Merge remote-tracking branch 'origin/main' into ndrh-2026-videos

# Conflicts:
#	content/events/hck26-2026-janelia-ndrh.md

Author: bendichter

.github/workflows/link-check.yml

@@ -22,5 +22,21 @@ jobs:
         id: lychee
         uses: lycheeverse/lychee-action@v2
         with:
-          # NOTE: Lychee (and sphinx) encounter issues with SSL certificates for INCF URLs, so use --insecure
-          args: --verbose --no-progress './content/**/*.md' './content/**/*.html' './content/**/*.rst' --insecure
+          # --base resolves root-relative paths (e.g. /events/) against the live site
+          # --accept includes 403/429 since many destinations (mathworks, hilton, doi.org,
+          #   slack invites) reject lychee's user-agent rather than the link being broken
+          # --insecure: lychee (and sphinx) hit SSL cert issues on INCF URLs
+          args: >-
+            --verbose
+            --no-progress
+            --base 'https://neurodatawithoutborders.github.io/'
+            --accept '200..=299,403,429'
+            --max-retries 2
+            --insecure
+            './content/**/*.md'
+            './content/**/*.html'
+            './content/**/*.rst'
+          # Don't block PRs on the report; the job summary still surfaces broken links
+          # so they can be triaged separately. Pre-existing dead links in archived
+          # event pages otherwise fail every PR.
+          fail: false

assets/css/style.css

@@ -1083,6 +1083,76 @@ ol.custom-ordered-list li::before {
   padding: 0 10px !important;
 }
 
+/* Site-wide search: icon toggle + dropdown panel */
+.site-search-wrapper {
+  position: relative;
+}
+.site-search-toggle {
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  width: 40px;
+  height: 40px;
+  border-radius: 50% !important;
+  cursor: pointer;
+}
+.site-search-toggle:hover,
+.site-search-toggle[aria-expanded="true"] {
+  background-color: rgba(255, 255, 255, 0.12) !important;
+}
+.site-search-toggle .bi-search {
+  font-size: 1.2rem;
+  line-height: 1;
+  color: #ffffff !important;
+}
+.site-search-toggle:hover .bi-search,
+.site-search-toggle[aria-expanded="true"] .bi-search {
+  color: #ffffff !important;
+}
+.site-search-panel {
+  position: absolute;
+  top: calc(100% + 8px);
+  right: 0;
+  width: min(420px, 92vw);
+  background: #fff;
+  border: 1px solid #ebebeb;
+  border-radius: 0.5rem;
+  box-shadow: 0 8px 24px rgba(33, 37, 41, 0.12);
+  padding: 12px;
+  z-index: 1050;
+}
+.site-search-panel[hidden] {
+  display: none;
+}
+.site-search-panel .pagefind-ui__search-input {
+  width: 100%;
+  height: 40px;
+  font-size: 14px;
+  padding: 8px 12px;
+  border: 1px solid #d0d4dd;
+  border-radius: 0.5rem;
+}
+.site-search-panel .pagefind-ui__drawer {
+  position: static !important;
+  top: auto !important;
+  right: auto !important;
+  left: auto !important;
+  width: 100% !important;
+  border: 0 !important;
+  box-shadow: none !important;
+  padding: 0 !important;
+  margin-top: 8px;
+  max-height: 60vh;
+  overflow-y: auto;
+}
+@media (max-width: 991.98px) {
+  .site-search-panel {
+    right: auto;
+    left: 0;
+    width: 100%;
+  }
+}
+
 /* Contact Us */
 .contactP a {
   color: #171b26 !important;

assets/js/main.js

@@ -108,7 +108,45 @@ document.addEventListener("DOMContentLoaded", function () {
 
   // PageFind Init
   window.addEventListener('DOMContentLoaded', (event) => {
-    new PagefindUI({ element: "#search", showSubResults: true });
+    if (document.getElementById("search")) {
+      new PagefindUI({ element: "#search", showSubResults: true });
+    }
+    if (document.getElementById("site-search")) {
+      new PagefindUI({
+        element: "#site-search",
+        showSubResults: true,
+        showImages: false,
+        resetStyles: false,
+      });
+    }
+
+    // Site-search toggle
+    const searchToggle = document.querySelector(".site-search-toggle");
+    const searchPanel = document.querySelector(".site-search-panel");
+    if (searchToggle && searchPanel) {
+      const closePanel = () => {
+        searchPanel.hidden = true;
+        searchToggle.setAttribute("aria-expanded", "false");
+      };
+      const openPanel = () => {
+        searchPanel.hidden = false;
+        searchToggle.setAttribute("aria-expanded", "true");
+        const input = searchPanel.querySelector(".pagefind-ui__search-input");
+        if (input) input.focus();
+      };
+      searchToggle.addEventListener("click", (e) => {
+        e.stopPropagation();
+        searchPanel.hidden ? openPanel() : closePanel();
+      });
+      document.addEventListener("click", (e) => {
+        if (!searchPanel.hidden && !searchPanel.contains(e.target) && e.target !== searchToggle) {
+          closePanel();
+        }
+      });
+      document.addEventListener("keydown", (e) => {
+        if (e.key === "Escape" && !searchPanel.hidden) closePanel();
+      });
+    }
   });
 
   if (logos) {

assets/jsconfig.json

@@ -3,8 +3,8 @@
   "baseUrl": ".",
   "paths": {
    "*": [
-    "../../../Library/Caches/hugo_cache/modules/filecache/modules/pkg/mod/github.com/gohugoio/hugo-mod-jslibs-dist/popperjs/v2@v2.21100.20000/package/dist/cjs/*",
-    "../../../Library/Caches/hugo_cache/modules/filecache/modules/pkg/mod/github.com/twbs/bootstrap@v5.3.2+incompatible/js/*"
+    "../../../../Library/Caches/hugo_cache/modules/filecache/modules/pkg/mod/github.com/gohugoio/hugo-mod-jslibs-dist/popperjs/v2@v2.21100.20000/package/dist/cjs/*",
+    "../../../../Library/Caches/hugo_cache/modules/filecache/modules/pkg/mod/github.com/twbs/bootstrap@v5.3.2+incompatible/js/*"
    ]
   }
  }

content/_index.md

@@ -9,7 +9,7 @@ hero_section:
       btn_link: "/about-nwb/"
 banner_section:
   enable: true
-  title: "NWB needs your urgent help! <a href='/supporting-nwb/' style='color: #664d03; font-weight: 600;'>Learn how you can support NWB</a>"
+  title: "<a href='/supporting-nwb/' style='color: #664d03; font-weight: 600;'>Learn how you can support NWB</a>"
 card_section:
   enable: true
   cards:

content/community/educators.md

@@ -52,7 +52,7 @@ resources_teaching_fair:
       url: "https://pynwb.readthedocs.io/en/stable/tutorials/index.html"
     - title: "MatNWB Tutorials"
       content: "MATLAB-based tutorials for working with NWB data. Ideal for courses already using MATLAB as a primary teaching language. Useful for MATLAB-based courses and labs."
-      url: "https://neurodatawithoutborders.github.io/matnwb/"
+      url: "https://matnwb.readthedocs.io/en/latest/pages/tutorials/index.html"
     - title: "NWB YouTube Channel"
       content: "Video tutorials, webinars, and recorded training sessions covering various aspects of NWB. Useful for visual demos and asynchronous learning."
       url: "https://www.youtube.com/@NeurodataWithoutBorders"

content/events/hck26-2026-janelia-ndrh.md

@@ -1,11 +1,11 @@
 ---
 title: "NeuroDataReHack 2026"
-date: 2026-07-13
+date: 2026-07-12
 endDate: 2026-07-17
 location: "HHMI Janelia Research Campus, Ashburn, VA"
 eventType: "Hackathon"
 image: "/images/events/hck_2x_2026-janelia-ndrh/ndrh_2026_banner.png"
-weight: 20260713
+weight: 20260712
 summary: "Unlock new discoveries in neurophysiology through secondary analysis."
 draft: false
 organizers:
@@ -177,10 +177,12 @@ Following the event, participants will be invited to apply for a Kavli Foundatio
 
 ## Eligibility
 
-This course is intended for PhD students, postdoctoral researchers, principal investigators, or similar.
+Eligibility is broad. This course is intended for PhD students, postdoctoral researchers, principal investigators, or similar.
 Advanced undergraduates may be considered on a case-by-case basis. We welcome applicants from all areas of
 neuroscience, including but not limited to experimentalists, computational neuroscientists, and data scientists.
 Applicants should have basic programming experience in Python or MATLAB and experience with neurophysiology research.
+Preference will be given to applicants who have a specific project in mind that involves reanalyzing existing
+neurophysiology data in NWB format and who has not previously attended a NeuroDataReHack event.
 
 ## Logistics
 

content/faq/_index.md

@@ -24,7 +24,7 @@ See the [Installing PyNWB](https://pynwb.readthedocs.io/en/stable/install_users.
 
 ### How do I install MatNWB? {#install-matnwb}
 
-See the [MatNWB documentation](https://matnwb.readthedocs.io/en/latest/pages/getting_started/installation_users.html) for details.
+See the [MatNWB documentation](https://matnwb.readthedocs.io/en/latest/pages/getting_started/installation.html) for details.
 
 ### What is the difference between PyNWB and nwb-schema? {#pynwb-vs-schema}
 

content/news/nwb-newsletter-2026-winter.md

@@ -0,0 +1,9 @@
+---
+title: "NWB & DANDI Newsletter Winter 2026"
+weight: 1
+date: "2026-05-08"
+subtitle: "NeuroDataReHack 2026 + Cosyne tutorial, leadership additions, new funding through 2027, NWB 2.9 schema, and PyNWB 3 / HDMF 4 / AqNWB 0.2 / NeuroConv 0.9 releases"
+image: "/images/newsletter_2026-winter_banner.png"
+ext_link: "https://us3.campaign-archive.com/?u=eacaccc485a4e5f36034bbdbd&id=86d4c15809"
+tags: announcement, newsletter
+---

content/news/pynwb-4.0.0-release.md

@@ -0,0 +1,67 @@
+---
+title: "PyNWB 4.0.0 Released"
+weight: 1
+date: "2026-06-30"
+subtitle: "A major release bringing HERD external resource annotations, the NWBEP001 EventsTable, and the NWB 2.10.0 schema to the Python reference API"
+image: "/images/pynwb_4.0.0_banner.png"
+tags: announcement, software, pynwb, release
+---
+
+We're excited to announce the release of [**PyNWB 4.0.0**](https://github.com/NeurodataWithoutBorders/pynwb/releases/tag/4.0.0), the latest major version of the Python reference API for reading and writing Neurodata Without Borders files. This release pairs two long-anticipated capabilities, **HERD** external resource annotations and the **NWBEP001 EventsTable**, with the new NWB **2.10.0** schema, alongside expanded Python support and a round of cleanup that removes long-deprecated functionality.
+
+## HERD: linking NWB data to external resources
+
+A headline feature of PyNWB 4.0.0 is support for **HERD** (the HDMF External Resources Data structure), exposed as the new `external_resources` field on `NWBFile`.
+
+HERD provides a standardized way to associate **external resource annotations** with the contents of your NWB file. The most common use case is mapping entries in your data, such as species, brain regions, genotypes, or behavioral conditions, to terms in external ontologies and controlled vocabularies. Instead of recording a free-text label like "mouse," you can link that value to a precise, globally resolvable identifier (for example, an NCBI Taxonomy term), making your data more **machine-readable, interoperable, and [FAIR](https://www.go-fair.org/fair-principles/)**.
+
+To get started, see the new tutorials: [Linking to External Resources (HERD)](https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_external_resources.html) and [Annotating Multiple Streamed NWB Files with a Single HERD](https://pynwb.readthedocs.io/en/stable/tutorials/general/resources_streaming.html).
+
+## NWBEP001 and the EventsTable
+
+PyNWB 4.0.0 also integrates [**NWBEP001**](https://github.com/nwb-extensions/nwbep-review/issues/4), the first [NWB Enhancement Proposal](/enhancement-proposals/) to graduate into the core standard. NWB Enhancement Proposals are the formal mechanism for proposing broadly useful additions to the NWB specification; they are typically prototyped and refined as NWB extensions (NDX) before being folded into the core schema. NWBEP001 followed exactly this path, and its acceptance brings a dedicated, standardized way to represent **events** in NWB.
+
+This release adds the new neurodata types defined by the proposal:
+
+- **`EventsTable`**: a table for storing events, including a `source_description` attribute documenting where the events came from
+- **`TimestampVectorData`** and **`DurationVectorData`**: column types for event timing and durations
+- A new **`events`** group on `NWBFile` to hold event tables
+- **`MeaningsTable`**: a table for documenting the meaning of categorical column values of another table, such as the events table
+
+`NWBFile` also gains convenience methods for managing multiple event tables, including `merge_events_tables()` to combine event tables and `get_all_events()` to retrieve all events across the file.
+
+## More new capabilities
+
+Beyond the two headline features, PyNWB 4.0.0 adds several quality-of-life improvements:
+
+- New `get_starting_time()` and `get_duration()` methods on `TimeSeries`, `TimeIntervals`, and `Units`
+- **Python 3.14** support, and a bump to **HDMF ≥ 6.1.0**
+- **pandas 3.0** compatibility
+
+It also resolves a number of bugs, including fixes to `TimeSeries.get_timestamps()` for numpy arrays, round-tripping of `Units` waveform metadata, and parsing of legacy `Device.model` strings.
+
+## Breaking changes
+
+As a major release, PyNWB 4.0.0 removes functionality that has been deprecated for some time. Highlights include:
+
+- Removal of the deprecated `ProcessingModule` methods `add_container`, `get_container`, `add_data_interface`, and `get_data_interface`
+- Removal of the `extensions` argument from `get_type_map`, `get_manager`, and `NWBHDF5IO`
+- Removal of the `notes` argument and property from `ScratchData`
+- Removal of the `ic_electrodes` argument from `NWBFile`
+- Removal of the `paths` argument from `pynwb.validate`
+- `NWBFile.icephys_filtering` is now read-only
+- **Python 3.9** is now deprecated
+
+If your code relies on any of these, review the [full release notes](https://github.com/NeurodataWithoutBorders/pynwb/releases/tag/4.0.0) before upgrading.
+
+## Get started
+
+You can upgrade today:
+
+```bash
+pip install --upgrade pynwb
+```
+
+For complete details, see the [PyNWB 4.0.0 release notes](https://github.com/NeurodataWithoutBorders/pynwb/releases/tag/4.0.0) and the [PyNWB documentation](https://pynwb.readthedocs.io/). Questions and feedback are always welcome on the [NWB Helpdesk](https://github.com/NeurodataWithoutBorders/helpdesk/discussions).
+
+Subscribe to our [mailing list](https://mailchi.mp/fe2a9bc55a1a/nwb-signup) to stay up to date on PyNWB releases and other NWB news.