eegdash 0.0.2__tar.gz → 0.5.0.dev170116588__tar.gz

eegdash-0.5.0.dev170116588/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2024-2025, EEGDash contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

eegdash-0.5.0.dev170116588/MANIFEST.in

@@ -0,0 +1,7 @@
+include README.md
+include LICENSE
+
+include eegdash/dataset/dataset_summary.csv
+
+recursive-include docs *.ipynb *.rst conf.py Makefile
+recursive-exclude docs *checkpoint.ipynb

eegdash-0.5.0.dev170116588/PKG-INFO

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+Metadata-Version: 2.4
+Name: eegdash
+Version: 0.5.0.dev170116588
+Summary: EEG data for machine learning
+Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@ucsd.edu>, Aviv Dotan <avivdot@bgu.post.ac.il>, Oren Shriki <shrikio@bgu.ac.il>, Bruno Aristimunha <b.aristimunha@gmail.com>
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://github.com/sccn/EEG-Dash-Data
+Project-URL: Issues, https://github.com/sccn/EEG-Dash-Data/issues
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python
+Classifier: Topic :: Software Development
+Classifier: Topic :: Scientific/Engineering
+Classifier: Development Status :: 3 - Alpha
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: braindecode[hub]>=1.3.2
+Requires-Dist: mne_bids>=0.18.0
+Requires-Dist: numba
+Requires-Dist: requests>=2.25.0
+Requires-Dist: s3fs
+Requires-Dist: tqdm
+Requires-Dist: pymatreader
+Requires-Dist: eeglabio
+Requires-Dist: tabulate
+Requires-Dist: rich
+Requires-Dist: pyarrow
+Requires-Dist: pandas>=2.0
+Requires-Dist: pydantic
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-sugar; extra == "tests"
+Requires-Dist: codecov; extra == "tests"
+Requires-Dist: pytest_cases; extra == "tests"
+Requires-Dist: pytest-benchmark; extra == "tests"
+Requires-Dist: pytest-xdist; extra == "tests"
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Requires-Dist: lightning>=2.0; extra == "dev"
+Requires-Dist: torchmetrics>=0.7; extra == "dev"
+Requires-Dist: scikit-learn; extra == "dev"
+Requires-Dist: tensorboard; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_design; extra == "docs"
+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"
+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"
+Requires-Dist: neato; extra == "docs"
+Requires-Dist: moabb; extra == "docs"
+Provides-Extra: digestion
+Requires-Dist: pybids; extra == "digestion"
+Requires-Dist: gql[requests]; extra == "digestion"
+Requires-Dist: requests_toolbelt; extra == "digestion"
+Requires-Dist: beautifulsoup4; extra == "digestion"
+Requires-Dist: python-dotenv; extra == "digestion"
+Requires-Dist: selenium; extra == "digestion"
+Requires-Dist: httpx; extra == "digestion"
+Requires-Dist: tenacity; extra == "digestion"
+Requires-Dist: hishel; extra == "digestion"
+Requires-Dist: pydantic>=2; extra == "digestion"
+Requires-Dist: PyGithub>=2; extra == "digestion"
+Provides-Extra: all
+Requires-Dist: eegdash[docs]; extra == "all"
+Requires-Dist: eegdash[dev]; extra == "all"
+Requires-Dist: eegdash[tests]; extra == "all"
+Requires-Dist: eegdash[digestion]; extra == "all"
+Dynamic: license-file
+
+# EEG-Dash
+
+[![PyPI version](https://img.shields.io/pypi/v/eegdash)](https://pypi.org/project/eegdash/)
+[![Docs](https://img.shields.io/badge/docs-stable-brightgreen.svg)](https://sccn.github.io/eegdash)
+
+[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD--3--Clause-blue.svg)](LICENSE)
+[![Python versions](https://img.shields.io/pypi/pyversions/eegdash.svg)](https://pypi.org/project/eegdash/)
+[![Downloads](https://pepy.tech/badge/eegdash)](https://pepy.tech/project/eegdash)
+[![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fraw.githubusercontent.com%2Feegdash%2FEEGDash%2Fmain%2Fcoverage.json&query=%24.totals.percent_covered_display&suffix=%25&label=coverage)](https://github.com/eegdash/EEGDash/blob/main/coverage.json)
+
+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. 
+
+## Data source
+
+The data in EEG-DaSh originates from a collaboration involving 25 laboratories, encompassing 27,053 participants. This extensive collection includes MEEG data, which is a combination of EEG and MEG signals. The data is sourced from various studies conducted by these labs, involving both healthy subjects and clinical populations with conditions such as ADHD, depression, schizophrenia, dementia, autism, and psychosis. Additionally, data spans different mental states like sleep, meditation, and cognitive tasks. In addition, EEG-DaSh will incorporate a subset of the data converted from NEMAR, which includes 330 MEEG BIDS-formatted datasets, further expanding the archive with well-curated, standardized neuroelectromagnetic data.
+
+## Data format
+
+EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine learning (ML) and deep learning (DL) applications. PyTorch Datasets are the best format for EEGDash queries because they provide an efficient, scalable, and flexible structure for machine learning (ML) and deep learning (DL) applications. They allow seamless integration with PyTorch’s DataLoader, enabling efficient batching, shuffling, and parallel data loading, which is essential for training deep learning models on large EEG datasets.
+
+## Data preprocessing
+
+EEGDash datasets are processed using the popular [braindecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are braindecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on braindecode datasets is also possible on EEGDash datasets. Refer to [braindecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
+
+## EEG-Dash usage
+
+### Install
+Use your preferred Python environment manager with Python > 3.10 to install the package.
+* To install the eegdash package, use the following command: `pip install eegdash`
+* To verify the installation, start a Python session and type: `from eegdash import EEGDash`
+
+Please check our tutorial webpages to explore what you can do with [eegdash](https://eegdash.org/)! 
+
+## Education -- Coming soon...
+
+We organize workshops and educational events to foster cross-cultural education and student training, offering both online and in-person opportunities in collaboration with US and Israeli partners. Events for 2025 will be announced via the EEGLABNEWS mailing list. Be sure to [subscribe](https://sccn.ucsd.edu/mailman/listinfo/eeglabnews).
+
+## About EEG-DaSh
+
+EEG-DaSh is a collaborative initiative between the United States and Israel, supported by the National Science Foundation (NSF). The partnership brings together experts from the Swartz Center for Computational Neuroscience (SCCN) at the University of California San Diego (UCSD) and Ben-Gurion University (BGU) in Israel. 
+
+![Screenshot 2024-10-03 at 09 14 06](https://github.com/user-attachments/assets/327639d3-c3b4-46b1-9335-37803209b0d3)
+
+
+

eegdash-0.5.0.dev170116588/README.md

@@ -0,0 +1,45 @@
+# EEG-Dash
+
+[![PyPI version](https://img.shields.io/pypi/v/eegdash)](https://pypi.org/project/eegdash/)
+[![Docs](https://img.shields.io/badge/docs-stable-brightgreen.svg)](https://sccn.github.io/eegdash)
+
+[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD--3--Clause-blue.svg)](LICENSE)
+[![Python versions](https://img.shields.io/pypi/pyversions/eegdash.svg)](https://pypi.org/project/eegdash/)
+[![Downloads](https://pepy.tech/badge/eegdash)](https://pepy.tech/project/eegdash)
+[![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fraw.githubusercontent.com%2Feegdash%2FEEGDash%2Fmain%2Fcoverage.json&query=%24.totals.percent_covered_display&suffix=%25&label=coverage)](https://github.com/eegdash/EEGDash/blob/main/coverage.json)
+
+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. 
+
+## Data source
+
+The data in EEG-DaSh originates from a collaboration involving 25 laboratories, encompassing 27,053 participants. This extensive collection includes MEEG data, which is a combination of EEG and MEG signals. The data is sourced from various studies conducted by these labs, involving both healthy subjects and clinical populations with conditions such as ADHD, depression, schizophrenia, dementia, autism, and psychosis. Additionally, data spans different mental states like sleep, meditation, and cognitive tasks. In addition, EEG-DaSh will incorporate a subset of the data converted from NEMAR, which includes 330 MEEG BIDS-formatted datasets, further expanding the archive with well-curated, standardized neuroelectromagnetic data.
+
+## Data format
+
+EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine learning (ML) and deep learning (DL) applications. PyTorch Datasets are the best format for EEGDash queries because they provide an efficient, scalable, and flexible structure for machine learning (ML) and deep learning (DL) applications. They allow seamless integration with PyTorch’s DataLoader, enabling efficient batching, shuffling, and parallel data loading, which is essential for training deep learning models on large EEG datasets.
+
+## Data preprocessing
+
+EEGDash datasets are processed using the popular [braindecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are braindecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on braindecode datasets is also possible on EEGDash datasets. Refer to [braindecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
+
+## EEG-Dash usage
+
+### Install
+Use your preferred Python environment manager with Python > 3.10 to install the package.
+* To install the eegdash package, use the following command: `pip install eegdash`
+* To verify the installation, start a Python session and type: `from eegdash import EEGDash`
+
+Please check our tutorial webpages to explore what you can do with [eegdash](https://eegdash.org/)! 
+
+## Education -- Coming soon...
+
+We organize workshops and educational events to foster cross-cultural education and student training, offering both online and in-person opportunities in collaboration with US and Israeli partners. Events for 2025 will be announced via the EEGLABNEWS mailing list. Be sure to [subscribe](https://sccn.ucsd.edu/mailman/listinfo/eeglabnews).
+
+## About EEG-DaSh
+
+EEG-DaSh is a collaborative initiative between the United States and Israel, supported by the National Science Foundation (NSF). The partnership brings together experts from the Swartz Center for Computational Neuroscience (SCCN) at the University of California San Diego (UCSD) and Ben-Gurion University (BGU) in Israel. 
+
+![Screenshot 2024-10-03 at 09 14 06](https://github.com/user-attachments/assets/327639d3-c3b4-46b1-9335-37803209b0d3)
+
+
+

eegdash-0.5.0.dev170116588/docs/Makefile

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+# 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) $(O)
+
+.PHONY: apidoc
+apidoc:
+	# Generate full API docs, then prune duplicates covered by autosummary
+	@rm -f "$(APIDIR)"/dataset/eegdash.features*
+	@SPHINX_APIDOC_OPTIONS=members,undoc-members,show-inheritance,noindex \
+		python -m sphinx.ext.apidoc -f -e -T -o "$(APIDIR)/dataset" "../$(PKG)" "../$(PKG)/features"
+
+
+# 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 --target $(BUILDDIR)
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" \
+		$(SPHINXOPTS) -D sphinx_gallery_conf.plot_gallery=0 $(O)
+
+# Very fast build: limit datasets to 5
+.PHONY: html-fast
+html-fast: apidoc
+	@EEGDASH_DOC_LIMIT=5 python prepare_summary_tables.py --target $(BUILDDIR)
+	@EEGDASH_DOC_LIMIT=5 $(SPHINXBUILD) -M html "$(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 --target $(BUILDDIR)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

eegdash-0.5.0.dev170116588/docs/source/_templates/autosummary/module.rst

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+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :member-order: bysource
+   :no-index:
+
+   {% block attributes %}
+   {%- if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block functions %}
+   {%- if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block classes %}
+   {%- if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block exceptions %}
+   {%- if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+{%- block modules %}
+{%- if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{%- endblock %}
+
+{% if sg_api_usage %}
+.. _sg_api_{{ fullname }}:
+
+API Usage
+---------
+
+.. raw:: html
+
+    <div class="sg-api-usage">
+
+{{ sg_api_usage }}
+
+.. raw:: html
+
+    </div>
+{% endif %}

eegdash-0.5.0.dev170116588/docs/source/api/api.rst

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+: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.
+
+.. raw:: html
+
+   <h2 class="hf-section-title">What's inside EEGDash</h2>
+   <p class="hf-section-subtitle">Everything you need to discover, prepare, and benchmark EEG and MEG data.</p>
+
+.. grid:: 1 1 2 2
+   :gutter: 4
+   :class-container: hf-feature-grid
+
+   .. grid-item-card:: Dataset discovery
+      :link: ../dataset_summary
+      :link-type: doc
+      :text-align: left
+      :class-card: feature-card hf-reveal hf-delay-1
+
+      :octicon:`search;1.5em;sd-text-primary`
+
+      Search metadata, modalities, tasks, and cohorts with unified filters.
+
+   .. grid-item-card:: Reproducible preprocessing
+      :link: ../user_guide
+      :link-type: doc
+      :text-align: left
+      :class-card: feature-card hf-reveal hf-delay-2
+
+      :octicon:`plug;1.5em;sd-text-primary`
+
+      One-command pipelines with EEGPrep, MNE, and BIDS alignment.
+
+   .. grid-item-card:: Benchmarks and features
+      :link: ../generated/auto_examples/index
+      :link-type: doc
+      :text-align: left
+      :class-card: feature-card hf-reveal hf-delay-3
+
+      :octicon:`rocket;1.5em;sd-text-primary`
+
+      Export model-ready features and compare baselines across datasets.
+
+   .. grid-item-card:: BIDS-first interoperability
+      :link: ../user_guide
+      :link-type: doc
+      :text-align: left
+      :class-card: feature-card hf-reveal hf-delay-3
+
+      .. image:: ../_static/bids_logo_black.svg
+         :alt: BIDS
+         :class: hf-feature-logo
+
+      Keep metadata consistent and portable across teams and tools.
+
+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
+
+
+********************
+REST API Endpoints
+********************
+
+The EEGDash metadata server exposes a FastAPI REST interface for discovery and
+querying. Base URL: `https://data.eegdash.org`_. Below is a concise map of the main
+entrypoints and their purpose.
+
+.. _https://data.eegdash.org: https://data.eegdash.org
+
+
+
+Meta Endpoints
+==============
+
+- ``GET /``
+  Returns API name, version, and available databases.
+- ``GET /health``
+  Returns API health and MongoDB connection status.
+- ``GET /metrics``
+  Prometheus metrics (if enabled).
+
+Public Data Endpoints
+=====================
+
+- ``GET /api/{database}/records``
+  Query records (files) with filter and pagination.
+- ``GET /api/{database}/count``
+  Count records matching a filter.
+- ``GET /api/{database}/datasets/names``
+  List unique dataset names from records.
+- ``GET /api/{database}/metadata/{dataset}``
+  Get metadata for a single dataset (from records).
+- ``GET /api/{database}/datasets/summary``
+  Get summary statistics and metadata for all datasets (with pagination, filtering).
+  Query params: ``limit`` (1-1000), ``skip``, ``modality`` (eeg/meg/ieeg), ``source`` (openneuro/nemar/zenodo/etc.).
+  Response includes aggregate totals for datasets, subjects, files, and size.
+- ``GET /api/{database}/datasets/summary/{dataset_id}``
+  Get detailed summary for a specific dataset.
+  ``dataset_id`` may be the dataset ID or dataset name.
+- ``GET /api/{database}/datasets/{dataset_id}``
+  Get a specific dataset document by ID.
+- ``GET /api/{database}/datasets``
+  List dataset documents (with filtering and pagination).
+- ``GET /api/{database}/datasets/stats/records``
+  Get aggregated ``nchans`` and ``sampling_frequency`` counts for all datasets.
+  Used to generate summary tables efficiently.
+
+Admin Endpoints (require Bearer token)
+======================================
+
+- ``POST /admin/{database}/records``
+  Insert a single record (file document).
+- ``POST /admin/{database}/records/bulk``
+  Insert multiple records (max 1000 per request).
+- ``POST /admin/{database}/datasets``
+  Insert or update a single dataset document (upsert by ``dataset_id``).
+- ``POST /admin/{database}/datasets/bulk``
+  Insert or update multiple dataset documents (max 500 per request).
+- ``PATCH /admin/{database}/records``
+  Update records matching a filter (only ``$set`` allowed).
+- ``GET /admin/security/blocked``
+  List blocked IPs and offense counts.
+- ``POST /admin/security/unblock``
+  Unblock a specific IP.
+    
+
+******************
+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
+   ../developer_notes