Updated index page style

docs/_static/custom.css

@@ -14,6 +14,54 @@ body[data-theme="dark"] .sidebar-brand-text {
     color: #58a6ff !important;
 }
 
+/* Make all heading levels match sidebar title blue color */
+.content h1,
+.content h2,
+.content h3,
+.content h4,
+.content h5,
+.content h6,
+article h1,
+article h2,
+article h3,
+article h4,
+article h5,
+article h6 {
+    color: #0969da !important;
+}
+
+body[data-theme="dark"] .content h1,
+body[data-theme="dark"] .content h2,
+body[data-theme="dark"] .content h3,
+body[data-theme="dark"] .content h4,
+body[data-theme="dark"] .content h5,
+body[data-theme="dark"] .content h6,
+body[data-theme="dark"] article h1,
+body[data-theme="dark"] article h2,
+body[data-theme="dark"] article h3,
+body[data-theme="dark"] article h4,
+body[data-theme="dark"] article h5,
+body[data-theme="dark"] article h6 {
+    color: #58a6ff !important;
+}
+
+@media (prefers-color-scheme: dark) {
+    body:not([data-theme="light"]) .content h1,
+    body:not([data-theme="light"]) .content h2,
+    body:not([data-theme="light"]) .content h3,
+    body:not([data-theme="light"]) .content h4,
+    body:not([data-theme="light"]) .content h5,
+    body:not([data-theme="light"]) .content h6,
+    body:not([data-theme="light"]) article h1,
+    body:not([data-theme="light"]) article h2,
+    body:not([data-theme="light"]) article h3,
+    body:not([data-theme="light"]) article h4,
+    body:not([data-theme="light"]) article h5,
+    body:not([data-theme="light"]) article h6 {
+        color: #58a6ff !important;
+    }
+}
+
 /* Quick Links sidebar styling - darker gray box with proper padding */
 .sidebar-quicklinks {
     margin: 1rem 0.75rem 1rem 0.75rem;
@@ -23,6 +71,35 @@ body[data-theme="dark"] .sidebar-brand-text {
     border: 1px solid #d0d0d0;
 }
 
+/* Style RST sidebar directive boxes to match left sidebar styling */
+.sidebar,
+aside.sidebar {
+    background-color: #e8e8e8 !important;
+    border: 1px solid #d0d0d0 !important;
+    border-radius: 0.25rem !important;
+    padding: 0.75rem 1rem !important;
+}
+
+body[data-theme="dark"] .sidebar,
+body[data-theme="dark"] aside.sidebar {
+    background-color: #0d0d0d !important;
+    border-color: #1a1a1a !important;
+}
+
+@media (prefers-color-scheme: dark) {
+    body:not([data-theme="light"]) .sidebar,
+    body:not([data-theme="light"]) aside.sidebar {
+        background-color: #0d0d0d !important;
+        border-color: #1a1a1a !important;
+    }
+}
+
+.sidebar p.sidebar-title,
+aside.sidebar p.sidebar-title {
+    font-weight: 600 !important;
+    margin-bottom: 0.5rem !important;
+}
+
 /* Dark mode styling for quick links - much darker background */
 body[data-theme="dark"] .sidebar-quicklinks {
     background-color: #0d0d0d;

docs/index.rst

@@ -1,16 +1,65 @@
-HED Python tools
-================
+Python HEDTools
+===============
 
-Welcome to the HED Python tools documentation. This package provides comprehensive tools for working with Hierarchical Event Descriptors (HED) in Python.
+
+.. sidebar:: Quick links
+
+   * `HED homepage <https://www.hedtags.org/>`_ 
+
+   * `HED vocabularies <https://www.hedtags.org/hed-schema-browser>`_
+
+   * `HED online tools <https://hedtools.org/hed/>`_
+
+   * `HED browser tools <https://www.hedtags.org/hed-javascript>`_
+
+   * `HED organization  <https://github.com/hed-standard/>`_  
+
+   * `HED specification <https://www.hedtags.org/hed-specification>`_ 
+
+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.
+
+What is HED?
+------------
+
+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:
+
+* `BIDS <https://bids.neuroimaging.io/>`_ (Brain Imaging Data Structure)
+* `NWB <https://www.nwb.org/>`_ (Neurodata Without Borders)
+
+Key features
+------------
+
+* **Validation**: Verify HED annotations against official schemas
+* **Analysis**: Search, filter, and summarize HED-annotated data
+* **BIDS integration**: Full support for BIDS dataset validation and processing
+* **NWB support**: Read and write HED annotations in NWB files using `ndx-hed <https://www.hedtags.org/ndx-hed>`_
+* **Multiple formats**: Work with JSON sidecars, TSV files, Excel spreadsheets
+
+Getting started
+---------------
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
    Introduction <introduction>
+
+Programming with HEDTools
+-------------------------
+
+.. toctree::
+   :maxdepth: 2
+
    User guide <user_guide>
+
+API documentation
+-----------------
+
+.. toctree::
+   :maxdepth: 2
+
    API reference <api/index>
 
+
 Indices and tables
 ==================
 

examples/extract_json_template.ipynb

@@ -11,7 +11,7 @@
     "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",
     "Ideally, this sidecar will contain all the annotations needed for users to understand and analyze the data.\n",
     "\n",
-    "(See the [**BIDS annotation quickstart**](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html) for additional information on this strategy.)\n",
+    "(See the [**BIDS annotation quickstart**](https://www.hedtags.org/hed-resources) for additional information on this strategy.)\n",
     "\n",
     "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",
     "\n",
@@ -27,9 +27,9 @@
     "\n",
     "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",
     "\n",
-    "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",
+    "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",
     "\n",
-    "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."
+    "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."
    ]
   },
   {

hed/errors/error_reporter.py

@@ -628,7 +628,7 @@ def create_doc_link(error_code):
     """
     if error_code in known_error_codes["hed_validation_errors"] or error_code in known_error_codes["schema_validation_errors"]:
         modified_error_code = error_code.replace("_", "-").lower()
-        return f"https://hed-specification.readthedocs.io/en/latest/Appendix_B.html#{modified_error_code}"
+        return f"https://www.hedtags.org/hed-specification/Appendix_B.html#{modified_error_code}"
     return None
 
 

pyproject.toml

@@ -63,7 +63,7 @@ dependencies = [
 "Repository" = "https://github.com/hed-standard/hed-python/"
 "Bug Tracker" = "https://github.com/hed-standard/hed-python/issues"
 "Changelog" = "https://github.com/hed-standard/hed-python/blob/main/CHANGELOG.md"
-"HED Resources" = "https://www.hed-resources.org"
+"HED Resources" = "https://www.hedtags.org/hed-resources/"
 
 [project.optional-dependencies]
 dev = [

tests/data/bids_tests/eeg_ds003645s_hed_demo/README.md

@@ -131,5 +131,5 @@ are inserted into the template, rather than concatenated:
 "(Experiment-participant, ID/sub-001),Age/3,Male,Healthy,Rested,Novide-level"
 ```
 
-See [Assembly and curly braces](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html#assembly-and-curly-braces)
-in the [HED annotation quickstart](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html#) for more information.
+See [Assembly and curly braces](https:/www.hedtags.org/hed-resources/HedAnnotationQuickstart.html#assembly-and-curly-braces)
+in the [HED annotation quickstart](https:/www.hedtags.org/hed-resources/HedAnnotationQuickstart.html) for more information.