oscura 0.5.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

oscura/session/session.py

@@ -1,520 +0,0 @@
-"""Analysis session management.
-
-This module provides session save/restore functionality for Oscura.
-
-
-Example:
-    >>> session = Session()
-    >>> session.load_trace('capture.wfm')
-    >>> session.save('debug_session.tks')
-    >>>
-    >>> # Later...
-    >>> session = load_session('debug_session.tks')
-"""
-
-from __future__ import annotations
-
-import gzip
-import hashlib
-import hmac
-import pickle
-from dataclasses import dataclass, field
-from datetime import datetime
-from pathlib import Path
-from typing import Any, cast
-
-import numpy as np
-
-from oscura.core.exceptions import SecurityError
-from oscura.session.annotations import AnnotationLayer
-from oscura.session.history import OperationHistory
-
-# Session file format constants
-_SESSION_MAGIC = b"OSC1"  # Magic bytes for new format with signature
-_SESSION_SIGNATURE_SIZE = 32  # SHA256 hash size in bytes
-_SECURITY_KEY = hashlib.sha256(b"oscura-session-v1").digest()
-
-
-@dataclass
-class Session:
-    """Analysis session container.
-
-    Manages traces, annotations, measurements, and history for a complete
-    analysis session. Sessions can be saved and restored.
-
-    Attributes:
-        name: Session name
-        traces: Dictionary of loaded traces (name -> trace)
-        annotation_layers: Annotation layers
-        measurements: Recorded measurements
-        history: Operation history
-        metadata: Session metadata
-        created_at: Creation timestamp
-        modified_at: Last modification timestamp
-    """
-
-    name: str = "Untitled Session"
-    traces: dict[str, Any] = field(default_factory=dict)
-    annotation_layers: dict[str, AnnotationLayer] = field(default_factory=dict)
-    measurements: dict[str, Any] = field(default_factory=dict)
-    history: OperationHistory = field(default_factory=OperationHistory)
-    metadata: dict[str, Any] = field(default_factory=dict)
-    created_at: datetime = field(default_factory=datetime.now)
-    modified_at: datetime = field(default_factory=datetime.now)
-    _file_path: Path | None = None
-
-    def __post_init__(self) -> None:
-        """Initialize default annotation layer."""
-        if "default" not in self.annotation_layers:
-            self.annotation_layers["default"] = AnnotationLayer("Default")
-
-    def load_trace(
-        self,
-        path: str | Path,
-        name: str | None = None,
-        **load_kwargs: Any,
-    ) -> Any:
-        """Load a trace into the session.
-
-        Args:
-            path: Path to trace file.
-            name: Name for trace in session (default: filename).
-            **load_kwargs: Additional arguments for load().
-
-        Returns:
-            Loaded trace.
-        """
-        from oscura.loaders import load
-
-        path = Path(path)
-        trace = load(str(path), **load_kwargs)
-
-        if name is None:
-            name = path.stem
-
-        self.traces[name] = trace
-        self._mark_modified()
-
-        self.history.record(
-            "load_trace",
-            {"path": str(path), "name": name},
-            result=f"Loaded {name}",
-        )
-
-        return trace
-
-    def add_trace(
-        self,
-        name: str,
-        trace: Any,
-    ) -> None:
-        """Add an in-memory trace to the session.
-
-        This method allows adding traces that were created programmatically
-        or loaded separately, rather than loading from a file.
-
-        Args:
-            name: Name for the trace in the session.
-            trace: Trace object (WaveformTrace, DigitalTrace, etc.).
-
-        Raises:
-            ValueError: If name is empty or already exists.
-            TypeError: If trace doesn't have expected attributes.
-
-        Example:
-            >>> session = Session()
-            >>> data = np.sin(np.linspace(0, 2*np.pi, 1000))
-            >>> trace = osc.WaveformTrace(data=data, metadata=osc.TraceMetadata(sample_rate=1e6))
-            >>> session.add_trace("my_trace", trace)
-        """
-        if not name:
-            raise ValueError("Trace name cannot be empty")
-
-        if not hasattr(trace, "data"):
-            raise TypeError("Trace must have a 'data' attribute")
-
-        self.traces[name] = trace
-        self._mark_modified()
-
-        self.history.record(
-            "add_trace",
-            {"name": name, "type": type(trace).__name__},
-            result=f"Added {name}",
-        )
-
-    def remove_trace(self, name: str) -> None:
-        """Remove a trace from the session.
-
-        Args:
-            name: Name of the trace to remove.
-
-        Raises:
-            KeyError: If trace not found.
-        """
-        if name not in self.traces:
-            raise KeyError(f"Trace '{name}' not found in session")
-
-        del self.traces[name]
-        self._mark_modified()
-
-        self.history.record(
-            "remove_trace",
-            {"name": name},
-            result=f"Removed {name}",
-        )
-
-    def get_trace(self, name: str) -> Any:
-        """Get trace by name.
-
-        Args:
-            name: Trace name.
-
-        Returns:
-            Trace object.
-        """
-        return self.traces[name]
-
-    def list_traces(self) -> list[str]:
-        """List all trace names."""
-        return list(self.traces.keys())
-
-    def annotate(
-        self,
-        text: str,
-        *,
-        time: float | None = None,
-        time_range: tuple[float, float] | None = None,
-        layer: str = "default",
-        **kwargs: Any,
-    ) -> None:
-        """Add annotation to session.
-
-        Args:
-            text: Annotation text.
-            time: Time point for annotation.
-            time_range: Time range for annotation.
-            layer: Annotation layer name.
-            **kwargs: Additional annotation parameters.
-        """
-        if layer not in self.annotation_layers:
-            self.annotation_layers[layer] = AnnotationLayer(layer)
-
-        self.annotation_layers[layer].add(
-            text=text,
-            time=time,
-            time_range=time_range,
-            **kwargs,
-        )
-        self._mark_modified()
-
-        self.history.record(
-            "annotate",
-            {"text": text, "time": time, "layer": layer},
-        )
-
-    def get_annotations(
-        self,
-        layer: str | None = None,
-        time_range: tuple[float, float] | None = None,
-    ) -> list[Any]:
-        """Get annotations.
-
-        Args:
-            layer: Filter by layer name (None for all layers).
-            time_range: Filter by time range.
-
-        Returns:
-            List of annotations.
-        """
-        annotations = []
-
-        layers = [self.annotation_layers[layer]] if layer else self.annotation_layers.values()
-
-        for ann_layer in layers:
-            if time_range:
-                annotations.extend(ann_layer.find_in_range(time_range[0], time_range[1]))
-            else:
-                annotations.extend(ann_layer.annotations)
-
-        return annotations
-
-    def record_measurement(
-        self,
-        name: str,
-        value: Any,
-        unit: str = "",
-        trace_name: str | None = None,
-        **metadata: Any,
-    ) -> None:
-        """Record a measurement result.
-
-        Args:
-            name: Measurement name (e.g., 'rise_time').
-            value: Measurement value.
-            unit: Unit of measurement.
-            trace_name: Associated trace name.
-            **metadata: Additional metadata.
-        """
-        self.measurements[name] = {
-            "value": value,
-            "unit": unit,
-            "trace": trace_name,
-            "timestamp": datetime.now().isoformat(),
-            **metadata,
-        }
-        self._mark_modified()
-
-        self.history.record(
-            f"measure_{name}",
-            {"trace": trace_name},
-            result=f"{value} {unit}".strip(),
-        )
-
-    def get_measurements(self) -> dict[str, Any]:
-        """Get all recorded measurements."""
-        return self.measurements.copy()
-
-    def save(
-        self,
-        path: str | Path | None = None,
-        *,
-        include_traces: bool = True,
-        compress: bool = True,
-    ) -> Path:
-        """Save session to file with HMAC signature for integrity verification.
-
-        Args:
-            path: Output path (default: use existing or generate).
-            include_traces: Include trace data in session file.
-            compress: Compress session file with gzip.
-
-        Returns:
-            Path to saved file.
-
-        Example:
-            >>> session.save('analysis.tks')
-
-        Security Note:
-            Session files now include HMAC signatures for integrity verification.
-            Files are still pickle-based - only load from trusted sources.
-            For secure data exchange with untrusted parties, use JSON or HDF5
-            export formats instead.
-        """
-        if path is None:
-            path = self._file_path or Path(f"{self.name.replace(' ', '_')}.tks")
-        else:
-            path = Path(path)
-
-        self._file_path = path
-        self._mark_modified()
-
-        # Build session data
-        data = self._to_dict(include_traces=include_traces)
-
-        # Serialize with pickle
-        serialized = pickle.dumps(data, protocol=pickle.HIGHEST_PROTOCOL)
-
-        # Compute HMAC signature
-        signature = hmac.new(_SECURITY_KEY, serialized, hashlib.sha256).digest()
-
-        # Write: magic bytes + signature + pickled data
-        if compress:
-            with gzip.open(path, "wb") as f:
-                f.write(_SESSION_MAGIC)
-                f.write(signature)
-                f.write(serialized)
-        else:
-            with open(path, "wb") as f:
-                f.write(_SESSION_MAGIC)
-                f.write(signature)
-                f.write(serialized)
-
-        self.history.record("save", {"path": str(path)})
-
-        return path
-
-    def _to_dict(self, include_traces: bool = True) -> dict[str, Any]:
-        """Convert session to dictionary."""
-        data: dict[str, Any] = {
-            "version": "1.0",
-            "name": self.name,
-            "created_at": self.created_at.isoformat(),
-            "modified_at": self.modified_at.isoformat(),
-            "annotation_layers": {
-                name: layer.to_dict() for name, layer in self.annotation_layers.items()
-            },
-            "measurements": self.measurements,
-            "history": self.history.to_dict(),
-            "metadata": self.metadata,
-        }
-
-        if include_traces:
-            # Store traces with their data
-            data["traces"] = {}
-            for name, trace in self.traces.items():
-                trace_data = {
-                    "type": type(trace).__name__,
-                    "data": trace.data.tolist() if hasattr(trace, "data") else None,
-                    "sample_rate": (
-                        trace.metadata.sample_rate if hasattr(trace, "metadata") else None
-                    ),
-                }
-                data["traces"][name] = trace_data
-        else:
-            data["traces"] = {}
-
-        return data
-
-    @classmethod
-    def _from_dict(cls, data: dict[str, Any]) -> Session:
-        """Create session from dictionary."""
-        session = cls(
-            name=data.get("name", "Untitled Session"),
-            metadata=data.get("metadata", {}),
-        )
-
-        if "created_at" in data:
-            session.created_at = datetime.fromisoformat(data["created_at"])
-        if "modified_at" in data:
-            session.modified_at = datetime.fromisoformat(data["modified_at"])
-
-        # Restore annotation layers
-        for name, layer_data in data.get("annotation_layers", {}).items():
-            session.annotation_layers[name] = AnnotationLayer.from_dict(layer_data)
-
-        # Restore measurements
-        session.measurements = data.get("measurements", {})
-
-        # Restore history
-        if "history" in data:
-            session.history = OperationHistory.from_dict(data["history"])
-
-        # Restore traces (if included)
-        if "traces" in data:
-            from oscura.core.types import WaveformTrace
-
-            for name, trace_data in data["traces"].items():
-                if trace_data.get("data") is not None:
-                    session.traces[name] = WaveformTrace(  # type: ignore[call-arg]
-                        data=np.array(trace_data["data"]),
-                        sample_rate=trace_data.get("sample_rate", 1.0),
-                    )
-
-        return session
-
-    def _mark_modified(self) -> None:
-        """Update modification timestamp."""
-        self.modified_at = datetime.now()
-
-    def summary(self) -> str:
-        """Get session summary."""
-        lines = [
-            f"Session: {self.name}",
-            f"Created: {self.created_at.strftime('%Y-%m-%d %H:%M')}",
-            f"Modified: {self.modified_at.strftime('%Y-%m-%d %H:%M')}",
-            f"Traces: {len(self.traces)}",
-            f"Annotations: {sum(len(l.annotations) for l in self.annotation_layers.values())}",  # noqa: E741
-            f"Measurements: {len(self.measurements)}",
-            f"History entries: {len(self.history.entries)}",
-        ]
-        return "\n".join(lines)
-
-
-def load_session(path: str | Path) -> Session:
-    """Load session from file with HMAC signature verification.
-
-    Session files must be in the current OSC1 format with HMAC signature.
-    Legacy session files without signatures are not supported.
-
-    Args:
-        path: Path to session file (.tks).
-
-    Returns:
-        Loaded Session object.
-
-    Raises:
-        SecurityError: If signature verification fails or file is not in OSC1 format.
-        gzip.BadGzipFile: If file is neither valid gzip nor uncompressed session.
-
-    Example:
-        >>> session = load_session('debug_session.tks')
-        >>> print(session.list_traces())
-
-    Security Warning:
-        Session files use pickle serialization. Only load session files from
-        trusted sources. Loading a malicious .tks file could execute arbitrary
-        code. Never load session files from untrusted or unknown sources.
-
-        All session files must include HMAC signatures for integrity verification.
-        For secure data exchange with untrusted parties, consider exporting to
-        JSON or HDF5 formats instead of using pickle-based session files.
-    """
-    path = Path(path)
-
-    def _load_with_verification(f: Any) -> dict[str, Any]:
-        """Load and verify session file with HMAC signature.
-
-        Args:
-            f: File object (gzip or regular).
-
-        Returns:
-            Deserialized session dictionary.
-
-        Raises:
-            SecurityError: If magic bytes or signature verification fails.
-        """
-        # Read magic bytes
-        magic = f.read(len(_SESSION_MAGIC))
-
-        if magic != _SESSION_MAGIC:
-            raise SecurityError(
-                "This is a legacy session file. Please re-save with current version.",
-                file_path=str(path),
-                check_type="Session format",
-                details="Expected OSC1 format with HMAC signature",
-            )
-
-        # Read signature and payload
-        signature = f.read(_SESSION_SIGNATURE_SIZE)
-        serialized = f.read()
-
-        if not signature or not serialized:
-            raise SecurityError(
-                "This is a legacy session file. Please re-save with current version.",
-                file_path=str(path),
-                check_type="Session format",
-                details="File is incomplete or corrupted",
-            )
-
-        # Verify HMAC signature
-        expected = hmac.new(_SECURITY_KEY, serialized, hashlib.sha256).digest()
-        if not hmac.compare_digest(signature, expected):
-            raise SecurityError(
-                "Session file signature verification failed",
-                file_path=str(path),
-                check_type="HMAC signature",
-                details="File may be corrupted or tampered with",
-            )
-
-        # Deserialize verified data
-        data = cast("dict[str, Any]", pickle.loads(serialized))
-        return data
-
-    # Try loading (compressed first, then uncompressed)
-    try:
-        with gzip.open(path, "rb") as f:
-            data = _load_with_verification(f)
-    except gzip.BadGzipFile:
-        with open(path, "rb") as f:  # type: ignore[assignment]
-            data = _load_with_verification(f)
-
-    session = Session._from_dict(data)
-    session._file_path = path
-
-    return session
-
-
-__all__ = [
-    "Session",
-    "load_session",
-]

oscura/workflow/__init__.py

@@ -1,13 +0,0 @@
-"""Workflow execution and DAG-based analysis.
-
-This module provides directed acyclic graph (DAG) execution for complex
-multi-step analysis workflows with automatic dependency resolution and
-parallel execution.
-"""
-
-from oscura.workflow.dag import TaskNode, WorkflowDAG
-
-__all__ = [
-    "TaskNode",
-    "WorkflowDAG",
-]