update docs

docs/intensity_normalization.cli.rst

@@ -0,0 +1,101 @@
+intensity\_normalization.cli package
+====================================
+
+Submodules
+----------
+
+intensity\_normalization.cli.coregister module
+----------------------------------------------
+
+.. automodule:: intensity_normalization.cli.coregister
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.fcm module
+---------------------------------------
+
+.. automodule:: intensity_normalization.cli.fcm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.histogram module
+---------------------------------------------
+
+.. automodule:: intensity_normalization.cli.histogram
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.kde module
+---------------------------------------
+
+.. automodule:: intensity_normalization.cli.kde
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.lsq module
+---------------------------------------
+
+.. automodule:: intensity_normalization.cli.lsq
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.nyul module
+----------------------------------------
+
+.. automodule:: intensity_normalization.cli.nyul
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.preprocess module
+----------------------------------------------
+
+.. automodule:: intensity_normalization.cli.preprocess
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.ravel module
+-----------------------------------------
+
+.. automodule:: intensity_normalization.cli.ravel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.tissue\_membership module
+------------------------------------------------------
+
+.. automodule:: intensity_normalization.cli.tissue_membership
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.whitestripe module
+-----------------------------------------------
+
+.. automodule:: intensity_normalization.cli.whitestripe
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+intensity\_normalization.cli.zscore module
+------------------------------------------
+
+.. automodule:: intensity_normalization.cli.zscore
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: intensity_normalization.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/intensity_normalization.rst

@@ -7,17 +7,18 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
+   intensity_normalization.cli
    intensity_normalization.normalize
    intensity_normalization.plot
    intensity_normalization.util
 
 Submodules
 ----------
 
-intensity\_normalization.cli module
------------------------------------
+intensity\_normalization.base\_cli module
+-----------------------------------------
 
-.. automodule:: intensity_normalization.cli
+.. automodule:: intensity_normalization.base_cli
    :members:
    :undoc-members:
    :show-inheritance:
@@ -30,14 +31,6 @@ intensity\_normalization.errors module
    :undoc-members:
    :show-inheritance:
 
-intensity\_normalization.parse module
--------------------------------------
-
-.. automodule:: intensity_normalization.parse
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 intensity\_normalization.type module
 ------------------------------------