minor channges in docs

.readthedocs.yml

 build:
-    image: latest
+  image: latest
+
 python:
-   pip_install: true
-   version: 3.6
- conda:
-   file: environment.yml
+  pip_install: false
+  version: 3.5
+
+conda:
+  file: environment.yml
+
 requirements_file: requirements.txt
+
 formats: []
\ No newline at end of file

README.md

 [![Documentation Status](https://readthedocs.org/projects/syconn/badge/?version=latest)](https://syconn.readthedocs.io/en/latest/?badge=latest)
 
-# SyConn v2
+# SyConn
 Refactored (still an early stage construction) version of SyConn for automated synaptic connectivity inference based on dense EM segmentation data.
 For v0.1 see the SyConn branch [dorkenwald2017nm](https://github.com/StructuralNeurobiologyLab/SyConn/tree/dorkenwald2017nm).
 
-Version 0.2 currently features:
+v0.2 currently features:
 - introduction of supervoxel and agglomerated supervoxel classes
 - added support for (sub-) cellular compartment (spines, axon/dendrite/soma) and cell type classification with [skeleton](https://www.nature.com/articles/nmeth.4206)- and [multiview-based](https://www.biorxiv.org/content/early/2018/07/06/364034) approaches
 - cell organelle prediction, extraction and mesh generation
@@ -14,8 +14,9 @@ Version 0.2 currently features:
 ## System requirements & installation
 * Python 3.5
 * The whole pipeline was designed and tested on Linux systems (CentOS, Arch)
-* SyConn is based on the packages [elektronn](http://elektronn.org), [knossos-utils](https://github.com/knossos-project/knossos_utils)
- is used for visualization and annotation of 3D EM data sets.
+* SyConn is primarily based on the packages [elektronn](http://elektronn.org) and [knossos-utils](https://github.com/knossos-project/knossos_utils)
+* We use [KNOSSOS](https://knossostool.org/)
+ for visualization and annotation of 3D EM data sets.
 * [VIGRA](https://ukoethe.github.io/vigra/), e.g. ``conda install -c ukoethe vigra``
 * osmesa, e.g.: ``conda install -c menpo osmesa``
 
@@ -28,7 +29,7 @@ You can install SyConn using  ``git`` and  ``pip``:
 
 ## Tutorials & documentation
 
-For the SyConn documentation see [here](docs/doc.md) or check out the latest readthedocs build [here](https://syconn.readthedocs.io/en/latest/). Alternatively you can build the API documentation lcoally by running `make html` in the `docs` folder.
+For the SyConn documentation see [here](docs/doc.md) or check out the latest readthedocs build [here](https://syconn.readthedocs.io/en/latest/). Alternatively you can build the API documentation locally by running `make html` in the `docs` folder.
 
 # The Team
 The Synaptic connectivity inference toolkit is developed at Max-Planck-Institute of Neurobiology, Munich.

docs/conf.py

@@ -36,6 +36,7 @@ extensions = [
     'sphinx.ext.githubpages',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
+    'sphinx_autodoc_typehints',
     'm2r',
 ]
 
@@ -61,8 +62,8 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'SyConn'
-copyright = u'2016, Sven Dorkenwald, Philipp Schubert, Jörgen Kornfeld'
-author = u'Sven Dorkenwald, Philipp Schubert, Jörgen Kornfeld'
+copyright = u'2018, SyConn team'
+author = u'Philipp Schubert, Sven Dorkenwald, Jörgen Kornfeld'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -138,9 +139,8 @@ html_theme = 'sphinxdoc'
 # documentation.
 #
 # html_theme_options = {}
-
 # Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
+# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
@@ -165,7 +165,7 @@ html_theme = 'sphinxdoc'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static', 'images']
+html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

docs/index.rst

@@ -25,7 +25,7 @@ API
    syconn
 
 Indices and tables
-==================
+------------------
 
 :ref:`genindex`
 :ref:`modindex`

docs/syconn.rst

-syconn package
-==============
+syconn API
+==========
 
 Subpackages
 -----------

environment.yml

@@ -28,5 +28,4 @@ dependencies:
 
   # For docs:
   - sphinx >=1.7.5
-  - sphinx_rtd_theme >=0.4.0
   - sphinx-autodoc-typehints >=1.3.0
\ No newline at end of file

requirements.txt

@@ -2,6 +2,7 @@ h5py
 matplotlib>=2.2.2
 scipy>=1.1.0
 networkx
+sphinx-autodoc-typehints >=1.3.0
 lz4
 configobj
 flask

setup.py

@@ -24,7 +24,8 @@ config = {
                          'numpy', 'scipy', 'lz4', 'h5py', 'networkx', 'numba',
                          'configobj', 'fasteners', 'flask', 'coloredlogs',
                          'opencv-python', 'pyopengl', 'scikit-learn',
-                         'scikit-image', 'm2r'],
+                         'scikit-image', 'm2r',
+                         'sphinx-autodoc-typehints'],
     'name': 'SyConn',
     'dependency_links': ['https://github.com/knossos-project/knossos_utils'
                          '/tarball/master#egg=knossos_utils',