yeatmanlab · arokem · Nov 13, 2023 · Nov 13, 2023 · Nov 13, 2023
diff --git a/docs/Makefile b/docs/Makefile
@@ -36,7 +36,7 @@ ARTIFACTS := $(strip \
 distclean: clean
 	@echo Removing files created by sphinx-build
 	rm -rf $(BUILDDIR)
-	rm -f $(SOURCEDIR)/usage/config.rst
+	rm -f $(SOURCEDIR)/usage/howto/config.rst
 	rm -rf $(SOURCEDIR)/auto_examples/
 	$(if $(ARTIFACTS),rm -f $(ARTIFACTS))
 

diff --git a/docs/source/explanations/_static/tract_modeling2.png b/docs/source/explanations/_static/tract_modeling2.png
diff --git a/docs/source/explanations/cleaning.rst b/docs/source/explanations/cleaning.rst
diff --git a/docs/source/explanations/tractometry_pipeline.rst b/docs/source/explanations/tractometry_pipeline.rst
@@ -16,20 +16,20 @@ AFQ Tractometry Pipeline
 ..      - |rArr| `Profiling <https://dipy.org/documentation/1.4.0./reference/dipy.stats/#afq-profile>`_
 ..      - |rArr| `Visualization <http://yeatmanlab.github.io/pyAFQ/autoapi/AFQ/viz/index.html>`_
 
-.. figure:: _static/tract_tractography.png
+.. figure:: _static/tract_modeling2.png
    :figclass: top-image
-   :target: tractography.html
+   :target: modeling.html
 
-   :ref:`tractography`
+   :ref:`modeling`
 
 .. figure:: _static/right_arrow.png
    :figclass: right-arrow
 
-.. figure:: _static/tract_modeling.png
+.. figure:: _static/tract_tractography.png
    :figclass: top-image
-   :target: modeling.html
+   :target: tractography.html
 
-   :ref:`modeling`
+   :ref:`tractography`
 
 .. figure:: _static/right_arrow.png
    :figclass: right-arrow
@@ -43,29 +43,11 @@ AFQ Tractometry Pipeline
 .. image:: _static/down_arrow.png
    :width: 8%
 
-.. figure:: _static/tract_cleaning.png
-   :figclass: bottom-image
-   :target: cleaning.html
-
-   :ref:`cleaning`
-
-.. figure:: _static/left_arrow.png
-   :figclass: left-arrow
-
-.. figure:: _static/tract_profiling.png
+.. figure:: _static/tract_visualization.png
    :figclass: bottom-image
    :target: profiling.html
 
    :ref:`profiling`
 
-.. figure:: _static/left_arrow.png
-   :figclass: left-arrow
-
-.. figure:: _static/tract_visualization.png
-   :figclass: bottom-image
-   :target: visualization.html
-
-   :ref:`visualization`
-
 
 
diff --git a/docs/source/explanations/visualization.rst b/docs/source/explanations/visualization.rst
diff --git a/docs/source/howto/index.rst b/docs/source/howto/index.rst
@@ -8,7 +8,7 @@ software.
     :maxdepth: 2
 
     installation_guide
-    usage
+    usage/index
     contributing
     developing/index
     getting_help

diff --git a/docs/source/howto/converter.rst → docs/source/howto/usage/converter.rst b/docs/source/howto/converter.rst → docs/source/howto/usage/converter.rst
diff --git a/docs/source/howto/data.rst → docs/source/howto/usage/data.rst b/docs/source/howto/data.rst → docs/source/howto/usage/data.rst
diff --git a/docs/source/howto/docker.rst → docs/source/howto/usage/docker.rst b/docs/source/howto/docker.rst → docs/source/howto/usage/docker.rst
diff --git a/docs/source/howto/usage/index.rst b/docs/source/howto/usage/index.rst
@@ -25,15 +25,9 @@ Examples of using the API are provided in the :ref:`examples` documentation sect
     :maxdepth: 2
 
     data
-    usage
     kwargs
-    methods
-    bundledict
     config
-    viz_backend
     mask
-    mapping
     scalars
     converter
-    tracking
     docker
diff --git a/docs/source/howto/scalars.rst → docs/source/howto/usage/scalars.rst b/docs/source/howto/scalars.rst → docs/source/howto/usage/scalars.rst
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -8,5 +8,5 @@ Reference Documentation
     bundledict
     kwargs
     methods
-    tracking
-    viz_backend
+    viz_backend
+    mapping
diff --git a/docs/source/reference/kwargs.rst b/docs/source/reference/kwargs.rst
@@ -99,10 +99,9 @@ brain_mask_definition: instance from `AFQ.definitions.image`, optional
 	If None, use B0Image()
 	Default: None
 
-bundle_info: strings, dict, or BundleDict, optional
-	List of bundle names to include in segmentation,
-	or a bundle dictionary (see BundleDict for inspiration),
-	or a BundleDict. See `Defining Custom Bundle Dictionaries`
+bundle_info: dict or BundleDict, optional
+	A dictionary or BundleDict for use in segmentation.
+	See `Defining Custom Bundle Dictionaries`
 	in the `usage` section of pyAFQ's documentation for details.
 	If None, will get all appropriate bundles for the chosen
 	segmentation algorithm.

diff --git a/docs/source/explanations/mapping.rst → docs/source/reference/mapping.rst b/docs/source/explanations/mapping.rst → docs/source/reference/mapping.rst
diff --git a/docs/source/reference/tracking.rst b/docs/source/reference/tracking.rst