obsidian

obsidian/bin/copy_folder.py

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+#!/usr/bin/env python3
+"""
+Recursively copy a folder to a destination, excluding hidden files and folders.
+
+This script copies all files and subfolders from a source directory to a destination directory,
+skipping any hidden files or folders (those starting with a dot).
+
+Usage:
+    ./copy_folder.py SOURCE DESTINATION
+
+Arguments:
+    SOURCE      Path to the source folder to copy from.
+    DESTINATION Path to the destination folder to copy to.
+
+Example:
+    ./copy_folder.py ~/my_project ~/backup/my_project
+
+Notes:
+    - Hidden files/folders (starting with a dot) are excluded.
+    - The destination folder will be created if it does not exist.
+    - Existing files in the destination will be overwritten.
+"""
+
+import argparse
+import os
+import shutil
+from pathlib import Path
+
+def copy_folder_excluding_hidden(src, dst):
+    """Recursively copy src to dst, excluding hidden files and folders."""
+    src_path = Path(src)
+    dst_path = Path(dst)
+
+    if not src_path.exists():
+        raise FileNotFoundError(f"Source folder does not exist: {src_path}")
+
+    if not dst_path.exists():
+        dst_path.mkdir(parents=True, exist_ok=True)
+
+    for item in src_path.iterdir():
+        if item.name.startswith('.'):
+            continue  # Skip hidden files/folders
+        if item.is_dir():
+            shutil.copytree(item, dst_path / item.name, ignore=shutil.ignore_patterns('.*'))
+        else:
+            shutil.copy2(item, dst_path / item.name)
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Recursively copy a folder, excluding hidden files and folders."
+    )
+    parser.add_argument(
+        "source",
+        type=str,
+        help="Source folder to copy from."
+    )
+    parser.add_argument(
+        "destination",
+        type=str,
+        help="Destination folder to copy to."
+    )
+
+    args = parser.parse_args()
+
+    try:
+        copy_folder_excluding_hidden(args.source, args.destination)
+        print(f"Successfully copied from {args.source} to {args.destination}")
+    except Exception as e:
+        print(f"Error: {e}")
+        exit(1)
+
+if __name__ == "__main__":
+    main()

obsidian/bin/obsidian_converter.py

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+#!/usr/bin/env python3
+"""
+Convert Obsidian-style wiki links to standard markdown links.
+
+This script processes markdown files containing Obsidian wiki links in the format:
+- [[ mypage ]] -> [mypage](mypage.md)
+- [[ myfolder/mypage ]] -> [myfolder/mypage](myfolder/mypage.md)
+- [[ myfolder/mypage | my description ]] -> [my description](myfolder/mypage.md)
+
+Usage:
+    python obsidian_converter.py source_folder destination_folder
+"""
+
+import os
+import re
+import sys
+import shutil
+import argparse
+from pathlib import Path
+
+
+def build_file_index(source_folder):
+    """
+    Build an index of all markdown files in the source folder.
+    Maps filename (without extension) to full relative paths.
+    
+    Args:
+        source_folder (Path): Root folder to index
+        
+    Returns:
+        dict: Map of filename -> list of relative paths
+    """
+    file_index = {}
+    
+    for md_file in source_folder.rglob('*.md'):
+        relative_path = md_file.relative_to(source_folder)
+        filename = md_file.stem  # filename without extension
+        
+        if filename not in file_index:
+            file_index[filename] = []
+        file_index[filename].append(relative_path)
+    
+    return file_index
+
+
+def convert_wiki_links(content, file_index, current_file_path, source_folder):
+    """
+    Convert wiki-style links to standard markdown links with relative paths.
+    
+    Args:
+        content (str): The markdown content to process
+        file_index (dict): Map of filenames to their paths
+        current_file_path (Path): Path of the current file being processed (relative to source)
+        source_folder (Path): Root source folder
+        
+    Returns:
+        tuple: (converted_content, list of warnings)
+    """
+    # Pattern to match wiki links: [[ link ]] or [[ link | description ]]
+    # Group 1: the link path
+    # Group 2: optional description (after |)
+    wiki_link_pattern = r'\[\[\s*([^|\]]+?)(?:\s*\|\s*([^\]]+?))?\s*\]\]'
+    
+    warnings = []
+    
+    def replace_wiki_link(match):
+        link_path = match.group(1).strip()
+        description = match.group(2)
+        
+        # If there's a custom description, use it; otherwise use the link text
+        if description:
+            display_text = description.strip()
+        else:
+            # Extract just the filename for display (without folder path)
+            display_text = os.path.basename(link_path)
+        
+        # Check if the link already includes a path separator
+        if '/' in link_path or '\\' in link_path:
+            # User specified a path - use it as-is
+            target_path = link_path
+            if not target_path.endswith('.md'):
+                target_path += '.md'
+            
+            # Verify the file exists
+            full_path = source_folder / target_path
+            if not full_path.exists():
+                warnings.append(f"File not found for link '[[ {link_path} ]]' -> {target_path}")
+                return f'[{display_text}]({target_path})'
+            
+            # Convert to relative path
+            target_path = Path(target_path)
+        else:
+            # Just a filename - search for it
+            filename = link_path
+            
+            if filename in file_index:
+                paths = file_index[filename]
+                
+                if len(paths) == 1:
+                    # Single match - use it
+                    target_path = paths[0]
+                else:
+                    # Multiple matches - warn and use the first one
+                    target_path = paths[0]
+                    paths_list = '\n    '.join(str(p) for p in paths)
+                    warnings.append(
+                        f"Multiple files found for '[[ {filename} ]]':\n    {paths_list}\n  Using: {target_path}"
+                    )
+            else:
+                # File not found
+                warnings.append(f"File not found for link '[[ {link_path} ]]' - no matching .md file")
+                # Still create a link, but it will be broken
+                target_path = link_path
+                if not target_path.endswith('.md'):
+                    target_path += '.md'
+                return f'[{display_text}]({target_path})'
+        
+        # Calculate relative path from current file to target file
+        # current_file_path is relative to source_folder (e.g., 'notes/index.md')
+        # target_path is also relative to source_folder (e.g., 'reference/MyPage.md')
+        
+        current_dir = current_file_path.parent
+        
+        # Calculate relative path
+        try:
+            relative_path = os.path.relpath(target_path, current_dir)
+            # Normalize path separators to forward slashes for markdown
+            relative_path = relative_path.replace('\\', '/')
+        except ValueError:
+            # Fallback if relpath fails (different drives on Windows)
+            relative_path = str(target_path)
+        
+        return f'[{display_text}]({relative_path})'
+    
+    # Replace all wiki links with standard markdown links
+    converted_content = re.sub(wiki_link_pattern, replace_wiki_link, content)
+    
+    return converted_content, warnings
+
+
+def process_markdown_file(source_path, dest_path, file_index, source_folder, dry_run=False, verbose=False):
+    """
+    Process a single markdown file, converting wiki links.
+    
+    Args:
+        source_path (Path): Source file path
+        dest_path (Path): Destination file path
+        file_index (dict): Map of filenames to their paths
+        source_folder (Path): Root source folder
+        dry_run (bool): If True, don't actually write files
+        verbose (bool): If True, show detailed output
+        
+    Returns:
+        tuple: (conversions_made, list of warnings)
+    """
+    try:
+        with open(source_path, 'r', encoding='utf-8') as f:
+            content = f.read()
+        
+        # Calculate relative path from source folder for this file
+        relative_file_path = source_path.relative_to(source_folder)
+        
+        # Convert wiki links
+        converted_content, warnings = convert_wiki_links(content, file_index, relative_file_path, source_folder)
+        
+        # Check if any conversions were made
+        conversions_made = content != converted_content
+        
+        if dry_run:
+            status = "WOULD CONVERT" if conversions_made else "NO CHANGES"
+            print(f"{status}: {source_path} -> {dest_path}")
+            if verbose and conversions_made:
+                # Show what wiki links were found
+                wiki_links = re.findall(r'\[\[\s*([^|\]]+?)(?:\s*\|\s*([^\]]+?))?\s*\]\]', content)
+                for link in wiki_links:
+                    if link[1]:  # Has custom description
+                        print(f"  [[ {link[0]} | {link[1]} ]]")
+                    else:
+                        print(f"  [[ {link[0]} ]]")
+            if warnings and verbose:
+                for warning in warnings:
+                    print(f"  ⚠ {warning}")
+        else:
+            # Ensure destination directory exists
+            dest_path.parent.mkdir(parents=True, exist_ok=True)
+            
+            # Write converted content
+            with open(dest_path, 'w', encoding='utf-8') as f:
+                f.write(converted_content)
+            
+            if verbose or conversions_made:
+                status = "CONVERTED" if conversions_made else "COPIED"
+                print(f"{status}: {source_path} -> {dest_path}")
+        
+        # Display warnings for this file
+        if warnings:
+            print(f"⚠ WARNING in {source_path.relative_to(source_folder)}:")
+            for warning in warnings:
+                print(f"  {warning}")
+        
+        return conversions_made, warnings
+        
+    except Exception as e:
+        print(f"ERROR processing {source_path}: {e}")
+        return False, []
+
+
+def main():
+    """Main function to handle command line arguments and process files."""
+    parser = argparse.ArgumentParser(
+        description="Convert Obsidian-style wiki links to standard markdown links.",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python obsidian_converter.py ./my_obsidian_vault ./converted_markdown
+  python obsidian_converter.py /path/to/obsidian /path/to/output
+
+Wiki link conversion examples:
+  [[ mypage ]]                    -> [mypage](mypage.md)
+  [[ myfolder/mypage ]]           -> [myfolder/mypage](myfolder/mypage.md)
+  [[ myfolder/mypage | My Title ]] -> [My Title](myfolder/mypage.md)
+        """
+    )
+    
+    parser.add_argument(
+        'source_folder',
+        help='Source folder containing Obsidian markdown files'
+    )
+    
+    parser.add_argument(
+        'destination_folder',
+        help='Destination folder for converted markdown files'
+    )
+    
+    parser.add_argument(
+        '--dry-run',
+        action='store_true',
+        help='Show what would be converted without actually converting files'
+    )
+    
+    parser.add_argument(
+        '--verbose', '-v',
+        action='store_true',
+        help='Show detailed output during conversion'
+    )
+    
+    args = parser.parse_args()
+    
+    source_folder = Path(args.source_folder)
+    dest_folder = Path(args.destination_folder)
+    
+    # Validate source folder
+    if not source_folder.exists():
+        parser.error(f"Source folder '{source_folder}' does not exist.")
+    
+    if not source_folder.is_dir():
+        parser.error(f"'{source_folder}' is not a directory.")
+    
+    # Create destination folder if it doesn't exist (unless dry run)
+    if not args.dry_run:
+        dest_folder.mkdir(parents=True, exist_ok=True)
+    
+    action = "Would convert" if args.dry_run else "Converting"
+    print(f"{action} Obsidian markdown files from '{source_folder}' to '{dest_folder}'")
+    if args.dry_run:
+        print("(DRY RUN - no files will be modified)")
+    print("-" * 60)
+    
+    # Build file index
+    print("Building file index...")
+    file_index = build_file_index(source_folder)
+    print(f"Indexed {len(file_index)} unique markdown files")
+    print("-" * 60)
+    
+    # Track statistics
+    total_files = 0
+    converted_files = 0
+    files_with_conversions = 0
+    all_warnings = []
+    
+    # Process all markdown files recursively
+    for source_path in source_folder.rglob('*.md'):
+        total_files += 1
+        
+        # Calculate relative path to maintain folder structure
+        relative_path = source_path.relative_to(source_folder)
+        dest_path = dest_folder / relative_path
+        
+        # Process the file
+        had_conversions, warnings = process_markdown_file(
+            source_path, dest_path, 
+            file_index, source_folder,
+            dry_run=args.dry_run, 
+            verbose=args.verbose
+        )
+        
+        converted_files += 1
+        if had_conversions:
+            files_with_conversions += 1
+        
+        all_warnings.extend(warnings)
+    
+    # Copy non-markdown files as well (images, etc.) - unless dry run
+    non_md_files = 0
+    if not args.dry_run:
+        for source_path in source_folder.rglob('*'):
+            if source_path.is_file() and not source_path.suffix == '.md':
+                relative_path = source_path.relative_to(source_folder)
+                dest_path = dest_folder / relative_path
+                
+                # Ensure destination directory exists
+                dest_path.parent.mkdir(parents=True, exist_ok=True)
+                
+                # Copy the file
+                shutil.copy2(source_path, dest_path)
+                non_md_files += 1
+                if args.verbose:
+                    print(f"COPIED: {source_path} -> {dest_path}")
+    
+    print("-" * 60)
+    if args.dry_run:
+        print("Dry run complete!")
+        print(f"Total markdown files: {total_files}")
+        print(f"Files with wiki links to convert: {files_with_conversions}")
+    else:
+        print("Conversion complete!")
+        print(f"Total markdown files processed: {converted_files}/{total_files}")
+        print(f"Files with wiki links converted: {files_with_conversions}")
+        if non_md_files > 0:
+            print(f"Non-markdown files copied: {non_md_files}")
+        print(f"Output directory: {dest_folder}")
+    
+    # Summary of warnings
+    if all_warnings:
+        print("-" * 60)
+        print(f"⚠ TOTAL WARNINGS: {len(all_warnings)}")
+        print("Review the warnings above to fix broken links.")
+
+
+if __name__ == "__main__":
+    main()

obsidian/mkdocs.yml

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+site_name: OptimDev course
+nav:
+  - course: IaaC/index.md
+#  - course: optimdev/index.md
+#  - llm: llm/index.md
+#  - agent: agent/index.md
+#  - exercices: optimdev/OptimDevExercices.md
+
+copyright: "copyright © Gwen"
+site_description: "Advanced user AI course"
+
+theme:
+  name: 'windmill'
+  custom_dir: "overrides"
+#  name: 'material'
+  language: en
+
+markdown_extensions:
+  - admonition
+  - pymdownx.arithmatex
+  - pymdownx.superfences
+
+extra_javascript:
+  - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-MML-AM_CHTML

obsidian/taskfile.yml

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+version: '3'
+# 
+# You can override the host variable by passing it as a command line parameter.
+# task upload -- UPLOAD_TARGET: "localvm"
+# 
+
+vars:
+  UPLOAD_TARGET:
+#  UPLOAD_TARGET: "remotevps"
+#  UPLOAD_TARGET: "localvm"
+
+tasks:
+
+  default:
+    desc: whole workflow
+    cmds:
+      - task: copy
+      - task: obsidian_convert
+     # - task: deadlinks
+      - task: mkdocs
+      # **CAREFULL** be sur you deploy on the right upload target
+      - task: upload
+
+  copy:
+    desc: copies the folder without the hidden files (and filter on a YAML frontmatter attribute)
+    cmds:
+      - cp ../ders/mkdocs.yml .
+      - ./bin/copy_folder.py ../ders/ders tmp0
+#      # filter the exercices
+#      - ./bin/filter_md_files.py --source tmp0 --destination tmp --filter-key kind --filter-value exercice
+#      - rm -rf tmp0
+      - mv tmp0 tmp
+
+  obsidian_convert:
+    desc: converts obsidian wiki syntax into a standard markdown
+    cmds:
+      - ./bin/obsidian_converter.py tmp/ docs
+      - rm -rf tmp
+    generates:
+      - docs
+
+#  deadlinks:
+#    desc: remove dead links
+#    cmds:
+#      - ./bin/md_link_cleaner.py --source tmp2 --destination docs
+#      - rm -rf tmp2
+#    generates:
+#      - docs
+
+  mkdocs:
+    desc: mkdocs html generation
+    cmds:
+      - ./.venv/bin/mkdocs build
+    generates:
+      - site
+
+  upload:
+    desc: uploads the generated html
+    cmds:
+      - |
+        if [ "{{.UPLOAD_TARGET}}" = "remotevps" ]; then
+          echo "deployment in remote VPS"
+          rsync -avH -e "ssh -i ./hosts/XXXXX.key" --force --stats ./site/* root@monvps.fr:/var/www/html/
+        elif [ "{{.UPLOAD_TARGET}}" = "localvm" ]; then
+          echo "deployment in the local VM"
+          rsync -avH -e "ssh -i ./hosts/localvm/toto_key" --force --stats ./site/* ubuntu@toto.local:/var/www/html/
+        else
+          echo "Unknown deployment target: {{.UPLOAD_TARGET}}"
+          exit 1
+        fi
+      - task: clean
+
+  clean:
+    desc: suppression of all data
+    cmds:
+      # generated files and folders
+      - rm -rf docs
+      - rm -rf site