deploy: c9113da

talmolab · Jun 30, 2023 · a5f7113 · a5f7113
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 408a4bc092f16fdf637adfcea5e6267f
+config: db6ef5d9def7f10b9e6dbff766d782a1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
@@ -9,7 +9,7 @@
     <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/" />
 
-    <title>Contributor Covenant Code of Conduct &#8212; SLEAP (v1.3.0)</title>
+    <title>Contributor Covenant Code of Conduct &#8212; SLEAP (v1.3.1)</title>
 
 
 
@@ -19,12 +19,12 @@
   </script>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
-<link href="_static/styles/bootstrap.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
+  <link href="_static/styles/theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="_static/styles/bootstrap.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />
 
 
-  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
+  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=e353d410970836974a52" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
@@ -36,8 +36,8 @@
     <link rel="stylesheet" type="text/css" href="_static/mystnb.css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=12da95d707ffb74b382d" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=12da95d707ffb74b382d" />
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
@@ -384,9 +384,15 @@ <h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to thi
 
 
                 <footer class="bd-footer-article">
-                  <!-- Previous / next buttons -->
+
+<div class="footer-article-items footer-article__inner">
+
+    <div class="footer-article-item"><!-- Previous / next buttons -->
 <div class="prev-next-area">
+</div></div>
+
 </div>
+
                 </footer>
 
             </div>
@@ -415,7 +421,7 @@ <h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to thi
 
           </div>
           <footer class="bd-footer-content">
-            <div class="bd-footer-content__inner">
+
 <div class="bd-footer-content__inner container">
 
   <div class="footer-item">
@@ -445,7 +451,7 @@ <h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to thi
 
   </div>
 
-</div></div>
+</div>
           </footer>
 
 
@@ -454,8 +460,8 @@ <h2>Attribution<a class="headerlink" href="#attribution" title="Permalink to thi
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="_static/scripts/bootstrap.js?digest=12da95d707ffb74b382d"></script>
-<script src="_static/scripts/pydata-sphinx-theme.js?digest=12da95d707ffb74b382d"></script>
+  <script src="_static/scripts/bootstrap.js?digest=e353d410970836974a52"></script>
+<script src="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
@@ -9,7 +9,7 @@
     <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/" />
 
-    <title>Contributing to SLEAP &#8212; SLEAP (v1.3.0)</title>
+    <title>Contributing to SLEAP &#8212; SLEAP (v1.3.1)</title>
 
 
 
@@ -19,12 +19,12 @@
   </script>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
-<link href="_static/styles/bootstrap.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
+  <link href="_static/styles/theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="_static/styles/bootstrap.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />
 
 
-  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=12da95d707ffb74b382d" rel="stylesheet" />
+  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=e353d410970836974a52" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
@@ -36,8 +36,8 @@
     <link rel="stylesheet" type="text/css" href="_static/mystnb.css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=12da95d707ffb74b382d" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=12da95d707ffb74b382d" />
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
@@ -444,9 +444,15 @@ <h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-f
 
 
                 <footer class="bd-footer-article">
-                  <!-- Previous / next buttons -->
+
+<div class="footer-article-items footer-article__inner">
+
+    <div class="footer-article-item"><!-- Previous / next buttons -->
 <div class="prev-next-area">
+</div></div>
+
 </div>
+
                 </footer>
 
             </div>
@@ -481,7 +487,7 @@ <h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-f
 
           </div>
           <footer class="bd-footer-content">
-            <div class="bd-footer-content__inner">
+
 <div class="bd-footer-content__inner container">
 
   <div class="footer-item">
@@ -511,7 +517,7 @@ <h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-f
 
   </div>
 
-</div></div>
+</div>
           </footer>
 
 
@@ -520,8 +526,8 @@ <h3>Thank you for contributing to SLEAP!<a class="headerlink" href="#thank-you-f
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="_static/scripts/bootstrap.js?digest=12da95d707ffb74b382d"></script>
-<script src="_static/scripts/pydata-sphinx-theme.js?digest=12da95d707ffb74b382d"></script>
+  <script src="_static/scripts/bootstrap.js?digest=e353d410970836974a52"></script>
+<script src="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/_sources/api.rst b/_sources/api.rst
@@ -19,6 +19,13 @@ Developer API
    sleap.message
    sleap.skeleton
    sleap.util
+   sleap.info.align
+   sleap.info.feature_suggestions
+   sleap.info.labels
+   sleap.info.metrics
+   sleap.info.summary
+   sleap.info.trackcleaner
+   sleap.info.write_tracking_h5
    sleap.io.asyncvideo
    sleap.io.convert
    sleap.io.dataset
@@ -43,13 +50,6 @@ Developer API
    sleap.io.format.nix
    sleap.io.format.sleap_analysis
    sleap.io.format.text
-   sleap.info.align
-   sleap.info.feature_suggestions
-   sleap.info.labels
-   sleap.info.metrics
-   sleap.info.summary
-   sleap.info.trackcleaner
-   sleap.info.write_tracking_h5
    sleap.nn.callbacks
    sleap.nn.evals
    sleap.nn.heads
@@ -64,21 +64,6 @@ Developer API
    sleap.nn.training
    sleap.nn.utils
    sleap.nn.viz
-   sleap.nn.architectures.common
-   sleap.nn.architectures.encoder_decoder
-   sleap.nn.architectures.hourglass
-   sleap.nn.architectures.hrnet
-   sleap.nn.architectures.leap
-   sleap.nn.architectures.pretrained_encoders
-   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.data.augmentation
    sleap.nn.data.confidence_maps
    sleap.nn.data.dataset_ops
@@ -96,5 +81,20 @@ Developer API
    sleap.nn.data.resizing
    sleap.nn.data.training
    sleap.nn.data.utils
+   sleap.nn.architectures.common
+   sleap.nn.architectures.encoder_decoder
+   sleap.nn.architectures.hourglass
+   sleap.nn.architectures.hrnet
+   sleap.nn.architectures.leap
+   sleap.nn.architectures.pretrained_encoders
+   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
diff --git a/_sources/guides/cli.md b/_sources/guides/cli.md
@@ -102,9 +102,9 @@ optional arguments:
   -u, --unrag UNRAG
                         Convert ragged tensors into regular tensors with NaN padding.
                         Defaults to True.
-  -i, --max_instances MAX_INSTANCES
+  -n, --max_instances MAX_INSTANCES
                         Limit maximum number of instances in multi-instance models.
-                        Defaults to None.
+                        Not available for ID models. Defaults to None.
 ```
 
 ## Inference and Tracking
@@ -178,6 +178,9 @@ optional arguments:
                         if retracking predictions.
   --no-empty-frames     Clear any empty frames that did not have any detected
                         instances before saving to output.
+  -n, --max_instances MAX_INSTANCES
+                        Limit maximum number of instances in multi-instance models.
+                        Not available for ID models. Defaults to None.
   --verbosity {none,rich,json}
                         Verbosity of inference progress reporting. 'none' does
                         not output anything during inference, 'rich' displays