Update all references to the Bio-Formats documentation to readthedocs

The Bio-Formats documentation has been migrated from being self-hosted
on OME infrastructure to readthedocs.io. All the
https://docs.openmicroscopy.org/bio-formats/ URLs are maintained but
redirect to https://bio-formats.readthedocs.io/.
This updates all the pages linking to the documentation for the current
version of Bio-Formats to use readthedocs.io directly, removing a layer
of indirection.

bio-formats/downloads/index.html

@@ -7,7 +7,7 @@
             <div class="row column text-center">
                 <h1>Bio-Formats {{ site.bf.version }} Downloads</h1>
                 <a href="{{ site.baseurl }}/2024/11/14/bio-formats-8-0-1.html" class="large btn-red button sites-button" style="text-shadow: none;">Read the Release Announcement</a>
-                <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/" target="_blank" class="hero-link">Read the Docs</a>
+                <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/" target="_blank" class="hero-link">Read the Docs</a>
             </div>
         </div>
 
@@ -22,7 +22,7 @@ <h3 class="text-center">Tools</h3>
                         <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_bio-formats.svg">
                         <h5>Bio-Formats Package</h5>
                         <h6>bioformats_package.jar</h6>
-                        <p class="card-caption">The complete bundle for end users containing everything needed to read images into ImageJ. Instructions for installing Bio-Formats in ImageJ are available in the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/users/imagej/installing.html" taget="_blank">user guide</a>.</p>
+                        <p class="card-caption">The complete bundle for end users containing everything needed to read images into ImageJ. Instructions for installing Bio-Formats in ImageJ are available in the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/users/imagej/installing.html" taget="_blank">user guide</a>.</p>
                         <a href="https://downloads.openmicroscopy.org/bio-formats/{{ site.bf.version }}/artifacts/bioformats_package.jar" class="button hollow small"><i class="fa fa-download"></i> Download (31.64 MB)</a>
                     </div>
                 </div>
@@ -33,7 +33,7 @@ <h6>bioformats_package.jar</h6>
                         <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_command-line.svg">
                         <h5>Command Line Tools</h5>
                         <h6>bftools.zip</h6>
-                        <p class="card-caption">A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included. For more info, see the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/users/comlinetools/index.html" target="_blank">command line tools documentation</a>.</p>
+                        <p class="card-caption">A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included. For more info, see the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/users/comlinetools/index.html" target="_blank">command line tools documentation</a>.</p>
                         <a href="https://downloads.openmicroscopy.org/bio-formats/{{ site.bf.version }}/artifacts/bftools.zip" class="button hollow small"><i class="fa fa-download"></i> Download (29.96 MB)</a>
                     </div>
                 </div>
@@ -44,7 +44,7 @@ <h6>bftools.zip</h6>
                         <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_matlab.svg">
                         <h5>MATLAB Toolbox</h5>
                         <h6>bfmatlab.zip</h6>
-                        <p class="card-caption">A bundle of functions for using Bio-Formats from MATLAB with bioformats_package.jar already included. For more info, see the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/users/matlab/index.html" target="_blank">MATLAB documentation</a>.</p>
+                        <p class="card-caption">A bundle of functions for using Bio-Formats from MATLAB with bioformats_package.jar already included. For more info, see the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/users/matlab/index.html" target="_blank">MATLAB documentation</a>.</p>
                         <a href="https://downloads.openmicroscopy.org/bio-formats/{{ site.bf.version }}/artifacts/bfmatlab.zip" class="button hollow small"><i class="fa fa-download"></i> Download (29.97 MB)</a>
                     </div>
                 </div>
@@ -55,7 +55,7 @@ <h6>bfmatlab.zip</h6>
                         <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_octave.svg">
                         <h5>Octave Package</h5>
                         <h6>bioformats-octave-{{ site.bf.version }}.tar.gz</h6>
-                        <p class="card-caption">A bundle of functions for using Bio-Formats from Octave. You’ll need to install bioformats_package.jar separately. For more info, see the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/users/octave/index.html" target="_blank">Octave documentation</a>.</p>
+                        <p class="card-caption">A bundle of functions for using Bio-Formats from Octave. You’ll need to install bioformats_package.jar separately. For more info, see the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/users/octave/index.html" target="_blank">Octave documentation</a>.</p>
                         <a href="https://downloads.openmicroscopy.org/bio-formats/{{ site.bf.version }}/artifacts/bioformats-octave-{{ site.bf.version }}.tar.gz" class="button hollow small"><i class="fa fa-download"></i> Download (37.44 KB)</a>
                     </div>
                 </div>

bio-formats/index.html

@@ -11,7 +11,7 @@ <h1 class="hero-main-header"><img src="{{ site.baseurl }}/img/logos/bio-formats-
                     <p class="hero-subheader small-12">The solution for reading proprietary microscopy image data and metadata</p>
                     <br>
                     <a href="{{ site.baseurl }}/bio-formats/downloads/" class="large button sites-button btn-red">Download Version {{ site.bf.version }}</a>
-                    <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/" target="_blank" class="hero-link">Read the Docs</a>
+                    <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/" target="_blank" class="hero-link">Read the Docs</a>
                 </div>
             </div>
         </header>
@@ -25,7 +25,7 @@ <h2>What is Bio-Formats?</h2>
         <div class="row column text-center">
             <p>Bio-Formats is a software tool for reading and writing image data using standardized, open formats. Bio-Formats is a community driven project with a standardized application interface that supports open source analysis programs like <a href="https://imagej.net/" target="_blank">ImageJ</a>, <a href="http://www.cellprofiler.org/" target="_blank">CellProfiler</a> and <a href="http://icy.bioimageanalysis.org/" target="_blank">Icy</a>, informatics solutions like <a href="{{ site.baseurl }}/omero/">OMERO</a>, and commercial programs like <a href="http://www.mathworks.com/products/matlab/" target="_blank">MATLAB</a>.</p>
             <p>Bio-Formats documentation includes a complete version history, guides for using Bio-Formats as a plugin for ImageJ/Fiji, extensive information on which formats are supported and the level of that support, and also information for developers wanting to extend Bio-Formats or use it in their own software.</p>
-            <p><a class="small button sites-button btn-blue" href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/" target="_blank">Read the Docs <i class="fa fa-long-arrow-right"></i></a></p>
+            <p><a class="small button sites-button btn-blue" href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/" target="_blank">Read the Docs <i class="fa fa-long-arrow-right"></i></a></p>
         </div>
         <!-- end -->
 
@@ -47,7 +47,7 @@ <h2>File Formats</h2>
         </div>
         <hr>
         <div class="row column text-center">
-            <p>Bio-Formats 5 improves support for High Content Screening, time lapse imaging, digital pathology and other complex multidimensional image formats, reading over <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/supported-formats.html">160 file formats</a> and their metadata to the <a href="https://ome-model.readthedocs.io/en/stable/">OME data model</a> standard. </p>
+            <p>Bio-Formats 5 improves support for High Content Screening, time lapse imaging, digital pathology and other complex multidimensional image formats, reading over <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/supported-formats.html">160 file formats</a> and their metadata to the <a href="https://ome-model.readthedocs.io/en/stable/">OME data model</a> standard. </p>
         </div>
         <!-- end -->
 
@@ -58,7 +58,7 @@ <h2>Our Community</h2>
         </div>
         <hr>
         <div class="row column text-center">
-            <p>Bio-Formats is a community project and we welcome <a href="{{ site.baseurl }}/contributors/">your input</a>. You can find guidance on how to  <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/about/bug-reporting.html" target="_blank">report bugs or upload files for testing</a>, and contact us via our mailing lists or forums. Further information about how the OME team works and how you can contribute to our projects is in the <a href="https://docs.openmicroscopy.org/contributing/" target="_blank">Contributing Developer Documentation</a>.</p>
+            <p>Bio-Formats is a community project and we welcome <a href="{{ site.baseurl }}/contributors/">your input</a>. You can find guidance on how to  <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/about/bug-reporting.html" target="_blank">report bugs or upload files for testing</a>, and contact us via our mailing lists or forums. Further information about how the OME team works and how you can contribute to our projects is in the <a href="https://docs.openmicroscopy.org/contributing/" target="_blank">Contributing Developer Documentation</a>.</p>
         </div>
         <!-- end -->
 

docs/index.html

@@ -25,7 +25,7 @@ <h4>OMERO</h4>
                 </a>
             </div>
             <div class="small-12 medium-12 large-4 columns">
-                <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/" target="_blank" class="card-as-link">
+                <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/" target="_blank" class="card-as-link">
                     <div class="card card-support">
                         <div class="card-section">
                             <div class="medium-2"><img class="thumbnail" alt="Bio-Formats logo" src="{{ site.baseurl }}/img/logos/bio-formats-logomark.svg"></div>

explore/index.html

@@ -25,7 +25,7 @@ <h2 class="header-red">OME for Scientists</h2>
             <img class="medium-3 medium-offset-1 columns" alt="OMERO for Scientists" src="{{ site.baseurl }}/img/icons/user-groups_scientists.svg">
             <div class="medium-8 columns">
                 <p>Sign up for our <a href="https://www.openmicroscopy.org/qa2/registry/demo_account/">OMERO demo server</a> to test out the functionality with your own data. If happy, <a href="{{ site.baseurl }}/omero/institution/getting-started.html"> check how to start with OMERO in your institution.</a></p>
-                <p><a href="{{ site.baseurl }}/bio-formats/">Bio-Formats</a> lets you read image data from Java, <a href="https://imagej.net/Welcome" target="_blank">ImageJ</a>/<a href="https://fiji.sc/" target="_blank">Fiji</a>, GNU Octave/MATLAB, Python and R. If you're already using Fiji, it comes bundled with the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/users/index.html#using-bio-formats-with-imagej-and-fiji">Bio-Formats plugin</a> automatically.</p>
+                <p><a href="{{ site.baseurl }}/bio-formats/">Bio-Formats</a> lets you read image data from Java, <a href="https://imagej.net/Welcome" target="_blank">ImageJ</a>/<a href="https://fiji.sc/" target="_blank">Fiji</a>, GNU Octave/MATLAB, Python and R. If you're already using Fiji, it comes bundled with the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/users/index.html#using-bio-formats-with-imagej-and-fiji">Bio-Formats plugin</a> automatically.</p>
                 <hr class="invisible">
                 <p><a class="button small" href="https://www.openmicroscopy.org/qa2/registry/demo_account/">Sign up for Demo Server</a>
             </div>
@@ -114,7 +114,7 @@ <h5>Image Analysis</h5>
                     <li><a href="https://github.com/aoles/RBioFormats">R and Bio-Formats</a></li>
                     <li><a href="https://github.com/openmicroscopy/bio-formats-examples">How to consume Bio-Formats</a></li>
                     <li><a href="https://pypi.python.org/pypi/python-bioformats">Python wrapper for Bio-Formats</a></li>
-                    <li><a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/developers/matlab-dev.html">Bio-Formats and MATLAB</a></li>
+                    <li><a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/developers/matlab-dev.html">Bio-Formats and MATLAB</a></li>
                     <li><a href="https://github.com/ome/scripts">Scripts</a> and <a href="https://github.com/openmicroscopy/omero-example-scripts">more scripts</a></li>
                     <li>Testing environments for <a href="https://www.gnu.org/software/octave/">Octave</a>:
                         <ul>

licensing/index.html

@@ -30,7 +30,7 @@ <h2>Bio-Formats</h2>
         </div>
         <hr>
         <div class="row column">
-            <p>Under the terms of the <a href="http://www.gnu.org/copyleft/" target="_blank">GNU public "copyleft" license</a>, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive <a href="https://github.com/openmicroscopy/bioformats/blob/master/components/formats-bsd/LICENSE.txt" target="_blank">BSD-2 license</a> which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/supported-formats.html" target="_blank">supported formats table</a>. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software</a>.</p>
+            <p>Under the terms of the <a href="http://www.gnu.org/copyleft/" target="_blank">GNU public "copyleft" license</a>, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive <a href="https://github.com/openmicroscopy/bioformats/blob/master/components/formats-bsd/LICENSE.txt" target="_blank">BSD-2 license</a> which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the <a href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/supported-formats.html" target="_blank">supported formats table</a>. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software</a>.</p>
         </div>
         <!-- end -->
 

omero/features/import/index.html

@@ -30,7 +30,7 @@ <h4>Supported file formats</h4>
                     <p>Import any of the 140+ formats read by Bio-Formats including
                         microscopy, HCS, tissue scanner and graphics file
                         formats.</p>
-                    <a class="button hollow tiny" href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/supported-formats.html" target="_blank">View formats guide</a>
+                    <a class="button hollow tiny" href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/supported-formats.html" target="_blank">View formats guide</a>
                 </div>
                 <div class="omero-feature-container tall-content column text-center">
                     <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_command-line.svg">

omero/features/view/index.html

@@ -40,7 +40,7 @@ <h4>Volumetric viewer</h4>
                 <h4>Supported file formats</h4>
                 <p>Work with the 150+ formats read by Bio-Formats including
                     microscopy, HCS, tissue scanner and graphics file formats.</p>
-                <a class="button hollow tiny" href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/supported-formats.html" target="_blank">View formats guide</a>
+                <a class="button hollow tiny" href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/supported-formats.html" target="_blank">View formats guide</a>
             </div>
             <div class="omero-feature-container tall-content column text-center">
                 <img class="thumbnail omero-feature" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_rendering-settings.svg">

omero/institution/index.html

@@ -49,7 +49,7 @@ <h3 class="header-green">Key Features</h3>
             <div class="omero-key-feature-container medium-3 columns">
                 <h4>Supported File Formats</h4>
                 <p>OMERO imports all the formats read by Bio-Formats including microscopy, HCS, tissue scanner and graphics file formats. Over 140 in total.</p>
-                <a class="button hollow tiny" href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/supported-formats.html" target="_blank">View Supported Formats</a>
+                <a class="button hollow tiny" href="https://bio-formats.readthedocs.io/en/v{{ site.bf.version }}/supported-formats.html" target="_blank">View Supported Formats</a>
                 <a class="button hollow tiny" href="{{ site.baseurl }}/omero/features/import/">Learn more about importing</a>
             </div>
             <div class="medium-1 columns"><img class="omero-feature thumbnail" alt="OMERO feature" src="{{ site.baseurl }}/img/icons/omero-features-icons_manage.svg"></div>