Merge pull request #1 from mdraw/master

Add autogenerating API docs with sphinx and readthedocs, update some dependencies

.gitignore

@@ -14,3 +14,5 @@ cache
 *.nbi
 *.nbc
 
+docs/_build/*
+docs/source/*

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = ELEKTRONN2
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,195 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# ELEKTRONN2 documentation build configuration file, created by
+# sphinx-quickstart on Tue Jan 17 17:07:17 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- Mock problematic libraries that are unnecessary for doc building -----
+
+import sys
+from unittest.mock import MagicMock
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return MagicMock()
+
+MOCK_MODULES = [
+    'knossos_utils',
+]
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'ELEKTRONN2'
+copyright = '2017, Marius Killinger'
+author = 'Marius Killinger'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+#html_theme = 'alabaster'
+
+import sphinx_rtd_theme
+
+html_theme = "sphinx_rtd_theme"
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ELEKTRONN2doc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'ELEKTRONN2.tex', 'ELEKTRONN2 Documentation',
+     'Marius Killinger', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'elektronn2', 'ELEKTRONN2 Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'ELEKTRONN2', 'ELEKTRONN2 Documentation',
+     author, 'ELEKTRONN2', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# From https://github.com/rtfd/readthedocs.org/issues/1139
+def run_apidoc(_):
+    from sphinx.apidoc import main
+    import os
+    import sys
+    sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+    cur_dir = os.path.abspath(os.path.dirname(__file__))
+    module = '../elektronn2'
+    output_path = os.path.join(cur_dir, 'source')
+    main(['-e', '-o', output_path, module, '--force'])
+
+def setup(app):
+    app.connect('builder-inited', run_apidoc)

docs/index.rst

@@ -0,0 +1,26 @@
+.. ELEKTRONN2 documentation master file, created by
+   sphinx-quickstart on Tue Jan 17 17:07:17 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ELEKTRONN2's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: API documentation:
+
+   source/elektronn2.neuromancer
+   source/elektronn2.training
+   source/elektronn2.config
+   source/elektronn2.data
+   source/elektronn2.utils
+   source/elektronn2.malis
+..    source/elektronn2.tests
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`

docs/sphinx-requirements.txt

@@ -0,0 +1,18 @@
+numpy>=1.11
+scipy>=0.18
+sklearn<=0.20
+scikit-image>=0.12.3
+matplotlib>=2.0
+h5py>=2.2
+theano>=0.8
+future>=0.15
+tqdm>=4
+colorlog>=2.7
+pydotplus
+seaborn
+prompt_toolkit>=1.0.3
+jedi>=0.9.0
+psutil
+
+sphinx
+sphinx_rtd_theme

requirements.txt

@@ -1,9 +1,10 @@
-sklearn
+sklearn<0.20
+scikit-image>=0.12.3
 numpy>=1.8
 scipy>=0.14
 matplotlib>=1.4
 h5py>=2.2
-theano>=0.7
+theano>=0.8
 future>=0.15
 tqdm>=4
 numba>=0.25
@@ -12,4 +13,4 @@ pydotplus
 seaborn
 prompt_toolkit>=1.0.3
 jedi>=0.9.0
-git+https://github.com/Theano/Theano.git
+psutil>=5.0.1

setup.py

@@ -46,6 +46,8 @@ def read(fname):
         'pydotplus',
         'seaborn',
         'scikit-learn<0.20',  # >=0.20 requires change, see todo-note in data.traindata import
+        'psutil>=5.0.1',
+        'scikit-image>=0.12.3',
     ],
     extras_require={
         'numba': ['numba>=0.25'],