scitex 2.10.3__py3-none-any.whl → 2.11.0__py3-none-any.whl

scitex/{fig → canvas}/io/_canvas.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: ./src/scitex/vis/io/canvas.py
 """
-Canvas JSON operations for scitex.fig.
+Canvas JSON operations for scitex.canvas.
 
 Handles saving, loading, and updating canvas.json files.
 """

scitex/{fig → canvas}/io/_data.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: ./src/scitex/vis/io/data.py
 """
-Data operations for scitex.fig.
+Data operations for scitex.canvas.
 
 Handles SHA256 hash computation and verification for data integrity.
 """

scitex/{fig → canvas}/io/_export.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: ./src/scitex/vis/io/export.py
 """
-Export operations for scitex.fig.
+Export operations for scitex.canvas.
 
 Handles composing and exporting canvas to various formats (PNG, PDF, SVG).
 """

scitex/{fig → canvas}/io/_load.py

@@ -115,7 +115,7 @@ def load_figure_model(
 
     Examples
     --------
-    >>> from scitex.fig.io import load_figure_model
+    >>> from scitex.canvas.io import load_figure_model
     >>> fig_model = load_figure_model("figure.json")
     >>> fig_model.width_mm
     180

scitex/{fig → canvas}/io/_panel.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: ./src/scitex/vis/io/panel.py
 """
-Panel operations for scitex.fig.
+Panel operations for scitex.canvas.
 
 Handles adding, removing, updating, and listing panels within a canvas.
 Panels can be either 'scitex' type (full stx.plt output) or 'image' type (static image).

scitex/{fig → canvas}/io/_save.py

@@ -119,7 +119,7 @@ def save_figure_model(
 
     Examples
     --------
-    >>> from scitex.fig.model import FigureModel
+    >>> from scitex.canvas.model import FigureModel
     >>> fig_model = FigureModel(width_mm=180, height_mm=120)
     >>> save_figure_model(fig_model, "figure.json")
     PosixPath('figure.json')

scitex/{fig → canvas}/model/__init__.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/__init__.py
 """
-JSON models for scitex.fig figure specifications.
+JSON models for scitex.canvas figure specifications.
 
 This module provides dataclass-based models for representing
 publication-quality figures as JSON structures.

scitex/{fig → canvas}/model/_annotations.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/annotations.py
-"""Annotation JSON model for scitex.fig."""
+"""Annotation JSON model for scitex.canvas."""
 
 from typing import Optional, Dict, Any, Tuple
 from dataclasses import dataclass, field, asdict

scitex/{fig → canvas}/model/_axes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/axes.py
-"""Axes JSON model for scitex.fig."""
+"""Axes JSON model for scitex.canvas."""
 
 from typing import Optional, List, Dict, Any
 from dataclasses import dataclass, field, asdict

scitex/{fig → canvas}/model/_figure.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/figure.py
-"""Figure JSON model for scitex.fig."""
+"""Figure JSON model for scitex.canvas."""
 
 from typing import Optional, List, Dict, Any
 from dataclasses import dataclass, field, asdict

scitex/{fig → canvas}/model/_guides.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/guides.py
-"""Guide elements (lines, spans) JSON model for scitex.fig."""
+"""Guide elements (lines, spans) JSON model for scitex.canvas."""
 
 from typing import Optional, List, Dict, Any
 from dataclasses import dataclass, field, asdict

scitex/{fig → canvas}/model/_plot.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/plot.py
-"""Plot JSON model for scitex.fig."""
+"""Plot JSON model for scitex.canvas."""
 
 from typing import Optional, List, Dict, Any
 from dataclasses import dataclass, field, asdict

scitex/{fig → canvas}/model/_styles.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/model/styles.py
 """
-Style dataclasses for scitex.fig objects.
+Style dataclasses for scitex.canvas objects.
 
 Separating style properties from data makes:
 - UI property panels easy to auto-generate

scitex/{fig → canvas}/utils/__init__.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 # File: ./src/scitex/vis/utils/__init__.py
 """
-Utilities for scitex.fig.
+Utilities for scitex.canvas.
 
 Includes validation functions and default templates for
 common publication formats.

scitex/cli/convert.py

@@ -227,17 +227,19 @@ def validate_bundles(paths: tuple, verbose: bool):
       scitex convert validate output.stx
       scitex convert validate ./figures/*.stx --verbose
     """
-    # Use FTS instead of deprecated io.bundle
+    # Use Bundle for validation
     try:
-        from scitex.fts import FTS as ZipBundle
+        from scitex.io.bundle import Bundle as ZipBundle
+
         def validate_stx_bundle(path):
             try:
                 bundle = ZipBundle(path)
                 return bundle.validate(level="strict")
             except Exception as e:
                 return {"valid": False, "errors": [str(e)]}
+
     except ImportError:
-        click.echo("Error: scitex.fts not available", err=True)
+        click.echo("Error: scitex.io.bundle not available", err=True)
         return
 
     valid = 0
@@ -303,9 +305,9 @@ def bundle_info(path: str):
       scitex convert info figure.stx
     """
     try:
-        from scitex.fts import FTS as ZipBundle
+        from scitex.io.bundle import Bundle as ZipBundle
     except ImportError:
-        click.echo("Error: scitex.fts not available", err=True)
+        click.echo("Error: scitex.io.bundle not available", err=True)
         return
 
     bundle_path = Path(path)
@@ -368,12 +370,14 @@ def _convert_bundle(input_path: Path, output_path: Path) -> None:
     """
     import json
     import tempfile
-    import zipfile
 
     # Generate bundle ID and normalize spec - inline functions since io.bundle is deprecated
     import uuid
+    import zipfile
+
     def generate_bundle_id():
         return str(uuid.uuid4())[:8]
+
     def normalize_spec(spec):
         return spec  # FTS handles normalization internally
 

scitex/diagram/README.md

@@ -50,23 +50,23 @@ title: SciTeX Figure Lifecycle
 paper:
   column: single
   mode: publication      # draft | publication
-  emphasize: [figz_bundle, editor]
+  emphasize: [figure_bundle, editor]
   return_edges:          # Hide in publication mode
-    - [editor, figz_bundle]
+    - [editor, figure_bundle]
 
 layout:
   layer_gap: tight
   layers:                # rank=same constraints
     - [python, savefig]
-    - [figz_bundle]
+    - [figure_bundle]
     - [editor, ai_review]
 
 nodes:
   - id: python
     label: Python
     shape: rounded
-  - id: figz_bundle
-    label: .figz Bundle
+  - id: figure_bundle
+    label: .figure Bundle
     shape: stadium
     emphasis: primary
 
@@ -74,7 +74,7 @@ edges:
   - from: python
     to: savefig
   - from: savefig
-    to: figz_bundle
+    to: figure_bundle
 ```
 
 ```python
@@ -98,7 +98,7 @@ d.to_mermaid("workflow.mmd")
 paper:
   mode: publication
   return_edges:
-    - [editor, figz_bundle]  # Will be invisible
+    - [editor, figure_bundle]  # Will be invisible
 ```
 
 ## Auto-Split Large Diagrams

scitex/io/__init__.py

@@ -9,21 +9,19 @@ __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 """Scitex IO module with lazy imports to avoid circular dependencies.
 
-Bundle I/O is handled via scitex.fts:
-    from scitex.fts import FTS
-    bundle = FTS("Figure1.stx")
+Bundle I/O is handled via scitex.io.bundle:
+    from scitex.io.bundle import Bundle
+    bundle = Bundle("Figure1.figure")
     bundle.save()
 """
 
 # Import commonly used functions directly
+# Bundle I/O - import the bundle submodule
+from . import bundle
 from ._cache import cache
 from ._flush import flush
 from ._glob import glob, parse_glob
 from ._load import load
-
-# Bundle I/O - import the bundle submodule
-from . import bundle
-
 from ._load_configs import load_configs
 from ._reload import reload
 from ._save import save
@@ -45,20 +43,10 @@ except ImportError:
     has_zarr_key = None
 
 # Import load cache control functions
-from ._load_cache import (
-    clear_cache as clear_load_cache,
-)
-from ._load_cache import (
-    configure_cache,
-    get_cache_info,
-)
+from ._load_cache import clear_cache as clear_load_cache
+from ._load_cache import configure_cache, get_cache_info
 
 # Import load cache control functions
-from ._load_cache import (
-    get_cache_info,
-    configure_cache,
-    clear_cache as clear_load_cache,
-)
 
 # Import save module functions
 try:

scitex/io/_load.py

@@ -16,11 +16,7 @@ from typing import Any, Union
 
 from scitex.decorators import preserve_doc
 
-from ._load_cache import (
-    cache_data,
-    get_cached_data,
-    load_npy_cached,
-)
+from ._load_cache import cache_data, get_cached_data, load_npy_cached
 
 # Core loaders (no special dependencies)
 from ._load_modules._bibtex import _load_bibtex
@@ -101,7 +97,7 @@ except ImportError:
 
 
 def _load_bundle(lpath, verbose=False, **kwargs):
-    """Load a .pltz, .figz, or .statsz bundle.
+    """Load a .plot, .figure, or .stats bundle.
 
     Parameters
     ----------
@@ -114,12 +110,12 @@ def _load_bundle(lpath, verbose=False, **kwargs):
 
     Returns
     -------
-    For .pltz bundles:
+    For .plot bundles:
         tuple: (fig, ax, data) where fig is reconstructed figure,
                ax is the axes, data is DataFrame or None.
-    For .figz bundles:
+    For .figure bundles:
         dict: Figure data with 'spec' and 'panels'.
-    For .statsz bundles:
+    For .stats bundles:
         dict: Stats data with 'spec' and 'comparisons'.
     """
     from .bundle import BundleType
@@ -128,8 +124,8 @@ def _load_bundle(lpath, verbose=False, **kwargs):
     bundle = load_bundle(lpath)
     bundle_type = bundle.get("type")
 
-    if bundle_type == BundleType.PLTZ:
-        # Return (fig, ax, data) tuple for .pltz bundles
+    if bundle_type == BundleType.PLOT:
+        # Return (fig, ax, data) tuple for .plot bundles
         # Note: We return the spec and data, not a reconstructed figure
         # as matplotlib figures cannot be perfectly serialized/deserialized
         from pathlib import Path
@@ -177,19 +173,19 @@ def _load_bundle(lpath, verbose=False, **kwargs):
                 if theme:
                     fig._scitex_theme = theme.get("mode")
 
-            # Data from bundle (merged in load_layered_pltz_bundle)
+            # Data from bundle (merged in load_layered_plot_bundle)
             data = bundle.get("data")
             return fig, ax, data
         else:
             # No PNG, return spec and data
             return bundle.get("spec"), None, bundle.get("data")
 
-    elif bundle_type == BundleType.FIGZ:
-        # Return figure dict for .figz bundles
+    elif bundle_type == BundleType.FIGURE:
+        # Return figure dict for .figure bundles
         return bundle
 
-    elif bundle_type == BundleType.STATSZ:
-        # Return stats dict for .statsz bundles
+    elif bundle_type == BundleType.STATS:
+        # Return stats dict for .stats bundles
         return bundle
 
     return bundle
@@ -300,10 +296,10 @@ def load(
         if verbose:
             print(f"[DEBUG] After Path conversion: {lpath}")
 
-    # Handle bundle formats (.pltz, .figz, .statsz and their .d variants)
-    bundle_extensions = (".figz", ".pltz", ".statsz")
+    # Handle bundle formats (.plot, .figure, .stats and their ZIP variants)
+    bundle_extensions = (".figure", ".plot", ".stats")
     for bext in bundle_extensions:
-        if lpath.endswith(bext) or lpath.endswith(f"{bext}.d"):
+        if lpath.endswith(bext) or lpath.endswith(f"{bext}.zip"):
             return _load_bundle(lpath, verbose=verbose, **kwargs)
 
     # Check if it's a glob pattern

scitex/io/_load_modules/_canvas.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_load_modules/_canvas.py
 """
-Load canvas directory (.canvas) for scitex.fig.
+Load canvas directory (.canvas) for scitex.canvas.
 
 Canvas directories are portable figure bundles containing:
     - canvas.json: Layout, panels, composition settings
@@ -100,7 +100,7 @@ def _load_canvas(
     # Return Canvas object by default
     if not as_dict:
         try:
-            from scitex.fig.canvas import Canvas
+            from scitex.canvas.canvas import Canvas
 
             canvas_obj = Canvas.from_dict(canvas_dict)
             # Store reference to original directory for copying

scitex/io/_load_modules/_con.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:51:45 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_con.py
 
@@ -11,10 +10,11 @@ import mne
 def _load_con(lpath: str, **kwargs) -> Any:
     if not lpath.endswith(".con"):
         raise ValueError("File must have .con extension")
-    obj = mne.io.read_raw_fif(lpath, preload=True, **kwargs)
-    obj = obj.to_data_frame()
-    obj["samp_rate"] = obj.info["sfreq"]
-    return obj
+    raw = mne.io.read_raw_fif(lpath, preload=True, **kwargs)
+    sfreq = raw.info["sfreq"]
+    df = raw.to_data_frame()
+    df["samp_rate"] = sfreq
+    return df
 
 
 # EOF

scitex/io/_load_modules/_eeg.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-14 07:56:27 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/io/_load_modules/_eeg.py
 
@@ -10,7 +9,7 @@ from typing import Any
 import mne
 
 
-def _load_eeg_data(path: str, **kwargs) -> Any:
+def _load_eeg_data(lpath: str, **kwargs) -> Any:
     """
     Load EEG data based on file extension and associated files using MNE-Python.
 
@@ -43,15 +42,15 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
     extension = lpath.split(".")[-1]
 
     allowed_extensions = [
-        ".vhdr",
-        ".vmrk",
-        ".edf",
-        ".bdf",
-        ".gdf",
-        ".cnt",
-        ".egi",
-        ".eeg",
-        ".set",
+        "vhdr",
+        "vmrk",
+        "edf",
+        "bdf",
+        "gdf",
+        "cnt",
+        "egi",
+        "eeg",
+        "set",
     ]
 
     if extension not in allowed_extensions:
@@ -59,6 +58,9 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
             f"File must have one of these extensions: {', '.join(allowed_extensions)}"
         )
 
+    # Remove preload from kwargs if present - we always use preload=True
+    kwargs.pop("preload", None)
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", RuntimeWarning)
 
@@ -98,9 +100,11 @@ def _load_eeg_data(path: str, **kwargs) -> Any:
                 lpath_v = lpath.replace(".eeg", ".vhdr")
                 raw = mne.io.read_raw_brainvision(lpath_v, preload=True, **kwargs)
             # Nihon Koden
-            if is_NihonKoden:
+            elif is_NihonKoden:
                 # raw = mne.io.read_raw_nihon(lpath, preload=True, **kwargs)
                 raw = mne.io.read_raw(lpath, preload=True, **kwargs)
+            else:
+                raise ValueError("No associated files found for .eeg file")
         else:
             raise ValueError(f"Unsupported file extension: {extension}")
 

scitex/io/_save.py

@@ -6,7 +6,7 @@
 Save utilities for various data types to different file formats.
 
 Supported formats include CSV, NPY, PKL, JOBLIB, PNG, HTML, TIFF, MP4, YAML,
-JSON, HDF5, PTH, MAT, CBM, and FTS bundles (.zip or directory).
+JSON, HDF5, PTH, MAT, CBM, and SciTeX bundles (.zip or directory).
 """
 
 import inspect
@@ -40,8 +40,6 @@ from ._save_modules import (
     save_npz,
     save_pickle,
     save_pickle_compressed,
-    save_pltz_bundle,
-    save_stx_bundle,
     save_tex,
     save_text,
     save_torch,
@@ -53,12 +51,9 @@ from ._save_modules import (
 
 logger = logging.getLogger()
 
-# Re-export for backward compatibility
 _get_figure_with_data = get_figure_with_data
 _symlink = symlink
 _symlink_to = symlink_to
-_save_stx_bundle = save_stx_bundle
-_save_pltz_bundle = save_pltz_bundle
 _handle_image_with_csv = handle_image_with_csv
 
 
@@ -278,17 +273,17 @@ def _save(
     """Core dispatcher for saving objects to various formats."""
     ext = _os.path.splitext(spath)[1].lower()
 
-    # Check if this is a matplotlib figure being saved to FTS bundle format
-    # FTS bundles use .zip (archive) or no extension (directory)
+    # Check if this is a matplotlib figure being saved to SciTeX bundle format
+    # SciTeX bundles use .zip (archive) or no extension (directory)
     if _is_matplotlib_figure(obj):
-        # Save as FTS bundle if:
+        # Save as SciTeX bundle if:
         # 1. Path ends with .zip (create ZIP bundle)
         # 2. Path has no extension and doesn't match other formats (create directory bundle)
         if ext == ".zip" or (ext == "" and not spath.endswith("/")):
-            # Check if explicitly requesting FTS bundle or just .zip
+            # Check if explicitly requesting SciTeX bundle or just .zip
             # Pop as_zip from kwargs to avoid duplicate parameter error
             as_zip = kwargs.pop("as_zip", ext == ".zip")
-            _save_fts_bundle(
+            _save_scitex_bundle(
                 obj, spath, as_zip, verbose, symlink_from_cwd, symlink_to, **kwargs
             )
             return
@@ -348,12 +343,12 @@ def _is_matplotlib_figure(obj):
         return False
 
 
-def _save_fts_bundle(
+def _save_scitex_bundle(
     obj, spath, as_zip, verbose, symlink_from_cwd, symlink_to_path, **kwargs
 ):
-    """Save matplotlib figure as FTS bundle (.zip or directory).
+    """Save matplotlib figure as SciTeX bundle (.zip or directory).
 
-    Delegates to scitex.fts.from_matplotlib as the single source of truth
+    Delegates to scitex.io.bundle.from_matplotlib as the single source of truth
     for bundle structure (canonical/artifacts/payload/children).
 
     When figrecipe is available and enabled on the figure, also saves
@@ -362,7 +357,7 @@ def _save_fts_bundle(
     # Get the actual matplotlib figure
     import matplotlib.figure
 
-    from scitex.fts import from_matplotlib
+    from scitex.io.bundle import from_matplotlib
 
     from ._save_modules._figure_utils import get_figure_with_data
 
@@ -390,7 +385,7 @@ def _save_fts_bundle(
             except Exception:
                 pass
 
-    # Delegate to FTS (single source of truth)
+    # Delegate to Bundle (single source of truth)
     # Encoding is built from CSV columns directly for consistency
     from_matplotlib(fig, spath, name=name, csv_df=csv_df, dpi=dpi)
 

scitex/io/_save_modules/__init__.py

@@ -55,14 +55,10 @@ from ._mp4 import _mk_mp4 as save_mp4
 from ._numpy import _save_npy as save_npy
 from ._numpy import _save_npz as save_npz
 from ._optuna_study_as_csv_and_pngs import save_optuna_study_as_csv_and_pngs
-from ._pickle import (
-    _save_pickle as save_pickle,
-)
-from ._pickle import (
-    _save_pickle_gz as save_pickle_compressed,
-)
-from ._pltz_bundle import save_pltz_bundle
-from ._pltz_stx import save_pltz_as_stx
+from ._pickle import _save_pickle as save_pickle
+from ._pickle import _save_pickle_gz as save_pickle_compressed
+from ._plot_bundle import save_plot_bundle
+from ._plot_scitex import save_plot_as_scitex
 from ._stx_bundle import save_stx_bundle
 from ._symlink import symlink, symlink_to
 from ._tex import _save_tex as save_tex
@@ -121,8 +117,8 @@ __all__ = [
     "save_optuna_study_as_csv_and_pngs",
     # Bundle save functions
     "save_stx_bundle",
-    "save_pltz_bundle",
-    "save_pltz_as_stx",
+    "save_plot_bundle",
+    "save_plot_as_scitex",
     "save_separate_legends",
     "handle_image_with_csv",
     # Utilities

scitex/io/_save_modules/_canvas.py

@@ -3,7 +3,7 @@
 # Timestamp: 2025-12-08
 # File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_save_modules/_canvas.py
 """
-Save canvas directory (.canvas) for scitex.fig.
+Save canvas directory (.canvas) for scitex.canvas.
 
 Canvas directories are portable figure bundles containing:
     - canvas.json: Layout, panels, composition settings
@@ -113,7 +113,7 @@ def _export_canvas_figures(
         formats = ["png", "pdf", "svg"]
 
     try:
-        from scitex.fig.io.export import _compose_and_export
+        from scitex.canvas.io.export import _compose_and_export
         import json
 
         # Load canvas.json
@@ -136,7 +136,7 @@ def _export_canvas_figures(
                 transparent=False,
             )
     except ImportError:
-        # scitex.fig not available
+        # scitex.canvas not available
         pass
     except Exception as e:
         # Log but don't fail save if export fails