Read the Docs build information Build id: 6381550 Project: cobrapy Version: master Commit: f61c9980cc2266aed775711b58e15d7d94f2c581 Date: 2017-12-07T18:18:30.208319Z State: finished Success: True [rtd-command-info] start-time: 2017-12-07T18:18:35.856269, end-time: 2017-12-07T18:18:39.227391, duration: 3, exit-code: 0 python3.5 -mvirtualenv --system-site-packages --no-download /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master Using base prefix '/usr' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/python3.5 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-12-07T18:18:39.302679, end-time: 2017-12-07T18:19:36.933823, duration: 57, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/pip install --use-wheel --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip -I Pygments==2.2.0 setuptools<37 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx==1.5.6 sphinx-rtd-theme<0.3 readthedocs-sphinx-ext<0.6 Collecting Pygments==2.2.0 Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB) Collecting setuptools<37 Downloading setuptools-36.8.0-py2.py3-none-any.whl (482kB) Collecting docutils==0.13.1 Downloading docutils-0.13.1-py3-none-any.whl (536kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861kB) Collecting pillow==2.6.1 Downloading Pillow-2.6.1.zip (7.5MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.10-py2.py3-none-any.whl Collecting commonmark==0.5.4 Downloading CommonMark-0.5.4.tar.gz (120kB) Collecting recommonmark==0.4.0 Downloading recommonmark-0.4.0-py2.py3-none-any.whl Collecting sphinx==1.5.6 Downloading Sphinx-1.5.6-py2.py3-none-any.whl (1.6MB) Collecting sphinx-rtd-theme<0.3 Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB) Collecting readthedocs-sphinx-ext<0.6 Downloading readthedocs_sphinx_ext-0.5.5-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx==1.5.6) Downloading requests-2.18.4-py2.py3-none-any.whl (88kB) Collecting imagesize (from sphinx==1.5.6) Downloading imagesize-0.7.1-py2.py3-none-any.whl Collecting Jinja2>=2.3 (from sphinx==1.5.6) Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB) Collecting babel!=2.0,>=1.3 (from sphinx==1.5.6) Downloading Babel-2.5.1-py2.py3-none-any.whl (6.8MB) Collecting snowballstemmer>=1.1 (from sphinx==1.5.6) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) Collecting six>=1.5 (from sphinx==1.5.6) Downloading six-1.11.0-py2.py3-none-any.whl Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6) Downloading nilsimsa-0.3.8.tar.gz (276kB) Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx==1.5.6) Downloading idna-2.6-py2.py3-none-any.whl (56kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.5.6) Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.5.6) Downloading certifi-2017.11.5-py2.py3-none-any.whl (330kB) Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx==1.5.6) Downloading urllib3-1.22-py2.py3-none-any.whl (132kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.5.6) Downloading MarkupSafe-1.0.tar.gz Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.5.6) Downloading pytz-2017.3-py2.py3-none-any.whl (511kB) Building wheels for collected packages: mock, pillow, commonmark, nilsimsa, MarkupSafe Running setup.py bdist_wheel for mock: started Running setup.py bdist_wheel for mock: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/b2/f8/fe/920b7d3b279878045354cde14646f73864cf944501f19e4a1b Running setup.py bdist_wheel for pillow: started Running setup.py bdist_wheel for pillow: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/d0/3d/6f/4a3dbe290c7053073e6c32734c146d7174f2ad7675030b6137 Running setup.py bdist_wheel for commonmark: started Running setup.py bdist_wheel for commonmark: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442 Running setup.py bdist_wheel for nilsimsa: started Running setup.py bdist_wheel for nilsimsa: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/77/f8/25/539c7b52ecbfcb7ed9b6c7189f9fdde48706c41fe529a64c9f Running setup.py bdist_wheel for MarkupSafe: started Running setup.py bdist_wheel for MarkupSafe: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built mock pillow commonmark nilsimsa MarkupSafe Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, idna, chardet, certifi, urllib3, requests, imagesize, MarkupSafe, Jinja2, pytz, babel, snowballstemmer, six, sphinx, sphinx-rtd-theme, nilsimsa, readthedocs-sphinx-ext Successfully installed Jinja2-2.10 MarkupSafe-1.0 Pygments-2.2.0 alabaster-0.7.10 babel-2.5.1 certifi-2017.11.5 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.6 imagesize-0.7.1 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2017.3 readthedocs-sphinx-ext-0.5.5 recommonmark-0.4.0 requests-2.18.4 setuptools-36.8.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.5.6 sphinx-rtd-theme-0.2.4 urllib3-1.22 [rtd-command-info] start-time: 2017-12-07T18:19:37.046220, end-time: 2017-12-07T18:19:53.833544, duration: 16, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip -rdocumentation_builder/requirements.txt Collecting nbsphinx>=0.2.4 (from -r documentation_builder/requirements.txt (line 1)) Downloading nbsphinx-0.2.18-py2.py3-none-any.whl Collecting ipykernel (from -r documentation_builder/requirements.txt (line 2)) Downloading ipykernel-4.7.0-py2.py3-none-any.whl (106kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/lib/python3.5/site-packages (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Collecting nbconvert (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading nbconvert-5.3.1-py2.py3-none-any.whl (387kB) Collecting nbformat (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading nbformat-4.4.0-py2.py3-none-any.whl (155kB) Collecting traitlets (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading traitlets-4.3.2-py2.py3-none-any.whl (74kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/lib/python3.5/site-packages (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Requirement already satisfied: sphinx!=1.5.0,>=1.3.2 in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/lib/python3.5/site-packages (from nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Collecting ipython>=4.0.0 (from ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading ipython-6.2.1-py3-none-any.whl (745kB) Collecting tornado>=4.0 (from ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading tornado-4.5.2.tar.gz (483kB) Collecting jupyter-client (from ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading jupyter_client-5.1.0-py2.py3-none-any.whl (84kB) Collecting testpath (from nbconvert->nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading testpath-0.3.1-py2.py3-none-any.whl (161kB) Collecting entrypoints>=0.2.2 (from nbconvert->nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading entrypoints-0.2.3-py2.py3-none-any.whl Collecting jupyter-core (from nbconvert->nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading jupyter_core-4.4.0-py2.py3-none-any.whl (126kB) Requirement already satisfied: pygments in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/lib/python3.5/site-packages (from 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prompt-toolkit<2.0.0,>=1.0.4 (from ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading prompt_toolkit-1.0.15-py3-none-any.whl (247kB) Collecting pickleshare (from ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading pickleshare-0.7.4-py2.py3-none-any.whl Requirement already satisfied: setuptools>=18.5 in /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/lib/python3.5/site-packages (from ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Collecting jedi>=0.10 (from ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading jedi-0.11.0-py2.py3-none-any.whl (146kB) Collecting pexpect; sys_platform != "win32" (from ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading pexpect-4.3.0-py2.py3-none-any.whl (55kB) Requirement already satisfied: python-dateutil>=2.1 in /usr/lib/python3/dist-packages (from 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wcwidth-0.1.7-py2.py3-none-any.whl Collecting parso==0.1.0 (from jedi>=0.10->ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading parso-0.1.0-py2.py3-none-any.whl (89kB) Collecting ptyprocess>=0.5 (from pexpect; sys_platform != "win32"->ipython>=4.0.0->ipykernel->-r documentation_builder/requirements.txt (line 2)) Downloading ptyprocess-0.5.2-py2.py3-none-any.whl Collecting webencodings (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->nbsphinx>=0.2.4->-r documentation_builder/requirements.txt (line 1)) Downloading webencodings-0.5.1-py2.py3-none-any.whl Building wheels for collected packages: tornado, pandocfilters, simplegeneric Running setup.py bdist_wheel for tornado: started Running setup.py bdist_wheel for tornado: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/b3/47/3a/96e12476829cb196adabc879fedb72f1bb2c8613b6961e78e7 Running setup.py bdist_wheel for pandocfilters: started Running setup.py bdist_wheel for pandocfilters: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/08/5b/5b/66b3cde6f8215f8345479ef3699d6ddbb860f6ea7072008f8b Running setup.py bdist_wheel for simplegeneric: started Running setup.py bdist_wheel for simplegeneric: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/.cache/pip/wheels/7b/31/08/c85e74c84188cbec6a6827beec4d640f2bd78ae003dc1ec09d Successfully built tornado pandocfilters simplegeneric Installing collected packages: testpath, jsonschema, ipython-genutils, traitlets, jupyter-core, nbformat, entrypoints, pandocfilters, mistune, webencodings, html5lib, bleach, nbconvert, nbsphinx, simplegeneric, wcwidth, prompt-toolkit, pickleshare, parso, jedi, ptyprocess, pexpect, ipython, tornado, pyzmq, jupyter-client, ipykernel Found existing installation: html5lib 0.999 Not uninstalling html5lib at /usr/lib/python3/dist-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master Successfully installed bleach-2.1.2 entrypoints-0.2.3 html5lib-1.0.1 ipykernel-4.7.0 ipython-6.2.1 ipython-genutils-0.2.0 jedi-0.11.0 jsonschema-2.6.0 jupyter-client-5.1.0 jupyter-core-4.4.0 mistune-0.8.3 nbconvert-5.3.1 nbformat-4.4.0 nbsphinx-0.2.18 pandocfilters-1.4.2 parso-0.1.0 pexpect-4.3.0 pickleshare-0.7.4 prompt-toolkit-1.0.15 ptyprocess-0.5.2 pyzmq-16.0.3 simplegeneric-0.8.1 testpath-0.3.1 tornado-4.5.2 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 [rtd-command-info] start-time: 2017-12-07T18:19:57.229238, end-time: 2017-12-07T18:19:57.274086, duration: 0, exit-code: 0 cat documentation_builder/conf.py # -*- coding: utf-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. # # 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. import sys import os # 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. sys.path.insert(0, os.path.abspath('..')) # In order to build documentation that requires libraries to import class Mock(object): def __init__(self, *args, **kwargs): return def __call__(self, *args, **kwargs): return Mock() @classmethod def __getattr__(cls, name): if name in ('__file__', '__path__'): return '/dev/null' else: return Mock() MOCK_MODULES = ['numpy', 'scipy', 'scipy.optimize', 'scipy.sparse', 'scipy.io', 'scipy.stats', 'pp', 'libsbml', 'pandas', 'tabulate', 'optlang', 'optlang.interface', 'sympy', 'sympy.core', 'sympy.core.singleton', 'future', 'future.utils', 'ruamel', 'ruamel.yaml'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() # -- General configuration ---------------------------------------------------- # 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.intersphinx', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.napoleon', 'sphinx.ext.mathjax', 'nbsphinx'] # The master toctree document. master_doc = 'index' # General information about the project. project = u'cobra' copyright = u'2016, The cobrapy core team' # 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. # 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', '.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 font size ('10pt', '11pt' or '12pt'). # 'pointsize': '10pt', # 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'The cobrapy core team', 'manual'), ] # -- Options for manual page output -------------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ ('index', 'cobra', u'cobra Documentation', [u'The cobrapy core team'], 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 = [ ('index', 'cobra', u'cobra Documentation', u'The cobrapy core team', '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 ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.org/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = 'https://media.readthedocs.org/static/' else: websupport2_static_url = 'https://media.readthedocs.org//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "master", 'MEDIA_URL': "https://media.readthedocs.org/", 'PRODUCTION_DOMAIN': "readthedocs.org", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("0.9.1", "/en/0.9.1/"), ("0.9.0", "/en/0.9.0/"), ("0.8.2", "/en/0.8.2/"), ("0.8.1", "/en/0.8.1/"), ("0.8.0", "/en/0.8.0/"), ("0.7.0", "/en/0.7.0/"), ("0.6.2", "/en/0.6.2/"), ("0.6.1", "/en/0.6.1/"), ("0.6.0", "/en/0.6.0/"), ("0.6.0a7", "/en/0.6.0a7/"), ("0.5.11", "/en/0.5.11/"), ("0.5.10", "/en/0.5.10/"), ("0.5.9", "/en/0.5.9/"), ("0.5.8", "/en/0.5.8/"), ("0.5.7", "/en/0.5.7/"), ("0.5.6", "/en/0.5.6/"), ("0.5.4", "/en/0.5.4/"), ("0.5.3", "/en/0.5.3/"), ("0.5.2", "/en/0.5.2/"), ("0.4.1", "/en/0.4.1/"), ("0.4.0", "/en/0.4.0/"), ("0.3.2", "/en/0.3.2/"), ("master", "/en/master/"), ("devel", "/en/devel/"), ], 'downloads': [ ("pdf", "//readthedocs.org/projects/cobrapy/downloads/pdf/master/"), ("htmlzip", "//readthedocs.org/projects/cobrapy/downloads/htmlzip/master/"), ("epub", "//readthedocs.org/projects/cobrapy/downloads/epub/master/"), ], 'subprojects': [ ], 'slug': 'cobrapy', 'name': u'cobrapy', 'rtd_language': u'en', 'canonical_url': 'http://cobrapy.readthedocs.io/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/documentation_builder/', 'api_host': 'https://readthedocs.org', 'github_user': 'opencobra', 'github_repo': 'cobrapy', 'github_version': 'origin/master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'origin/master', 'display_bitbucket': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-1', 'commit': 'f61c9980', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2017-12-07T18:19:57.358382, end-time: 2017-12-07T18:20:30.959325, duration: 33, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.5.6 making output directory... loading translations [en]... done loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/numpy/objects.inv -> https://docs.scipy.org/doc/numpy/objects.inv loading intersphinx inventory from http://docs.python.org/objects.inv... intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/2/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/reference/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 22 source files that are out of date updating environment: 22 added, 0 changed, 0 removed reading sources... [ 4%] building_model reading sources... [ 9%] cobra reading sources... [ 13%] cobra.core reading sources... [ 18%] cobra.design reading sources... [ 22%] cobra.flux_analysis reading sources... [ 27%] cobra.io reading sources... [ 31%] cobra.manipulation reading sources... [ 36%] cobra.topology reading sources... [ 40%] cobra.util reading sources... [ 45%] constraints_objectives reading sources... [ 50%] deletions reading sources... [ 54%] faq reading sources... [ 59%] gapfilling reading sources... [ 63%] getting_started reading sources... [ 68%] index reading sources... [ 72%] io reading sources... [ 77%] loopless reading sources... [ 81%] phenotype_phase_plane reading sources... [ 86%] pymatbridge reading sources... [ 90%] sampling reading sources... [ 95%] simulating reading sources... [100%] solvers /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/solvers/__init__.py:73: UserWarning: No LP solvers found warn("No LP solvers found") /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:9: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/model.py:docstring of cobra.core.model.Model.add_boundary:15: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.get_coefficients:4: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.subtract_metabolites:18: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:11: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:22: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:6: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:7: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:37: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:31: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:39: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:47: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:5: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:9: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:78: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:85: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler.sample:6: SEVERE: Unexpected section title. Paramters --------- /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:48: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:52: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_gene_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_reaction_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:56: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:61: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:20: ERROR: Unknown target name: "3". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:64: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:7: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:12: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:41: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:47: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.nullspace:15: WARNING: Field list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 4%] building_model writing output... [ 9%] cobra writing output... [ 13%] cobra.core writing output... [ 18%] cobra.design writing output... [ 22%] cobra.flux_analysis writing output... [ 27%] cobra.io writing output... [ 31%] cobra.manipulation writing output... [ 36%] cobra.topology writing output... [ 40%] cobra.util writing output... [ 45%] constraints_objectives writing output... [ 50%] deletions writing output... [ 54%] faq writing output... [ 59%] gapfilling writing output... [ 63%] getting_started writing output... [ 68%] index writing output... [ 72%] io writing output... [ 77%] loopless writing output... [ 81%] phenotype_phase_plane writing output... [ 86%] pymatbridge writing output... [ 90%] sampling writing output... [ 95%] simulating writing output... [100%] solvers generating indices... genindex py-modindex highlighting module code... [ 2%] cobra.design.design_algorithms highlighting module code... [ 5%] cobra.util.util highlighting module code... 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[ 94%] cobra.core.species highlighting module code... [ 97%] cobra.flux_analysis.phenotype_phase_plane highlighting module code... [100%] cobra.manipulation.modify writing additional pages... search copying images... [ 25%] _build/doctrees-readthedocs/nbsphinx/loopless_11_0.png copying images... [ 50%] _build/doctrees-readthedocs/nbsphinx/constraints_objectives_17_0.png copying images... [ 75%] _build/doctrees-readthedocs/nbsphinx/loopless_7_1.png copying images... [100%] _build/doctrees-readthedocs/nbsphinx/phenotype_phase_plane_10_1.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 40 warnings. [rtd-command-info] start-time: 2017-12-07T18:20:31.130970, end-time: 2017-12-07T18:21:04.293076, duration: 33, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.5.6 making output directory... loading translations [en]... done loading pickled environment... not yet created loading intersphinx inventory from http://docs.python.org/objects.inv... intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/2/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/reference/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/numpy/objects.inv -> https://docs.scipy.org/doc/numpy/objects.inv building [mo]: targets for 0 po files that are out of date building [json]: targets for 22 source files that are out of date updating environment: 22 added, 0 changed, 0 removed reading sources... [ 4%] building_model reading sources... [ 9%] cobra reading sources... [ 13%] cobra.core reading sources... [ 18%] cobra.design reading sources... [ 22%] cobra.flux_analysis reading sources... [ 27%] cobra.io reading sources... [ 31%] cobra.manipulation reading sources... [ 36%] cobra.topology reading sources... [ 40%] cobra.util reading sources... [ 45%] constraints_objectives reading sources... [ 50%] deletions reading sources... [ 54%] faq reading sources... [ 59%] gapfilling reading sources... [ 63%] getting_started reading sources... [ 68%] index reading sources... [ 72%] io reading sources... [ 77%] loopless reading sources... [ 81%] phenotype_phase_plane reading sources... [ 86%] pymatbridge reading sources... [ 90%] sampling reading sources... [ 95%] simulating reading sources... [100%] solvers /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/solvers/__init__.py:73: UserWarning: No LP solvers found warn("No LP solvers found") /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:9: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/model.py:docstring of cobra.core.model.Model.add_boundary:15: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.get_coefficients:4: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.subtract_metabolites:18: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:11: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:22: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:6: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:7: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:37: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:31: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:39: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:47: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:5: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:9: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:78: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:85: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler.sample:6: SEVERE: Unexpected section title. Paramters --------- /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:48: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:52: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_gene_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_reaction_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:56: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:61: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:20: ERROR: Unknown target name: "3". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:64: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:7: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:12: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:41: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:47: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.nullspace:15: WARNING: Field list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 4%] building_model writing output... [ 9%] cobra writing output... [ 13%] cobra.core writing output... [ 18%] cobra.design writing output... [ 22%] cobra.flux_analysis writing output... [ 27%] cobra.io writing output... [ 31%] cobra.manipulation writing output... [ 36%] cobra.topology writing output... [ 40%] cobra.util writing output... [ 45%] constraints_objectives writing output... [ 50%] deletions writing output... [ 54%] faq writing output... [ 59%] gapfilling writing output... [ 63%] getting_started writing output... [ 68%] index writing output... [ 72%] io writing output... [ 77%] loopless writing output... [ 81%] phenotype_phase_plane writing output... [ 86%] pymatbridge writing output... [ 90%] sampling writing output... [ 95%] simulating writing output... [100%] solvers generating indices... genindex py-modindex highlighting module code... [ 2%] cobra.core.reaction highlighting module code... [ 5%] cobra.flux_analysis.single_deletion highlighting module code... [ 7%] cobra.io.sbml3 highlighting module code... [ 10%] cobra.manipulation.validate highlighting module code... [ 12%] cobra.io.mat highlighting module code... [ 15%] cobra.manipulation.modify highlighting module code... [ 17%] cobra.core.solution highlighting module code... [ 20%] cobra.core.object highlighting module code... [ 23%] cobra.flux_analysis.summary highlighting module code... [ 25%] cobra.util.context highlighting module code... [ 28%] cobra.flux_analysis.reaction highlighting module code... [ 30%] cobra.core.dictlist highlighting module code... [ 33%] logging highlighting module code... [ 35%] cobra.io.sbml highlighting module code... [ 38%] cobra.core.model highlighting module code... [ 41%] cobra.flux_analysis.variability highlighting module code... [ 43%] cobra.util.array highlighting module code... [ 46%] cobra.core.species highlighting module code... [ 48%] cobra.core.arraybasedmodel highlighting module code... 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[ 92%] cobra.core.gene highlighting module code... [ 94%] cobra.flux_analysis.sampling highlighting module code... [ 97%] cobra.flux_analysis.phenotype_phase_plane highlighting module code... [100%] cobra.flux_analysis.parsimonious writing additional pages... search copying images... [ 25%] _build/doctrees-json/nbsphinx/phenotype_phase_plane_10_1.png copying images... [ 50%] _build/doctrees-json/nbsphinx/loopless_7_1.png copying images... [ 75%] _build/doctrees-json/nbsphinx/loopless_11_0.png copying images... [100%] _build/doctrees-json/nbsphinx/constraints_objectives_17_0.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 40 warnings. [rtd-command-info] start-time: 2017-12-07T18:21:04.614849, end-time: 2017-12-07T18:21:36.087706, duration: 31, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.5.6 making output directory... loading translations [en]... done loading pickled environment... not yet created loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/numpy/objects.inv -> https://docs.scipy.org/doc/numpy/objects.inv loading intersphinx inventory from http://docs.python.org/objects.inv... intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/2/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/reference/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 22 added, 0 changed, 0 removed reading sources... [ 4%] building_model reading sources... [ 9%] cobra reading sources... [ 13%] cobra.core reading sources... [ 18%] cobra.design reading sources... [ 22%] cobra.flux_analysis reading sources... [ 27%] cobra.io reading sources... [ 31%] cobra.manipulation reading sources... [ 36%] cobra.topology reading sources... [ 40%] cobra.util reading sources... [ 45%] constraints_objectives reading sources... [ 50%] deletions reading sources... [ 54%] faq reading sources... [ 59%] gapfilling reading sources... [ 63%] getting_started reading sources... [ 68%] index reading sources... [ 72%] io reading sources... [ 77%] loopless reading sources... [ 81%] phenotype_phase_plane reading sources... [ 86%] pymatbridge reading sources... [ 90%] sampling reading sources... [ 95%] simulating reading sources... [100%] solvers /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/solvers/__init__.py:73: UserWarning: No LP solvers found warn("No LP solvers found") /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:9: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/model.py:docstring of cobra.core.model.Model.add_boundary:15: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.get_coefficients:4: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.subtract_metabolites:18: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:11: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:22: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:6: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:7: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:37: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:31: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:39: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:47: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:5: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:9: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:78: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:85: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler.sample:6: SEVERE: Unexpected section title. Paramters --------- /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:48: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:52: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_gene_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_reaction_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:56: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:61: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:20: ERROR: Unknown target name: "3". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:64: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:7: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:12: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:41: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:47: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.nullspace:15: WARNING: Field list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... getting_started building_model io simulating deletions phenotype_phase_plane sampling loopless gapfilling solvers constraints_objectives pymatbridge faq cobra cobra.core cobra.design cobra.flux_analysis cobra.io cobra.manipulation cobra.topology cobra.util writing... done writing additional files... copying images... [ 25%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/phenotype_phase_plane_10_1.png copying images... [ 50%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/loopless_11_0.png copying images... [ 75%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/constraints_objectives_17_0.png copying images... [100%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/loopless_7_1.png copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 40 warnings. [rtd-command-info] start-time: 2017-12-07T18:21:36.265101, end-time: 2017-12-07T18:22:04.275033, duration: 28, exit-code: 0 python /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/envs/master/bin/sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.5.6 making output directory... loading translations [en]... done loading pickled environment... not yet created loading intersphinx inventory from http://docs.python.org/objects.inv... intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/2/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/reference/objects.inv loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... intersphinx inventory has moved: http://docs.scipy.org/doc/numpy/objects.inv -> https://docs.scipy.org/doc/numpy/objects.inv building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 22 added, 0 changed, 0 removed reading sources... [ 4%] building_model reading sources... [ 9%] cobra reading sources... [ 13%] cobra.core reading sources... [ 18%] cobra.design reading sources... [ 22%] cobra.flux_analysis reading sources... [ 27%] cobra.io reading sources... [ 31%] cobra.manipulation reading sources... [ 36%] cobra.topology reading sources... [ 40%] cobra.util reading sources... [ 45%] constraints_objectives reading sources... [ 50%] deletions reading sources... [ 54%] faq reading sources... [ 59%] gapfilling reading sources... [ 63%] getting_started reading sources... [ 68%] index reading sources... [ 72%] io reading sources... [ 77%] loopless reading sources... [ 81%] phenotype_phase_plane reading sources... [ 86%] pymatbridge reading sources... [ 90%] sampling reading sources... [ 95%] simulating reading sources... [100%] solvers /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/solvers/__init__.py:73: UserWarning: No LP solvers found warn("No LP solvers found") /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:6: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/dictlist.py:docstring of cobra.core.dictlist.DictList.query:9: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/model.py:docstring of cobra.core.model.Model.add_boundary:15: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.get_coefficients:4: WARNING: Inline literal start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/core/reaction.py:docstring of cobra.core.reaction.Reaction.subtract_metabolites:18: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:11: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:22: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:6: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_fva_iter:7: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:37: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/moma.py:docstring of cobra.flux_analysis.moma.add_moma:31: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:39: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/parsimonious.py:docstring of cobra.flux_analysis.parsimonious.pfba:47: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:5: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/phenotype_phase_plane.py:docstring of cobra.flux_analysis.phenotype_phase_plane.calculate_phenotype_phase_plane:9: WARNING: Field list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:78: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:85: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler.sample:6: SEVERE: Unexpected section title. Paramters --------- /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:48: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:52: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_gene_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/single_deletion.py:docstring of cobra.flux_analysis.single_deletion.single_reaction_deletion:21: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:56: WARNING: Duplicate explicit target name: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:61: WARNING: Duplicate explicit target name: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:3: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/gapfilling.py:docstring of cobra.flux_analysis.gapfilling.GapFiller:20: ERROR: Unknown target name: "3". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.add_loopless:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/loopless.py:docstring of cobra.flux_analysis.loopless.loopless_solution:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.ACHRSampler:64: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.OptGPSampler:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:7: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/sampling.py:docstring of cobra.flux_analysis.sampling.sample:12: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:41: ERROR: Duplicate target name, cannot be used as a unique reference: "1". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/flux_analysis/variability.py:docstring of cobra.flux_analysis.variability.flux_variability_analysis:47: ERROR: Duplicate target name, cannot be used as a unique reference: "2". /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:24: ERROR: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.constraint_matrices:25: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/cobra/util/array.py:docstring of cobra.util.array.nullspace:15: WARNING: Field list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done processing cobra.tex... index getting_started building_model io simulating deletions phenotype_phase_plane sampling loopless gapfilling solvers constraints_objectives pymatbridge faq cobra cobra.core cobra.design cobra.flux_analysis cobra.io cobra.manipulation cobra.topology cobra.util resolving references... writing... done copying images... _build/doctrees/nbsphinx/constraints_objectives_17_0.pdf _build/doctrees/nbsphinx/phenotype_phase_plane_10_1.png _build/doctrees/nbsphinx/loopless_7_1.pdf _build/doctrees/nbsphinx/loopless_11_0.pdf copying TeX support files... done build succeeded, 39 warnings. [rtd-command-info] start-time: 2017-12-07T18:22:04.381104, end-time: 2017-12-07T18:22:05.937099, duration: 1, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/documentation_builder/_build/latex/cobra.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cobrapy/checkouts/master/docu mentation_builder/_build/latex/cobra.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.5.4 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [4] [5] [6] [7] [8] Chapter 2. [9] [10] [11] [12] Chapter 3. [13] [14] [15] [16] Chapter 4. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [17] [18] [19] [20] [21] [22] Chapter 5. [23] [24] [25] [26] Chapter 6. [27] [28 <./phenotype_phase_plane_10_1.png>] Chapter 7. [29] [30] [31] [32] Chapter 8. LaTeX Warning: Hyper reference `loopless:Method' on page 33 undefined on input line 1952. [33] [34 <./loopless_7_1.pdf>] [35 <./loopless_11_0.pdf>] ! Missing \endgroup inserted. \endgroup l.2178 \end{eqnarray}\end{split} ! Missing } inserted. } l.2178 \end{eqnarray}\end{split} ! You can't use `\halign' in math mode. \H@eqnarray ...let \\\@eqncr $$\everycr {}\halign to\displaywidth \bgroup \h... l.2178 \end{eqnarray}\end{split} ! Missing number, treated as zero. \bgroup l.2178 \end{eqnarray}\end{split} ! 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