eegdash 0.4.0.dev132__tar.gz → 0.4.0.dev144__tar.gz

{eegdash-0.4.0.dev132/eegdash.egg-info → eegdash-0.4.0.dev144}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev132
+Version: 0.4.0.dev144
 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
@@ -65,6 +65,7 @@ Requires-Dist: ipython; extra == "docs"
 Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
 Requires-Dist: nbformat; extra == "docs"
+Requires-Dist: graphviz; extra == "docs"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"

eegdash-0.4.0.dev144/docs/Makefile

@@ -0,0 +1,69 @@
+# Minimal makefile for Sphinx documentation
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+PKG ?= eegdash
+APIDIR := $(SOURCEDIR)/api
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: apidoc
+apidoc:
+	# Generate full API docs, then prune duplicates covered by autosummary
+	@python -m sphinx.ext.apidoc -f -e -M -o "$(APIDIR)/dataset" "../$(PKG)"
+	# Remove top-level package page and modules covered elsewhere
+	@rm -f "$(APIDIR)/dataset/eegdash.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.api.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.bids_eeg_metadata.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.const.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.data_utils.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.logging.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.mongodb.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.paths.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.utils.rst"
+	@rm -f "$(APIDIR)/dataset/eegdash.features.rst"
+	@rm -f $(APIDIR)/dataset/eegdash.features.*.rst
+	@rm -f "$(APIDIR)/dataset/eegdash.hbn.rst"
+	@rm -f $(APIDIR)/dataset/eegdash.hbn.*.rst
+	@rm -f "$(APIDIR)/dataset/modules.rst"
+
+.PHONY: dataset-pages
+dataset-pages:
+	# Generate individual dataset documentation pages
+	@python generate_dataset_pages.py
+
+# Standard build runs examples
+html: apidoc dataset-pages
+
+# Fast build: do NOT execute examples (sphinx-gallery)
+.PHONY: html-noplot
+html-noplot: apidoc dataset-pages
+	@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" \
+		$(SPHINXOPTS) -D sphinx_gallery_conf.plot_gallery=0 $(O)
+
+# Custom clean target to remove generated API docs and build files
+.PHONY: clean
+clean:
+	@echo "Removing generated API documentation..."
+	@rm -rf "$(APIDIR)/dataset"
+	@rm -rf "$(APIDIR)/generated"
+	@echo "Removing generated dataset pages..."
+	@rm -rf "$(APIDIR)/datasets"
+	@rm -f "$(APIDIR)/api_dataset.rst"
+	@echo "Removing other generated directories..."
+	@rm -rf "$(SOURCEDIR)/generated"
+	@rm -rf "$(SOURCEDIR)/gen_modules"
+	@echo "Removing build directory..."
+	@rm -rf "$(BUILDDIR)"
+	@echo "Clean completed."
+
+.PHONY: help apidoc
+Makefile: ;          
+
+%: Makefile
+	@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
+	@python generate_dataset_pages.py
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

{eegdash-0.4.0.dev132/docs/source → eegdash-0.4.0.dev144/docs/source/api}/api.rst

@@ -1,10 +1,12 @@
+:html_theme.sidebar_primary.remove: true
+
 .. _api:
 
 API Reference
 =============
 
-.. grid:: 2
-   :gutter: 2
+.. grid:: 1
+   :gutter: 3
 
    .. grid-item-card:: Core
       :class-header: sd-bg-primary sd-text-white sd-font-weight-bold
@@ -20,20 +22,16 @@ API Reference
 
       Feature extraction and processing routines.
 
-Datasets
---------
-
-.. toctree::
-   :maxdepth: 2
-
-   api/dataset/modules
+   .. grid-item-card:: Dataset
+      :class-header: sd-bg-primary sd-text-white sd-font-weight-bold
+      :link: api_dataset
+      :link-type: doc
 
-.. note::
-   The dataset API above is generated automatically during the build.
+      Datasets available at EEGDash.
 
 .. toctree::
    :hidden:
 
    api_core
    api_features
-
+   api_dataset

{eegdash-0.4.0.dev132/docs/source → eegdash-0.4.0.dev144/docs/source/api}/api_core.rst

@@ -11,8 +11,8 @@ Core API
    bids_eeg_metadata
    const
    data_utils
+   logging
    hbn
    mongodb
    paths
    utils
-

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/docs/source/conf.py

@@ -32,16 +32,20 @@ extensions = [
     "sphinx.ext.linkcode",
     "sphinx.ext.napoleon",
     "sphinx_design",
-    # "autoapi.extension",
     "numpydoc",
     "sphinx_gallery.gen_gallery",
-    # Generate sitemap.xml for search engines
     "sphinx_sitemap",
 ]
 
 templates_path = ["_templates"]
 exclude_patterns = ["build", "Thumbs.db", ".DS_Store"]
 
+# Suppress benign warnings
+suppress_warnings = [
+    # Sphinx-Gallery uses functions/classes in config which are not picklable
+    "config.cache",
+]
+
 # -- Options for HTML output -------------------------------------------------
 
 html_theme = "pydata_sphinx_theme"
@@ -55,7 +59,7 @@ html_js_files = []
 
 # Required for sphinx-sitemap: set the canonical base URL of the site
 # Make sure this matches the actual published docs URL and ends with '/'
-html_baseurl = "https://sccn.github.io/eegdash/"
+html_baseurl = "https://eegdash.org/"
 
 html_theme_options = {
     "icon_links_label": "External Links",  # for screen reader
@@ -91,7 +95,7 @@ html_theme_options = {
         },
         {
             "name": "Docs (Stable)",
-            "url": "https://sccn.github.io/EEGDash",
+            "url": "https://eegdash.org/EEGDash",
             "icon": "fa-solid fa-book",
             "type": "fontawesome",
         },
@@ -182,7 +186,7 @@ numpydoc_show_class_members = False
 # Sphinx Gallery
 EX_DIR = "../../examples"  # relative to docs/source
 sphinx_gallery_conf = {
-    "examples_dirs": [EX_DIR],
+    "examples_dirs": [f"{EX_DIR}"],
     "gallery_dirs": ["generated/auto_examples"],
     "nested_sections": False,
     "backreferences_dir": "gen_modules/backreferences",
@@ -198,13 +202,7 @@ sphinx_gallery_conf = {
         "# `pip install eegdash`\n"
         "%matplotlib inline"
     ),
-    "subsection_order": ExplicitOrder(
-        [
-            f"{EX_DIR}/core",
-            # f"{EX_DIR}/eeg2025",
-            "*",
-        ]
-    ),
+    "subsection_order": ExplicitOrder([f"{EX_DIR}/core", "*"]),
     "within_subsection_order": FileNameSortKey,
 }
 

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/docs/source/dataset_summary.rst

@@ -4,8 +4,8 @@
 
 .. _data_summary:
 
-EEGDash 
-========
+Dataset Summary 
+===============
 
 To leverage recent and ongoing advancements in large-scale computational methods and to ensure the preservation of scientific data generated from publicly funded research, the EEG-DaSh data archive will create a data-sharing resource for MEEG (EEG, MEG) data contributed by collaborators for machine learning (ML) and deep learning (DL) applications.
 

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/docs/source/index.rst

@@ -1,7 +1,7 @@
 :html_theme.sidebar_secondary.remove: true
 
-EEGDASH Documentation
-=====================
+EEGDASH Homepage
+=================
 
 .. title:: EEG Dash
 
@@ -55,6 +55,6 @@ The archive is currently still in :bdg-danger:`beta testing` mode, so be kind.
 
    Overview <overview>
    Install <install/install>
-   API <api>
+   API <api/api>
    Dataset Summary <dataset_summary>
    Examples <generated/auto_examples/index>

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/docs/source/install/install.rst

@@ -6,7 +6,7 @@
 Installation
 ================
 
-EEGDash is written in Python 3, specifically for version 3.8 or above.
+EEGDash is written in Python 3, specifically for version 3.10 or above.
 
 The package is distributed via Python package index (`PyPI <eegdash-pypi_>`_), and you can access the
 source code via `Github <eegdash-github_>`_ repository.

eegdash-0.4.0.dev144/eegdash/__init__.py

@@ -0,0 +1,21 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""EEGDash: A comprehensive platform for EEG data management and analysis.
+
+EEGDash provides a unified interface for accessing, querying, and analyzing large-scale
+EEG datasets. It integrates with cloud storage, MongoDB databases, and machine learning
+frameworks to streamline EEG research workflows.
+"""
+
+from .api import EEGDash, EEGDashDataset
+from .dataset import EEGChallengeDataset
+from .hbn import preprocessing
+from .utils import _init_mongo_client
+
+_init_mongo_client()
+
+__all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
+
+__version__ = "0.4.0.dev144"

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/api.py

@@ -1,3 +1,15 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""High-level interface to the EEGDash metadata database.
+
+This module provides the main EEGDash class which serves as the primary entry point for
+interacting with the EEGDash ecosystem. It offers methods to query, insert, and update
+metadata records stored in the EEGDash MongoDB database, and includes utilities to load
+EEG data from S3 for matched records.
+"""
+
 import os
 from pathlib import Path
 from typing import Any, Mapping
@@ -549,16 +561,54 @@ class EEGDashDataset(BaseConcatDataset, metaclass=NumpyDocstringInheritanceInitM
 
     Examples
     --------
-    # Find by single subject
-    >>> ds = EEGDashDataset(dataset="ds005505", subject="NDARCA153NKE")
-
-    # Find by a list of subjects and a specific task
-    >>> subjects = ["NDARCA153NKE", "NDARXT792GY8"]
-    >>> ds = EEGDashDataset(dataset="ds005505", subject=subjects, task="RestingState")
-
-    # Use a raw MongoDB query for advanced filtering
-    >>> raw_query = {"dataset": "ds005505", "subject": {"$in": subjects}}
-    >>> ds = EEGDashDataset(query=raw_query)
+    Basic usage with dataset and subject filtering:
+
+    >>> from eegdash import EEGDashDataset
+    >>> dataset = EEGDashDataset(
+    ...     cache_dir="./data",
+    ...     dataset="ds002718",
+    ...     subject="012"
+    ... )
+    >>> print(f"Number of recordings: {len(dataset)}")
+
+    Filter by multiple subjects and specific task:
+
+    >>> subjects = ["012", "013", "014"]
+    >>> dataset = EEGDashDataset(
+    ...     cache_dir="./data",
+    ...     dataset="ds002718",
+    ...     subject=subjects,
+    ...     task="RestingState"
+    ... )
+
+    Load and inspect EEG data from recordings:
+
+    >>> if len(dataset) > 0:
+    ...     recording = dataset[0]
+    ...     raw = recording.load()
+    ...     print(f"Sampling rate: {raw.info['sfreq']} Hz")
+    ...     print(f"Number of channels: {len(raw.ch_names)}")
+    ...     print(f"Duration: {raw.times[-1]:.1f} seconds")
+
+    Advanced filtering with raw MongoDB queries:
+
+    >>> from eegdash import EEGDashDataset
+    >>> query = {
+    ...     "dataset": "ds002718",
+    ...     "subject": {"$in": ["012", "013"]},
+    ...     "task": "RestingState"
+    ... }
+    >>> dataset = EEGDashDataset(cache_dir="./data", query=query)
+
+    Working with dataset collections and braindecode integration:
+
+    >>> # EEGDashDataset is a braindecode BaseConcatDataset
+    >>> for i, recording in enumerate(dataset):
+    ...     if i >= 2:  # limit output
+    ...         break
+    ...     print(f"Recording {i}: {recording.description}")
+    ...     raw = recording.load()
+    ...     print(f"  Channels: {len(raw.ch_names)}, Duration: {raw.times[-1]:.1f}s")
 
     Parameters
     ----------

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/bids_eeg_metadata.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""BIDS metadata processing and query building utilities.
+
+This module provides functions for processing BIDS-formatted EEG metadata, building database
+queries from user parameters, and enriching metadata records with participant information.
+It handles the translation between user-friendly query parameters and MongoDB query syntax.
+"""
+
 import re
 from pathlib import Path
 from typing import Any

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/const.py

@@ -1,3 +1,21 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Configuration constants and mappings for EEGDash.
+
+This module contains global configuration settings, allowed query fields, and mapping
+constants used throughout the EEGDash package. It defines the interface between EEGDash
+releases and OpenNeuro dataset identifiers, as well as validation rules for database queries.
+"""
+
+__all__ = [
+    "config",
+    "ALLOWED_QUERY_FIELDS",
+    "RELEASE_TO_OPENNEURO_DATASET_MAP",
+    "SUBJECT_MINI_RELEASE_MAP",
+]
+
 ALLOWED_QUERY_FIELDS = {
     "data_name",
     "dataset",

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/data_utils.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Data utilities and dataset classes for EEG data handling.
+
+This module provides core dataset classes for working with EEG data in the EEGDash ecosystem,
+including classes for individual recordings and collections of datasets. It integrates with
+braindecode for machine learning workflows and handles data loading from both local and remote sources.
+"""
+
 import io
 import json
 import os

eegdash-0.4.0.dev144/eegdash/dataset/__init__.py

@@ -0,0 +1,22 @@
+"""Public API for dataset helpers and dynamically generated datasets."""
+
+from . import dataset as _dataset_mod  # triggers dynamic class registration
+from .dataset import EEGChallengeDataset
+from .registry import register_openneuro_datasets
+
+# Re-export dynamically generated dataset classes at the package level so that
+# ``eegdash.dataset`` shows them in the API docs and users can import as
+# ``from eegdash.dataset import DSXXXXX``.
+_dyn_names = []
+for _name in getattr(_dataset_mod, "__all__", []):
+    if _name == "EEGChallengeDataset":
+        # Already imported explicitly above
+        continue
+    _obj = getattr(_dataset_mod, _name, None)
+    if _obj is not None:
+        globals()[_name] = _obj
+        _dyn_names.append(_name)
+
+__all__ = ["EEGChallengeDataset", "register_openneuro_datasets"] + _dyn_names
+
+del _dataset_mod, _name, _obj, _dyn_names

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/dataset/dataset_summary.csv

@@ -10,7 +10,6 @@
 8,ds005508,3342,324,10,129,500,269.281,229.81 GB,246753736933,0,,,,,
 9,ds005507,1812,184,10,129,500,168.649,139.37 GB,149646718160,0,,,,,
 10,ds005506,1405,150,10,129,500,127.896,111.88 GB,120126449650,0,,,,,
-11,test,2,1,1,64,500,20.556,0 B,0,0,,,,,
 12,ds004854,1,1,1,64,128,0.535,79.21 MB,83057080,0,,,,,
 13,ds004853,1,1,1,64,128,0.535,79.21 MB,83057080,0,,,,,
 14,ds004844,68,17,1,64,1024,21.252,22.33 GB,23976121966,0,ds004844,,,Multisensory,Decision-making

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/dataset/registry.py

@@ -57,14 +57,8 @@ def register_openneuro_datasets(
 
         init = make_init(dataset_id)
 
-        doc = f"""OpenNeuro dataset ``{dataset_id}``.
-
-        {_markdown_table(row_series)}
-
-        This class is a thin convenience wrapper for the dataset ``{dataset_id}``.
-        Constructor arguments are forwarded to :class:`{base_class.__name__}`; see the
-        base class documentation for parameter details and examples.
-        """
+        # Generate rich docstring with dataset metadata
+        doc = _generate_rich_docstring(dataset_id, row_series, base_class)
 
         # init.__doc__ = doc
 
@@ -90,6 +84,94 @@ def register_openneuro_datasets(
     return registered
 
 
+def _generate_rich_docstring(dataset_id: str, row_series: pd.Series, base_class) -> str:
+    """Generate a comprehensive docstring for a dataset class."""
+    # Extract metadata with safe defaults
+    n_subjects = row_series.get("n_subjects", "Unknown")
+    n_records = row_series.get("n_records", "Unknown")
+    n_tasks = row_series.get("n_tasks", "Unknown")
+    modality = row_series.get("modality of exp", "")
+    exp_type = row_series.get("type of exp", "")
+    subject_type = row_series.get("Type Subject", "")
+    duration = row_series.get("duration_hours_total", "Unknown")
+    size = row_series.get("size", "Unknown")
+
+    # Create description based on available metadata
+    description_parts = []
+    if modality and str(modality).strip():
+        description_parts.append(f"**Modality**: {modality}")
+    if exp_type and str(exp_type).strip():
+        description_parts.append(f"**Type**: {exp_type}")
+    if subject_type and str(subject_type).strip():
+        description_parts.append(f"**Subjects**: {subject_type}")
+
+    description = (
+        " | ".join(description_parts)
+        if description_parts
+        else "EEG dataset from OpenNeuro"
+    )
+
+    # Generate the docstring
+    docstring = f"""OpenNeuro dataset ``{dataset_id}``.
+
+{description}
+
+This dataset contains {n_subjects} subjects with {n_records} recordings across {n_tasks} tasks.
+Total duration: {duration} hours. Dataset size: {size}.
+
+{_markdown_table(row_series)}
+
+This dataset class provides convenient access to the ``{dataset_id}`` dataset through the EEGDash interface.
+It inherits all functionality from :class:`~{base_class.__module__}.{base_class.__name__}` with the dataset filter pre-configured.
+
+Parameters
+----------
+cache_dir : str
+    Directory to cache downloaded data.
+query : dict, optional
+    Additional MongoDB-style filters to AND with the dataset selection.
+    Must not contain the key ``dataset``.
+s3_bucket : str, optional
+    Base S3 bucket used to locate the data.
+**kwargs
+    Additional arguments passed to the base dataset class.
+
+Examples
+--------
+Basic usage:
+
+>>> from eegdash.dataset import {dataset_id.upper()}
+>>> dataset = {dataset_id.upper()}(cache_dir="./data")
+>>> print(f"Number of recordings: {{len(dataset)}}")
+
+Load a specific recording:
+
+>>> if len(dataset) > 0:
+...     recording = dataset[0]
+...     raw = recording.load()
+...     print(f"Sampling rate: {{raw.info['sfreq']}} Hz")
+...     print(f"Number of channels: {{len(raw.ch_names)}}")
+
+Filter by additional criteria:
+
+>>> # Get subset with specific task or subject
+>>> filtered_dataset = {dataset_id.upper()}(
+...     cache_dir="./data",
+...     query={{"task": "RestingState"}}  # if applicable
+... )
+
+Notes
+-----
+More details available in the `NEMAR documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`__.
+
+See Also
+--------
+{base_class.__name__} : Base dataset class with full API documentation
+"""
+
+    return docstring
+
+
 def _markdown_table(row_series: pd.Series) -> str:
     """Create a reStructuredText grid table from a pandas Series."""
     if row_series.empty:
@@ -128,7 +210,12 @@ def _markdown_table(row_series: pd.Series) -> str:
     table = tabulate(df, headers="keys", tablefmt="rst", showindex=False)
 
     # Add a caption for the table
-    caption = f"Short overview of dataset {dataset_id} more details in the `Nemar documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`_."
+    # Use an anonymous external link (double underscore) to avoid duplicate
+    # target warnings when this docstring is repeated across many classes.
+    caption = (
+        f"Short overview of dataset {dataset_id} more details in the "
+        f"`NeMAR documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`__."
+    )
     # adding caption below the table
     # Indent the table to fit within the admonition block
     indented_table = "\n".join("    " + line for line in table.split("\n"))

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/downloader.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""File downloading utilities for EEG data from cloud storage.
+
+This module provides functions for downloading EEG data files and BIDS dependencies from
+AWS S3 storage, with support for caching and progress tracking. It handles the communication
+between the EEGDash metadata database and the actual EEG data stored in the cloud.
+"""
+
 import re
 import tempfile
 from pathlib import Path

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/features/serialization.py

@@ -1,6 +1,8 @@
-"""Convenience functions for storing and loading of features datasets.
+"""Convenience functions for storing and loading features datasets.
+
+See Also:
+    https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
 
-see also: https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
 """
 
 from pathlib import Path
@@ -15,7 +17,7 @@ from .datasets import FeaturesConcatDataset, FeaturesDataset
 
 
 def load_features_concat_dataset(path, ids_to_load=None, n_jobs=1):
-    """Load a stored FeaturesConcatDataset of FeaturesDatasets from files.
+    """Load a stored features dataset from files.
 
     Parameters
     ----------
@@ -28,7 +30,9 @@ def load_features_concat_dataset(path, ids_to_load=None, n_jobs=1):
 
     Returns
     -------
-    concat_dataset: FeaturesConcatDataset of FeaturesDatasets
+    concat_dataset: eegdash.features.datasets.FeaturesConcatDataset
+        A concatenation of multiple eegdash.features.datasets.FeaturesDataset
+        instances loaded from the given directory.
 
     """
     # Make sure we always work with a pathlib.Path

eegdash-0.4.0.dev144/eegdash/hbn/__init__.py

@@ -0,0 +1,28 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Healthy Brain Network (HBN) specific utilities and preprocessing.
+
+This module provides specialized functions for working with the Healthy Brain Network
+dataset, including preprocessing pipelines, annotation handling, and windowing utilities
+tailored for HBN EEG data analysis.
+"""
+
+from .preprocessing import hbn_ec_ec_reannotation
+from .windows import (
+    add_aux_anchors,
+    add_extras_columns,
+    annotate_trials_with_target,
+    build_trial_table,
+    keep_only_recordings_with,
+)
+
+__all__ = [
+    "hbn_ec_ec_reannotation",
+    "build_trial_table",
+    "annotate_trials_with_target",
+    "add_aux_anchors",
+    "add_extras_columns",
+    "keep_only_recordings_with",
+]

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/hbn/preprocessing.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Preprocessing utilities specific to the Healthy Brain Network dataset.
+
+This module contains preprocessing classes and functions designed specifically for
+HBN EEG data, including specialized annotation handling for eyes-open/eyes-closed
+paradigms and other HBN-specific preprocessing steps.
+"""
+
 import mne
 import numpy as np
 

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/hbn/windows.py

@@ -1,3 +1,15 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Windowing and trial processing utilities for HBN datasets.
+
+This module provides functions for building trial tables, adding auxiliary anchors,
+annotating trials with targets, and filtering recordings based on various criteria.
+These utilities are specifically designed for working with HBN EEG data structures
+and experimental paradigms.
+"""
+
 import logging
 
 import mne

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/logging.py

@@ -1,3 +1,13 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Logging configuration for EEGDash.
+
+This module sets up centralized logging for the EEGDash package using Rich for enhanced
+console output formatting. It provides a consistent logging interface across all modules.
+"""
+
 import logging
 
 from rich.logging import RichHandler

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/mongodb.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""MongoDB connection and operations management.
+
+This module provides thread-safe MongoDB connection management and high-level database
+operations for the EEGDash metadata database. It includes methods for finding, adding,
+and updating EEG data records with proper connection pooling and error handling.
+"""
+
 import threading
 
 from pymongo import MongoClient

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/paths.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Path utilities and cache directory management.
+
+This module provides functions for resolving consistent cache directories and path
+management throughout the EEGDash package, with integration to MNE-Python's
+configuration system.
+"""
+
 from __future__ import annotations
 
 import os

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash/utils.py

@@ -1,3 +1,13 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""General utility functions for EEGDash.
+
+This module contains miscellaneous utility functions used across the EEGDash package,
+including MongoDB client initialization and configuration helpers.
+"""
+
 from mne.utils import get_config, set_config, use_log_level
 
 

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144/eegdash.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev132
+Version: 0.4.0.dev144
 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
@@ -65,6 +65,7 @@ Requires-Dist: ipython; extra == "docs"
 Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
 Requires-Dist: nbformat; extra == "docs"
+Requires-Dist: graphviz; extra == "docs"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash.egg-info/SOURCES.txt

@@ -3,13 +3,13 @@ MANIFEST.in
 README.md
 pyproject.toml
 docs/Makefile
-docs/source/api.rst
-docs/source/api_core.rst
-docs/source/api_features.rst
 docs/source/conf.py
 docs/source/dataset_summary.rst
 docs/source/index.rst
 docs/source/overview.rst
+docs/source/api/api.rst
+docs/source/api/api_core.rst
+docs/source/api/api_features.rst
 docs/source/install/install.rst
 docs/source/install/install_pip.rst
 docs/source/install/install_source.rst

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/eegdash.egg-info/requires.txt

@@ -40,6 +40,7 @@ ipython
 lightgbm
 plotly
 nbformat
+graphviz
 
 [tests]
 pytest

{eegdash-0.4.0.dev132 → eegdash-0.4.0.dev144}/pyproject.toml

@@ -87,6 +87,7 @@ docs = [
   "lightgbm",
   "plotly",
   "nbformat",
+  "graphviz",
 ]
 
 all = [

eegdash-0.4.0.dev132/docs/Makefile

@@ -1,33 +0,0 @@
-# Minimal makefile for Sphinx documentation
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
-PKG ?= eegdash
-APIDIR := $(SOURCEDIR)/api
-
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: apidoc
-apidoc:
-	# Generate API docs using the top-level package so modules are importable
-	# as eegdash.* instead of an unimportable bare 'dataset.*'
-	@python -m sphinx.ext.apidoc -o "$(APIDIR)/dataset" "../$(PKG)" -f -e -M
-
-# Standard build runs examples
-html: apidoc
-
-# Fast build: do NOT execute examples (sphinx-gallery)
-.PHONY: html-noplot
-html-noplot: apidoc
-	@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
-	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" \
-		$(SPHINXOPTS) -D sphinx_gallery_conf.plot_gallery=0 $(O)
-
-.PHONY: help apidoc
-Makefile: ;          
-
-%: Makefile
-	@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

eegdash-0.4.0.dev132/eegdash/__init__.py

@@ -1,10 +0,0 @@
-from .api import EEGDash, EEGDashDataset
-from .dataset import EEGChallengeDataset
-from .hbn import preprocessing
-from .utils import _init_mongo_client
-
-_init_mongo_client()
-
-__all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
-
-__version__ = "0.4.0.dev132"

eegdash-0.4.0.dev132/eegdash/dataset/__init__.py

@@ -1,4 +0,0 @@
-from .dataset import EEGChallengeDataset
-from .registry import register_openneuro_datasets
-
-__all__ = ["EEGChallengeDataset", "register_openneuro_datasets"]

eegdash-0.4.0.dev132/eegdash/hbn/__init__.py

@@ -1,17 +0,0 @@
-from .preprocessing import hbn_ec_ec_reannotation
-from .windows import (
-    add_aux_anchors,
-    add_extras_columns,
-    annotate_trials_with_target,
-    build_trial_table,
-    keep_only_recordings_with,
-)
-
-__all__ = [
-    "hbn_ec_ec_reannotation",
-    "build_trial_table",
-    "annotate_trials_with_target",
-    "add_aux_anchors",
-    "add_extras_columns",
-    "keep_only_recordings_with",
-]