eegdash 0.4.0.dev132__tar.gz → 0.4.0.dev150__tar.gz

{eegdash-0.4.0.dev132/eegdash.egg-info → eegdash-0.4.0.dev150}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev132
+Version: 0.4.0.dev150
 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
@@ -35,7 +35,6 @@ Requires-Dist: python-dotenv
 Requires-Dist: s3fs
 Requires-Dist: scipy
 Requires-Dist: tqdm
-Requires-Dist: xarray
 Requires-Dist: h5io>=0.2.4
 Requires-Dist: pymatreader
 Requires-Dist: eeglabio
@@ -58,6 +57,7 @@ Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: pydata-sphinx-theme; extra == "docs"
 Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
 Requires-Dist: sphinx-sitemap; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: memory_profiler; extra == "docs"
@@ -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.dev150/docs/Makefile

@@ -0,0 +1,51 @@
+# 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) $(O)
+
+.PHONY: apidoc
+apidoc:
+	# Generate full API docs, then prune duplicates covered by autosummary
+	@SPHINX_APIDOC_OPTIONS=members,undoc-members,show-inheritance,noindex \
+		python -m sphinx.ext.apidoc -f -e -M -o "$(APIDIR)/dataset" "../$(PKG)"
+	# Remove top-level package page and modules covered elsewhere
+
+
+# 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 $(O)
+
+# Custom clean target to remove generated API docs and build files
+.PHONY: clean
+clean:
+	@echo "Removing generated API documentation..."
+	@rm -rf "$(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/ $(BUILDDIR)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

eegdash-0.4.0.dev150/docs/source/api/api.rst

@@ -0,0 +1,122 @@
+:html_theme.sidebar_primary.remove: true
+:html_theme.sidebar_secondary.remove: true
+
+.. _api:
+
+#############
+API Reference
+#############
+
+The EEGDash API reference curates everything you need to integrate, extend,
+and automate EEGDash—from core dataset helpers to feature extraction and rich
+dataset metadata. The focus is interoperability, extensibility, and ease of use.
+
+The API is organized into three main components:
+
+
+.. grid:: 1
+   :gutter: 4
+   :class-container: sd-gap-4 sd-mb-4
+
+   .. grid-item-card::
+      :link: api_core
+      :link-type: doc
+      :text-align: center
+      :class-card: api-grid-card
+      :class-header: api-grid-card__header
+      :class-body: api-grid-card__body
+      :class-footer: api-grid-card__footer
+
+      .. raw:: html
+
+         <span class="fa-solid fa-microchip api-grid-card__icon" aria-hidden="true"></span>
+
+      .. rst-class:: api-grid-card__title
+
+      **Core API**
+      ^^^
+
+      Build, query, and manage EEGDash datasets and utilities.
+
+      +++
+
+      .. button-ref:: api_core
+         :color: primary
+         :class: api-grid-card__button
+         :click-parent:
+
+         → Explore Core API
+
+   .. grid-item-card::
+      :link: api_features
+      :link-type: doc
+      :text-align: center
+      :class-card: api-grid-card
+      :class-header: api-grid-card__header
+      :class-body: api-grid-card__body
+      :class-footer: api-grid-card__footer
+
+      .. raw:: html
+
+         <span class="fa-solid fa-wave-square api-grid-card__icon" aria-hidden="true"></span>
+
+      .. rst-class:: api-grid-card__title
+
+      **Feature engineering**
+      ^^^
+
+      Extract statistical, spectral, and machine-learning-ready features.
+
+      +++
+
+      .. button-ref:: api_features
+         :color: primary
+         :class: api-grid-card__button
+         :click-parent:
+
+         → Explore Feature Engineering
+
+   .. grid-item-card::
+      :link: dataset/api_dataset
+      :link-type: doc
+      :text-align: center
+      :class-card: api-grid-card
+      :class-header: api-grid-card__header
+      :class-body: api-grid-card__body
+      :class-footer: api-grid-card__footer
+
+      .. raw:: html
+
+         <span class="fa-solid fa-database api-grid-card__icon" aria-hidden="true"></span>
+
+      .. rst-class:: api-grid-card__title
+
+      **Dataset catalog**
+      ^^^
+
+      Browse dynamically generated dataset classes with rich metadata.
+
+      +++
+
+      .. button-ref:: dataset/api_dataset
+         :color: primary
+         :class: api-grid-card__button
+         :click-parent:
+
+         → Explore the Dataset API
+    
+
+******************
+Related Guides
+******************
+
+- :doc:`Tutorial gallery <../generated/auto_examples/index>`
+- :doc:`Dataset summary <../dataset_summary>`
+- :doc:`Installation guide <../install/install>`
+
+.. toctree::
+   :hidden:
+
+   api_core
+   api_features
+   dataset/api_dataset

eegdash-0.4.0.dev150/docs/source/api/api_core.rst

@@ -0,0 +1,79 @@
+:html_theme.sidebar_secondary.remove: true
+
+Core API
+========
+
+EEGDash provides a comprehensive interface for accessing and processing EEG data through 
+a three-tier architecture that combines metadata management, cloud storage, and standardized 
+data organization.
+
+Architecture Overview
+---------------------
+
+The EEGDash core API is built around three interconnected components:
+
+.. code-block:: text
+
+      +-----------------+
+      |     MongoDB     |
+      |    (Metadata)   |
+      +-----------------+
+            |
+            |
+      +-----------v-----------+      +-----------------+
+      |       eegdash         |<---->|   S3 Filesystem |
+      |     Interface         |      |    (Raw Data)   |
+      +-----------------------+      +-----------------+
+            |
+            |
+      +-----------v-----------+
+      |      BIDS Parser      |
+      +-----------------------+
+
+**MongoDB Metadata Layer**
+    Centralized NoSQL database storing EEG dataset metadata including subject information,
+    session details, task parameters, and experimental conditions. Enables fast querying
+    and filtering of large-scale datasets.
+
+**File Cloud Storage**
+    Scalable object storage for raw EEG data files. Provides reliable access to large
+    datasets with on-demand downloading capabilities, reducing local storage requirements.
+    At the moment, AWS S3 is the only supported storage backend.
+
+**BIDS Standardization**
+    Brain Imaging Data Structure (BIDS) parser ensuring consistent data organization
+    and interpretation across different datasets and experiments.
+    Use to perform the digest of BIDS datasets and extract relevant metadata for
+    the mongodb.
+
+Core Modules
+------------
+
+The API is organized into focused modules that handle specific aspects of EEG data processing:
+
+* :mod:`~eegdash.api` - Main interface for data access and manipulation
+* :mod:`~eegdash.const` - Constants and enumerations used throughout the package
+* :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
+
+API Reference
+-------------
+
+.. currentmodule:: eegdash
+
+.. autosummary::
+   :toctree: generated/api-core
+   :recursive:
+
+   api
+   bids_eeg_metadata
+   const
+   data_utils
+   logging
+   hbn
+   mongodb
+   paths
+   utils