scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/__init__.py

@@ -29,8 +29,8 @@ Example:
 from .api import generate_paper
 from .models import ProgressUpdate, PaperResult, PaperMetadata, PaperFiles
 
-__version__ = "2.1.1"
-__author__ = "Scientific Writer Contributors"
+__version__ = "2.2.2"
+__author__ = "K-Dense"
 __license__ = "MIT"
 
 __all__ = [

scientific_writer/api.py

@@ -15,6 +15,7 @@ from .core import (
     get_data_files,
     process_data_files,
     create_data_context_message,
+    setup_claude_skills,
 )
 from .models import ProgressUpdate, PaperResult, PaperMetadata, PaperFiles
 from .utils import (
@@ -76,10 +77,16 @@ async def generate_paper(
     if cwd:
         work_dir = Path(cwd).resolve()
     else:
-        # Default to package parent directory (project root)
-        work_dir = Path(__file__).parent.parent.absolute()
+        # Default to user's current working directory
+        work_dir = Path.cwd()
     
-    # Ensure output folder exists
+    # Get package directory for loading system instructions and skills
+    package_dir = Path(__file__).parent.absolute()  # scientific_writer/ directory
+    
+    # Set up Claude skills in the working directory
+    setup_claude_skills(package_dir, work_dir)
+    
+    # Ensure output folder exists in user's directory
     output_folder = ensure_output_folder(work_dir, output_dir)
     
     # Initial progress update
@@ -89,8 +96,8 @@ async def generate_paper(
         percentage=0,
     ).to_dict()
     
-    # Load system instructions
-    system_instructions = load_system_instructions(work_dir)
+    # Load system instructions from package
+    system_instructions = load_system_instructions(package_dir)
     
     # Add conversation continuity instruction
     system_instructions += "\n\n" + """
@@ -120,8 +127,8 @@ IMPORTANT - CONVERSATION CONTINUITY:
         model=model,
         allowed_tools=["Read", "Write", "Edit", "Bash", "research-lookup"],
         permission_mode="bypassPermissions",
-        setting_sources=["project"],
-        cwd=str(work_dir),
+        setting_sources=["project"],  # Load skills from project .claude directory
+        cwd=str(work_dir),  # User's working directory
     )
     
     # Track progress through message analysis

scientific_writer/cli.py

@@ -20,6 +20,7 @@ from .core import (
     get_data_files,
     process_data_files,
     create_data_context_message,
+    setup_claude_skills,
 )
 from .utils import find_existing_papers, detect_paper_reference
 
@@ -33,14 +34,18 @@ async def main():
         print(f"Error: {e}")
         sys.exit(1)
     
-    # Get the current working directory (project root)
-    cwd = Path(__file__).parent.parent.absolute()
+    # Get the current working directory (user's directory) and package directory
+    cwd = Path.cwd()  # User's current working directory
+    package_dir = Path(__file__).parent.absolute()  # Package installation directory (scientific_writer/)
     
-    # Ensure paper_outputs folder exists
+    # Set up Claude skills in the working directory
+    setup_claude_skills(package_dir, cwd)
+    
+    # Ensure paper_outputs folder exists in user's directory
     output_folder = ensure_output_folder(cwd)
     
-    # Load system instructions from CLAUDE.md
-    system_instructions = load_system_instructions(cwd)
+    # Load system instructions from package CLAUDE.md
+    system_instructions = load_system_instructions(package_dir)
     
     # Add conversation continuity instruction  
     # Note: The Python CLI handles session tracking via current_paper_path
@@ -60,8 +65,8 @@ IMPORTANT - CONVERSATION CONTINUITY:
         model="claude-sonnet-4-20250514",  # Always use Claude Sonnet 4.5
         allowed_tools=["Read", "Write", "Edit", "Bash", "research-lookup"],  # Default Claude Code tools + research lookup
         permission_mode="bypassPermissions",  # Execute immediately without approval prompts
-        setting_sources=["project"],  # Load skills from .claude/skills/
-        cwd=str(cwd),  # Set working directory to project root
+        setting_sources=["project"],  # Load skills from project .claude directory
+        cwd=str(cwd),  # Set working directory to user's current directory
     )
     
     # Track conversation state

scientific_writer/core.py

@@ -10,6 +10,28 @@ from dotenv import load_dotenv
 load_dotenv()
 
 
+def setup_claude_skills(package_dir: Path, work_dir: Path) -> None:
+    """
+    Set up Claude skills by copying from package to working directory.
+    
+    Args:
+        package_dir: Package installation directory containing .claude/
+        work_dir: User's working directory where .claude/ should be copied
+    """
+    source_claude = package_dir / ".claude"
+    dest_claude = work_dir / ".claude"
+    
+    # Only copy if source exists and destination doesn't
+    if source_claude.exists() and not dest_claude.exists():
+        try:
+            shutil.copytree(source_claude, dest_claude)
+            print(f"✓ Initialized Claude skills in {dest_claude}")
+        except Exception as e:
+            print(f"Warning: Could not copy Claude skills: {e}")
+    elif not source_claude.exists():
+        print(f"Warning: Skills directory not found in package: {source_claude}")
+
+
 def get_api_key(api_key: Optional[str] = None) -> str:
     """
     Get the Anthropic API key.
@@ -35,23 +57,23 @@ def get_api_key(api_key: Optional[str] = None) -> str:
     return env_key
 
 
-def load_system_instructions(cwd: Path) -> str:
+def load_system_instructions(package_dir: Path) -> str:
     """
-    Load system instructions from CLAUDE.md file.
+    Load system instructions from package's CLAUDE.md file.
     
     Args:
-        cwd: Current working directory (project root).
+        package_dir: Package installation directory containing CLAUDE.md.
         
     Returns:
         System instructions string.
     """
-    instructions_file = cwd / "CLAUDE.md"
+    instructions_file = package_dir / "CLAUDE.md"
     
     if instructions_file.exists():
         with open(instructions_file, 'r', encoding='utf-8') as f:
             return f.read()
     else:
-        # Fallback if CLAUDE.md doesn't exist
+        # Fallback if CLAUDE.md doesn't exist in package
         return (
             "You are a scientific writing assistant. Follow best practices for "
             "scientific communication and always present a plan before execution."

{scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scientific-writer
-Version: 2.1.1
+Version: 2.2.2
 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
@@ -22,6 +22,7 @@ A Python package and CLI for generating publication-ready scientific papers, rep
 - Programmatic Python API with async support
 - Research lookup with Perplexity Sonar Pro
 - Intelligent paper detection (auto-resume editing)
+- Clinical reports (case reports, diagnostic reports, trial reports, HIPAA compliance)
 - Grant proposal generation (NSF, NIH, DOE, DARPA)
 - Research posters with LaTeX
 - Scientific schematics (CONSORT, circuits, pathways)
@@ -85,6 +86,7 @@ asyncio.run(main())
 
 ### 📝 Document Generation
 - **Scientific papers** with IMRaD structure (Nature, Science, NeurIPS, etc.)
+- **Clinical reports** (case reports, diagnostic reports, trial reports, patient documentation)
 - **Research posters** using LaTeX (beamerposter, tikzposter, baposter)
 - **Grant proposals** (NSF, NIH, DOE, DARPA) with agency-specific formatting
 - **Literature reviews** with systematic citation management
@@ -158,6 +160,7 @@ asyncio.run(main())
 | Task | Command Example |
 |------|----------------|
 | **Scientific Paper** | `> Create a Nature paper on CRISPR gene editing` |
+| **Clinical Report** | `> Create a clinical case report for rare disease presentation` |
 | **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` |
@@ -184,6 +187,7 @@ asyncio.run(main())
 | Type | Example |
 |------|---------|
 | **Papers** | Nature, Science, NeurIPS, ICML, IEEE, ACM |
+| **Clinical Reports** | Case reports, diagnostic reports, trial reports, patient notes |
 | **Grants** | NSF, NIH R01/R21/K, DOE, DARPA |
 | **Posters** | Conference posters (A0, A1, custom sizes) |
 | **Reviews** | Systematic literature reviews |

scientific_writer-2.2.2.dist-info/RECORD

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+scientific_writer/utils.py,sha256=z2nX3PDEcfW4pN_w47TDDC6Kmdcw5uFUGrT8T6lZYSg,9032
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