eegdash 0.4.1__tar.gz → 0.4.1.dev185__tar.gz

{eegdash-0.4.1/eegdash.egg-info → eegdash-0.4.1.dev185}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.1
+Version: 0.4.1.dev185
 Summary: EEG data for machine learning
 Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License-Expression: GPL-3.0-only
@@ -60,6 +60,7 @@ Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
 Requires-Dist: nbformat; extra == "docs"
 Requires-Dist: graphviz; extra == "docs"
+Requires-Dist: neato; extra == "docs"
 Provides-Extra: digestion
 Requires-Dist: pybids; extra == "digestion"
 Requires-Dist: python-dotenv; extra == "digestion"

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/docs/Makefile

@@ -12,9 +12,9 @@ help:
 .PHONY: apidoc
 apidoc:
 	# Generate full API docs, then prune duplicates covered by autosummary
+	@rm -f "$(APIDIR)"/dataset/eegdash.features*
 	@SPHINX_APIDOC_OPTIONS=members,undoc-members,show-inheritance,noindex \
-		python -m sphinx.ext.apidoc -f -e -M -o "$(APIDIR)/dataset" "../$(PKG)"
-	# Remove top-level package page and modules covered elsewhere
+		python -m sphinx.ext.apidoc -f -e -T -o "$(APIDIR)/dataset" "../$(PKG)" "../$(PKG)/features"
 
 
 # Standard build runs examples

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/docs/source/api/api_core.rst

@@ -53,8 +53,8 @@ The API is organized into focused modules that handle specific aspects of EEG da
 
 * :mod:`~eegdash.api` - Main interface for data access and manipulation
 * :mod:`~eegdash.const` - Constants and enumerations used throughout the package
+* :doc:`dataset/api_dataset` - Dataset object management and operations
 * :mod:`~eegdash.bids_eeg_metadata` - BIDS-compliant metadata handling  
-* :mod:`~eegdash.data_utils` - Data preprocessing and transformation utilities
 * :mod:`~eegdash.mongodb` - Database connection and query operations
 * :mod:`~eegdash.paths` - File system and storage path management
 * :mod:`~eegdash.utils` - General utility functions and helpers
@@ -71,7 +71,6 @@ API Reference
    api
    bids_eeg_metadata
    const
-   data_utils
    logging
    hbn
    mongodb

eegdash-0.4.1.dev185/docs/source/api/api_features.rst

@@ -0,0 +1,24 @@
+Feature API
+===========
+
+.. toctree::
+   :maxdepth: 1
+
+   Feature Package Overview <features_overview>
+
+.. autosummary::
+   :toctree: generated/api-features
+
+   eegdash.features.datasets
+   eegdash.features.decorators
+   eegdash.features.extractors
+   eegdash.features.inspect
+   eegdash.features.serialization
+   eegdash.features.utils
+   eegdash.features.feature_bank.complexity
+   eegdash.features.feature_bank.connectivity
+   eegdash.features.feature_bank.csp
+   eegdash.features.feature_bank.dimensionality
+   eegdash.features.feature_bank.signal
+   eegdash.features.feature_bank.spectral
+   eegdash.features.feature_bank.utils

eegdash-0.4.1.dev185/docs/source/api/features_overview.rst

@@ -0,0 +1,37 @@
+Feature Package Overview
+========================
+
+.. currentmodule:: eegdash.features
+
+The :mod:`eegdash.features` namespace re-exports feature extractors,
+decorators, and dataset utilities from the underlying submodules so callers can
+import the most common helpers from a single place. To avoid duplicated
+documentation in the API reference, the classes themselves are documented in
+their defining modules (see the links below). This page focuses on the
+high-level orchestration helpers that only live in the package ``__init__``.
+
+High-level discovery helpers
+----------------------------
+
+.. autofunction:: get_all_features
+.. autofunction:: get_feature_kind
+.. autofunction:: get_feature_predecessors
+.. autofunction:: get_all_feature_extractors
+.. autofunction:: get_all_feature_kinds
+
+Dataset and extraction utilities
+--------------------------------
+
+.. autofunction:: extract_features
+.. autofunction:: fit_feature_extractors
+.. autofunction:: load_features_concat_dataset
+
+See also
+--------
+
+- :mod:`eegdash.features.extractors` for the feature-extraction base classes
+  such as :class:`~eegdash.features.extractors.FeatureExtractor`.
+- :mod:`eegdash.features.datasets` for dataset wrappers like
+  :class:`~eegdash.features.datasets.FeaturesConcatDataset`.
+- :mod:`eegdash.features.feature_bank.*` for the concrete feature families
+  (complexity, connectivity, spectral, and more).

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/docs/source/conf.py

@@ -65,6 +65,16 @@ suppress_warnings = [
     "config.cache",
 ]
 
+autodoc_type_aliases = {
+    "FeatureExtractor": "eegdash.features.extractors.FeatureExtractor",
+    "MultivariateFeature": "eegdash.features.extractors.MultivariateFeature",
+    "FeaturesConcatDataset": "eegdash.features.datasets.FeaturesConcatDataset",
+    "FeaturesDataset": "eegdash.features.datasets.FeaturesDataset",
+    "TrainableFeature": "eegdash.features.extractors.TrainableFeature",
+}
+
+python_use_unqualified_type_names = False
+
 # -- Options for HTML output -------------------------------------------------
 
 html_theme = "pydata_sphinx_theme"
@@ -223,6 +233,8 @@ EX_DIR = "../../examples"  # relative to docs/source
 sphinx_gallery_conf = {
     "examples_dirs": [f"{EX_DIR}"],
     "gallery_dirs": ["generated/auto_examples"],
+    # Disable plotting during doc builds; matches `html-noplot` behaviour.
+    "plot_gallery": False,
     "binder": {
         "org": "sccn",
         "repo": "EEGDash",
@@ -258,8 +270,8 @@ LOGGER = logging.getLogger(__name__)
 
 
 AUTOGEN_NOTICE = """..
-   This file is auto-generated during the Sphinx build.
-   Do not edit by hand; changes will be overwritten.
+   This documentation page is generated during the Sphinx build.
+   The underlying code is manually maintained and not autogenerated.
 
 """
 
@@ -294,7 +306,9 @@ See Also
 """
 
 
-DATASET_INDEX_TEMPLATE = """{notice}Datasets API
+DATASET_INDEX_TEMPLATE = """{notice}.. _api/dataset/api_dataset:
+
+Datasets API
 =======================
 
 The :mod:`eegdash.dataset` package exposes dynamically registered dataset
@@ -314,6 +328,7 @@ Base Dataset API
 .. toctree::
    :maxdepth: 1
 
+   eegdash.EEGDashDataset
    eegdash.dataset.EEGChallengeDataset
 
 .. list-table:: Dataset counts by experimental type
@@ -353,6 +368,39 @@ EEGChallengeDataset
 """
 
 
+PRIMARY_DATASET_TEMPLATE = """{notice}.. _api_eegdash_dataset:
+
+.. currentmodule:: eegdash
+
+EEGDashDataset
+==============
+
+.. autoclass:: eegdash.EEGDashDataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+   :member-order: bysource
+
+Usage Example
+-------------
+
+.. code-block:: python
+
+   from eegdash import EEGDashDataset
+
+   dataset = EEGDashDataset(cache_dir="./data", dataset="ds002718")
+   print(f"Number of recordings: {{len(dataset)}}")
+
+See Also
+--------
+
+* :mod:`eegdash.dataset`
+* :class:`eegdash.dataset.EEGChallengeDataset`
+
+"""
+
+
 def _write_if_changed(path: Path, content: str) -> bool:
     """Write ``content`` to ``path`` if it differs from the current file."""
     existing = path.read_text(encoding="utf-8") if path.exists() else None
@@ -365,7 +413,7 @@ def _write_if_changed(path: Path, content: str) -> bool:
 def _iter_dataset_classes() -> Sequence[str]:
     """Return the sorted dataset class names exported by ``eegdash.dataset``."""
     import eegdash.dataset as dataset_module  # local import for clarity
-    from eegdash.api import EEGDashDataset
+    from eegdash.dataset import EEGDashDataset
 
     class_names: list[str] = []
     for name in getattr(dataset_module, "__all__", []):
@@ -584,6 +632,11 @@ def _generate_dataset_docs(app) -> None:
     if _write_if_changed(base_path, base_content):
         LOGGER.info("[dataset-docs] Updated %s", base_path.relative_to(app.srcdir))
 
+    primary_content = PRIMARY_DATASET_TEMPLATE.format(notice=AUTOGEN_NOTICE)
+    primary_path = dataset_dir / "eegdash.EEGDashDataset.rst"
+    if _write_if_changed(primary_path, primary_content):
+        LOGGER.info("[dataset-docs] Updated %s", primary_path.relative_to(app.srcdir))
+
     generated_paths: set[Path] = set()
     for name in dataset_names:
         title = f"eegdash.dataset.{name}"
@@ -715,7 +768,7 @@ def _inject_counter_values(app, docname, source) -> None:
 
 
 def setup(app):
-    """Create the back-references directory if it doesn't exist."""
+    """Create the back-references directory and setup Sphinx events."""
     backreferences_dir = os.path.join(
         app.srcdir, sphinx_gallery_conf["backreferences_dir"]
     )

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/docs/source/developer_notes.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. _developer_notes:
 
 Developer Notes
@@ -104,6 +106,15 @@ Metadata & Database Management
 
      python scripts/data_ingest.py
 
+API Gateway Endpoint
+--------------------
+
+The public HTTP gateway that fronts the MongoDB metadata service lives at
+``|api-base-url|``. Point external tooling, health probes, and API examples at
+that hostname instead of the raw server IP so future migrations only require
+updating the ``|api-base-url|`` substitution in ``docs/source/links.inc``.
+
+
 Remote Storage Mounting
 -----------------------
 

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/docs/source/user_guide.rst

@@ -205,3 +205,8 @@ Once you have your :class:`~eegdash.api.EEGDashDataset` object, you can access i
         print(f"Number of channels: {len(raw.ch_names)}")
 
 This provides a powerful and flexible way to integrate ``eegdash`` into your data analysis pipelines, whether you are working with remote or local data. For contributor resources, see :doc:`Developer Notes </developer_notes>`.
+
+
+.. seealso::
+
+   :doc:`developer_notes` captures contributor workflows for the core package.

{eegdash-0.4.1 → eegdash-0.4.1.dev185}/eegdash/__init__.py

@@ -9,8 +9,8 @@ EEG datasets. It integrates with cloud storage, MongoDB databases, and machine l
 frameworks to streamline EEG research workflows.
 """
 
-from .api import EEGDash, EEGDashDataset
-from .dataset import EEGChallengeDataset
+from .api import EEGDash
+from .dataset import EEGChallengeDataset, EEGDashDataset
 from .hbn import preprocessing
 from .utils import _init_mongo_client
 
@@ -18,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.1"
+__version__ = "0.4.1.dev185"