Merge branch 'refs/heads/dev' into add-matnwb

# Conflicts:
#	content/working-groups/_index.md

Author: bendichter

.github/workflows/link-check.yml

@@ -0,0 +1,23 @@
+# Workflow for link checking with lychee
+name: Link Check Source Files with Lychee
+
+on:
+  # Runs on pull requests targeting the dev branch
+  pull_request:
+    branches: ["dev"]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  link_check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Link Checker
+        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

.gitignore

@@ -3,3 +3,6 @@
 /public/**
 .hugo_build.lock
 /todo.md
+
+# PyCharm
+.idea/

content/working-groups/_index.md

@@ -17,8 +17,9 @@ sections:
       NWB standard to integrate and leverage these resources for storing
       relevant metadata on the genotypes and genetic backgrounds of individual
       mice, linking neurophysiological data to the databases and literature that
-      characterize the experimental animals. <br><br> <a href=''>[NDX
-      Proposal]</a>
+      characterize the experimental animals. <br><br>
+      <a href='https://docs.google.com/document/d/12EVToclVEKXF8OP5hd6eaTYT6vj-ewhHYVM54u7h-tU/edit#heading=h.xk81rob2tb1l'>
+      [NDX Proposal]</a>
     image: /images/genotype.png
   - title: Spatial coordinates representation
     content: Reporting of spatial coordinates within the brain is a complex problem,
@@ -31,7 +32,9 @@ sections:
       stimuli) within a spatial coordinate system. This type of standardization
       will facilitate the programmatic integration and comparison of data
       represented in NWB with other datasets that have been mapped to the same
-      coordinate system. <br><br> <a href=''>[NDX Proposal]</a>
+      coordinate system. <br><br>
+      <a href='https://docs.google.com/document/u/0/d/13frfqavbj4e0T-cmR3B8zGanrEe-f74Sa_s1yp_0LcI/edit'>
+      [NDX Proposal]</a>
     image: /images/spatial.png
   - title: Behavioral task representation
     content: Behavioral tasks are an increasingly important component in
@@ -45,30 +48,17 @@ sections:
       building a standard markup language (BEADL) to build state machine
       descriptions of task logic and control flow within a trial and across
       trials in a session, including tools for visualization, construction, and
-      emulation of tasks from these machine-readable descriptions. <br><br> <a
-      href=''>[NDX Proposal]</a>
+      emulation of tasks from these machine-readable descriptions. <br><br>
+      <a href='https://docs.google.com/document/d/1QQLbon-29Td5SblvB2AdWlGzCzgG7MNHloUD8C3tNdc/edit#heading=h.xk81rob2tb1l'>
+      [NDX Proposal]</a>
     image: /images/behavioral.png
-  - title: Spatial coordinates representation
-    content: Reporting of spatial coordinates within the brain is a complex problem,
-      requiring registration between data collected with multiple recording
-      modalities (imaging, probes) and across brain preparations (in vivo whole
-      brain, slice) with common reference atlases and controlled vocabularies.
-      The focus of this working group is to create an NWB extension to capture
-      spatial coordinate systems, spatial mappings between two systems, and the
-      representation of objects (e.g. cells, probes, injections, and optogenetic
-      stimuli) within a spatial coordinate system. This type of standardization
-      will facilitate the programmatic integration and comparison of data
-      represented in NWB with other datasets that have been mapped to the same
-      coordinate system. <br><br> <a href=''>[NDX Proposal]</a>
-    image: /images/spatial.png
   - title: External Working Groups
     bg_white: true
     content: NWB team members also participate in numerous external working groups.
       While the charge of external working groups are often broader than just
       NWB,  they all involve components that are relevant to NWB and commonly
       use NWB or are creating a Neurodata Extension (NDX) as part of their
       charge.
-    image: /images/external-group.png
   - title: INCF Working Group on standardization of a directory structure containing
       neurophysiology data
     bg_white: true
@@ -81,9 +71,9 @@ sections:
       facilitate obtaining reproducible research and data sharing following the
       FAIR principles. In addition to data structures, the working group will
       discuss what experimental metadata is essential, and which formats and
-      structures are appropriate for different metadata types. <br><br> <a
-      href=''>Working Groups Page</a>
-    image: /images/incf.png
+      structures are appropriate for different metadata types. <br><br>
+      <a href='https://github.com/INCF/neuroscience-data-structure/'>Working Group Page</a>
+    image: /images/incf-wg-genaral-image.jpg
   - title: INCF Electrophysiology Stimulation Ontology Working Group
     bg_white: true
     content: Stimulus protocols are an essential component of neurophysiological
@@ -100,8 +90,10 @@ sections:
       protocols use very similar protocols with waveforms that have stereotyped
       profiles (e.g., long steps, ramps, chirps). This working group will also
       draft recommendations for representation in NWB of parameterized stimuli
-      beyond 1-D waveforms. <br><br> <a href=''>Working Groups Page</a>
-    image: /images/incf-ontology-group.png
+      beyond 1-D waveforms. <br><br>
+      <a href='https://www.incf.org/sig/electrophysiology-stimulation-ontology-working-group'>
+      Working Group Page</a>
+    image: /images/incf-wg-genaral-image.jpg
   - title: Standardization of data/file formats for simulation outputs in
       computational neuroscience
     bg_white: true
@@ -115,7 +107,8 @@ sections:
       data. Tasks for this working group include compiling a list of existing
       formats, defining evaluation criteria and evaluating the different
       formats, and identifying avenues for improving interoperability. <br><br>
-      <a href=''>Source</a>, <a href=''>NDX</a>
+      <a href='https://github.com/catalystneuro/ndx-simulation-output'>Source</a>,
+      <a href='https://github.com/nwb-extensions/ndx-simulation-output-record'>NDX</a>
     image: /images/simulation.png
 past_groups:
   enable: true
@@ -136,13 +129,23 @@ past_groups:
     title: Outcomes
     content: The working group drafted an extension for the NWB schema that
       implements these tables for testing and evaluation of the proposed changes
-      (see “<a href=''>Source</a>” “<a href=''>NDX</a>” “<a href=''>NDX
-      Proposal</a>” “<a href=''>YouTube</a>”). The proposed extension underwent
+      (see <a href='https://github.com/oruebel/ndx-icephys-meta'>Source</a>, 
+      <a href='https://github.com/nwb-extensions/ndx-icephys-meta-record'>NDX</a>,
+      <a href='https://docs.google.com/document/d/1cAgsXv26BmQoVfa7Greyxs0oc4IGH-t5aJsm-AwUAAE/edit'>
+      NDX Proposal</a>, <a href='https://www.youtube.com/watch?v=TClUoKA1pEU'>YouTube</a>
+      ). The proposed extension underwent
       community review and has been merged with NWB after completion of the
       review. The new structures developed by this working group have been
-      released as part of <a href=''>NWB Schema version 2.4</a> and
+      released as part of
+      <a href='https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html#aug-11-2021'>
+      NWB Schema version 2.4</a> and
       corresponding PyNWB 2.0 and MatNWB 2.4.0.0. These new features are
-      documented in the <a href=''>Intracellular electrophysiology tutorial</a>
-      as part o PyNWB and <a href=''>AlignedDynamicTable tutorial</a> and <a
-      href=''>AlignedDynmaicTable</a> schema as part of HDMF.
+      documented in the
+      <a href='https://pynwb.readthedocs.io/en/stable/tutorials/domain/plot_icephys.html#sphx-glr-tutorials-domain-plot-icephys-py'>
+      Intracellular electrophysiology tutorial</a>
+      as part of PyNWB and the
+      <a href='https://hdmf.readthedocs.io/en/stable/tutorials/plot_aligneddynamictable.html#sphx-glr-tutorials-plot-aligneddynamictable-py'>
+      AlignedDynamicTable tutorial</a> and
+      <a href='https://hdmf-common-schema.readthedocs.io/en/latest/format.html#aligneddynamictable'>AlignedDynmaicTable</a>
+      schema as part of HDMF.
 ---

images/incf-wg-genaral-image.jpg

@@ -1,3 +1,5 @@
-# Basic Bootstrap and Hugo Starter
+# Neurodata Without Borders Website
 
-See more starters at https://github.com/hugo-starters/
+**Status** The repo and website are available for community feedback and review. This will become the official NWB website, once the initial community review has been completed. While this website is being finalized, please see the current NWB website at https://www.nwb.org/ for the latest updates. 
+
+This website uses HUGO. See more starters at https://github.com/hugo-starters/