Script that converts a python repo to markdown

pyqmmm/cli.py

@@ -41,12 +41,14 @@ def cli():
 @click.option("--delete_pdb_atoms", "-dpa", is_flag=True, help="Deletes atoms from PDB trajectory.")
 @click.option("--translate_pdb_to_center", "-tc", is_flag=True, help="Translates PDB traj to new center.")
 @click.option("--xyz2pdb", "-x2p", is_flag=True, help="Converts an xyz file or traj to a PDB.")
+@click.option("--repo2markdown", "-r2m", is_flag=True, help="Converts python package to markdown file.")
 def io(
     ppm2png,
     delete_xyz_atoms,
     delete_pdb_atoms,
     translate_pdb_to_center,
     xyz2pdb,
+    repo2markdown
     ):
     """
     Tools for useful manipulations of common file types.
@@ -114,6 +116,12 @@ def io(
         output_pdb = "pdb_trajectory.pdb"
         pyqmmm.io.xyz2pdb.xyz2pdb_traj(xyz_traj, output_pdb, template)
 
+    elif repo2markdown:
+        click.echo("Converts a Python package to a single markdown file")
+        click.echo("Loading...")
+        import pyqmmm.io.repo2markdown
+        pyqmmm.io.repo2markdown.main()
+
 
 @cli.command()
 @click.option("--gbsa_submit", "-gs", is_flag=True, help="Prepares and submits a mmGBSA job.")

pyqmmm/io/repo2markdown.py

@@ -0,0 +1,131 @@
+import os
+import ast
+from pathlib import Path
+
+# Configuration
+ROOT_DIR = Path(".").resolve()
+OUTPUT_FILE = f"{ROOT_DIR.name}_LLM_readable.md"
+
+INCLUDE_EXTENSIONS = {".py", ".md", ".txt", ".yaml", ".yml", ".json", ".toml", ".csv"}
+SKIP_DIRS = {".git", "__pycache__", ".mypy_cache", ".venv", "env", "venv", ".idea", ".vscode"}
+INDENT = "    "
+
+
+def should_include_file(file_path: Path):
+    return file_path.suffix in INCLUDE_EXTENSIONS
+
+
+def generate_tree_structure(root: Path) -> str:
+    tree_lines = ["# Repository Structure\n"]
+
+    def _walk(path: Path, prefix=""):
+        dir_entries = [p for p in path.iterdir() if p.is_dir() and p.name not in SKIP_DIRS]
+        file_entries = [p for p in path.iterdir() if p.is_file() and should_include_file(p)]
+        entries = sorted(dir_entries + file_entries, key=lambda p: p.name.lower())
+        for i, entry in enumerate(entries):
+            connector = "└── " if i == len(entries) - 1 else "├── "
+            tree_lines.append(f"{prefix}{connector}{entry.name}{ '/' if entry.is_dir() else ''}")
+            if entry.is_dir():
+                extension = "    " if i == len(entries) - 1 else "│   "
+                _walk(entry, prefix + extension)
+
+    _walk(root)
+    return "\n".join(tree_lines) + "\n"
+
+
+def get_readme_content(root: Path) -> str:
+    for filename in ["README.md", "readme.md", "Readme.md"]:
+        readme_path = root / filename
+        if readme_path.exists():
+            try:
+                with open(readme_path, "r", encoding="utf-8") as f:
+                    return "# README\n\n" + f.read() + "\n\n"
+            except Exception as e:
+                return f"# README\n\n⚠️ Could not read README: {e}\n\n"
+    return ""
+
+
+def get_imported_modules(file_path: Path) -> list:
+    imported = set()
+    try:
+        with open(file_path, "r", encoding="utf-8") as f:
+            tree = ast.parse(f.read(), filename=str(file_path))
+        for node in ast.walk(tree):
+            if isinstance(node, ast.Import):
+                for alias in node.names:
+                    imported.add(alias.name)
+            elif isinstance(node, ast.ImportFrom):
+                if node.module:
+                    dots = "." * node.level
+                    imported.add(dots + node.module)
+    except Exception:
+        pass
+    return sorted(imported)
+
+
+def write_imports_section(root_dir: Path):
+    markdown_lines = ["# Module Imports\n"]
+    py_files = sorted(root_dir.rglob("*.py"), key=lambda p: str(p.relative_to(root_dir)))
+    for file_path in py_files:
+        if not should_include_file(file_path):  # Though rglob *.py should be fine
+            continue
+        rel_path = file_path.relative_to(root_dir)
+        imported = get_imported_modules(file_path)
+        markdown_lines.append(f"\n## `{rel_path}`\n")
+        if imported:
+            markdown_lines.append("Imported modules:\n")
+            for mod in imported:
+                markdown_lines.append(f"- {mod}")
+        else:
+            markdown_lines.append("No imported modules.")
+        markdown_lines.append("\n")
+    return "\n".join(markdown_lines) + "\n"
+
+
+def write_file_contents(root_dir: Path):
+    markdown_lines = ["# File Contents\n"]
+    readme_names = {"readme.md", "readme.md", "readme.md"}  # Lowercase set
+
+    for dirpath, dirnames, filenames in os.walk(root_dir):
+        dirnames[:] = sorted([d for d in dirnames if d not in SKIP_DIRS])
+        rel_path = Path(dirpath).relative_to(root_dir)
+        for filename in sorted(filenames):
+            if filename.lower() in readme_names and rel_path == Path("."):
+                continue  # Skip README since it's added separately
+            file_path = Path(dirpath) / filename
+            if not should_include_file(file_path):
+                continue
+            markdown_lines.append(f"\n### `{file_path.relative_to(root_dir)}`\n")
+            lang = file_path.suffix[1:] if file_path.suffix else "text"
+            if lang == "md":
+                lang = "markdown"
+            elif lang == "txt":
+                lang = "text"
+            markdown_lines.append(f"```{lang}")
+            try:
+                with open(file_path, "r", encoding="utf-8") as f:
+                    markdown_lines.append(f.read())
+            except Exception as e:
+                markdown_lines.append(f"⚠️ Could not read file: {e}")
+            markdown_lines.append("```")
+    return "\n".join(markdown_lines) + "\n"
+
+
+def main():
+    print(f"Generating markdown from: {ROOT_DIR}")
+    readme_section = get_readme_content(ROOT_DIR)
+    tree_diagram = generate_tree_structure(ROOT_DIR)
+    imports_section = write_imports_section(ROOT_DIR)
+    file_content_section = write_file_contents(ROOT_DIR)
+
+    with open(OUTPUT_FILE, "w", encoding="utf-8") as f:
+        f.write(readme_section)
+        f.write(tree_diagram)
+        f.write(imports_section)
+        f.write(file_content_section)
+
+    print(f"✅ Output written to {OUTPUT_FILE}")
+
+
+if __name__ == "__main__":
+    main()