scientific-writer 2.2.2__tar.gz → 2.3.0__tar.gz

{scientific_writer-2.2.2 → scientific_writer-2.3.0}/CHANGELOG.md

@@ -6,6 +6,76 @@ All notable changes to the Scientific Writer project will be documented in this
 
 ---
 
+## [2.3.0] - 2025-11-04
+
+### ✨ Added
+
+#### Manuscript Editing Workflow
+
+- **Automatic Editing Mode Detection** - Smart file routing based on file type
+  - Manuscript files (`.tex`, `.md`, `.docx`, `.pdf`) automatically copied to `drafts/` folder
+  - Image files routed to `figures/` folder
+  - Data files routed to `data/` folder
+  - System recognizes manuscripts in drafts/ as editing tasks, not creation from scratch
+  
+- **EDITING MODE Context** - Clear feedback and instructions
+  - Prominent `⚠️ EDITING MODE` warning displayed when manuscripts detected
+  - Agent receives explicit instructions to edit existing manuscript
+  - Visual `[EDITING MODE]` indicators in CLI output
+  - Progress messages show manuscript file counts separately
+  
+- **Enhanced File Processing** - Improved data file handling
+  - New `get_manuscript_extensions()` function in `core.py`
+  - Updated `process_data_files()` to handle three file categories
+  - Updated `create_data_context_message()` with editing mode detection
+  - Manuscript files tracked separately in processed_info dictionary
+
+### 🔧 Improvements
+
+- **System Instructions (WRITER.md)** - Added comprehensive manuscript editing workflow section
+  - Clear instructions for handling manuscript files from data folder
+  - Defined file routing rules by file type
+  - Detailed editing workflow for the agent
+  - Example scenarios demonstrating the workflow
+  
+- **CLI User Experience** - Better visibility into file processing
+  - Welcome message explains manuscript file routing
+  - File processing shows separate counts for manuscripts, data, and images
+  - Help text updated with manuscript editing information
+  - Consistent `[EDITING MODE]` indicators throughout
+  
+- **API Progress Updates** - Enhanced feedback in programmatic mode
+  - Progress messages report manuscript files separately
+  - Clear indication when manuscripts are copied to drafts/
+  - Better tracking of file processing stages
+
+### 📝 Files Modified
+
+- `scientific_writer/.claude/WRITER.md` - Added "CRITICAL: Manuscript Editing Workflow" section
+- `scientific_writer/core.py` - Added manuscript detection and routing logic
+- `scientific_writer/cli.py` - Updated UI to show editing mode indicators
+- `scientific_writer/api.py` - Enhanced progress reporting for manuscript files
+
+### 🎯 Usage Example
+
+```bash
+# Place a manuscript file in the data folder
+cp my_paper.tex data/
+
+# Run scientific writer
+scientific-writer
+
+# The system will:
+# ✓ Detect my_paper.tex as a manuscript file
+# ✓ Copy it to drafts/ folder (not data/)
+# ✓ Display [EDITING MODE] indicator
+# ✓ Treat the task as editing, not creation
+
+> "Improve the introduction and add 5 more citations"
+```
+
+---
+
 ## [2.2.1] - 2025-11-04
 
 ### 🔧 Improvements

{scientific_writer-2.2.2 → scientific_writer-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scientific-writer
-Version: 2.2.2
+Version: 2.3.0
 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

scientific_writer-2.3.0/RELEASE_NOTES_2.3.0.md

@@ -0,0 +1,208 @@
+# Scientific Writer v2.3.0 - Edit Papers Anywhere 📝
+
+## 🎉 Write & Edit Scientific Papers Anywhere
+
+This release introduces **Manuscript Editing Mode** - a powerful new workflow that lets you edit existing papers from anywhere! Simply place your manuscript file (`.tex`, `.md`, `.docx`, `.pdf`) in the `data/` folder, and the system automatically recognizes it as an editing task.
+
+## ✨ What's New
+
+### Automatic Editing Mode Detection
+
+The system now intelligently routes files based on their type:
+
+| 📄 File Type | 📁 Destination | 🎯 Purpose |
+|-------------|---------------|-----------|
+| **Manuscript files** (`.tex`, `.md`, `.docx`, `.pdf`) | `drafts/` | Editing existing manuscripts |
+| **Image files** (`.png`, `.jpg`, `.svg`, etc.) | `figures/` | Figures for your paper |
+| **Data files** (`.csv`, `.txt`, `.json`, etc.) | `data/` | Data for analysis |
+
+### How It Works
+
+```bash
+# 1. Place your manuscript in the data folder
+cp my_research_paper.tex data/
+
+# 2. Run scientific writer
+scientific-writer
+
+# The system automatically:
+# ✓ Detects it's a manuscript file
+# ✓ Copies it to drafts/ folder
+# ✓ Displays [EDITING MODE] indicator
+# ✓ Treats this as an editing task
+
+# 3. Request your edits
+> "Improve the introduction and add 5 more citations to the methods section"
+
+# Result:
+# - Original manuscript preserved
+# - New version created (v2_my_research_paper.tex)
+# - All changes documented in revision_notes.md
+```
+
+### Clear Visual Feedback
+
+When editing mode is active, you'll see clear indicators:
+
+```
+⚠️  EDITING MODE - Manuscript files detected!
+
+📦 Processing files...
+   ✓ Copied 1 manuscript file(s) to drafts/ [EDITING MODE]
+   ✓ Copied 2 image(s) to figures/
+   ✓ Deleted original files from data folder
+
+🔧 TASK: This is an EDITING task, not creating from scratch.
+```
+
+## 🚀 Key Features
+
+### 1. **Works with Multiple Formats**
+- LaTeX (`.tex`) - Your complete paper
+- Markdown (`.md`) - Research notes or drafts
+- Word (`.docx`) - Documents from collaborators
+- PDF (`.pdf`) - Existing publications to revise
+
+### 2. **Smart File Organization**
+- Manuscripts automatically go to `drafts/` folder
+- Images automatically go to `figures/` folder
+- Data files stay in `data/` folder
+- No manual organization needed!
+
+### 3. **Version Control Built-In**
+- Original manuscript preserved
+- New versions created (v2, v3, etc.)
+- Changes documented in `revision_notes.md`
+- Full audit trail of all edits
+
+### 4. **Works in Both CLI and API**
+- Same behavior in interactive CLI mode
+- Same behavior when using programmatic API
+- Consistent experience everywhere
+
+## 💡 Use Cases
+
+### Edit a Paper from a Collaborator
+```bash
+# Collaborator sends you draft.docx
+cp draft.docx data/
+scientific-writer
+> "Convert to LaTeX and add citations for all claims in the introduction"
+```
+
+### Improve an Existing LaTeX Paper
+```bash
+# Working on your submission
+cp neurips_submission.tex data/
+scientific-writer
+> "Address reviewer comments: strengthen methods section and add ablation study"
+```
+
+### Revise Based on Feedback
+```bash
+# Got feedback from advisor
+cp thesis_chapter.tex data/
+scientific-writer
+> "Rewrite the discussion section to address concerns about generalizability"
+```
+
+## 🔧 Technical Details
+
+### Files Modified
+- `scientific_writer/.claude/WRITER.md` - Added manuscript editing workflow instructions
+- `scientific_writer/core.py` - Added manuscript detection and routing logic
+- `scientific_writer/cli.py` - Updated UI with editing mode indicators
+- `scientific_writer/api.py` - Enhanced progress reporting for manuscripts
+
+### New Functions
+- `get_manuscript_extensions()` - Defines manuscript file types
+- Enhanced `process_data_files()` - Routes files intelligently
+- Enhanced `create_data_context_message()` - Provides editing mode context
+
+### Backward Compatibility
+✅ **100% backward compatible**
+- All existing functionality preserved
+- New behavior only activates for manuscript files
+- No breaking changes to API or CLI
+- Existing workflows continue to work
+
+## 📦 Installation
+
+```bash
+# Update to the latest version
+cd claude-scientific-writer
+git pull origin main
+uv sync
+
+# Verify installation
+scientific-writer --version  # Should show 2.3.0
+```
+
+## 📚 Documentation
+
+For detailed information, see:
+- [CHANGELOG.md](CHANGELOG.md) - Complete version history
+- [WRITER.md](scientific_writer/.claude/WRITER.md) - System instructions
+- [README.md](README.md) - Full documentation
+
+## 🎯 Example Workflow
+
+Here's a complete workflow showing the power of editing mode:
+
+```bash
+# You receive a paper draft from a colleague
+cp colleague_draft.docx data/
+
+# Start scientific writer
+scientific-writer
+
+# Request comprehensive edits
+> "Please:
+1. Convert this Word document to LaTeX
+2. Improve the introduction with better flow
+3. Add 10 more recent citations (2023-2024)
+4. Strengthen the methods section
+5. Create a new figure summarizing the results
+6. Format for Nature journal submission"
+
+# The system will:
+# ✓ Recognize this as an editing task
+# ✓ Read the existing document
+# ✓ Apply all requested changes
+# ✓ Create properly versioned outputs
+# ✓ Document all changes
+# ✓ Generate publication-ready LaTeX
+```
+
+## 🙏 What This Means for You
+
+### Before v2.3.0
+- Had to manually specify you're editing
+- Files could go to wrong folders
+- No clear indication of editing vs. creation
+- Manual file organization required
+
+### After v2.3.0
+- ✨ Automatic detection of editing tasks
+- ✨ Smart file routing by type
+- ✨ Clear visual feedback throughout
+- ✨ Zero manual organization needed
+- ✨ Edit papers from **anywhere**!
+
+## 🎊 Summary
+
+Version 2.3.0 makes it effortless to edit scientific papers from any source:
+- Drop manuscript files in `data/` folder
+- System automatically recognizes editing mode
+- Smart routing to correct folders
+- Clear feedback and version control
+- Works with LaTeX, Markdown, Word, and PDF
+
+**Write and edit scientific papers anywhere! 🚀**
+
+---
+
+**Full Changelog**: [CHANGELOG.md](CHANGELOG.md)
+
+**Questions or Issues?** Open an issue on GitHub or check the [documentation](README.md).
+

{scientific_writer-2.2.2 → scientific_writer-2.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scientific-writer"
-version = "2.2.2"
+version = "2.3.0"
 description = "AI-powered scientific writing with programmatic API and CLI - powered by Claude Sonnet 4.5 and the Claude Agents SDK"
 readme = "README.md"
 requires-python = ">=3.10"