scitex 2.15.5__py3-none-any.whl → 2.16.1__py3-none-any.whl

scitex/dataset/__init__.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+"""
+SciTeX Dataset - Thin wrapper delegating to scitex-dataset package.
+
+This module provides access to scientific dataset discovery functionality
+by delegating to the scitex-dataset package.
+
+Usage:
+    >>> from scitex import dataset
+    >>> datasets = dataset.fetch_all_datasets(max_datasets=10)
+    >>> results = dataset.search_datasets(datasets, modality="eeg")
+
+    >>> # Or use the database for fast local search
+    >>> dataset.db.build()
+    >>> results = dataset.db.search("alzheimer EEG")
+"""
+
+try:
+    from scitex_dataset import (
+        OPENNEURO_API,
+        __version__,
+        database,
+        fetch_all_datasets,
+        fetch_datasets,
+        format_dataset,
+        general,
+        neuroscience,
+        search_datasets,
+        sort_datasets,
+    )
+
+    # Alias for consistency
+    db = database
+
+    __all__ = [
+        "__version__",
+        # Domains
+        "neuroscience",
+        "general",
+        # Database
+        "database",
+        "db",
+        # Convenience (OpenNeuro)
+        "fetch_datasets",
+        "fetch_all_datasets",
+        "format_dataset",
+        "OPENNEURO_API",
+        # Search
+        "search_datasets",
+        "sort_datasets",
+    ]
+
+except ImportError as e:
+    import warnings
+
+    warnings.warn(
+        f"scitex-dataset package not installed. "
+        f"Install with: pip install scitex-dataset\n{e}",
+        ImportWarning,
+        stacklevel=2,
+    )
+
+    # Provide stub for error messages
+    def _not_installed(*args, **kwargs):
+        raise ImportError(
+            "scitex-dataset package not installed. "
+            "Install with: pip install scitex-dataset"
+        )
+
+    fetch_datasets = _not_installed
+    fetch_all_datasets = _not_installed
+    format_dataset = _not_installed
+    search_datasets = _not_installed
+    sort_datasets = _not_installed
+    database = None
+    db = None
+    neuroscience = None
+    general = None
+    OPENNEURO_API = None
+    __version__ = "0.0.0"
+
+    __all__ = []
+
+
+# EOF

scitex/introspect/_list_api.py

@@ -146,13 +146,19 @@ def _list_api_impl(
             obj_name = f"{full_path}.{name}"
 
             if inspect.ismodule(obj):
-                if obj.__name__ not in visited:
+                # Only recurse into direct submodules (not sibling packages)
+                obj_mod_name = getattr(obj, "__name__", "")
+                # Check if this is a direct submodule of current module
+                if (
+                    obj_mod_name.startswith(module_name + ".")
+                    and obj_mod_name not in visited
+                ):
                     content_list.append(
                         (
                             "M",
                             obj_name,
                             obj.__doc__ if docstring and obj.__doc__ else "",
-                            current_depth,
+                            current_depth + 1,  # Children are one level deeper
                         )
                     )
                     try:
@@ -175,23 +181,35 @@ def _list_api_impl(
                     except Exception as err:
                         print(f"Error processing module {obj_name}: {err}")
             elif inspect.isfunction(obj):
-                content_list.append(
-                    (
-                        "F",
-                        obj_name,
-                        obj.__doc__ if docstring and obj.__doc__ else "",
-                        current_depth,
+                # Only include functions defined in this module (not re-exported from siblings)
+                obj_module = getattr(obj, "__module__", "")
+                # Check if function is defined in current module or its submodules
+                if obj_module == module_name or obj_module.startswith(
+                    module_name + "."
+                ):
+                    content_list.append(
+                        (
+                            "F",
+                            obj_name,
+                            obj.__doc__ if docstring and obj.__doc__ else "",
+                            current_depth + 1,  # Children are one level deeper
+                        )
                     )
-                )
             elif inspect.isclass(obj):
-                content_list.append(
-                    (
-                        "C",
-                        obj_name,
-                        obj.__doc__ if docstring and obj.__doc__ else "",
-                        current_depth,
+                # Only include classes defined in this module (not re-exported from siblings)
+                obj_module = getattr(obj, "__module__", "")
+                # Check if class is defined in current module or its submodules
+                if obj_module == module_name or obj_module.startswith(
+                    module_name + "."
+                ):
+                    content_list.append(
+                        (
+                            "C",
+                            obj_name,
+                            obj.__doc__ if docstring and obj.__doc__ else "",
+                            current_depth + 1,  # Children are one level deeper
+                        )
                     )
-                )
 
     except Exception as err:
         print(f"Error processing module structure: {err}")

scitex/io/__init__.py

@@ -28,17 +28,21 @@ from ._save import save
 
 # Optional: HDF5 explorer (requires h5py)
 try:
-    from ._load_modules._H5Explorer import H5Explorer, explore_h5, has_h5_key
+    from ._load_modules._H5Explorer import H5Explorer as _H5Explorer  # Internal class
+    from ._load_modules._H5Explorer import explore_h5, has_h5_key
 except ImportError:
-    H5Explorer = None
+    _H5Explorer = None
     explore_h5 = None
     has_h5_key = None
 
 # Optional: Zarr explorer (requires zarr)
 try:
-    from ._load_modules._ZarrExplorer import ZarrExplorer, explore_zarr, has_zarr_key
+    from ._load_modules._ZarrExplorer import (
+        ZarrExplorer as _ZarrExplorer,
+    )  # Internal class
+    from ._load_modules._ZarrExplorer import explore_zarr, has_zarr_key
 except ImportError:
-    ZarrExplorer = None
+    _ZarrExplorer = None
     explore_zarr = None
     has_zarr_key = None
 
@@ -67,25 +71,25 @@ except ImportError:
     save_listed_scalars_as_csv = None
     save_optuna_study_as_csv_and_pngs = None
 
-# Optional imports that might fail
+# Optional internal imports
 try:
-    from ._path import path
+    from ._path import path as _path  # Internal helper
 except ImportError:
-    path = None
+    _path = None
 
 try:
-    from ._mv_to_tmp import mv_to_tmp
+    from ._mv_to_tmp import mv_to_tmp as _mv_to_tmp  # Internal helper
 except ImportError:
-    mv_to_tmp = None
+    _mv_to_tmp = None
 
 try:
     from ._json2md import json2md
 except ImportError:
     json2md = None
 
-# Import utils
+# Import from internal utils module (hidden)
 try:
-    from .utils import migrate_h5_to_zarr, migrate_h5_to_zarr_batch
+    from ._utils import migrate_h5_to_zarr, migrate_h5_to_zarr_batch
 except ImportError:
     migrate_h5_to_zarr = None
     migrate_h5_to_zarr_batch = None

scitex/io/_save_modules/_tex.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Timestamp: "2025-10-01 21:30:00 (ywatanabe)"
 # File: /home/ywatanabe/proj/scitex_repo/src/scitex/io/_save_modules/_tex.py
 # ----------------------------------------
@@ -19,7 +18,7 @@ Supports multiple input types:
 - matplotlib figures → TikZ/PGFPlots (future enhancement)
 """
 
-from typing import Union, Optional, Any
+from typing import Any, Optional
 
 from scitex import logging
 
@@ -88,7 +87,7 @@ def save_tex(
     Notes
     -----
     - For DataFrames, uses pandas.DataFrame.to_latex()
-    - For dicts/lists, attempts to use scitex.stats.utils.convert_results()
+    - For dicts/lists, attempts to use scitex.stats._utils.convert_results()
     - For strings, writes content directly
     - The document=True option creates a complete compilable LaTeX document
     """
@@ -115,7 +114,7 @@ def save_tex(
     elif isinstance(obj, (dict, list)):
         # Try to convert using stats module's convert_results
         try:
-            from scitex.stats.utils._normalizers import convert_results
+            from scitex.stats._utils._normalizers import convert_results
 
             tex_content = convert_results(obj, return_as="latex", **kwargs)
 
@@ -126,7 +125,7 @@ def save_tex(
         except ImportError:
             logger.warning(
                 "Cannot convert dict/list to LaTeX: "
-                "scitex.stats.utils.convert_results not available. "
+                "scitex.stats._utils.convert_results not available."
                 "Converting to string instead."
             )
             tex_content = str(obj)
@@ -183,8 +182,6 @@ def _dataframe_to_latex(
     str
         LaTeX table string
     """
-    import pandas as pd
-
     # Build to_latex arguments
     latex_kwargs = {
         "index": False,

scitex/logging/__init__.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Timestamp: "2025-08-21 20:09:30 (ywatanabe)"
 # File: /home/ywatanabe/proj/SciTeX-Code/src/scitex/logging/__init__.py
 # ----------------------------------------
 from __future__ import annotations
+
 import os
 
 __FILE__ = __file__
@@ -39,88 +39,112 @@ Usage:
 
 import logging as _logging
 
-from ._Tee import Tee, tee
-
-# Import modular components
-from ._levels import SUCCESS, FAIL, DEBUG, INFO, WARNING, ERROR, CRITICAL
-from ._logger import SciTeXLogger, setup_logger_class
-from ._formatters import SciTeXConsoleFormatter, SciTeXFileFormatter
-from ._handlers import create_console_handler, create_file_handler, get_default_log_path
 from ._config import (
-    set_level,
-    get_level,
-    enable_file_logging,
-    is_file_logging_enabled,
     configure,
+    enable_file_logging,
+    get_level,
     get_log_path,
-)
-from ._print_capture import (
-    PrintCapture,
-    enable_print_capture,
-    disable_print_capture,
-    is_print_capture_enabled,
+    is_file_logging_enabled,
+    set_level,
 )
 from ._context import log_to_file
 
-# Warnings (like Python's warnings module)
-from ._warnings import (
-    SciTeXWarning,
-    UnitWarning,
-    StyleWarning,
-    SciTeXDeprecationWarning,
-    PerformanceWarning,
-    DataLossWarning,
-    warn,
-    filterwarnings,
-    resetwarnings,
-    warn_deprecated,
-    warn_performance,
-    warn_data_loss,
-)
-
 # Errors (exceptions)
 from ._errors import (
-    SciTeXError,
-    ConfigurationError,
+    AuthenticationError,
+    AxisError,
+    BibTeXEnrichmentError,
     ConfigFileNotFoundError,
     ConfigKeyError,
-    IOError,
+    ConfigurationError,
+    DataError,
+    DOIResolutionError,
+    DTypeError,
+    EnrichmentError,
+    FigureNotFoundError,
     FileFormatError,
-    SaveError,
+    InvalidPathError,
+    IOError,
     LoadError,
-    ScholarError,
-    SearchError,
-    EnrichmentError,
+    ModelError,
+    NNError,
+    PathError,
+    PathNotFoundError,
     PDFDownloadError,
-    DOIResolutionError,
     PDFExtractionError,
-    BibTeXEnrichmentError,
-    TranslatorError,
-    AuthenticationError,
     PlottingError,
-    FigureNotFoundError,
-    AxisError,
-    DataError,
+    SaveError,
+    ScholarError,
+    SciTeXError,
+    SearchError,
     ShapeError,
-    DTypeError,
-    PathError,
-    InvalidPathError,
-    PathNotFoundError,
+    StatsError,
     TemplateError,
     TemplateViolationError,
-    NNError,
-    ModelError,
-    StatsError,
     TestError,
-    check_path,
+    TranslatorError,
     check_file_exists,
+    check_path,
     check_shape_compatibility,
 )
+from ._formatters import (
+    SciTeXConsoleFormatter as _SciTeXConsoleFormatter,
+)
+from ._formatters import (
+    SciTeXFileFormatter as _SciTeXFileFormatter,
+)
+from ._handlers import (
+    create_console_handler as _create_console_handler,
+)
+from ._handlers import (
+    create_file_handler as _create_file_handler,
+)
+from ._handlers import (
+    get_default_log_path as _get_default_log_path,
+)
+
+# Import modular components
+from ._levels import CRITICAL, DEBUG, ERROR, FAIL, INFO, SUCCESS, WARNING
+from ._logger import (
+    SciTeXLogger as _SciTeXLogger,
+)
+from ._logger import (
+    setup_logger_class as _setup_logger_class,
+)
+from ._print_capture import (
+    PrintCapture as _PrintCapture,
+)
+from ._print_capture import (
+    disable_print_capture as _disable_print_capture,
+)
+from ._print_capture import (
+    enable_print_capture as _enable_print_capture,
+)
+from ._print_capture import (
+    is_print_capture_enabled as _is_print_capture_enabled,
+)
+from ._Tee import Tee, tee
+
+# Warnings (like Python's warnings module)
+from ._warnings import (
+    DataLossWarning,
+    PerformanceWarning,
+    SciTeXDeprecationWarning,
+    SciTeXWarning,
+    StyleWarning,
+    UnitWarning,
+    filterwarnings,
+    resetwarnings,
+    warn,
+    warn_data_loss,
+    warn_deprecated,
+    warn_performance,
+)
 
 # Re-export standard logging functions for compatibility
 getLogger = _logging.getLogger
-basicConfig = _logging.basicConfig
-disable = _logging.disable
+_basicConfig = _logging.basicConfig
+_disable = _logging.disable
 
 level_by_env = os.getenv("SCITEX_LOGGING_LEVEL", "INFO").upper()
 level_map = {
@@ -156,6 +180,10 @@ __all__ = [
     "FAIL",
     # Configuration
     "configure",
+    "set_level",
+    "get_level",
+    "enable_file_logging",
+    "is_file_logging_enabled",
     "get_log_path",
     "Tee",
     "tee",

scitex/schema/_stats.py

@@ -21,14 +21,12 @@ Note: This is the SOURCE OF TRUTH. Other modules (stats, plt, vis) should
 import from here, not define their own versions.
 """
 
-from dataclasses import dataclass
-from dataclasses import field, asdict
-from typing import Optional
-from typing import Dict, Any, List, Literal, Union
-from datetime import datetime
 import json
-import numpy as np
+from dataclasses import asdict, dataclass, field
+from datetime import datetime
+from typing import Any, Dict, List, Literal, Optional, Union
 
+import numpy as np
 
 # Schema version for statistical result schemas
 STATS_SCHEMA_VERSION = "0.1.0"
@@ -647,22 +645,16 @@ class StatResult:
                     self.effect_size.get("value") if self.effect_size else None
                 ),
                 "group1": (
-                    self.samples.get("group1", {}).get("name")
-                    if self.samples
-                    else None
+                    self.samples.get("group1", {}).get("name") if self.samples else None
                 ),
                 "group2": (
-                    self.samples.get("group2", {}).get("name")
-                    if self.samples
-                    else None
+                    self.samples.get("group2", {}).get("name") if self.samples else None
                 ),
                 "statistic": self.statistic.get("value"),
                 "method": self.test_type,
                 "formatted_output": self.format_text(style="compact"),
             },
-            "positioning": (
-                self.positioning.to_dict() if self.positioning else None
-            ),
+            "positioning": (self.positioning.to_dict() if self.positioning else None),
             "styling": self.styling.to_dict() if self.styling else None,
         }
 
@@ -710,7 +702,7 @@ def create_stat_result(
     ... )
     """
     # Import here to avoid circular dependency
-    from scitex.stats.utils import p2stars
+    from scitex.stats._utils import p2stars
 
     # Determine category from test type
     category_map = {

scitex/scholar/__init__.py

@@ -17,10 +17,10 @@ Installation:
     pip install scitex[scholar]
 """
 
-# Check for missing dependencies and warn user
-from scitex._install_guide import warn_module_deps
+# Check for missing dependencies and warn user (internal)
+from scitex._install_guide import warn_module_deps as _warn_module_deps
 
-_missing = warn_module_deps("scholar")
+_missing = _warn_module_deps("scholar")
 
 # Import configuration - wrap all in try/except for graceful degradation
 try:
@@ -66,9 +66,9 @@ except ImportError:
     ScholarURLFinder = None
 
 try:
-    from . import utils
+    from . import _utils  # Internal utilities
 except ImportError:
-    utils = None
+    _utils = None
 
 # Local database integrations (crossref-local, openalex-local)
 try:
@@ -82,15 +82,18 @@ except ImportError:
     openalex_scitex = None
 
 __all__ = [
+    # Core classes
+    "Scholar",
+    "Paper",
+    "Papers",
+    # Configuration and managers
     "ScholarConfig",
     "ScholarEngine",
     "ScholarURLFinder",
     "ScholarAuthManager",
     "ScholarBrowserManager",
-    "Paper",
-    "Papers",
-    "Scholar",
-    "utils",
+    "ScholarLibrary",
+    "ScholarPDFDownloader",
     # Local database integrations
     "crossref_scitex",  # CrossRef (167M+ papers via crossref-local)
     "openalex_scitex",  # OpenAlex (284M+ works via openalex-local)

scitex/scholar/examples/03_02-engine-for-bibtex.py

@@ -54,7 +54,7 @@ async def search_bibtex_metadata(
 ) -> list:
     """Search for metadata of papers from BibTeX file."""
     from scitex.scholar import ScholarConfig, ScholarEngine
-    from scitex.scholar.utils import parse_bibtex
+    from scitex.scholar._utils import parse_bibtex
 
     entries = parse_bibtex(bibtex_path)
     if n_samples:

scitex/scholar/examples/04_02-url-for-bibtex.py

@@ -83,7 +83,7 @@ async def process_bibtex_urls(
         ScholarEngine,
         ScholarURLFinder,
     )
-    from scitex.scholar.utils import parse_bibtex
+    from scitex.scholar._utils import parse_bibtex
 
     print(f"📚 Parsing BibTeX file: {bibtex_path}")
     entries = parse_bibtex(bibtex_path)

scitex/scholar/examples/06_parse_bibtex.py

@@ -66,7 +66,7 @@ def demonstrate_bibtex_parsing(
     dict
         Parsed BibTeX entries
     """
-    from scitex.scholar.utils import parse_bibtex
+    from scitex.scholar._utils import parse_bibtex
 
     results = {}
 

scitex/scholar/examples/99_fullpipeline-for-bibtex.py

@@ -85,7 +85,7 @@ async def process_bibtex_entries(
         ScholarPDFDownloader,
         ScholarURLFinder,
     )
-    from scitex.scholar.utils import parse_bibtex
+    from scitex.scholar._utils import parse_bibtex
 
     # Parse BibTeX entries
     entries = parse_bibtex(bibtex_path)

scitex/scholar/pipelines/ScholarPipelineMetadataSingle.py

@@ -32,7 +32,7 @@ from scitex.scholar.core import Paper
 from scitex.scholar.metadata_engines import ScholarEngine
 from scitex.scholar.impact_factor import ImpactFactorEngine
 from scitex.scholar.config import ScholarConfig
-from scitex.scholar.utils import DOIValidator
+from scitex.scholar._utils import DOIValidator
 
 logger = logging.getLogger(__name__)
 

scitex/scholar/storage/_mixins/_paper_saving.py

@@ -15,7 +15,7 @@ from datetime import datetime
 from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
 from scitex import logging
-from scitex.scholar.utils import TextNormalizer
+from scitex.scholar._utils import TextNormalizer
 
 if TYPE_CHECKING:
     from scitex.scholar.core.Paper import Paper

scitex/scholar/storage/_mixins/_resolution.py

@@ -14,7 +14,7 @@ from datetime import datetime
 from typing import Any, Dict, List, Optional
 
 from scitex import logging
-from scitex.scholar.utils import TextNormalizer
+from scitex.scholar._utils import TextNormalizer
 
 logger = logging.getLogger(__name__)
 

scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Timestamp: "2025-10-13 06:32:08 (ywatanabe)"
 # File: /home/ywatanabe/proj/scitex_repo/src/scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py
 # ----------------------------------------
 from __future__ import annotations
+
 import os
 
 __FILE__ = (
@@ -38,10 +38,10 @@ Usage:
 from typing import List
 
 from playwright.async_api import Page
-from scitex.scholar.url_finder.translators.core.registry import TranslatorRegistry
 
 from scitex import logging
 from scitex.browser import browser_logger
+from scitex.scholar.url_finder.translators._core.registry import TranslatorRegistry
 
 logger = logging.getLogger(__name__)
 
@@ -67,11 +67,13 @@ async def find_pdf_urls_by_zotero_translators(
         config: ScholarConfig instance (unused, for signature consistency)
         func_name: Function name for logging
 
-    Returns:
+    Returns
+    -------
         List of PDF URLs extracted by matching translators
         Empty list if no translator matches or extraction fails
 
-    Examples:
+    Examples
+    --------
         >>> async with async_playwright() as p:
         ...     browser = await p.chromium.launch()
         ...     page = await browser.new_page()

scitex/scholar/url_finder/translators/__init__.py

@@ -21,11 +21,12 @@ Internal modules (not part of public API):
 """
 
 # Public API - only expose what users need
-from .core.registry import TranslatorRegistry
-from .core.base import BaseTranslator
+from ._core.base import (
+    BaseTranslator as _BaseTranslator,
+)  # Hidden, use TranslatorRegistry
+from ._core.registry import TranslatorRegistry
 
 # Everything else is internal implementation
 __all__ = [
     "TranslatorRegistry",
-    "BaseTranslator",
 ]