DOC: Display API per module

README.md

@@ -4,6 +4,7 @@
 [![codecov](https://codecov.io/gh/poldracklab/nitransforms/branch/master/graph/badge.svg)](https://codecov.io/gh/poldracklab/nitransforms)
 [![doi](https://img.shields.io/badge/doi-10.31219%2Fosf.io%2F8aq7b-blue.svg)](https://doi.org/10.31219/osf.io/8aq7b)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/poldracklab/nitransforms/master?filepath=docs%2Fnotebooks%2F)
+[![Docs](https://readthedocs.org/projects/nitransforms/badge/?version=latest)](http://nitransforms.readthedocs.io/en/latest/?badge=latest)
 
 A development repo for [nipy/nibabel#656](https://github.com/nipy/nibabel/pull/656)
 
@@ -23,6 +24,6 @@ to apply transforms generated by the most popular neuroimaging packages and libr
 (AFNI, FSL, FreeSurfer, ITK, and SPM).
 The proposed software is subject to continuous integration tests to check the
 compatibility with each supported tool after every change to the code base.
-Compatibility between software tools and imaging formats is a necessary bridge 
+Compatibility between software tools and imaging formats is a necessary bridge
 to ensure the reproducibility of results and enable the optimization and evaluation
 of current image processing and analysis workflows.

docs/_api/base.rst

@@ -0,0 +1,6 @@
+====
+Base
+====
+
+.. automodule:: nitransforms.base
+    :members:

docs/_api/io.rst

@@ -0,0 +1,39 @@
+===
+IO
+===
+
+Reading and writing of transform files.
+
+--------
+Base I/O
+--------
+.. automodule:: nitransforms.io.base
+    :members:
+
+-----------------
+Tool Specific I/O
+-----------------
+
+^^^^
+AFNI
+^^^^
+.. automodule:: nitransforms.io.afni
+    :members:
+
+^^^
+FSL
+^^^
+.. automodule:: nitransforms.io.fsl
+    :members:
+
+^^^
+ITK
+^^^
+.. automodule:: nitransforms.io.itk
+    :members:
+
+^^^^^^^^^^^^^^
+FreeSurfer/LTA
+^^^^^^^^^^^^^^
+.. automodule:: nitransforms.io.lta
+    :members:

docs/_api/linear.rst

@@ -0,0 +1,6 @@
+=================
+Linear Transforms
+=================
+
+.. automodule:: nitransforms.linear
+    :members:

docs/_api/manip.rst

@@ -0,0 +1,6 @@
+=============
+Manipulations
+=============
+
+.. automodule:: nitransforms.manip
+    :members:

docs/_api/nonlinear.rst

@@ -0,0 +1,6 @@
+====================
+Nonlinear Transforms
+====================
+
+.. automodule:: nitransforms.nonlinear
+    :members:

docs/_api/patched.rst

@@ -0,0 +1,6 @@
+=========================
+Patched Nibabel Functions
+=========================
+
+.. automodule:: nitransforms.patched
+    :members:

docs/api.rst

@@ -3,12 +3,11 @@ Library API (application program interface)
 Information on specific functions, classes, and methods for developers.
 
 .. toctree::
-   :glob:
+   :maxdepth: 1
 
-   api/nitransforms.base
-   api/nitransforms.cli
-   api/nitransforms.io
-   api/nitransforms.linear
-   api/nitransforms.manip
-   api/nitransforms.nonlinear
-   api/nitransforms.patched
+   _api/base
+   _api/io
+   _api/linear
+   _api/manip
+   _api/nonlinear
+   _api/patched