Merge pull request #69 from childmindresearch/pybids

Adds pybids compatability layer to bids2table

Author: kaitj

bids2table/pybids/__init__.py

@@ -0,0 +1,8 @@
+__all__ = ["BIDSLayout", "BIDSFile", "Query", "listify"]
+
+from ._bidsfile import BIDSFile
+from ._layout import BIDSLayout
+from ._utils import (
+    Query,
+    listify,
+)

bids2table/pybids/_bidsfile.py

@@ -0,0 +1,95 @@
+"""
+BIDSFile wrapper for file paths with entity access.
+
+Provides a PyBIDS-compatible file object that can parse and cache
+BIDS entities from file paths.
+"""
+
+from typing import Any
+
+from .._entities import parse_bids_entities
+
+
+class BIDSFile:
+    """
+    Wrapper around a BIDS file path with entity parsing.
+
+    Provides PyBIDS-compatible interface for accessing file entities.
+    Entities are lazily parsed and cached on first access.
+
+    Example:
+        >>> from bids2table_compat import BIDSFile
+        >>> f = BIDSFile('sub-01/func/sub-01_task-rest_bold.nii.gz')
+        >>> entities = f.get_entities()
+        >>> print(entities)
+        {'sub': '01', 'task': 'rest', 'suffix': 'bold', 'ext': '.nii.gz'}
+    """
+
+    def __init__(self, path: str):
+        """
+        Initialize BIDSFile.
+
+        Args:
+            path: Path to BIDS file (absolute or relative)
+        """
+        self.path = str(path)
+        self._entities: dict[str, Any] | None = None
+
+    def get_entities(self) -> dict[str, Any]:
+        """
+        Parse and return BIDS entities from filename.
+
+        Entities are cached after first parse for performance.
+
+        Returns:
+            Dictionary of BIDS entities (e.g., {'sub': '01', 'task': 'rest'})
+        """
+        if self._entities is None:
+            self._entities = parse_bids_entities(self.path)
+        return self._entities
+
+    def __str__(self) -> str:
+        """String representation showing file path."""
+        return self.path
+
+    def __repr__(self) -> str:
+        """Developer-friendly representation."""
+        return f"BIDSFile('{self.path}')"
+
+    def __eq__(self, other) -> bool:
+        """Equality based on path."""
+        if isinstance(other, BIDSFile):
+            return self.path == other.path
+        return False
+
+    def __hash__(self) -> int:
+        """Allow use in sets/dicts."""
+        return hash(self.path)
+
+    def __lt__(self, other) -> bool:
+        """Less-than comparison based on path (for sorting)."""
+        if isinstance(other, BIDSFile):
+            return self.path < other.path
+        return NotImplemented
+
+    def __le__(self, other) -> bool:
+        """Less-than-or-equal comparison based on path."""
+        if isinstance(other, BIDSFile):
+            return self.path <= other.path
+        return NotImplemented
+
+    def __gt__(self, other) -> bool:
+        """Greater-than comparison based on path."""
+        if isinstance(other, BIDSFile):
+            return self.path > other.path
+        return NotImplemented
+
+    def __ge__(self, other) -> bool:
+        """Greater-than-or-equal comparison based on path."""
+        if isinstance(other, BIDSFile):
+            return self.path >= other.path
+        return NotImplemented
+
+    def __contains__(self, item) -> bool:
+        """Check if substring is in the file path (for 'in' operator)."""
+        return item in self.path