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Updated index page style
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‎docs/_static/custom.css‎

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@@ -14,6 +14,54 @@ body[data-theme="dark"] .sidebar-brand-text {
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color: #58a6ff !important;
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}
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/* Make all heading levels match sidebar title blue color */
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.content h1,
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.content h2,
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.content h3,
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.content h4,
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.content h5,
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.content h6,
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article h1,
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article h2,
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article h3,
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article h4,
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article h5,
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article h6 {
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color: #0969da !important;
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}
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body[data-theme="dark"] .content h1,
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body[data-theme="dark"] .content h2,
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body[data-theme="dark"] .content h3,
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body[data-theme="dark"] .content h4,
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body[data-theme="dark"] .content h5,
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body[data-theme="dark"] .content h6,
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body[data-theme="dark"] article h1,
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body[data-theme="dark"] article h2,
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body[data-theme="dark"] article h3,
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body[data-theme="dark"] article h4,
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body[data-theme="dark"] article h5,
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body[data-theme="dark"] article h6 {
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color: #58a6ff !important;
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}
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@media (prefers-color-scheme: dark) {
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body:not([data-theme="light"]) .content h1,
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body:not([data-theme="light"]) .content h2,
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body:not([data-theme="light"]) .content h3,
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body:not([data-theme="light"]) .content h4,
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body:not([data-theme="light"]) .content h5,
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body:not([data-theme="light"]) .content h6,
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body:not([data-theme="light"]) article h1,
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body:not([data-theme="light"]) article h2,
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body:not([data-theme="light"]) article h3,
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body:not([data-theme="light"]) article h4,
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body:not([data-theme="light"]) article h5,
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body:not([data-theme="light"]) article h6 {
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color: #58a6ff !important;
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}
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}
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/* Quick Links sidebar styling - darker gray box with proper padding */
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.sidebar-quicklinks {
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margin: 1rem 0.75rem 1rem 0.75rem;
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border: 1px solid #d0d0d0;
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}
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/* Style RST sidebar directive boxes to match left sidebar styling */
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.sidebar,
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aside.sidebar {
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background-color: #e8e8e8 !important;
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border: 1px solid #d0d0d0 !important;
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border-radius: 0.25rem !important;
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padding: 0.75rem 1rem !important;
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}
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body[data-theme="dark"] .sidebar,
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body[data-theme="dark"] aside.sidebar {
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background-color: #0d0d0d !important;
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border-color: #1a1a1a !important;
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}
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@media (prefers-color-scheme: dark) {
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body:not([data-theme="light"]) .sidebar,
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body:not([data-theme="light"]) aside.sidebar {
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background-color: #0d0d0d !important;
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border-color: #1a1a1a !important;
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}
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}
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.sidebar p.sidebar-title,
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aside.sidebar p.sidebar-title {
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font-weight: 600 !important;
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margin-bottom: 0.5rem !important;
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}
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/* Dark mode styling for quick links - much darker background */
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body[data-theme="dark"] .sidebar-quicklinks {
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background-color: #0d0d0d;

‎docs/index.rst‎

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HED Python tools
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================
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Python HEDTools
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===============
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Welcome to the HED Python tools documentation. This package provides comprehensive tools for working with Hierarchical Event Descriptors (HED) in Python.
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.. sidebar:: Quick links
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* `HED homepage <https://www.hedtags.org/>`_
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* `HED vocabularies <https://www.hedtags.org/hed-schema-browser>`_
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* `HED online tools <https://hedtools.org/hed/>`_
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* `HED browser tools <https://www.hedtags.org/hed-javascript>`_
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* `HED organization <https://github.com/hed-standard/>`_
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* `HED specification <https://www.hedtags.org/hed-specification>`_
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Welcome to the Python HEDTools documentation! This package provides comprehensive tools for working with **Hierarchical Event Descriptors (HED)** - a standardized framework for annotating events and experimental metadata in neuroscience and beyond.
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What is HED?
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------------
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HED is a standardized vocabulary and annotation framework designed to systematically describe events experimental data, particularly neuroimaging and behavioral data. It's integrated into major neuroimaging standards:
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* `BIDS <https://bids.neuroimaging.io/>`_ (Brain Imaging Data Structure)
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* `NWB <https://www.nwb.org/>`_ (Neurodata Without Borders)
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Key features
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------------
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* **Validation**: Verify HED annotations against official schemas
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* **Analysis**: Search, filter, and summarize HED-annotated data
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* **BIDS integration**: Full support for BIDS dataset validation and processing
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* **NWB support**: Read and write HED annotations in NWB files using `ndx-hed <https://www.hedtags.org/ndx-hed>`_
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* **Multiple formats**: Work with JSON sidecars, TSV files, Excel spreadsheets
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Getting started
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---------------
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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Introduction <introduction>
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Programming with HEDTools
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-------------------------
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.. toctree::
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:maxdepth: 2
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User guide <user_guide>
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API documentation
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-----------------
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.. toctree::
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:maxdepth: 2
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API reference <api/index>
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Indices and tables
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==================
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‎examples/extract_json_template.ipynb‎

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"General strategy for machine-actionable annotation using HED in BIDS is to create a single `events.json` sidecar file in the BIDS dataset root directory.\n",
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"Ideally, this sidecar will contain all the annotations needed for users to understand and analyze the data.\n",
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"\n",
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"(See the [**BIDS annotation quickstart**](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html) for additional information on this strategy.)\n",
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"(See the [**BIDS annotation quickstart**](https://www.hedtags.org/hed-resources) for additional information on this strategy.)\n",
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"\n",
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"This notebook shows how to create a JSON sidecar template from the information in all the event files in a BIDS dataset. To use this notebook, substitute the specifics of your BIDS dataset for the following variables:\n",
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"\n",
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"\n",
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"Typical `skip_columns` include the `onset`, `duration`, and `sample` columns, which have well-defined meanings according to BIDS. The `value_columns` just require a single annotation, applicable to each value in the column.\n",
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"\n",
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"For additional information see the tutorial [**Create a JSON template**](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html#create-a-json-template) which illustrates the creation of a template from a single event file using the online tools.\n",
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"For additional information see the tutorial [**Create a JSON template**](https://hedtags.org/hed-resources/BidsAnnotationQuickstart.html#create-a-json-template) which illustrates the creation of a template from a single event file using the online tools.\n",
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"\n",
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"Additional information about this notebook can be found in [**Extract JSON template**](https://www.hed-resources.org/en/latest/HedPythonTools.html#extract-json-template) in the Python HEDTools user guide."
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"See [**Sidecar template extraction**](https://www.hedtags.org/hed-python/user_guide.html#sidecar-template-extraction) in the HEDTools documentation for an example of how to directly extract a template using command line tools."
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]
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},
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{

‎hed/errors/error_reporter.py‎

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"""
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if error_code in known_error_codes["hed_validation_errors"] or error_code in known_error_codes["schema_validation_errors"]:
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modified_error_code = error_code.replace("_", "-").lower()
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return f"https://hed-specification.readthedocs.io/en/latest/Appendix_B.html#{modified_error_code}"
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return f"https://www.hedtags.org/hed-specification/Appendix_B.html#{modified_error_code}"
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return None
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‎pyproject.toml‎

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"Repository" = "https://github.com/hed-standard/hed-python/"
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"Bug Tracker" = "https://github.com/hed-standard/hed-python/issues"
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"Changelog" = "https://github.com/hed-standard/hed-python/blob/main/CHANGELOG.md"
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"HED Resources" = "https://www.hed-resources.org"
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"HED Resources" = "https://www.hedtags.org/hed-resources/"
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[project.optional-dependencies]
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dev = [

‎tests/data/bids_tests/eeg_ds003645s_hed_demo/README.md‎

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"(Experiment-participant, ID/sub-001),Age/3,Male,Healthy,Rested,Novide-level"
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```
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See [Assembly and curly braces](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html#assembly-and-curly-braces)
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in the [HED annotation quickstart](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html#) for more information.
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See [Assembly and curly braces](https:/www.hedtags.org/hed-resources/HedAnnotationQuickstart.html#assembly-and-curly-braces)
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in the [HED annotation quickstart](https:/www.hedtags.org/hed-resources/HedAnnotationQuickstart.html) for more information.

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