scientific-writer 2.2.2__py3-none-any.whl → 2.2.3__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__ = "2.2.2"
+__version__ = "2.2.3"
 __author__ = "K-Dense"
 __license__ = "MIT"
 

scientific_writer/api.py

@@ -80,10 +80,10 @@ async def generate_paper(
         # Default to user's current working directory
         work_dir = Path.cwd()
     
-    # Get package directory for loading system instructions and skills
+    # Get package directory for copying skills to working directory
     package_dir = Path(__file__).parent.absolute()  # scientific_writer/ directory
     
-    # Set up Claude skills in the working directory
+    # Set up Claude skills in the working directory (includes WRITER.md)
     setup_claude_skills(package_dir, work_dir)
     
     # Ensure output folder exists in user's directory
@@ -96,8 +96,8 @@ async def generate_paper(
         percentage=0,
     ).to_dict()
     
-    # Load system instructions from package
-    system_instructions = load_system_instructions(package_dir)
+    # Load system instructions from .claude/WRITER.md in working directory
+    system_instructions = load_system_instructions(work_dir)
     
     # Add conversation continuity instruction
     system_instructions += "\n\n" + """

scientific_writer/cli.py

@@ -38,14 +38,14 @@ async def main():
     cwd = Path.cwd()  # User's current working directory
     package_dir = Path(__file__).parent.absolute()  # Package installation directory (scientific_writer/)
     
-    # Set up Claude skills in the working directory
+    # Set up Claude skills in the working directory (includes WRITER.md)
     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 package CLAUDE.md
-    system_instructions = load_system_instructions(package_dir)
+    # Load system instructions from .claude/WRITER.md in working directory
+    system_instructions = load_system_instructions(cwd)
     
     # Add conversation continuity instruction  
     # Note: The Python CLI handles session tracking via current_paper_path
@@ -62,7 +62,7 @@ IMPORTANT - CONVERSATION CONTINUITY:
     # Configure the Claude agent options
     options = ClaudeAgentOptions(
         system_prompt=system_instructions,
-        model="claude-sonnet-4-20250514",  # Always use Claude Sonnet 4.5
+        model="claude-sonnet-4-5",  # 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 project .claude directory

scientific_writer/core.py

@@ -12,7 +12,7 @@ load_dotenv()
 
 def setup_claude_skills(package_dir: Path, work_dir: Path) -> None:
     """
-    Set up Claude skills by copying from package to working directory.
+    Set up Claude skills and WRITER.md by copying .claude/ from package to working directory.
     
     Args:
         package_dir: Package installation directory containing .claude/
@@ -21,15 +21,16 @@ def setup_claude_skills(package_dir: Path, work_dir: Path) -> None:
     source_claude = package_dir / ".claude"
     dest_claude = work_dir / ".claude"
     
-    # Only copy if source exists and destination doesn't
+    # Copy .claude directory (which includes skills/ and WRITER.md) 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}")
+            print(f"✓ Initialized Claude configuration in {dest_claude}")
+            print(f"✓ Skills and system instructions (WRITER.md) ready")
         except Exception as e:
-            print(f"Warning: Could not copy Claude skills: {e}")
+            print(f"Warning: Could not copy Claude configuration: {e}")
     elif not source_claude.exists():
-        print(f"Warning: Skills directory not found in package: {source_claude}")
+        print(f"Warning: .claude directory not found in package: {source_claude}")
 
 
 def get_api_key(api_key: Optional[str] = None) -> str:
@@ -57,23 +58,23 @@ def get_api_key(api_key: Optional[str] = None) -> str:
     return env_key
 
 
-def load_system_instructions(package_dir: Path) -> str:
+def load_system_instructions(work_dir: Path) -> str:
     """
-    Load system instructions from package's CLAUDE.md file.
+    Load system instructions from .claude/WRITER.md in the working directory.
     
     Args:
-        package_dir: Package installation directory containing CLAUDE.md.
+        work_dir: Working directory containing .claude/WRITER.md.
         
     Returns:
         System instructions string.
     """
-    instructions_file = package_dir / "CLAUDE.md"
+    instructions_file = work_dir / ".claude" / "WRITER.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 in package
+        # Fallback if WRITER.md doesn't exist
         return (
             "You are a scientific writing assistant. Follow best practices for "
             "scientific communication and always present a plan before execution."

{scientific_writer-2.2.2.dist-info → scientific_writer-2.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scientific-writer
-Version: 2.2.2
+Version: 2.2.3
 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-2.2.2.dist-info → scientific_writer-2.2.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
-scientific_writer/CLAUDE.md,sha256=O-ThWtw-XJmeZF8MqGoF_bwGq3XNRKsF_Xog81k_3FM,32256
-scientific_writer/__init__.py,sha256=f7DQaHTD_J8ZLqjCN9KWj7rMIDuX9BagEbWbVwZjZfc,1159
-scientific_writer/api.py,sha256=-9ZXhTqDt3wDC-iL3d2BeKEk5RlkqrNFYVZNftRMigo,12826
-scientific_writer/cli.py,sha256=zEF7EZkJT7xOa5SeWATa3mHoHBmOF3oFXz7fkpK9QHw,14913
-scientific_writer/core.py,sha256=phsDtLIngod4MyVh9wQB1pNDkni7XvYUu-WGT6CyuX4,7486
+scientific_writer/__init__.py,sha256=9BVGd3cosRJSt25lC0pEHoZBxHlbvmepGPx1AXsnagc,1159
+scientific_writer/api.py,sha256=E2PKi3gszuw_PZU8edswkvk8enBOfhIM8S_KxNWRcUc,12872
+scientific_writer/cli.py,sha256=PzwcNwPY_af4VcLFtIBSTk3xJQ7D79dSfOXUZxIcBM0,14940
+scientific_writer/core.py,sha256=EXhh9p_y0gkuXFD0a47F9vlVaRipQ6W5Ng5Lyzieg4A,7656
 scientific_writer/models.py,sha256=KjRjMjn4GtbHLIUrx2EZB4omGcZeLbflaTJmfNV1M6Y,2629
 scientific_writer/utils.py,sha256=z2nX3PDEcfW4pN_w47TDDC6Kmdcw5uFUGrT8T6lZYSg,9032
+scientific_writer/.claude/WRITER.md,sha256=O-ThWtw-XJmeZF8MqGoF_bwGq3XNRKsF_Xog81k_3FM,32256
 scientific_writer/.claude/settings.local.json,sha256=PVPFjrrlwJo6J3KgeGwxqfh2w0N4xW9r5cefTC36fX8,780
 scientific_writer/.claude/skills/citation-management/SKILL.md,sha256=guNDqOIuvqK1YHbVc5JGiM4MwSmyiytoUqzahNZHrrw,29916
 scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib,sha256=vwPMZG5rxqq6hdYyuOJbJsKDBBmJLzwXp9hEgF06ch4,9201
@@ -305,8 +305,8 @@ scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.m
 scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py,sha256=ikTF2rMjexS4y3udwtZR8XauleXwU1drG9RDf1M2-Co,6875
 scientific_writer/.claude/skills/venue-templates/scripts/query_template.py,sha256=RI0dzZB-igJZl8dJjbA7teiJy3T-j3reGf62sQpN8g4,8959
 scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py,sha256=acRsRY4hqDsHrkzKIHeRZT7vle9q5SEjkFG3S4Vc5PQ,8766
-scientific_writer-2.2.2.dist-info/METADATA,sha256=mktLf2jN9bfv6WfoTaaezfbVs1LmXnzWwD7TrdTFbzU,9992
-scientific_writer-2.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scientific_writer-2.2.2.dist-info/entry_points.txt,sha256=pI1zUsWVV6eMkNEKfEmkKozOlLRZnhAZfXBsEyqXtqg,69
-scientific_writer-2.2.2.dist-info/licenses/LICENSE,sha256=H6FOLY6X6QMEnqcbDoq5BM0sBf-K-e1SIBAv0zSwxa4,1070
-scientific_writer-2.2.2.dist-info/RECORD,,
+scientific_writer-2.2.3.dist-info/METADATA,sha256=2vKPGJa5r18o5uw_Mgyaav94gBA74cLldMEjUV4iX20,9992
+scientific_writer-2.2.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scientific_writer-2.2.3.dist-info/entry_points.txt,sha256=pI1zUsWVV6eMkNEKfEmkKozOlLRZnhAZfXBsEyqXtqg,69
+scientific_writer-2.2.3.dist-info/licenses/LICENSE,sha256=H6FOLY6X6QMEnqcbDoq5BM0sBf-K-e1SIBAv0zSwxa4,1070
+scientific_writer-2.2.3.dist-info/RECORD,,