Updated guide, index page, and order of packages

b-heifets · Jun 10, 2024 · a33ee3d · a33ee3d
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diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
@@ -18,6 +18,14 @@ jobs:
       with:
         python-version: '3.x'
 
+    - name: Cache pip dependencies
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+  
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/unravel/docs/_build/doctrees/environment.pickle b/unravel/docs/_build/doctrees/environment.pickle
diff --git a/unravel/docs/_build/doctrees/guide.doctree b/unravel/docs/_build/doctrees/guide.doctree
diff --git a/unravel/docs/_build/doctrees/index.doctree b/unravel/docs/_build/doctrees/index.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.cluster_stats.doctree b/unravel/docs/_build/doctrees/unravel.cluster_stats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.cluster_stats.effect_sizes.doctree b/unravel/docs/_build/doctrees/unravel.cluster_stats.effect_sizes.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.core.doctree b/unravel/docs/_build/doctrees/unravel.core.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.doctree b/unravel/docs/_build/doctrees/unravel.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.image_io.doctree b/unravel/docs/_build/doctrees/unravel.image_io.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.image_tools.atlas.doctree b/unravel/docs/_build/doctrees/unravel.image_tools.atlas.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.image_tools.doctree b/unravel/docs/_build/doctrees/unravel.image_tools.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.region_stats.doctree b/unravel/docs/_build/doctrees/unravel.region_stats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.register.doctree b/unravel/docs/_build/doctrees/unravel.register.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.segment.doctree b/unravel/docs/_build/doctrees/unravel.segment.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.utilities.doctree b/unravel/docs/_build/doctrees/unravel.utilities.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.voxel_stats.doctree b/unravel/docs/_build/doctrees/unravel.voxel_stats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel.warp.doctree b/unravel/docs/_build/doctrees/unravel.warp.doctree
diff --git a/unravel/docs/_build/html/_modules/index.html b/unravel/docs/_build/html/_modules/index.html
@@ -28,7 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/brain_model.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/brain_model.html
@@ -28,7 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/crop_clusters.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/crop_clusters.html
@@ -28,7 +28,7 @@
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     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes.html
@@ -28,7 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />
@@ -382,8 +382,8 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 
 <span class="s2">The effect size is calculated as the unbiased Hedge</span><span class="se">\&#39;</span><span class="s2">s g effect sizes (corrected for sample size): </span>
 
-<span class="s2">Hegde&#39;\s g = ((c2-c1)/spooled*corr_factor)</span>
-<span class="s2">CI = Hedge&#39;s g +/- t * SE</span>
+<span class="s2">Hedges&#39; g = ((c2-c1)/spooled*corr_factor)</span>
+<span class="s2">CI = Hedges&#39; g +/- t * SE</span>
 <span class="s2">0.2 - 0.5 = small effect; 0.5 - 0.8 = medium; 0.8+ = large&quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
 

diff --git a/...build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html b/...build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html
@@ -28,7 +28,7 @@
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     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />
@@ -384,8 +384,8 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__abso
 
 <span class="s2">The effect size is calculated as the unbiased Hedge</span><span class="se">\&#39;</span><span class="s2">s g effect sizes (corrected for sample size): </span>
 
-<span class="s2">Hegde&#39;\s g = ((c2-c1)/spooled*corr_factor)</span>
-<span class="s2">CI = Hedge&#39;s g +/- t * SE</span>
+<span class="s2">Hedges&#39; g = ((c2-c1)/spooled*corr_factor)</span>
+<span class="s2">CI = Hedges&#39; g +/- t * SE</span>
 <span class="s2">0.2 - 0.5 = small effect; 0.5 - 0.8 = medium; 0.8+ = large&quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
 

diff --git a/...build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html b/...build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html
@@ -28,7 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />
@@ -384,8 +384,8 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__rela
 
 <span class="s2">The effect size is calculated as the unbiased Hedge</span><span class="se">\&#39;</span><span class="s2">s g effect sizes (corrected for sample size): </span>
 
-<span class="s2">Hegde&#39;\s g = ((c2-c1)/spooled*corr_factor)</span>
-<span class="s2">CI = Hedge&#39;s g +/- t * SE</span>
+<span class="s2">Hedges&#39; g = ((c2-c1)/spooled*corr_factor)</span>
+<span class="s2">CI = Hedges&#39; g +/- t * SE</span>
 <span class="s2">0.2 - 0.5 = small effect; 0.5 - 0.8 = medium; 0.8+ = large&quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
 

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/fdr.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/fdr.html
@@ -28,7 +28,7 @@
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     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/fdr_range.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/fdr_range.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/find_incongruent_clusters.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/find_incongruent_clusters.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/group_bilateral_data.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/group_bilateral_data.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/legend.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/legend.html
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+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/org_data.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/org_data.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/prism.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/prism.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/...cs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html b/...cs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/stats.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/stats.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/stats_table.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/stats_table.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/sunburst.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/sunburst.html
@@ -28,7 +28,7 @@
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html
@@ -28,7 +28,7 @@
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/valid_clusters_summary.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/valid_clusters_summary.html
@@ -28,7 +28,7 @@
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+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/validate_clusters.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/validate_clusters.html
@@ -28,7 +28,7 @@
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
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diff --git a/unravel/docs/_build/html/_modules/unravel/core/argparse_utils.html b/unravel/docs/_build/html/_modules/unravel/core/argparse_utils.html
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diff --git a/unravel/docs/_build/html/_modules/unravel/core/argparse_utils_rich.html b/unravel/docs/_build/html/_modules/unravel/core/argparse_utils_rich.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/core/config.html b/unravel/docs/_build/html/_modules/unravel/core/config.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/core/img_io.html b/unravel/docs/_build/html/_modules/unravel/core/img_io.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/core/img_tools.html b/unravel/docs/_build/html/_modules/unravel/core/img_tools.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/core/utils.html b/unravel/docs/_build/html/_modules/unravel/core/utils.html
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-    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=122099b5" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />

diff --git a/unravel/docs/_build/html/_modules/unravel/image_io/h5_to_tifs.html b/unravel/docs/_build/html/_modules/unravel/image_io/h5_to_tifs.html
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+    <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
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   <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />