chore(rebuild): Merge pull request ome#230 from melonora/rfc_code

RFC1 review SHA: 031c5af Reason: push, by @d-v-b Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
d-v-b · Mar 22, 2024 · 914e6b9 · 914e6b9
1 parent 4c7f718
commit 914e6b9
Show file tree

Hide file tree

Showing 6 changed files with 31 additions and 36 deletions.
diff --git a/0.1/index.html b/0.1/index.html
@@ -1488,10 +1488,10 @@
 		}
 	}
 </style>
-  <meta content="Bikeshed version d29f71adb, updated Wed Jul 19 11:08:56 2023 -0700" name="generator">
+  <meta content="Bikeshed version 82ce88815, updated Thu Sep 7 16:33:55 2023 -0700" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.1/" rel="canonical">
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
-  <meta content="99b8765c0f1b9aa6072b030c8f15f75c082a1e5e" name="document-revision">
+  <meta content="031c5af3c6c902d5ac5783abf1a77dc891ca4980" name="document-revision">
 <style>/* Boilerplate: style-autolinks */
 .css.css, .property.property, .descriptor.descriptor {
     color: var(--a-normal-text);
@@ -2019,7 +2019,7 @@
   <div class="head">
     <img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;"> 
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2023-08-01">1 August 2023</time></span></h2>
+   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2024-03-22">22 March 2024</time></span></h2>
    <div data-fill-with="spec-metadata">
     <dl>
      <dt>This version:
@@ -2033,7 +2033,7 @@ <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="cont
     </dl>
    </div>
    <div data-fill-with="warning"></div>
-   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2023 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2024 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
 OME trademark rules apply. </p>
    <hr title="Separator for header">
   </div>

diff --git a/0.2/index.html b/0.2/index.html
@@ -1488,10 +1488,10 @@
 		}
 	}
 </style>
-  <meta content="Bikeshed version d29f71adb, updated Wed Jul 19 11:08:56 2023 -0700" name="generator">
+  <meta content="Bikeshed version 82ce88815, updated Thu Sep 7 16:33:55 2023 -0700" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.2/" rel="canonical">
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
-  <meta content="99b8765c0f1b9aa6072b030c8f15f75c082a1e5e" name="document-revision">
+  <meta content="031c5af3c6c902d5ac5783abf1a77dc891ca4980" name="document-revision">
 <style>/* Boilerplate: style-autolinks */
 .css.css, .property.property, .descriptor.descriptor {
     color: var(--a-normal-text);
@@ -2019,7 +2019,7 @@
   <div class="head">
     <img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;"> 
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2023-08-01">1 August 2023</time></span></h2>
+   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2024-03-22">22 March 2024</time></span></h2>
    <div data-fill-with="spec-metadata">
     <dl>
      <dt>This version:
@@ -2033,7 +2033,7 @@ <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="cont
     </dl>
    </div>
    <div data-fill-with="warning"></div>
-   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2023 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2024 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
 OME trademark rules apply. </p>
    <hr title="Separator for header">
   </div>
@@ -2270,7 +2270,7 @@ <h3 class="heading settled" data-level="3.1" id="multiscale-md"><span class="sec
             <c- p>],</c->
             <c- f>"type"</c-><c- p>:</c-> <c- u>"gaussian"</c-><c- p>,</c->
             <c- f>"metadata"</c-><c- p>:</c-> <c- p>{</c->                                       # <c- kc>t</c->he <c- kc>f</c->ields i<c- kc>n</c-> me<c- kc>ta</c->da<c- kc>ta</c-> depe<c- kc>n</c->d o<c- kc>n</c-> <c- kc>t</c->he dow<c- kc>ns</c->cali<c- kc>n</c->g impleme<c- kc>ntat</c->io<c- kc>n</c->
-                <c- f>"method"</c-><c- p>:</c-> <c- u>"skimage.transform.pyramid_gaussian"</c-><c- p>,</c-> # here<c- p>,</c-> <c- kc>t</c->he param<c- kc>ters</c-> passed <c- kc>t</c->o <c- kc>t</c->he skimage <c- kc>fun</c->c<c- kc>t</c->io<c- kc>n</c-> are give<c- kc>n</c->
+                <c- f>"method"</c-><c- p>:</c-> <c- u>"skimage.transform.pyramid_gaussian"</c-><c- p>,</c-> # here<c- p>,</c-> <c- kc>t</c->he parame<c- kc>ters</c-> passed <c- kc>t</c->o <c- kc>t</c->he skimage <c- kc>fun</c->c<c- kc>t</c->io<c- kc>n</c-> are give<c- kc>n</c->
                 <c- f>"version"</c-><c- p>:</c-> <c- u>"0.16.1"</c-><c- p>,</c->
                 <c- f>"args"</c-><c- p>:</c-> <c- u>"[true]"</c-><c- p>,</c->
                 <c- f>"kwargs"</c-><c- p>:</c-> <c- p>{</c-><c- f>"multichannel"</c-><c- p>:</c-> <c- kc>true</c-><c- p>}</c->

diff --git a/0.3/index.html b/0.3/index.html
@@ -5,10 +5,10 @@
   <title>Next-generation file formats (NGFF)</title>
   <meta content="w3c/CG-FINAL" name="w3c-status">
   <link href="https://www.w3.org/StyleSheets/TR/2021/cg-final" rel="stylesheet">
-  <meta content="Bikeshed version d29f71adb, updated Wed Jul 19 11:08:56 2023 -0700" name="generator">
+  <meta content="Bikeshed version 82ce88815, updated Thu Sep 7 16:33:55 2023 -0700" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.3/" rel="canonical">
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
-  <meta content="99b8765c0f1b9aa6072b030c8f15f75c082a1e5e" name="document-revision">
+  <meta content="031c5af3c6c902d5ac5783abf1a77dc891ca4980" name="document-revision">
 <style>/* Boilerplate: style-autolinks */
 .css.css, .property.property, .descriptor.descriptor {
     color: var(--a-normal-text);
@@ -536,7 +536,7 @@
   <div class="head">
    <p data-fill-with="logo"><a class="logo" href="https://www.w3.org/"> <img alt="W3C" height="48" src="https://www.w3.org/StyleSheets/TR/2021/logos/W3C" width="72"> </a> </p>
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2023-08-01">1 August 2023</time></p>
+   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2024-03-22">22 March 2024</time></p>
    <details open>
     <summary>More details about this document</summary>
     <div data-fill-with="spec-metadata">
@@ -554,7 +554,7 @@ <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
     </div>
    </details>
    <div data-fill-with="warning"></div>
-   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2023 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2024 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
 OME trademark rules apply. </p>
    <hr title="Separator for header">
   </div>
@@ -801,7 +801,7 @@ <h3 class="heading settled" data-level="3.1" id="multiscale-md"><span class="sec
             <c- p>],</c->
             <c- f>"type"</c-><c- p>:</c-> <c- u>"gaussian"</c-><c- p>,</c->
             <c- f>"metadata"</c-><c- p>:</c-> <c- p>{</c->                                       # <c- kc>t</c->he <c- kc>f</c->ields i<c- kc>n</c-> me<c- kc>ta</c->da<c- kc>ta</c-> depe<c- kc>n</c->d o<c- kc>n</c-> <c- kc>t</c->he dow<c- kc>ns</c->cali<c- kc>n</c->g impleme<c- kc>ntat</c->io<c- kc>n</c->
-                <c- f>"method"</c-><c- p>:</c-> <c- u>"skimage.transform.pyramid_gaussian"</c-><c- p>,</c-> # here<c- p>,</c-> <c- kc>t</c->he param<c- kc>ters</c-> passed <c- kc>t</c->o <c- kc>t</c->he skimage <c- kc>fun</c->c<c- kc>t</c->io<c- kc>n</c-> are give<c- kc>n</c->
+                <c- f>"method"</c-><c- p>:</c-> <c- u>"skimage.transform.pyramid_gaussian"</c-><c- p>,</c-> # here<c- p>,</c-> <c- kc>t</c->he parame<c- kc>ters</c-> passed <c- kc>t</c->o <c- kc>t</c->he skimage <c- kc>fun</c->c<c- kc>t</c->io<c- kc>n</c-> are give<c- kc>n</c->
                 <c- f>"version"</c-><c- p>:</c-> <c- u>"0.16.1"</c-><c- p>,</c->
                 <c- f>"args"</c-><c- p>:</c-> <c- u>"[true]"</c-><c- p>,</c->
                 <c- f>"kwargs"</c-><c- p>:</c-> <c- p>{</c-><c- f>"multichannel"</c-><c- p>:</c-> <c- kc>true</c-><c- p>}</c->

diff --git a/0.4/index.html b/0.4/index.html
@@ -5,10 +5,10 @@
   <title>Next-generation file formats (NGFF)</title>
   <meta content="w3c/CG-FINAL" name="w3c-status">
   <link href="https://www.w3.org/StyleSheets/TR/2021/cg-final" rel="stylesheet">
-  <meta content="Bikeshed version d29f71adb, updated Wed Jul 19 11:08:56 2023 -0700" name="generator">
+  <meta content="Bikeshed version 82ce88815, updated Thu Sep 7 16:33:55 2023 -0700" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.4/" rel="canonical">
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
-  <meta content="99b8765c0f1b9aa6072b030c8f15f75c082a1e5e" name="document-revision">
+  <meta content="031c5af3c6c902d5ac5783abf1a77dc891ca4980" name="document-revision">
 <style>/* Boilerplate: style-autolinks */
 .css.css, .property.property, .descriptor.descriptor {
     color: var(--a-normal-text);
@@ -589,7 +589,7 @@
   <div class="head">
    <p data-fill-with="logo"><a class="logo" href="https://www.w3.org/"> <img alt="W3C" height="48" src="https://www.w3.org/StyleSheets/TR/2021/logos/W3C" width="72"> </a> </p>
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2023-08-01">1 August 2023</time></p>
+   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2024-03-22">22 March 2024</time></p>
    <details open>
     <summary>More details about this document</summary>
     <div data-fill-with="spec-metadata">
@@ -607,7 +607,7 @@ <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
     </div>
    </details>
    <div data-fill-with="warning"></div>
-   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2023 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+   <p class="copyright" data-fill-with="copyright">Copyright © 2020-2024 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
 OME trademark rules apply. </p>
    <hr title="Separator for header">
   </div>
@@ -736,7 +736,7 @@ <h3 class="heading settled" data-level="1.3" id="document-conventions"><span cla
 encouraged (SHOULD) to support the reading of the data, but writing will usually
 be optional (MAY). Examples of transitional metadata include custom additions by
 implementations that are later submitted as a formal specification. (See <a href="#bf2raw">§ 3.2 "bioformats2raw.layout" (transitional)</a>) </p>
-   <p>Some of the JSON examples in this document include commments. However, these are only for
+   <p>Some of the JSON examples in this document include comments. However, these are only for
 clarity purposes and comments MUST NOT be included in JSON objects.</p>
    <h2 class="heading settled" data-level="2" id="on-disk"><span class="secno">2. </span><span class="content">On-disk (or in-cloud) layout</span><a class="self-link" href="#on-disk"></a></h2>
    <p>An overview of the layout of an OME-Zarr fileset should make
@@ -764,7 +764,7 @@ <h3 class="heading settled" data-level="2.1" id="image-layout"><span class="secn
     ├── .zgroup               # Each image is a Zarr group, or a folder, of other groups and arrays.
     ├── .zattrs               # Group level attributes are stored in the .zattrs file and include
     │                         # "multiscales" and "omero" (see below). In addition, the group level attributes
-    │                         # must also contain "_ARRAY_DIMENSIONS" if this group directly contains multi-scale arrays.
+    │                         # may also contain "_ARRAY_DIMENSIONS" for compatibility with xarray if this group directly contains multi-scale arrays.
     │
     ├── 0                     # Each multiscale level is stored as a separate Zarr array,
     │   ...                   # which is a folder containing chunk files which compose the array.
@@ -1225,14 +1225,14 @@ <h3 class="heading settled" data-level="3.8" id="plate-md"><span class="secno">3
 other <code>name</code> in the <code>rows</code> list. Care SHOULD be taken to avoid collisions on
 case-insensitive filesystems (e.g. avoid using both <code>Aa</code> and <code>aA</code>).</p>
    <p>The <code>plate</code> dictionary SHOULD contain a <code>version</code> key whose value MUST be a string specifying the
-version of the plate specificaton.</p>
+version of the plate specification.</p>
    <p>The <code>plate</code> dictionary MUST contain a <code>wells</code> key whose value MUST be a list of JSON objects
 defining the wells of the plate. Each well object MUST contain a <code>path</code> key whose value MUST
 be a string specifying the path to the well subgroup. The <code>path</code> MUST consist of a <code>name</code> in
 the <code>rows</code> list, a file separator (<code>/</code>), and a <code>name</code> from the <code>columns</code> list, in that order.
 The <code>path</code> MUST NOT contain additional leading or trailing directories.
 Each well object MUST contain both a <code>rowIndex</code> key whose value MUST be an integer identifying
-the index into the <code>rows</code> list and a <code>columnIndex</code> key whose value MUST be an integer indentifying
+the index into the <code>rows</code> list and a <code>columnIndex</code> key whose value MUST be an integer identifying
 the index into the <code>columns</code> list. <code>rowIndex</code> and <code>columnIndex</code> MUST be 0-based. The <code>rowIndex</code>, <code>columnIndex</code>, and <code>path</code> MUST all refer to the same row/column pair.</p>
    <p>For example the following JSON object defines a plate with two acquisitions and
 6 wells (2 rows and 3 columns), containing up to 2 fields of view per acquisition.</p>