fix: rtd (#451)

* fix: rtd

missing mock modules

* Bump version: 0.6.0a1 → 0.6.0a2

cobra/__init__.py

@@ -12,7 +12,7 @@
 from cobra.core import (
     DictList, Gene, Metabolite, Model, Object, Reaction, Species)
 
-__version__ = "0.6.0a1"
+__version__ = "0.6.0a2"
 
 # set the warning format to be prettier and fit on one line
 _cobra_path = _dirname(_abspath(__file__))

documentation_builder/conf.py

@@ -3,7 +3,8 @@
 # cobra documentation build configuration file, created by
 # sphinx-quickstart on Wed Jun 13 19:17:34 2012.
 #
-# This file is execfile()d with the current directory set to its containing dir.
+# 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.
@@ -35,9 +36,10 @@ def __getattr__(cls, name):
         else:
             return Mock()
 
-MOCK_MODULES = ['numpy', 'scipy', 'scipy.sparse', 'scipy.io', 'scipy.stats',
-                'glpk', 'gurobipy', 'gurobipy.GRB', 'cplex', 'pp', 'libsbml',
-                'cplex.exceptions', 'pandas', 'tabulate']
+
+MOCK_MODULES = ['numpy', 'scipy', 'scipy.optimize', 'scipy.sparse', 'scipy.io',
+                'scipy.stats', 'pp', 'libsbml', 'pandas', 'tabulate',
+                'optlang', 'optlang.interface']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()
 
@@ -60,41 +62,37 @@ def __getattr__(cls, name):
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-from cobra.version import get_version, read_release_version
-version = read_release_version()
-# The full version, including alpha/beta/rc tags.
-release = get_version()
+from cobra import __version__ as release
+version = '.'.join(release.split('.')[:2])
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', 'version.py', '.ipynb_checkpoints']
+exclude_patterns = ['_build', '.ipynb_checkpoints']
 
 pygments_style = 'sphinx'
 
-
 # -- Options for HTML output --------------------------------------------------
 
 mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-'preamble': r'\usepackage{amsmath,amssymb}',
+    # Additional stuff for the LaTeX preamble.
+    'preamble': r'\usepackage{amsmath,amssymb}',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'cobra.tex', u'cobra Documentation',
-   u'Daniel Robert Hyduke and Ali Ebrahim', 'manual'),
+    ('index', 'cobra.tex', u'cobra Documentation',
+     u'Daniel Robert Hyduke and Ali Ebrahim', 'manual'),
 ]
 
 # -- Options for manual page output --------------------------------------------
@@ -112,14 +110,14 @@ def __getattr__(cls, name):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'cobra', u'cobra Documentation',
-   u'Daniel Robert Hyduke and Ali Ebrahim', 'cobra',
-   'A package for constraints-based modeling of biological networks',
-   'Miscellaneous'),
+    ('index', 'cobra', u'cobra Documentation',
+     u'Daniel Robert Hyduke and Ali Ebrahim', 'cobra',
+     'A package for constraints-based modeling of biological networks',
+     'Miscellaneous'),
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {"http://docs.python.org/": None,
                        "http://docs.scipy.org/doc/numpy/": None,
                        "http://docs.scipy.org/doc/scipy/reference": None}
-intersphinx_cache_limit = 10     # days to keep the cached inventories
+intersphinx_cache_limit = 10  # days to keep the cached inventories

setup.cfg

@@ -1,20 +1,20 @@
 [bumpversion]
-current_version = 0.6.0a1
+current_version = 0.6.0a2
 commit = True
 tag = True
 parse = (?P<major>\d+)
 	\.(?P<minor>\d+)
 	\.(?P<patch>\d+)
 	((?P<release>[ab])(?P<num>\d+))?
-serialize =
+serialize = 
 	{major}.{minor}.{patch}{release}{num}
 	{major}.{minor}.{patch}
 tag_name = {new_version}
 
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = a
-values =
+values = 
 	a
 	b
 	placeholder

setup.py

@@ -144,7 +144,7 @@ def build_extension(self, ext):
 
 setup(
     name="cobra",
-    version="0.6.0a1",
+    version="0.6.0a2",
     packages=find_packages(),
     setup_requires=setup_requirements,
     install_requires=["future", "swiglpk", "optlang",