scitex 2.4.3__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/git/_validation.py

@@ -30,27 +30,27 @@ def validate_branch_name(name: str) -> Tuple[bool, str]:
 
     name = name.strip()
 
-    if name.startswith('-'):
+    if name.startswith("-"):
         return False, "Branch name cannot start with '-'"
 
-    if name.endswith('.lock'):
+    if name.endswith(".lock"):
         return False, "Branch name cannot end with '.lock'"
 
-    if '..' in name:
+    if ".." in name:
         return False, "Branch name cannot contain '..'"
 
-    invalid_chars = ['~', '^', ':', '?', '*', '[', '\\', ' ', '\t']
+    invalid_chars = ["~", "^", ":", "?", "*", "[", "\\", " ", "\t"]
     for char in invalid_chars:
         if char in name:
             return False, f"Branch name cannot contain '{char}'"
 
-    if name.endswith('/'):
+    if name.endswith("/"):
         return False, "Branch name cannot end with '/'"
 
-    if name.startswith('/'):
+    if name.startswith("/"):
         return False, "Branch name cannot start with '/'"
 
-    if '//' in name:
+    if "//" in name:
         return False, "Branch name cannot contain consecutive slashes"
 
     return True, ""
@@ -99,7 +99,7 @@ def validate_path(path: Path, must_exist: bool = False) -> Tuple[bool, str]:
             return False, f"Path does not exist: {path}"
 
         path_str = str(resolved)
-        if '..' in path.parts:
+        if ".." in path.parts:
             return False, "Path contains parent directory references"
 
         return True, ""

scitex/git/_workflow.py

@@ -37,7 +37,9 @@ def setup_branches(repo_path: Path, template_name: str, verbose: bool = True) ->
     if not git_add_all(repo_path, verbose=verbose):
         return False
 
-    if not git_commit(repo_path, f"Initial commit from {template_name}", verbose=verbose):
+    if not git_commit(
+        repo_path, f"Initial commit from {template_name}", verbose=verbose
+    ):
         return False
 
     if not git_branch_rename(repo_path, "main", verbose=verbose):
@@ -70,9 +72,7 @@ def _rollback_commit(repo_path: Path, verbose: bool = True) -> None:
 
     with _in_directory(repo_path):
         result = sh(
-            ["git", "reset", "--soft", "HEAD~1"],
-            verbose=verbose,
-            return_as="dict"
+            ["git", "reset", "--soft", "HEAD~1"], verbose=verbose, return_as="dict"
         )
         if result["success"]:
             logger.info("Rolled back commit due to workflow failure")

scitex/io/__init__.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/io/__init__.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -24,7 +25,7 @@ from ._load_modules._ZarrExplorer import ZarrExplorer, explore_zarr, has_zarr_ke
 from ._load_cache import (
     get_cache_info,
     configure_cache,
-    clear_cache as clear_load_cache
+    clear_cache as clear_load_cache,
 )
 
 # Import save module functions

scitex/io/_glob.py

@@ -23,7 +23,7 @@ def glob(expression: Union[str, Path], parse=False, ensure_one=False):
     Parameters:
     -----------
     expression : Union[str, Path]
-        The glob pattern to match against file paths. Can be a string or pathlib.Path object. 
+        The glob pattern to match against file paths. Can be a string or pathlib.Path object.
         Supports standard glob syntax and curly brace expansion (e.g., 'dir/{a,b}/*.txt').
     parse : bool, optional
         Whether to parse the matched paths. Default is False.
@@ -56,7 +56,7 @@ def glob(expression: Union[str, Path], parse=False, ensure_one=False):
     # Convert Path objects to strings for consistency
     if isinstance(expression, Path):
         expression = str(expression)
-        
+
     glob_pattern = _re.sub(r"{[^}]*}", "*", expression)
     # Enable recursive globbing for ** patterns
     recursive = "**" in glob_pattern

scitex/io/_json2md.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/io/_json2md.py"
-)
+
+__FILE__ = "./src/scitex/io/_json2md.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -15,6 +14,7 @@ import json
 import sys
 import argparse
 
+
 def json2md(obj, level=1):
     output = []
     if isinstance(obj, dict):

scitex/io/_load.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -44,6 +45,7 @@ from ._load_modules._txt import _load_txt
 from ._load_modules._xml import _load_xml
 from ._load_modules._yaml import _load_yaml
 from ._load_modules._zarr import _load_zarr
+from ._load_modules._canvas import _load_canvas
 
 
 def load(
@@ -151,20 +153,20 @@ def load(
         if verbose:
             print(f"[DEBUG] After Path conversion: {lpath}")
 
+    # Handle .canvas directories (special case - directory not file)
+    if lpath.endswith(".canvas"):
+        return _load_canvas(lpath, verbose=verbose, **kwargs)
+
     # Check if it's a glob pattern
     if "*" in lpath or "?" in lpath or "[" in lpath:
         # Handle glob pattern
         matched_files = sorted(glob.glob(lpath))
         if not matched_files:
-            raise FileNotFoundError(
-                f"No files found matching pattern: {lpath}"
-            )
+            raise FileNotFoundError(f"No files found matching pattern: {lpath}")
         # Load all matched files
         results = []
         for file_path in matched_files:
-            results.append(
-                load(file_path, show=show, verbose=verbose, **kwargs)
-            )
+            results.append(load(file_path, show=show, verbose=verbose, **kwargs))
         return results
 
     # Handle broken symlinks - os.path.exists() returns False for broken symlinks
@@ -175,7 +177,7 @@ def load(
             target = os.readlink(lpath)
             resolved_target = os.path.join(symlink_dir, target)
             resolved_target = os.path.abspath(resolved_target)
-            
+
             if os.path.exists(resolved_target):
                 lpath = resolved_target
             else:
@@ -263,7 +265,7 @@ def load(
     # Determine extension: use explicit ext parameter or detect from filename
     if ext is not None:
         # Use explicitly provided extension (strip leading dot if present)
-        detected_ext = ext.lstrip('.')
+        detected_ext = ext.lstrip(".")
     else:
         # Auto-detect from filename
         detected_ext = lpath.split(".")[-1] if "." in lpath else ""
@@ -302,4 +304,5 @@ def load(
     except (ValueError, FileNotFoundError) as e:
         raise ValueError(f"Error loading file {lpath}: {str(e)}")
 
+
 # EOF

scitex/io/_load_cache.py

@@ -22,29 +22,25 @@ _file_metadata_cache: Dict[str, Tuple[float, int, str]] = {}
 _file_data_cache = weakref.WeakValueDictionary()
 
 # Cache statistics
-_cache_stats = {
-    'hits': 0,
-    'misses': 0,
-    'evictions': 0
-}
+_cache_stats = {"hits": 0, "misses": 0, "evictions": 0}
 
 # Configuration
 _cache_config = {
-    'enabled': True,
-    'max_size': 32,  # Maximum number of files to track
-    'verbose': False
+    "enabled": True,
+    "max_size": 32,  # Maximum number of files to track
+    "verbose": False,
 }
 
 
 def get_file_key(file_path: str) -> Tuple[str, float, int]:
     """
     Get cache key based on file path, modification time, and size.
-    
+
     Parameters
     ----------
     file_path : str
         Path to the file
-        
+
     Returns
     -------
     Tuple[str, float, int]
@@ -58,12 +54,12 @@ def get_file_key(file_path: str) -> Tuple[str, float, int]:
 def get_file_hash(file_path: str) -> str:
     """
     Get a hash based on file metadata.
-    
+
     Parameters
     ----------
     file_path : str
         Path to the file
-        
+
     Returns
     -------
     str
@@ -77,30 +73,29 @@ def get_file_hash(file_path: str) -> str:
 def is_cache_valid(file_path: str) -> bool:
     """
     Check if cached data for a file is still valid.
-    
+
     Parameters
     ----------
     file_path : str
         Path to the file
-        
+
     Returns
     -------
     bool
         True if cache is valid, False otherwise
     """
     abs_path = os.path.abspath(file_path)
-    
+
     if abs_path not in _file_metadata_cache:
         return False
-    
+
     # Get current file metadata
     try:
         current_key = get_file_key(file_path)
         cached_mtime, cached_size, cached_hash = _file_metadata_cache[abs_path]
-        
+
         # Check if file has been modified
-        return (current_key[1] == cached_mtime and 
-                current_key[2] == cached_size)
+        return current_key[1] == cached_mtime and current_key[2] == cached_size
     except (OSError, KeyError):
         return False
 
@@ -108,42 +103,42 @@ def is_cache_valid(file_path: str) -> bool:
 def get_cached_data(file_path: str) -> Optional[Any]:
     """
     Retrieve cached data if available and valid.
-    
+
     Parameters
     ----------
     file_path : str
         Path to the file
-        
+
     Returns
     -------
     Optional[Any]
         Cached data if available, None otherwise
     """
-    if not _cache_config['enabled']:
+    if not _cache_config["enabled"]:
         return None
-    
+
     abs_path = os.path.abspath(file_path)
-    
+
     # Check if cache is valid
     if not is_cache_valid(file_path):
-        _cache_stats['misses'] += 1
+        _cache_stats["misses"] += 1
         return None
-    
+
     # Try to get data from weak reference cache
     if abs_path in _file_data_cache:
-        _cache_stats['hits'] += 1
-        if _cache_config['verbose']:
+        _cache_stats["hits"] += 1
+        if _cache_config["verbose"]:
             logging.info(f"[Cache HIT] {file_path}")
         return _file_data_cache[abs_path]
-    
-    _cache_stats['misses'] += 1
+
+    _cache_stats["misses"] += 1
     return None
 
 
 def cache_data(file_path: str, data: Any) -> None:
     """
     Cache data for a file.
-    
+
     Parameters
     ----------
     file_path : str
@@ -151,19 +146,19 @@ def cache_data(file_path: str, data: Any) -> None:
     data : Any
         Data to cache
     """
-    if not _cache_config['enabled']:
+    if not _cache_config["enabled"]:
         return
-    
+
     abs_path = os.path.abspath(file_path)
-    
+
     # Update metadata cache
     key = get_file_key(file_path)
     _file_metadata_cache[abs_path] = (key[1], key[2], get_file_hash(file_path))
-    
+
     # Try to cache the data (may fail for non-weakref-able types)
     try:
         # For numpy arrays and other special types, we need to wrap them
-        if hasattr(data, '__array__'):
+        if hasattr(data, "__array__"):
             # Numpy arrays can't be weakly referenced directly
             # We'll skip caching for now (could implement a wrapper)
             pass
@@ -171,15 +166,15 @@ def cache_data(file_path: str, data: Any) -> None:
             _file_data_cache[abs_path] = data
     except TypeError:
         # Some objects can't be weakly referenced
-        if _cache_config['verbose']:
+        if _cache_config["verbose"]:
             logging.debug(f"Cannot cache {type(data).__name__} objects")
-    
+
     # Implement cache size limit
-    if len(_file_metadata_cache) > _cache_config['max_size']:
+    if len(_file_metadata_cache) > _cache_config["max_size"]:
         # Remove oldest entries (simple FIFO for metadata)
         oldest = list(_file_metadata_cache.keys())[0]
         del _file_metadata_cache[oldest]
-        _cache_stats['evictions'] += 1
+        _cache_stats["evictions"] += 1
 
 
 def clear_cache() -> None:
@@ -188,34 +183,36 @@ def clear_cache() -> None:
     _file_data_cache.clear()
     _numpy_cache_keys.clear()
     _cached_load_npy.cache_clear()  # Clear LRU cache
-    _cache_stats['hits'] = 0
-    _cache_stats['misses'] = 0
-    _cache_stats['evictions'] = 0
+    _cache_stats["hits"] = 0
+    _cache_stats["misses"] = 0
+    _cache_stats["evictions"] = 0
 
 
 def get_cache_info() -> Dict[str, Any]:
     """
     Get cache statistics and configuration.
-    
+
     Returns
     -------
     Dict[str, Any]
         Cache information including stats and config
     """
     return {
-        'stats': _cache_stats.copy(),
-        'config': _cache_config.copy(),
-        'metadata_size': len(_file_metadata_cache),
-        'data_size': len(_file_data_cache)
+        "stats": _cache_stats.copy(),
+        "config": _cache_config.copy(),
+        "metadata_size": len(_file_metadata_cache),
+        "data_size": len(_file_data_cache),
     }
 
 
-def configure_cache(enabled: Optional[bool] = None,
-                   max_size: Optional[int] = None,
-                   verbose: Optional[bool] = None) -> None:
+def configure_cache(
+    enabled: Optional[bool] = None,
+    max_size: Optional[int] = None,
+    verbose: Optional[bool] = None,
+) -> None:
     """
     Configure cache settings.
-    
+
     Parameters
     ----------
     enabled : Optional[bool]
@@ -226,27 +223,28 @@ def configure_cache(enabled: Optional[bool] = None,
         Enable verbose logging
     """
     if enabled is not None:
-        _cache_config['enabled'] = enabled
+        _cache_config["enabled"] = enabled
     if max_size is not None:
-        _cache_config['max_size'] = max_size
+        _cache_config["max_size"] = max_size
     if verbose is not None:
-        _cache_config['verbose'] = verbose
+        _cache_config["verbose"] = verbose
 
 
-# Track numpy cache separately  
+# Track numpy cache separately
 _numpy_cache_keys = set()
 
+
 # Specialized cache for numpy arrays (using LRU cache)
 @lru_cache(maxsize=16)
 def _cached_load_npy(file_key: Tuple[str, float, int]) -> Any:
     """
     Cached numpy loader using LRU cache.
-    
+
     Parameters
     ----------
     file_key : Tuple[str, float, int]
         Cache key (path, mtime, size)
-        
+
     Returns
     -------
     Any
@@ -255,49 +253,51 @@ def _cached_load_npy(file_key: Tuple[str, float, int]) -> Any:
     file_path = file_key[0]
     # Import here to avoid circular imports
     from ._load_modules._numpy import _load_npy
+
     result = _load_npy(file_path)
-    
+
     # Track that we've cached this key
     _numpy_cache_keys.add(file_key)
-    
+
     return result
 
 
 def load_npy_cached(file_path: str, **kwargs) -> Any:
     """
     Load numpy file with caching.
-    
+
     Parameters
     ----------
     file_path : str
         Path to numpy file
     **kwargs
         Additional arguments for numpy.load
-        
+
     Returns
     -------
     Any
         Loaded numpy array
     """
-    if not _cache_config['enabled']:
+    if not _cache_config["enabled"]:
         from ._load_modules._numpy import _load_npy
+
         return _load_npy(file_path, **kwargs)
-    
+
     # Check if we have a cache hit
     file_key = get_file_key(file_path)
-    
+
     # Check if this key is already cached
     if file_key in _numpy_cache_keys:
-        _cache_stats['hits'] += 1
-        if _cache_config['verbose']:
+        _cache_stats["hits"] += 1
+        if _cache_config["verbose"]:
             print(f"[Cache HIT] Loaded from cache: {file_path}")
     else:
-        _cache_stats['misses'] += 1
-        if _cache_config['verbose']:
+        _cache_stats["misses"] += 1
+        if _cache_config["verbose"]:
             print(f"[Cache MISS] Loading from disk: {file_path}")
-    
+
     # Use LRU cache for numpy files
     return _cached_load_npy(file_key)
 
 
-# EOF
+# EOF

scitex/io/_load_configs.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/io/_load_configs.py"
-)
+
+__FILE__ = "./src/scitex/io/_load_configs.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 

scitex/io/_load_modules/_H5Explorer.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/io/_H5Explorer.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -59,9 +60,7 @@ class H5Explorer:
         if hasattr(self, "file") and self.file:
             self.file.close()
 
-    def explore(
-        self, path: str = "/", max_depth: Optional[int] = None
-    ) -> None:
+    def explore(self, path: str = "/", max_depth: Optional[int] = None) -> None:
         """Explore HDF5 file structure interactively."""
         self.show(path, max_depth)
 
@@ -90,9 +89,7 @@ class H5Explorer:
                 print(f"{indent}[{path.split('/')[-1]}]")
             for key in sorted(item.keys()):
                 subpath = f"{path}/{key}".replace("//", "/")
-                self.show(
-                    subpath, max_depth, indent + "  ", _current_depth + 1
-                )
+                self.show(subpath, max_depth, indent + "  ", _current_depth + 1)
         elif isinstance(item, h5py.Dataset):
             name = path.split("/")[-1]
             shape = item.shape
@@ -208,9 +205,7 @@ class H5Explorer:
         matches = []
 
         def _search(current_path):
-            item = (
-                self.file[current_path] if current_path != "/" else self.file
-            )
+            item = self.file[current_path] if current_path != "/" else self.file
 
             if isinstance(item, h5py.Group):
                 for key in item.keys():
@@ -327,9 +322,7 @@ def has_h5_key(h5_path, key, max_retries=3, action_on_corrupted="delete"):
                 else:
                     return False
 
-            elif any(
-                indicator in error_msg for indicator in corruption_indicators
-            ):
+            elif any(indicator in error_msg for indicator in corruption_indicators):
                 if action_on_corrupted == "delete":
                     if _delete_corrupted_entry(h5_path, key):
                         return False
@@ -352,4 +345,5 @@ def _delete_corrupted_entry(h5_path, key):
         pass
     return False
 
+
 # EOF

scitex/io/_load_modules/_ZarrExplorer.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/io/_ZarrExplorer.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -54,9 +55,7 @@ class ZarrExplorer:
 
             for key in sorted(target.keys()):
                 subpath = f"{path}/{key}".replace("//", "/")
-                self.show(
-                    subpath, max_depth, indent + "  ", _current_depth + 1
-                )
+                self.show(subpath, max_depth, indent + "  ", _current_depth + 1)
 
         else:  # Array
             name = path.split("/")[-1]
@@ -111,4 +110,5 @@ def has_zarr_key(zarr_path: str, key: str) -> bool:
     except (KeyError, ValueError):
         return False
 
+
 # EOF