Merge pull request #136 from inferno-pytorch/super-dev

Super dev
inferno-pytorch · Sep 18, 2018 · 5493e9e · 5493e9e
2 parents b7e2444 + 9a73f60
commit 5493e9e
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Showing 72 changed files with 2,192 additions and 568 deletions.
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -111,3 +111,29 @@ Tips
 To run a subset of tests::
 
     $ python -m unittest tests.test_inferno
+
+
+
+Sphinx Apidoc
+--------------
+before building the documentation
+one needs to generate the auto-generated
+sphinxs api documentation.
+These files need to be in the github repository.
+
+.. code:: bash
+  
+    cd docs
+    sphinx-apidoc -o inferno-apidoc ../inferno
+
+.. warning::
+
+    Do not make changes to `inferno/docs/inferno-apidoc` This folder is auto-generated
+    by the above mentioned command.
+
+The following combines all the commands necessary to build the html documentation:
+
+.. code:: bash
+  
+    ./build_docs.sh
+
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -45,3 +45,9 @@ History
 ------------------
 
 * setup.py critical bugix in install procedure
+
+
+
+CURRENT CHANGES
+-----------------
+* Flexible Unet
diff --git a/README.rst b/README.rst
@@ -48,7 +48,7 @@ Current features include:
   *   `various utility layers <https://github.com/nasimrahaman/inferno/tree/master/inferno/extensions/layers>`_ with more underway,
   *   `a submodule <https://github.com/nasimrahaman/inferno/blob/master/inferno/io/volumetric>`_ for volumetric datasets, and more!
 
-
+  
 
 
 
@@ -147,10 +147,9 @@ Planned features include:
 Credits
 ---------
 All contributors are listed here_. 
+.. _here: https://inferno-pytorch.github.io/inferno/html/authors.html
 
-.. _here: https://pytorch-inferno.readthedocs.io/en/latest/authors.html
-
-This packag was partially generated with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template + lots of work by Thorsten. 
+This package was partially generated with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template + lots of work by Thorsten. 
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

diff --git a/_requirements_readthedocs.txt b/_requirements_readthedocs.txt
diff --git a/build_docs.sh b/build_docs.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+cd docs
+rm -r -f inferno-apidoc
+sphinx-apidoc -o inferno-apidoc ../inferno
+make html
+cd ..
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -27,10 +27,13 @@ requirements:
         - pyyaml
         - scipy
         - scikit-image
+        - scikit-learn
         - h5py
         - dill
         - networkx 1.11
         - tensorboardx
+        - sphinx_rtd_theme
+
 
 test:
     imports:

diff --git a/docs/conf.py b/docs/conf.py
@@ -62,6 +62,9 @@ def __getattr__(cls, name):
 
 import inferno
 import inferno.extensions
+import inferno.extensions.layers
+from inferno.extensions.layers import *
+from inferno.extensions.layers.reshape import *
 
 # -- General configuration ---------------------------------------------
 
@@ -81,7 +84,8 @@ def __getattr__(cls, name):
     'sphinx.ext.graphviz',
     'sphinx_gallery.gen_gallery',
     'sphinxcontrib.bibtex',
-    'sphinx.ext.napoleon'
+    'sphinx.ext.napoleon',
+    'sphinxcontrib.inlinesyntaxhighlight'
 ]
 
 
@@ -98,7 +102,7 @@ def __getattr__(cls, name):
     'scan_used_functions':
         True,
     'doc_module' :
-        ('inferno'),
+        ('inferno','inferno.extensions','inferno.extensions.layers','inferno.extensions.layers.convolutional'),
 
     'docs_resolv': True,
 
@@ -148,7 +152,7 @@ def __getattr__(cls, name):
 
 # General information about the project.
 project = u'inferno'
-copyright = u"2017, Nasim Rahaman"
+copyright = u"2018, f"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -203,7 +207,7 @@ def __getattr__(cls, name):
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -302,7 +306,7 @@ def __getattr__(cls, name):
 latex_documents = [
     ('index', 'inferno.tex',
      u'inferno Documentation',
-     u'Nasim Rahaman', 'manual'),
+     u'Inferno Team', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at
@@ -333,7 +337,7 @@ def __getattr__(cls, name):
 man_pages = [
     ('index', 'inferno',
      u'inferno Documentation',
-     [u'Nasim Rahaman'], 1)
+     [u'Inferno Team'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -348,7 +352,7 @@ def __getattr__(cls, name):
 texinfo_documents = [
     ('index', 'inferno',
      u'inferno Documentation',
-     u'Nasim Rahaman',
+     u'Inferno Team',
      'inferno',
      'One line description of project.',
      'Miscellaneous'),

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -18,4 +18,4 @@ dependencies:
      - sphinx-gallery
      - sphinxcontrib-napoleon
      - sphinxcontrib-bibtex
-
+     - sphinxcontrib-inlinesyntaxhighlight
diff --git a/docs/index.rst b/docs/index.rst
@@ -4,13 +4,12 @@ Welcome to inferno's documentation!
 Contents:
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 1
 
    readme
    installation
    usage
    examples
-   modules
    contributing
    inferno-apidoc/modules
    authors

diff --git a/docs/inferno-apidoc/inferno.extensions.containers.rst b/docs/inferno-apidoc/inferno.extensions.containers.rst
@@ -1,19 +1,19 @@
-inferno\.extensions\.containers package
-=======================================
+inferno.extensions.containers package
+=====================================
 
 Submodules
 ----------
 
-inferno\.extensions\.containers\.graph module
----------------------------------------------
+inferno.extensions.containers.graph module
+------------------------------------------
 
 .. automodule:: inferno.extensions.containers.graph
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.containers\.sequential module
---------------------------------------------------
+inferno.extensions.containers.sequential module
+-----------------------------------------------
 
 .. automodule:: inferno.extensions.containers.sequential
     :members:

diff --git a/docs/inferno-apidoc/inferno.extensions.criteria.rst b/docs/inferno-apidoc/inferno.extensions.criteria.rst
@@ -1,19 +1,35 @@
-inferno\.extensions\.criteria package
-=====================================
+inferno.extensions.criteria package
+===================================
 
 Submodules
 ----------
 
-inferno\.extensions\.criteria\.core module
-------------------------------------------
+inferno.extensions.criteria.core module
+---------------------------------------
 
 .. automodule:: inferno.extensions.criteria.core
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.criteria\.set\_similarity\_measures module
----------------------------------------------------------------
+inferno.extensions.criteria.elementwise\_measures module
+--------------------------------------------------------
+
+.. automodule:: inferno.extensions.criteria.elementwise_measures
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.criteria.regularized module
+----------------------------------------------
+
+.. automodule:: inferno.extensions.criteria.regularized
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.criteria.set\_similarity\_measures module
+------------------------------------------------------------
 
 .. automodule:: inferno.extensions.criteria.set_similarity_measures
     :members:

diff --git a/docs/inferno-apidoc/inferno.extensions.initializers.rst b/docs/inferno-apidoc/inferno.extensions.initializers.rst
@@ -1,19 +1,19 @@
-inferno\.extensions\.initializers package
-=========================================
+inferno.extensions.initializers package
+=======================================
 
 Submodules
 ----------
 
-inferno\.extensions\.initializers\.base module
-----------------------------------------------
+inferno.extensions.initializers.base module
+-------------------------------------------
 
 .. automodule:: inferno.extensions.initializers.base
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.initializers\.presets module
--------------------------------------------------
+inferno.extensions.initializers.presets module
+----------------------------------------------
 
 .. automodule:: inferno.extensions.initializers.presets
     :members:

diff --git a/docs/inferno-apidoc/inferno.extensions.layers.rst b/docs/inferno-apidoc/inferno.extensions.layers.rst
@@ -1,41 +1,89 @@
-inferno\.extensions\.layers package
-===================================
+inferno.extensions.layers package
+=================================
 
 Submodules
 ----------
 
-inferno\.extensions\.layers\.activations module
------------------------------------------------
+inferno.extensions.layers.activations module
+--------------------------------------------
 
 .. automodule:: inferno.extensions.layers.activations
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.convolutional module
+inferno.extensions.layers.building\_blocks module
 -------------------------------------------------
 
+.. automodule:: inferno.extensions.layers.building_blocks
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.convolutional module
+----------------------------------------------
+
 .. automodule:: inferno.extensions.layers.convolutional
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.device module
-------------------------------------------
+inferno.extensions.layers.device module
+---------------------------------------
 
 .. automodule:: inferno.extensions.layers.device
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.reshape module
--------------------------------------------
+inferno.extensions.layers.identity module
+-----------------------------------------
+
+.. automodule:: inferno.extensions.layers.identity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.prefab module
+---------------------------------------
+
+.. automodule:: inferno.extensions.layers.prefab
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.res\_unet module
+------------------------------------------
+
+.. automodule:: inferno.extensions.layers.res_unet
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.reshape module
+----------------------------------------
 
 .. automodule:: inferno.extensions.layers.reshape
     :members:
     :undoc-members:
     :show-inheritance:
 
+inferno.extensions.layers.sampling module
+-----------------------------------------
+
+.. automodule:: inferno.extensions.layers.sampling
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.unet\_base module
+-------------------------------------------
+
+.. automodule:: inferno.extensions.layers.unet_base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------