Merge branch 'ajc-namespace-cleanup' of https://github.com/spacetx/st…

…arfish into ajc-namespace-cleanup

* 'ajc-namespace-cleanup' of https://github.com/spacetx/starfish:
  more travis-only errors...
  fix error that only occurs on travis
  get docs building
  update makefile rules to ignore import ordering in top-level starfish __init__.py
  appease flake8
  refactor packages to exclude from public namespace
  Reorganize the presentation of the image filtering docs (#1229)

docs/source/_static/tutorials/exec_image_corrections.py

@@ -108,7 +108,7 @@
 # The point spread function can be determined in several ways. Ideally, it is approximated during
 # calibration of the microscope, in which case it can be removed by the
 # `Richardson-Lucy algorithm <richardson-lucy-web>`_ (API:
-# :ref:`Richardson-Lucy <richardson-lucy>`)
+# :py:class:`~starfish.image.Filter.DeconvolvePSF`)
 #
 # .. _richardson-lucy-web: https://en.wikipedia.org/wiki/Richardson%E2%80%93Lucy_deconvolution
 #

docs/source/api/image/index.rst

@@ -3,13 +3,73 @@
 Image Manipulation
 ==================
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-.. toctree::
-   filtering/index
-   learn_transform/index
-   apply_transform/index
-   segmentation/index
-   deconvolution/index
+
+starfish provides a variety of image manipulation methods that aid in the quantification of image-based transcriptomics
+experiments. These include :py:class:`~starfish.image.Filter`, which remove background fluorescence and enhance spots,
+:py:class:`~starfish.image.LearnTransform`, which learn transforms to align images across rounds and channels,
+:py:class:`~starfish.image.ApplyTransform`, which apply learned transforms to images, and finally,
+:py:class:`~starfish.image.Segmentation`, to identify the locations of cells.
+
+
+.. _filtering:
+
+Filtering
+---------
+
+Filters can be imported using ``starfish.image.Filter``, which registers all classes that subclass
+``FilterAlgorithmBase``:
+
+.. code-block:: python
+
+    from starfish.image import Filter
+
+.. autoclass:: starfish.image.Filter
+   :members:
+
+
+.. _learn_transform:
+
+Learn Transform
+---------------
+
+LearnTransform can be imported using ``starfish.image.LearnTransform``, the subclasses of
+``LearnTransformBase`` are available for transform learning.
+
+.. code-block:: python
+
+    from starfish.image import LearnTransform
+
+.. autoclass:: starfish.image.LearnTransform
+   :members:
+
+
+.. _apply_transform:
+
+Apply Transform
+---------------
+
+ApplyTransform can be imported using ``starfish.image.ApplyTransform``, the subclasses of
+``ApplyTransformBase`` are available for transform learning.
+
+.. code-block:: python
+
+    from starfish.image import ApplyTransform
+
+.. autoclass:: starfish.image.ApplyTransform
+   :members:
+
+
+.. _segmentation:
+
+Segmentation
+------------
+
+Segmentation can be imported using ``starfish.image.Segment``, which registers all classes that subclass
+``SegmentAlgorithmBase``:
+
+.. code-block:: python
+
+    from starfish.image import Segment
+
+.. autoclass:: starfish.image.Segment
+   :members: