deploy: 7991f14

talmolab · Dec 19, 2024 · 7e9354b · 7e9354b
1 parent cba51d6
commit 7e9354b
Showing 184 changed files with 26,732 additions and 5,883 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
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+config: 061a3cab3e5ef79e32ad32ceda8f5410
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
@@ -3,13 +3,13 @@
 <!DOCTYPE html>
 
 
-<html >
+<html lang="en" >
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>Contributor Covenant Code of Conduct &#8212; SLEAP (v1.3.3)</title>
+    <title>Contributor Covenant Code of Conduct &#8212; SLEAP (v1.4.1)</title>
 
 
 
@@ -32,8 +32,8 @@
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-    <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="_static/mystnb.css" />
+    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tabs.css" />
 
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@@ -42,22 +42,19 @@
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
+    <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
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+    <script src="_static/sphinx_highlight.js"></script>
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     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
-  <meta name="docsearch:language" content="None"/>
+  <meta name="docsearch:language" content="en"/>
   </head>
 
 
@@ -163,6 +160,7 @@
 <li class="toctree-l2"><a class="reference internal" href="guides/colab.html">Run training and inference on Colab</a></li>
 <li class="toctree-l2"><a class="reference internal" href="guides/custom-training.html">Creating a custom training profile</a></li>
 <li class="toctree-l2"><a class="reference internal" href="guides/remote.html">Running SLEAP remotely</a></li>
+<li class="toctree-l2"><a class="reference internal" href="guides/bonsai.html">Using Bonsai with SLEAP</a></li>
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="notebooks/index.html">Notebooks</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
@@ -333,13 +331,13 @@ <h2> Contents </h2>
                 <article class="bd-article" role="main">
 
   <section class="tex2jax_ignore mathjax_ignore" id="contributor-covenant-code-of-conduct">
-<h1>Contributor Covenant Code of Conduct<a class="headerlink" href="#contributor-covenant-code-of-conduct" title="Permalink to this headline">#</a></h1>
+<h1>Contributor Covenant Code of Conduct<a class="headerlink" href="#contributor-covenant-code-of-conduct" title="Permalink to this heading">#</a></h1>
 <section id="our-pledge">
-<h2>Our Pledge<a class="headerlink" href="#our-pledge" title="Permalink to this headline">#</a></h2>
+<h2>Our Pledge<a class="headerlink" href="#our-pledge" title="Permalink to this heading">#</a></h2>
 <p>In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.</p>
 </section>
 <section id="our-standards">
-<h2>Our Standards<a class="headerlink" href="#our-standards" title="Permalink to this headline">#</a></h2>
+<h2>Our Standards<a class="headerlink" href="#our-standards" title="Permalink to this heading">#</a></h2>
 <p>Examples of behavior that contributes to creating a positive environment include:</p>
 <ul class="simple">
 <li><p>Using welcoming and inclusive language</p></li>
@@ -358,21 +356,21 @@ <h2>Our Standards<a class="headerlink" href="#our-standards" title="Permalink to
 </ul>
 </section>
 <section id="our-responsibilities">
-<h2>Our Responsibilities<a class="headerlink" href="#our-responsibilities" title="Permalink to this headline">#</a></h2>
+<h2>Our Responsibilities<a class="headerlink" href="#our-responsibilities" title="Permalink to this heading">#</a></h2>
 <p>Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.</p>
 <p>Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.</p>
 </section>
 <section id="scope">
-<h2>Scope<a class="headerlink" href="#scope" title="Permalink to this headline">#</a></h2>
+<h2>Scope<a class="headerlink" href="#scope" title="Permalink to this heading">#</a></h2>
 <p>This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.</p>
 </section>
 <section id="enforcement">
-<h2>Enforcement<a class="headerlink" href="#enforcement" title="Permalink to this headline">#</a></h2>
+<h2>Enforcement<a class="headerlink" href="#enforcement" title="Permalink to this heading">#</a></h2>
 <p>Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at <a class="reference external" href="mailto:talmo&#37;&#52;&#48;salk&#46;edu">talmo<span>&#64;</span>salk<span>&#46;</span>edu</a>. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.</p>
 <p>Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.</p>
 </section>
 <section id="attribution">
-<h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to this headline">#</a></h2>
+<h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to this heading">#</a></h2>
 <p>This Code of Conduct is adapted from the <a class="reference external" href="https://contributor-covenant.org">Contributor Covenant</a>, version 1.4, available at <a class="reference external" href="https://contributor-covenant.org/version/1/4/">https://contributor-covenant.org/version/1/4</a></p>
 </section>
 </section>
@@ -436,7 +434,7 @@ <h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to thi
 
   <p class="copyright">
 
-      © Copyright 2019–2023, Talmo Lab.
+      © Copyright 2019–2024, Talmo Lab.
       <br/>
 
   </p>

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
@@ -3,13 +3,13 @@
 <!DOCTYPE html>
 
 
-<html >
+<html lang="en" >
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>Contributing to SLEAP &#8212; SLEAP (v1.3.3)</title>
+    <title>Contributing to SLEAP &#8212; SLEAP (v1.4.1)</title>
 
 
 
@@ -32,8 +32,8 @@
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" href="_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="_static/mystnb.css" />
+    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tabs.css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
@@ -42,22 +42,19 @@
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
+    <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="_static/doctools.js"></script>
+    <script src="_static/sphinx_highlight.js"></script>
     <script src="_static/clipboard.min.js"></script>
     <script src="_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="_static/togglebutton.js"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'CONTRIBUTING';</script>
     <link rel="canonical" href="/develop/CONTRIBUTING.html" />
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
-  <meta name="docsearch:language" content="None"/>
+  <meta name="docsearch:language" content="en"/>
   </head>
 
 
@@ -163,6 +160,7 @@
 <li class="toctree-l2"><a class="reference internal" href="guides/colab.html">Run training and inference on Colab</a></li>
 <li class="toctree-l2"><a class="reference internal" href="guides/custom-training.html">Creating a custom training profile</a></li>
 <li class="toctree-l2"><a class="reference internal" href="guides/remote.html">Running SLEAP remotely</a></li>
+<li class="toctree-l2"><a class="reference internal" href="guides/bonsai.html">Using Bonsai with SLEAP</a></li>
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="notebooks/index.html">Notebooks</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
@@ -339,11 +337,11 @@ <h2> Contents </h2>
                 <article class="bd-article" role="main">
 
   <section class="tex2jax_ignore mathjax_ignore" id="contributing-to-sleap">
-<h1>Contributing to SLEAP<a class="headerlink" href="#contributing-to-sleap" title="Permalink to this headline">#</a></h1>
+<h1>Contributing to SLEAP<a class="headerlink" href="#contributing-to-sleap" title="Permalink to this heading">#</a></h1>
 <p>As our community grows it is important to adhere to a set of contribution guidelines. These guidelines may change as needed. Please feel free to propose changes to source code in a pull request!</p>
 <section id="table-of-contents">
-<h2>Table Of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">#</a></h2>
-<ol class="simple">
+<h2>Table Of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this heading">#</a></h2>
+<ol class="arabic simple">
 <li><p><a class="reference internal" href="#code-of-conduct"><span class="std std-doc">Code of Conduct</span></a></p></li>
 <li><p><a class="reference internal" href="#contributing"><span class="std std-doc">Contributing</span></a></p>
 <ul class="simple">
@@ -356,21 +354,21 @@ <h2>Table Of Contents<a class="headerlink" href="#table-of-contents" title="Perm
 </ol>
 </section>
 <section id="code-of-conduct">
-<h2>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Permalink to this headline">#</a></h2>
+<h2>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Permalink to this heading">#</a></h2>
 <p>Everyone contributing to SLEAP is governed by the <a class="reference internal" href="CODE_OF_CONDUCT.html"><span class="doc std std-doc">SLEAP Code of Conduct</span></a>. As such, all are expected to abide by this code. Please report any unacceptable behavior to <code class="docutils literal notranslate"><span class="pre">talmo&#64;salk.edu</span></code>.</p>
 </section>
 <section id="contributing">
-<h2>Contributing<a class="headerlink" href="#contributing" title="Permalink to this headline">#</a></h2>
+<h2>Contributing<a class="headerlink" href="#contributing" title="Permalink to this heading">#</a></h2>
 <p>Github has made it easy to separate issues from discussions. Generally speaking, if something warrants a pull request (e.g. bug fixes, TODOs) it should be submitted as an issue. Conversely, general questions about usage and improvement ideas should go into discussions. These both act as staging areas before adding the items to the SLEAP Roadmap. Once added to the Roadmap, items can be given priority, status, assignee(s), etc.</p>
 <section id="issues">
-<h3>Issues<a class="headerlink" href="#issues" title="Permalink to this headline">#</a></h3>
+<h3>Issues<a class="headerlink" href="#issues" title="Permalink to this heading">#</a></h3>
 <ul class="simple">
 <li><p>Check <a class="reference external" href="https://github.com/talmolab/sleap/issues">open/closed issues</a>, <a class="reference external" href="https://github.com/talmolab/sleap/discussions/categories/ideas">ideas</a>, and <a class="reference external" href="https://github.com/talmolab/sleap/discussions/categories/help">the help page</a> to make sure issue doesn’t already exist / has been solved.</p></li>
 <li><p>Create new issue using the <a class="reference external" href="https://github.com/talmolab/sleap/blob/arlo/contributing_guide/.github/ISSUE_TEMPLATE/bug_report.md">issue template</a>.</p></li>
 </ul>
 </section>
 <section id="discussions">
-<h3>Discussions<a class="headerlink" href="#discussions" title="Permalink to this headline">#</a></h3>
+<h3>Discussions<a class="headerlink" href="#discussions" title="Permalink to this heading">#</a></h3>
 <ul class="simple">
 <li><p>This is a place to go to ask questions and propose new ideas.</p></li>
 <li><p>3 categories: Help, Ideas, General</p>
@@ -383,8 +381,8 @@ <h3>Discussions<a class="headerlink" href="#discussions" title="Permalink to thi
 </ul>
 </section>
 <section id="pull-requests">
-<h3>Pull Requests<a class="headerlink" href="#pull-requests" title="Permalink to this headline">#</a></h3>
-<ol class="simple">
+<h3>Pull Requests<a class="headerlink" href="#pull-requests" title="Permalink to this heading">#</a></h3>
+<ol class="arabic simple">
 <li><p>Install source code <a class="reference external" href="https://sleap.ai/installation.html#conda-from-source"><code class="docutils literal notranslate"><span class="pre">develop</span></code> branch</a> and follow instructions to create conda env, etc.</p></li>
 <li><p>Create a fork from the <code class="docutils literal notranslate"><span class="pre">develop</span></code> branch.</p>
 <ul class="simple">
@@ -424,14 +422,14 @@ <h3>Pull Requests<a class="headerlink" href="#pull-requests" title="Permalink to
 </section>
 </section>
 <section id="style-guides">
-<h2>Style Guides<a class="headerlink" href="#style-guides" title="Permalink to this headline">#</a></h2>
+<h2>Style Guides<a class="headerlink" href="#style-guides" title="Permalink to this heading">#</a></h2>
 <ul class="simple">
 <li><p><strong>Lint</strong> - <a class="reference external" href="https://black.readthedocs.io/en/stable/">Black</a> version 21.6b0 (see <a class="reference external" href="https://github.com/talmolab/sleap/blob/develop/dev_requirements.txt">dev_requirements</a> for any changes).</p></li>
 <li><p><strong>Code</strong> - Generally follow <a class="reference external" href="https://peps.python.org/pep-0008/">PEP8</a>. Type hinting is encouraged.</p></li>
 <li><p><strong>Documentation</strong> - Use <span class="xref myst">Google-style comments and docstrings</span> to document code.</p></li>
 </ul>
 <section id="thank-you-for-contributing-to-sleap">
-<h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-for-contributing-to-sleap" title="Permalink to this headline">#</a></h3>
+<h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-for-contributing-to-sleap" title="Permalink to this heading">#</a></h3>
 <p>:heart:</p>
 </section>
 </section>
@@ -502,7 +500,7 @@ <h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-f
 
   <p class="copyright">
 
-      © Copyright 2019–2023, Talmo Lab.
+      © Copyright 2019–2024, Talmo Lab.
       <br/>
 
   </p>

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diff --git a/_images/d2b61f464140b9d880c782c1347c1961ff1a43b6b62847e515dadb3047025028.png b/_images/d2b61f464140b9d880c782c1347c1961ff1a43b6b62847e515dadb3047025028.png
diff --git a/_images/d8517178d972bc0703903cfab70470e9c921794a84a0af190ce345f8321a14e9.png b/_images/d8517178d972bc0703903cfab70470e9c921794a84a0af190ce345f8321a14e9.png
diff --git a/_images/dc4bfaee117747c1eeba0b62c375704e720b95ba9694ecd512a2cc28d501fbab.png b/_images/dc4bfaee117747c1eeba0b62c375704e720b95ba9694ecd512a2cc28d501fbab.png
diff --git a/_sources/api.rst b/_sources/api.rst
@@ -57,6 +57,12 @@ Developer API
    sleap.nn.data.resizing
    sleap.nn.data.training
    sleap.nn.data.utils
+   sleap.nn.config.data
+   sleap.nn.config.model
+   sleap.nn.config.optimization
+   sleap.nn.config.outputs
+   sleap.nn.config.training_job
+   sleap.nn.config.utils
    sleap.nn.architectures.common
    sleap.nn.architectures.encoder_decoder
    sleap.nn.architectures.hourglass
@@ -66,15 +72,8 @@ Developer API
    sleap.nn.architectures.resnet
    sleap.nn.architectures.unet
    sleap.nn.architectures.upsampling
-   sleap.nn.config.data
-   sleap.nn.config.model
-   sleap.nn.config.optimization
-   sleap.nn.config.outputs
-   sleap.nn.config.training_job
-   sleap.nn.config.utils
    sleap.nn.tracker.components
    sleap.nn.tracker.kalman
-   sleap.io.asyncvideo
    sleap.io.convert
    sleap.io.dataset
    sleap.io.legacy