Merge branch 'main' into favicon-5

Author: jakirkham

.gitignore

@@ -2,4 +2,5 @@ _site
 .sass-cache
 .jekyll-metadata
 .DS_Store
+.swp
 *~

.readthedocs.yml

@@ -0,0 +1,16 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  commands:
+    - gpg --keyserver hkp://keyserver.ubuntu.com --recv-keys 409b6b1796c275462a1703113804bb82d39dc0e3 7d2baf1cf37b13e2069d6956105bd0e739499bdb && curl -sSL https://get.rvm.io | bash -s stable
+    - ~/.rvm/bin/rvm autolibs disable && ~/.rvm/bin/rvm install ruby 3.1.2
+    - PATH="$HOME/.rvm/rubies/ruby-3.1.2/bin:$PATH" gem install bundler
+    - PATH="$HOME/.rvm/rubies/ruby-3.1.2/bin:$PATH" bundle install
+    - PATH="$HOME/.rvm/rubies/ruby-3.1.2/bin:$PATH" bundle exec jekyll build --destination _readthedocs/html --baseurl $(echo -n "$READTHEDOCS_CANONICAL_URL" | cut -d '/' -f 4-)

Gemfile.lock

@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.0.4.4)
+    activesupport (6.0.6.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -16,7 +16,7 @@ GEM
     colorator (1.1.0)
     commonmarker (0.17.13)
       ruby-enum (~> 0.5)
-    concurrent-ruby (1.1.9)
+    concurrent-ruby (1.2.0)
     dnsruby (1.61.9)
       simpleidn (~> 0.1)
     em-websocket (0.5.3)
@@ -226,14 +226,14 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
-    mini_portile2 (2.8.0)
+    mini_portile2 (2.8.1)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.15.0)
+    minitest (5.17.0)
     multipart-post (2.1.1)
-    nokogiri (1.13.4)
+    nokogiri (1.14.3)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
     octokit (4.22.0)
@@ -242,7 +242,7 @@ GEM
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     public_suffix (4.0.6)
-    racc (1.6.0)
+    racc (1.6.2)
     rb-fsevent (0.11.1)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
@@ -268,14 +268,14 @@ GEM
     thread_safe (0.3.6)
     typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    tzinfo (1.2.9)
+    tzinfo (1.2.11)
       thread_safe (~> 0.1)
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8)
     unicode-display_width (1.8.0)
     webrick (1.7.0)
-    zeitwerk (2.5.4)
+    zeitwerk (2.6.6)
 
 PLATFORMS
   ruby

_config.yml

@@ -28,12 +28,19 @@ baseurl: "" # the subpath of your site, e.g. /blog
 
 url: "" # the base hostname & protocol for your site, e.g. http://example.com
 
+analytics:
+  provider: "google"
+  google:
+    tracking_id: "G-BCRR9QE7Z0"
+    anonymize_ip: true
+
 github_username:  zarr-developers
 gitter_url: https://gitter.im/zarr-developers/community
 
 # Build settings
 markdown: kramdown
 remote_theme: "mmistakes/minimal-mistakes@4.24.0"
+minimal_mistakes_skin: "dirt"
 
 plugins:
   - jekyll-feed

_data/navigation.yml

@@ -17,17 +17,23 @@ sidebar:
         url: '#features'
       - title: "Sponsorship"
         url: "#sponsorship"
-      - title: "Slides"
-        url: "/slides"
       - title: "Videos"
         url: "#videos"
-      - title: "Community Meetings"
-        url: '#community-meetings'
-      - title: "Blog"
-        url: '#blog'
-  - title: Other sites
+  - title: Subpages
     children:
-      - title: "Specification"
-        url: https://zarr-specs.readthedocs.io/en/core-protocol-v3.0-dev/
+      - title: "Adopters"
+        url: "/adopters"
+      - title: "Blog"
+        url: '/blog'
+      - title: "Community"
+        url: '/community'
       - title: "Implementations"
-        url: https://github.com/zarr-developers/zarr_implementations
+        url: '/implementations'
+      - title: "Office Hours"
+        url: "/office-hours"
+      - title: "Slides"
+        url: "/slides"
+      - title: "Specification"
+        url: https://zarr-specs.readthedocs.io/
+      - title: "ZEPs"
+        url: '/zeps'

adopters/adopters.md

@@ -0,0 +1,93 @@
+---
+layout: single
+author_profile: false
+title: Zarr Adopters
+permalink: /adopters/
+sidebar:
+  title: "Content"
+  nav: sidebar
+---
+
+<p style="font-family:Trebuchet MS"><font size="4">💡 If you're using Zarr in any way and would like to be added on this page, please drop your logo and blurb <a href="https://github.com/zarr-developers/community/issues/60">here</a>.</font></p>
+
+<p style="font-family:Trebuchet MS"><font size="4"> Thanks to the amazing community, Zarr is widely adopted and used by these groups. Here are the logos (in alphabetical order):</font></p>
+
+<a href="https://carbonplan.org/"><img src="../adopters/logos/carbonplan.svg" alt="Carbonplan" width="600" height="300"></a>
+
+<font size="3">→ Zarr is used by <a href="https://carbonplan.org/">CarbonPlan</a> as a storage format for analysis and visualization of climate data.</font>
+
+---
+
+<a href="https://www.columbia.edu/"><img src="../adopters/logos/columbia.png" alt="Columbia" width="700" height="300"></a>
+
+---
+
+<a href="https://lamont.columbia.edu/"><img src="../adopters/logos/ldeo.png" alt="LDEO" width="700" height="400"></a>
+
+---
+
+<a href="https://dandiarchive.org/"><img src="../adopters/logos/dandi.svg" alt="DANDI" width="500" height="300"></a>
+
+<font size="3">→ Zarr is currently used by DANDI for lightsheet microscopy and some ex vivo MRI datasets, and is being considered as a backend for Neurodata Without Borders (NWB) neurophysiology datasets.</font>
+
+---
+
+<a href="https://www.janelia.org/"><img src="../adopters/logos/hhmi.png" alt="HHMI" width="600" height="300"></a>
+
+<font size="3">→ Zarr is used extensively within Janelia Research Campus for efficiently storing and accessing large imaging datasets</font>
+
+---
+
+<a href="https://leap.columbia.edu/"><img src="../adopters/logos/leap.webp" alt="LEAP" width="550" height="300"></a>
+
+<font size="3">→ Zarr is used by the <a href="https://leap.columbia.edu/">LEAP Project</a> (Learning the Earth with Artificial Intelligence and Physics) at Columbia University as the data format for the LEAP-Pangeo data library. LEAP researchers use Zarr to perform data analytics and machine learning for climate modeling.</font>
+
+---
+
+<a href="https://planetarycomputer.microsoft.com/catalog?filter=zarr"><img src="../adopters/logos/microsoft.png" alt="Microsoft" width="600" height="300"></a>
+
+<font size="3">→ Zarr is used by the <a href="https://planetarycomputer.microsoft.com/">Microsoft Planetary Computer</a> as a cloud-native storage format for chunked, N-dimensional arrays of geospatial data.</font>
+
+---
+
+<a href="https://www.nasa.gov/"><img src="../adopters/logos/nasa.webp" alt="NASA" width="600" height="300"></a>
+
+<font size="3">→ Zarr is used by NASA as an analysis-ready data store for chunked, N-dimensional arrays of geospatial data.</font>
+
+---
+
+<a href="https://ncar.ucar.edu/"><img src="../adopters/logos/ncar.svg" alt="NCAR" width="600" height="300"></a>
+
+---
+
+<a href="https://www.openmicroscopy.org/"><img src="../adopters/logos/ome_logo.svg" alt="OME" width="600" height="300"></a>
+
+<font size="3">→ The <a href="https://www.openmicroscopy.org/">Open Microscopy Environment (OME)</a> community is developing a format, OME-Zarr, using Zarr to store large, n-dimensional biological images as part of the <a href="https://ngff.openmicroscopy.org/">Next-generation file format (NGFF)</a> effort."
+
+OME logo used by <a href="https://www.openmicroscopy.org/artwork/">permission</a>, trademarked <a href="https://www.glencoesoftware.com/">Glencoe Software, Inc.</a></font>
+
+---
+
+<a href="https://pangeo.io/"><img src="../adopters/logos/pangeo.png" alt="Pangeo" width="550" height="300"></a>
+
+<font size="3">→ Zarr is used extensively within the <a href="https://pangeo.io/">Pangeo Project</a> as a cloud native storage format for ocean, weather, climate, and geospatial data.</font>
+
+---
+
+<a href="https://scalableminds.com/"><img src="../adopters/logos/scalableminds.svg" alt="scalableminds" width="500" height="250"></a>
+
+<font size="3">→ scalable minds uses Zarr to store and process peta-scale 3D images of brain tissue for Connectomics analyses.</font>
+
+---
+
+<a href="https://www.unidata.ucar.edu/"><img src="../adopters/logos/unidata.png" alt="Unidata" width="600" height="300"></a>
+
+<font size="3">→ <a href="https://www.unidata.ucar.edu/">Unidata</a> is developing its netCDF libaries to support Zarr datasets amongst the atmospheric and geoscientific community.</font>
+
+---
+
+<a href="https://webknossos.org/"><img src="../adopters/logos/webknossos.svg" alt="Webknossos" width="600" height="300"></a>
+
+<font size="3">→ WEBKNOSSOS is a web-based platform for visualizing, collaboratively annotating and sharing large 3D images. Zarr is used for accessing remotely stored images as well as securely streaming annotation data to client applications.</font>
+
+---