Update documentation

b-heifets · Jun 24, 2024 · 92e858f · 92e858f
1 parent ebf5ebf
commit 92e858f
Show file tree

Hide file tree

Showing 103 changed files with 3 additions and 3 deletions.
diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
@@ -3,7 +3,7 @@ name: Deploy Sphinx Docs to GitHub Pages
 on:
   push:
     branches:
-      - dev
+      - main
 
 jobs:
   deploy:

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/installation.doctree b/unravel/docs/_build/doctrees/installation.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/brain_model.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/brain_model.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/cluster_summary.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/cluster_summary.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/cluster_validation.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/cluster_validation.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/crop.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/crop.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes.doctree
diff --git a/.../_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.doctree b/.../_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.doctree
diff --git a/.../_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.doctree b/.../_build/doctrees/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/effect_sizes/toc.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/effect_sizes/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/fdr.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/fdr.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/fdr_range.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/fdr_range.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/find_incongruent_clusters.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/find_incongruent_clusters.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/group_bilateral_data.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/group_bilateral_data.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/index.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/index.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/legend.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/legend.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/org_data.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/org_data.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/prism.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/prism.doctree
diff --git a/...docs/_build/doctrees/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.doctree b/...docs/_build/doctrees/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/stats.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/stats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/stats_table.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/stats_table.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/sunburst.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/sunburst.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/table.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/table.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/cluster_stats/toc.doctree b/unravel/docs/_build/doctrees/unravel/cluster_stats/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/argparse_utils.doctree b/unravel/docs/_build/doctrees/unravel/core/argparse_utils.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/argparse_utils_rich.doctree b/unravel/docs/_build/doctrees/unravel/core/argparse_utils_rich.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/config.doctree b/unravel/docs/_build/doctrees/unravel/core/config.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/img_io.doctree b/unravel/docs/_build/doctrees/unravel/core/img_io.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/img_tools.doctree b/unravel/docs/_build/doctrees/unravel/core/img_tools.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/toc.doctree b/unravel/docs/_build/doctrees/unravel/core/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/core/utils.doctree b/unravel/docs/_build/doctrees/unravel/core/utils.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/h5_to_tifs.doctree b/unravel/docs/_build/doctrees/unravel/image_io/h5_to_tifs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/img_to_npy.doctree b/unravel/docs/_build/doctrees/unravel/image_io/img_to_npy.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/io_img.doctree b/unravel/docs/_build/doctrees/unravel/image_io/io_img.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/io_nii.doctree b/unravel/docs/_build/doctrees/unravel/image_io/io_nii.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/metadata.doctree b/unravel/docs/_build/doctrees/unravel/image_io/metadata.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/nii_hd.doctree b/unravel/docs/_build/doctrees/unravel/image_io/nii_hd.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/nii_info.doctree b/unravel/docs/_build/doctrees/unravel/image_io/nii_info.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/nii_to_tifs.doctree b/unravel/docs/_build/doctrees/unravel/image_io/nii_to_tifs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/nii_to_zarr.doctree b/unravel/docs/_build/doctrees/unravel/image_io/nii_to_zarr.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/reorient_nii.doctree b/unravel/docs/_build/doctrees/unravel/image_io/reorient_nii.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/tif_to_tifs.doctree b/unravel/docs/_build/doctrees/unravel/image_io/tif_to_tifs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/toc.doctree b/unravel/docs/_build/doctrees/unravel/image_io/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_io/zarr_to_nii.doctree b/unravel/docs/_build/doctrees/unravel/image_io/zarr_to_nii.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/DoG.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/DoG.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/atlas/relabel_nii.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/atlas/relabel_nii.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/atlas/toc.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/atlas/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/atlas/wireframe.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/atlas/wireframe.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/avg.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/avg.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/bbox.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/bbox.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/extend.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/extend.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/max.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/max.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/pad.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/pad.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/rb.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/rb.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/spatial_averaging.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/spatial_averaging.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/toc.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/transpose_axes.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/transpose_axes.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/image_tools/unique_intensities.doctree b/unravel/docs/_build/doctrees/unravel/image_tools/unique_intensities.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/rstats.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/rstats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF_summary.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/rstats_mean_IF_summary.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/rstats_summary.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/rstats_summary.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/region_stats/toc.doctree b/unravel/docs/_build/doctrees/unravel/region_stats/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/affine_initializer.doctree b/unravel/docs/_build/doctrees/unravel/register/affine_initializer.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/reg.doctree b/unravel/docs/_build/doctrees/unravel/register/reg.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/reg_check.doctree b/unravel/docs/_build/doctrees/unravel/register/reg_check.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/reg_check_brain_mask.doctree b/unravel/docs/_build/doctrees/unravel/register/reg_check_brain_mask.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/reg_prep.doctree b/unravel/docs/_build/doctrees/unravel/register/reg_prep.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/register/toc.doctree b/unravel/docs/_build/doctrees/unravel/register/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/brain_mask.doctree b/unravel/docs/_build/doctrees/unravel/segment/brain_mask.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/copy_tifs.doctree b/unravel/docs/_build/doctrees/unravel/segment/copy_tifs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/ilastik_pixel_classification.doctree b/unravel/docs/_build/doctrees/unravel/segment/ilastik_pixel_classification.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/toc.doctree b/unravel/docs/_build/doctrees/unravel/segment/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/toc.doctree b/unravel/docs/_build/doctrees/unravel/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/unravel_commands.doctree b/unravel/docs/_build/doctrees/unravel/unravel_commands.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/aggregate_files_from_sample_dirs.doctree b/unravel/docs/_build/doctrees/unravel/utilities/aggregate_files_from_sample_dirs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/aggregate_files_w_recursive_search.doctree b/unravel/docs/_build/doctrees/unravel/utilities/aggregate_files_w_recursive_search.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/clean_tif_dirs.doctree b/unravel/docs/_build/doctrees/unravel/utilities/clean_tif_dirs.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/prepend_conditions.doctree b/unravel/docs/_build/doctrees/unravel/utilities/prepend_conditions.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/rename.doctree b/unravel/docs/_build/doctrees/unravel/utilities/rename.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree b/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/utilities/toggle_samples.doctree b/unravel/docs/_build/doctrees/unravel/utilities/toggle_samples.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/apply_mask.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/apply_mask.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/hemi_to_LR_avg.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/hemi_to_LR_avg.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/mirror.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/mirror.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/other/IF_outliers.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/other/IF_outliers.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/other/r_to_p.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/other/r_to_p.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/other/toc.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/other/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/toc.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats_prep.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats_prep.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/whole_to_LR_avg.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/whole_to_LR_avg.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/z_score.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/z_score.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/to_atlas.doctree b/unravel/docs/_build/doctrees/unravel/warp/to_atlas.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/to_native.doctree b/unravel/docs/_build/doctrees/unravel/warp/to_native.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/toc.doctree b/unravel/docs/_build/doctrees/unravel/warp/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/warp.doctree b/unravel/docs/_build/doctrees/unravel/warp/warp.doctree
diff --git a/unravel/docs/_build/html/_sources/guide.md.txt b/unravel/docs/_build/html/_sources/guide.md.txt
@@ -244,7 +244,7 @@ unravel_commands runs ./\<repo_root_dir\>/unravel/unravel_commands.py
 
 Its help guide is here: {py:mod}`unravel.unravel_commands` 
 
-Commands are defined in the `[project.scripts]` section of the [pyproject.toml](https://github.com/b-heifets/UNRAVEL/blob/dev/pyproject.toml) in the root directory of the UNRAVEL repository (repo).
+Commands are defined in the `[project.scripts]` section of the [pyproject.toml](https://github.com/b-heifets/UNRAVEL/blob/main/pyproject.toml) in the root directory of the UNRAVEL repository (repo).
 
 If new commands are added to run new scripts (a.k.a. modules), reinstall the unravel package with pip. 
 

diff --git a/unravel/docs/_build/html/guide.html b/unravel/docs/_build/html/guide.html
@@ -653,7 +653,7 @@ <h2>Common commands<a class="headerlink" href="#common-commands" title="Link to
 <p class="admonition-title">More info on commands</p>
 <p>unravel_commands runs ./&lt;repo_root_dir&gt;/unravel/unravel_commands.py</p>
 <p>Its help guide is here: <a class="reference internal" href="unravel/unravel_commands.html#module-unravel.unravel_commands" title="unravel.unravel_commands"><code class="xref py py-mod docutils literal notranslate"><span class="pre">unravel.unravel_commands</span></code></a></p>
-<p>Commands are defined in the <code class="docutils literal notranslate"><span class="pre">[project.scripts]</span></code> section of the <a class="reference external" href="https://github.com/b-heifets/UNRAVEL/blob/dev/pyproject.toml">pyproject.toml</a> in the root directory of the UNRAVEL repository (repo).</p>
+<p>Commands are defined in the <code class="docutils literal notranslate"><span class="pre">[project.scripts]</span></code> section of the <a class="reference external" href="https://github.com/b-heifets/UNRAVEL/blob/main/pyproject.toml">pyproject.toml</a> in the root directory of the UNRAVEL repository (repo).</p>
 <p>If new commands are added to run new scripts (a.k.a. modules), reinstall the unravel package with pip.</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>&lt;path<span class="w"> </span>to<span class="w"> </span>the<span class="w"> </span>root<span class="w"> </span>directory<span class="w"> </span>of<span class="w"> </span>the<span class="w"> </span>UNRAVEL<span class="w"> </span>repo&gt;
 pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.