+
+## Support
+- Open an issue on GitHub
+- See [docs/TROUBLESHOOTING.md](docs/TROUBLESHOOTING.md) for common problems
+
+## ⭐ Show Your Support
+
+If you find this project helpful for your research or work, please consider giving it a star on GitHub! It helps others discover the tool and motivates continued development. Thank you! 🙏
+
+![GitHub stars](https://img.shields.io/github/stars/K-Dense-AI/claude-scientific-writer?style=social)
+
+## Star History
+
+[![Star History Chart](https://api.star-history.com/svg?repos=K-Dense-AI/claude-scientific-writer&type=Date)](https://star-history.com/#K-Dense-AI/claude-scientific-writer&Date)

{scientific_writer-2.0.0.dist-info → scientific_writer-2.0.1.dist-info}/RECORD

@@ -1,11 +1,11 @@
-scientific_writer/__init__.py,sha256=SRUR4yXJ9cTBAUYsit7d4g_4v-8zVPWmh2jCCJRwPMU,1182
+scientific_writer/__init__.py,sha256=4kM6vsHCtuymCtc_NfnboW8xKwIz9X5bdBL_WEkRmf4,1182
 scientific_writer/api.py,sha256=nWzBIvsTfCD_Are1-7kamhjqCHn37zc86js7S3QTdi0,12464
 scientific_writer/cli.py,sha256=Hox01o87h33HSumLVHl70AkNinS-OT6KduSzmwqmx40,14592
 scientific_writer/core.py,sha256=XsdXb-GuKY3ER9VXN1aBdcp4hcJXb4H6-e9wkZjJ1h4,6553
 scientific_writer/models.py,sha256=KjRjMjn4GtbHLIUrx2EZB4omGcZeLbflaTJmfNV1M6Y,2629
 scientific_writer/utils.py,sha256=z2nX3PDEcfW4pN_w47TDDC6Kmdcw5uFUGrT8T6lZYSg,9032
-scientific_writer-2.0.0.dist-info/METADATA,sha256=hh-NsQdiVEOc-92EqmyoUhIr2NdBREx4R5uMQ860ZWc,3237
-scientific_writer-2.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scientific_writer-2.0.0.dist-info/entry_points.txt,sha256=pI1zUsWVV6eMkNEKfEmkKozOlLRZnhAZfXBsEyqXtqg,69
-scientific_writer-2.0.0.dist-info/licenses/LICENSE,sha256=H6FOLY6X6QMEnqcbDoq5BM0sBf-K-e1SIBAv0zSwxa4,1070
-scientific_writer-2.0.0.dist-info/RECORD,,
+scientific_writer-2.0.1.dist-info/METADATA,sha256=Q5oY8ZXiYk6h-X3O0Ozv99VTfEskGmGyLaGFk53GVgY,9630
+scientific_writer-2.0.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scientific_writer-2.0.1.dist-info/entry_points.txt,sha256=pI1zUsWVV6eMkNEKfEmkKozOlLRZnhAZfXBsEyqXtqg,69
+scientific_writer-2.0.1.dist-info/licenses/LICENSE,sha256=H6FOLY6X6QMEnqcbDoq5BM0sBf-K-e1SIBAv0zSwxa4,1070
+scientific_writer-2.0.1.dist-info/RECORD,,

scientific_writer-2.0.0.dist-info/METADATA

@@ -1,98 +0,0 @@
-Metadata-Version: 2.4
-Name: scientific-writer
-Version: 2.0.0
-Summary: AI-powered scientific writing with programmatic API and CLI - powered by Claude Sonnet 4.5 and the Claude Agents SDK
-License: MIT
-License-File: LICENSE
-Requires-Python: <=3.12,>=3.10
-Requires-Dist: claude-agent-sdk>=0.1.0
-Requires-Dist: python-dotenv>=1.0.0
-Requires-Dist: requests>=2.31.0
-Description-Content-Type: text/markdown
-
-# Claude Scientific Writer
-
-A Python package and CLI for generating publication-ready scientific papers with Claude Sonnet. Version 2.0 adds a fully typed, programmatic API while keeping the CLI 100% backward compatible.
-
-## Quick Start
-
-### Prerequisites
-- Python 3.10+
-- uv (package and environment manager)
-- ANTHROPIC_API_KEY (required), OPENROUTER_API_KEY (optional for research lookup)
-
-### Install
-```bash
-git clone https://github.com/yourusername/claude-scientific-writer.git
-cd claude-scientific-writer
-uv sync
-```
-
-### Configure API keys
-```bash
-# .env file (recommended)
-echo "ANTHROPIC_API_KEY=your_key" > .env
-echo "OPENROUTER_API_KEY=your_openrouter_key" >> .env
-# or export in your shell
-export ANTHROPIC_API_KEY='your_key'
-```
-
-### Use the CLI
-```bash
-uv run scientific-writer
-```
-
-### Use the Python API
-```python
-import asyncio
-from scientific_writer import generate_paper
-
-async def main():
-    async for update in generate_paper("Create a Nature paper on CRISPR gene editing"):
-        if update["type"] == "progress":
-            print(f"[{update['percentage']}%] {update['message']}")
-        else:
-            print(f"PDF: {update['files']['pdf_final']}")
-
-asyncio.run(main())
-```
-
-## Features
-- Scientific writing (IMRaD) with LaTeX and BibTeX outputs
-- Real-time progress streaming and transparent logging
-- Automatic bibliography and citation management
-- Data and figure integration from a local data/ folder
-- Research lookup via OpenRouter (optional)
-- CLI and programmatic API with full type hints
-
-## Typical Workflow
-1. Place figures and data in data/ at the project root (images -> figures/, files -> data/ automatically).
-2. Run the CLI (or use the API) and describe what you want (venue, topic, constraints).
-3. Follow progress updates; outputs are saved under paper_outputs/<timestamp>_<topic>/.
-
-## Documentation
-- API Reference: Docs/API.md
-- Troubleshooting: Docs/TROUBLESHOOTING.md
-- Skills Overview: Docs/SKILLS.md
-- Development and Contributing: Docs/DEVELOPMENT.md
-- Releasing (versioning & publishing): Docs/RELEASING.md
-- Release Notes: CHANGELOG.md
-- System Instructions (for the agent): CLAUDE.md
-
-## Versioning and Publishing (short)
-Use `uv` and the helper scripts:
-- Bump version (keeps pyproject + __init__ in sync): `uv run scripts/bump_version.py [patch|minor|major]`
-- Build and publish: `uv run scripts/publish.py` (or `--bump patch|minor|major`)
-See Docs/RELEASING.md for prerequisites, dry runs, tagging, and verification.
-
-## Migration (v1.x -> v2.0)
-- CLI remains unchanged (scientific-writer).
-- New programmatic API: from scientific_writer import generate_paper.
-- Legacy single-file script is replaced by a proper package; no action needed for CLI users.
-
-## License
-MIT - see LICENSE.
-
-## Support
-- Open an issue on GitHub
-- See Docs/TROUBLESHOOTING.md for common problems