{"action":"created","issue":{"url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/31","repository_url":"https://api.github.com/repos/xinbian/langevin_dynamics","labels_url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/31/comments","events_url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/31/events","html_url":"https://github.com/xinbian/langevin_dynamics/pull/31","id":202381181,"number":31,"title":"Update sphinx to 1.5.2","user":{"login":"pyup-bot","id":16239342,"avatar_url":"https://avatars.githubusercontent.com/u/16239342?v=3","gravatar_id":"","url":"https://api.github.com/users/pyup-bot","html_url":"https://github.com/pyup-bot","followers_url":"https://api.github.com/users/pyup-bot/followers","following_url":"https://api.github.com/users/pyup-bot/following{/other_user}","gists_url":"https://api.github.com/users/pyup-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/pyup-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pyup-bot/subscriptions","organizations_url":"https://api.github.com/users/pyup-bot/orgs","repos_url":"https://api.github.com/users/pyup-bot/repos","events_url":"https://api.github.com/users/pyup-bot/events{/privacy}","received_events_url":"https://api.github.com/users/pyup-bot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-01-22T12:55:45Z","updated_at":"2017-02-26T11:57:36Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/xinbian/langevin_dynamics/pulls/31","html_url":"https://github.com/xinbian/langevin_dynamics/pull/31","diff_url":"https://github.com/xinbian/langevin_dynamics/pull/31.diff","patch_url":"https://github.com/xinbian/langevin_dynamics/pull/31.patch"},"body":"\nThere's a new version of [Sphinx](https://pypi.python.org/pypi/Sphinx) available.\nYou are currently using **1.4.4**. I have updated it to **1.5.2**\n\n\n\nThese links might come in handy:  <a href=\"http://pypi.python.org/pypi/Sphinx\">PyPI</a> | <a href=\"https://pyup.io/changelogs/sphinx/\">Changelog</a> | <a href=\"http://sphinx-doc.org/\">Homepage</a> \n\n\n\n### Changelog\n> \n>### 1.5.2\n\n>===============================\n\n>Incompatible changes\n>--------------------\n\n>* Dependency requirement updates: requests 2.4.0 or above (refs: 3268, 3310)\n\n>Features added\n>--------------\n\n>* 3241: emit latex warning if buggy titlesec (ref 3210)\n>* 3194: Refer the $MAKE environment variable to determine ``make`` command\n>* Emit warning for nested numbered toctrees (refs: 3142)\n>* 978: `intersphinx_mapping` also allows a list as a parameter\n>* 3340: (LaTeX) long lines in :dudir:`parsed-literal` are wrapped like in\n>  :rst:dir:`code-block`, inline math and footnotes are fully functional.\n\n>Bugs fixed\n>----------\n\n>* 3246: xapian search adapter crashes\n>* 3253: In Py2 environment, building another locale with a non-captioned\n>  toctree produces ``None`` captions\n>* 185: References to section title including raw node has broken\n>* 3255: In Py3.4 environment, autodoc doesn&#39;t support documentation for\n>  attributes of Enum class correctly.\n>* 3261: ``latex_use_parts`` makes sphinx crash\n>* The warning type ``misc.highlighting_failure`` does not work\n>* 3294: ``add_latex_package()`` make crashes non-LaTeX builders\n>* The caption of table are rendered as invalid HTML (refs: 3287)\n>* 3268: Sphinx crashes with requests package from Debian jessie\n>* 3284: Sphinx crashes on parallel build with an extension which raises\n>  unserializable exception\n>* 3315: Bibliography crashes on latex build with docclass &#39;memoir&#39;\n>* 3328: Could not refer rubric implicitly\n>* 3329: emit warnings if po file is invalid and can&#39;t read it. Also writing mo too\n>* 3337: Ugly rendering of definition list term&#39;s classifier\n>* 3335: gettext does not extract field_name of a field in a field_list\n>* 2952: C++, fix refs to operator() functions.\n>* Fix Unicode super- and subscript digits in :rst:dir:`code-block` and\n>  parsed-literal LaTeX output (ref 3342)\n>* LaTeX writer: leave ``&quot;`` character inside parsed-literal as is (ref 3341)\n>* 3234: intersphinx failed for encoded inventories\n>* 3158: too much space after captions in PDF output\n>* 3317: An URL in parsed-literal contents gets wrongly rendered in PDF if\n>  with hyphen\n>* LaTeX crash if the filename of an image inserted in parsed-literal\n>  via a substitution contains an hyphen (ref 3340)\n>* LaTeX rendering of inserted footnotes in parsed-literal is wrong (ref 3340)\n>* Inline math in parsed-literal is not rendered well by LaTeX (ref 3340)\n>* 3308: Parsed-literals don&#39;t wrap very long lines with pdf builder (ref 3340)\n>* 3295: Could not import extension sphinx.builders.linkcheck\n>* 3285: autosummary: asterisks are escaped twice\n>* LaTeX, pass dvipdfm option to geometry package for Japanese documents (ref 3363)\n\n\n\n\n>### 1.5.1\n\n>=====================================\n\n>Features added\n>--------------\n\n>* 3214: Allow to suppress &quot;unknown mimetype&quot; warnings from epub builder using\n>  :confval:`suppress_warnings`.\n\n>Bugs fixed\n>----------\n\n>* 3195: Can not build in parallel\n>* 3198: AttributeError is raised when toctree has &#39;self&#39;\n>* 3211: Remove untranslated sphinx locale catalogs (it was covered by\n>  untranslated it_IT)\n>* 3212: HTML Builders crashes with docutils-0.13\n>* 3207: more latex problems with references inside parsed-literal directive\n>  (``\\DUrole``)\n>* 3205: sphinx.util.requests crashes with old pyOpenSSL (&lt; 0.14)\n>* 3220: KeyError when having a duplicate citation\n>* 3200: LaTeX: xref inside desc_name not allowed\n>* 3228: ``build_sphinx`` command crashes when missing dependency\n>* 2469: Ignore updates of catalog files for gettext builder. Thanks to\n>  Hiroshi Ohkubo.\n>* 3183: Randomized jump box order in generated index page.\n\n\n\n>### 1.5\n\n\n>* 3069: Even if ``&#39;babel&#39;`` key is set to empty string, LaTeX output contains\n>  one ``\\addto\\captions...``\n>* 3123: user ``&#39;babel&#39;`` key setting is not obeyed anymore\n>* 3155: Fix JavaScript for `html_sourcelink_suffix` fails with IE and Opera\n>* 3085: keep current directory after breaking build documentation. Thanks to\n>  Timotheus Kampik.\n>* 3181: pLaTeX crashes with a section contains endash\n>* 3180: latex: add stretch/shrink between successive singleline or\n>  multipleline cpp signatures (ref 3072)\n>* 3128: globing images does not support .svgz file\n>* 3015: fix a broken test on Windows.\n>* 1843: Fix documentation of descriptor classes that have a custom metaclass.\n>  Thanks to Erik Bray.\n>* 3190: util.split_docinfo fails to parse multi-line field bodies\n>* 3024, 3037: In Python3, application.Sphinx._log crushed when the log message cannot\n>  be encoded into console encoding.\n\n>Testing\n>--------\n\n>* To simplify, sphinx uses external mock package even if unittest.mock exists.\n\n\n\n\n>### 1.5b1\n\n\n>* 2432: Fix unwanted * between varargs and keyword only args. Thanks to Alex Grönholm.\n>* 3062: Failed to build PDF using 1.5a2 (undefined ``\\hypersetup`` for\n>  Japanese documents since PR3030)\n>* Better rendering of multiline signatures in html.\n>* 777: LaTeX output &quot;too deeply nested&quot; (ref 3096)\n>* Let LaTeX image inclusion obey ``scale`` before textwidth fit (ref 2865, 3059)\n>* 3019: LaTeX fails on description of C function with arguments (ref 3083)\n>* fix latex inline literals where ``&lt; &gt; -`` gobbled a space\n\n\n\n>### 1.5a2\n\n\n>* 2810: Problems with pdflatex in an Italian document\n>* Use ``latex_elements.papersize`` to specify papersize of LaTeX in Makefile\n>* 2988: linkcheck: retry with GET request if denied HEAD request\n>* 2990: linkcheck raises &quot;Can&#39;t convert &#39;bytes&#39; object to str implicitly&quot; error\n>  if linkcheck_anchors enabled\n>* 3004: Invalid link types &quot;top&quot; and &quot;up&quot; are used\n>* 3009: Bad rendering of parsed-literals in LaTeX since Sphinx 1.4.4\n>* 3000: ``option`` directive generates invalid HTML anchors\n>* 2984: Invalid HTML has been generated if `html_split_index` enabled\n>* 2986: themes/basic/defindex.html should be changed for html5 friendly\n>* 2987: Invalid HTML has been generated if multiple IDs are assigned to a list\n>* 2891: HTML search does not provide all the results\n>* 1986: Title in PDF Output\n>* 147: Problem with latex chapter style\n>* 3018: LaTeX problem with page layout dimensions and chapter titles\n>* Fix an issue with ``\\pysigline`` in LaTeX style file (ref 3023)\n>* 3038: ``sphinx.ext.math*`` raises TypeError if labels are duplicated\n>* 3031: incompatibility with LaTeX package ``tocloft``\n>* 3003: literal blocks in footnotes are not supported by Latex\n>* 3047: spacing before footnote in pdf output is not coherent and allows breaks\n>* 3045: HTML search index creator should ignore &quot;raw&quot; content if now html\n>* 3039: English stemmer returns wrong word if the word is capitalized\n>* Fix make-mode Makefile template (ref 3056, 2936)\n\n\n\n>### 1.5a1\n\n\n>* 2707: (latex) the column width is badly computed for tabular\n>* 2799: Sphinx installs roles and directives automatically on importing sphinx\n>  module.  Now Sphinx installs them on running application.\n>* `sphinx.ext.autodoc` crashes if target code imports * from mock modules\n>  by `autodoc_mock_imports`.\n>* 1953: ``Sphinx.add_node`` does not add handlers the translator installed by\n>  ``html_translator_class``\n>* 1797: text builder inserts blank line on top\n>* 2894: quickstart main() doesn&#39;t use argv argument\n>* 2874: gettext builder could not extract all text under the ``only``\n>  directives\n>* 2485: autosummary crashes with multiple source_suffix values\n>* 1734: Could not translate the caption of toctree directive\n>* Could not translate the content of meta directive (ref: 1734)\n>* 2550: external links are opened in help viewer\n>* 2687: Running Sphinx multiple times produces &#39;already registered&#39; warnings\n\n\n\n>### 1.4.9\n\n>=====================================\n\n>Bugs fixed\n>----------\n\n>* 2936: Fix doc/Makefile that can&#39;t build man because doc/man exists\n>* 3058: Using the same &#39;caption&#39; attribute in multiple &#39;toctree&#39; directives\n>  results in warning / error\n>* 3068: Allow the &#39;=&#39; character in the -D option of sphinx-build.py\n>* 3074: ``add_source_parser()`` crashes in debug mode\n>* 3135: ``sphinx.ext.autodoc`` crashes with plain Callable\n>* 3150: Fix query word splitter in JavaScript. It behaves as same as Python&#39;s regular expression.\n>* 3093: gettext build broken on substituted images.\n>* 3093: gettext build broken on image node under ``note`` directive.\n>* imgmath: crashes on showing error messages if image generation failed\n>* 3117: LaTeX writer crashes if admonition is placed before first section title\n>* 3164: Change search order of ``sphinx.ext.inheritance_diagram``\n\n\n\n>### 1.4.8\n\n>====================================\n\n>Bugs fixed\n>----------\n\n>* 2996: The wheel package of Sphinx got crash with ImportError\n\n\n\n>### 1.4.7\n\n>====================================\n\n>Bugs fixed\n>----------\n\n>* 2890: Quickstart should return an error consistently on all error conditions\n>* 2870: flatten genindex columns&#39; heights.\n>* 2856: Search on generated HTML site doesnt find some symbols\n>* 2882: Fall back to a GET request on 403 status in linkcheck\n>* 2902: jsdump.loads fails to load search index if keywords starts with\n>  underscore\n>* 2900: Fix epub content.opf: add auto generated orphan files to spine.\n>* 2899: Fix ``hasdoc()`` function in Jinja2 template. It can detect ``genindex``, ``search`` collectly.\n>* 2901: Fix epub result: skip creating links from image tags to original image files.\n>* 2917: inline code is hyphenated on HTML\n>* 1462: autosummary warns for namedtuple with attribute with trailing underscore\n>* Could not reference equations if ``:nowrap:`` option specified\n>* 2873: code-block overflow in latex (due to commas)\n>* 1060, 2056: sphinx.ext.intersphinx: broken links are generated if relative\n>  paths are used in `intersphinx_mapping`\n>* 2931: code-block directive with same :caption: causes warning of duplicate\n>  target.  Now `code-block` and `literalinclude` does not define hyperlink\n>  target using its caption automatially.\n>* 2962: latex: missing label of longtable\n>* 2968: autodoc: show-inheritance option breaks docstrings\n\n\n\n>### 1.4.6\n\n>=====================================\n\n>Incompatible changes\n>--------------------\n\n>* 2867: linkcheck builder crashes with six-1.4.  Now Sphinx depends on six-1.5 or\n>  later\n\n>Bugs fixed\n>----------\n\n>* applehelp: Sphinx crashes if ``hiutil`` or ``codesign`` commands not found\n>* Fix ``make clean`` abort issue when build dir contains regular files like ``DS_Store``.\n>* Reduce epubcheck warnings/errors:\n\n>  * Fix DOCTYPE to html5\n>  * Change extension from .html to .xhtml.\n>  * Disable search page on epub results\n\n>* 2778: Fix autodoc crashes if obj.__dict__ is a property method and raises exception\n>* Fix duplicated toc in epub3 output.\n>* 2775: Fix failing linkcheck with servers not supporting identidy encoding\n>* 2833: Fix formatting instance annotations in ext.autodoc.\n>* 1911: ``-D`` option of ``sphinx-build`` does not override the ``extensions`` variable\n>* 2789: `sphinx.ext.intersphinx` generates wrong hyperlinks if the inventory is given\n>* parsing errors for caption of code-blocks are displayed in document (ref: 2845)\n>* 2846: ``singlehtml`` builder does not include figure numbers\n>* 2816: Fix data from builds cluttering the ``Domain.initial_data`` class attributes\n\n\n\n>### 1.4.5\n\n>=====================================\n\n>Incompatible changes\n>--------------------\n\n>* latex, inclusion of non-inline images from image directive resulted in\n>  non-coherent whitespaces depending on original image width; new behaviour\n>  by necessity differs from earlier one in some cases. (ref: 2672)\n>* latex, use of ``\\includegraphics`` to refer to Sphinx custom variant is\n>  deprecated; in future it will revert to original LaTeX macro, custom one\n>  already has alternative name ``\\sphinxincludegraphics``.\n\n>Features added\n>--------------\n\n>* new config option ``latex_keep_old_macro_names``, defaults to True. If False,\n>  lets macros (for text styling) be defined only with ``\\sphinx``-prefixed names.\n>* latex writer allows user customization of &quot;shadowed&quot; boxes (topics), via\n>  three length variables.\n>* woff-format web font files now supported by the epub builder.\n\n>Bugs fixed\n>----------\n\n>* jsdump fix for python 3: fixes the HTML search on python &gt; 3\n>* 2676: (latex) Error with verbatim text in captions since Sphinx 1.4.4\n>* 2629: memoir class crashes LaTeX. Fixed ``by latex_keep_old_macro_names=False`` (ref 2675)\n>* 2684: `sphinx.ext.intersphinx` crashes with six-1.4.1\n>* 2679: ``float`` package needed for ``&#39;figure_align&#39;: &#39;H&#39;`` latex option\n>* 2671: image directive may lead to inconsistent spacing in pdf\n>* 2705: ``toctree`` generates empty bullet_list if ``:titlesonly:`` specified\n>* 2479: `sphinx.ext.viewcode` uses python2 highlighter by default\n>* 2700: HtmlHelp builder has hard coded index.html\n>* latex, since 1.4.4 inline literal text is followed by spurious space\n>* 2722: C++, fix id generation for var/member declarations to include namespaces.\n>* latex, images (from image directive) in lists or quoted blocks did not obey\n>  indentation (fixed together with 2671)\n>* 2733: since Sphinx-1.4.4 ``make latexpdf`` generates lots of hyperref warnings\n>* 2731: `sphinx.ext.autodoc` does not access propertymethods which raises any\n>  exceptions\n>* 2666: C++, properly look up nested names involving constructors.\n>* 2579: Could not refer a label including both spaces and colons via\n>  `sphinx.ext.intersphinx`\n>* 2718: Sphinx crashes if the document file is not readable\n>* 2699: hyperlinks in help HTMLs are broken if `html_file_suffix` is set\n>* 2723: extra spaces in latex pdf output from multirow cell\n>* 2735: latexpdf ``Underfull \\hbox (badness 10000)`` warnings from title page\n>* 2667: latex crashes if resized images appeared in section title\n>* 2763: (html) Provide default value for required ``alt`` attribute for image\n>  tags of SVG source, required to validate and now consistent w/ other formats.\n\n\n\n\n\n\n\n\n*Got merge conflicts? Close this PR and delete the branch. I'll create a new PR for you.*\n\nHappy merging! 🤖\n"},"comment":{"url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/comments/282550954","html_url":"https://github.com/xinbian/langevin_dynamics/pull/31#issuecomment-282550954","issue_url":"https://api.github.com/repos/xinbian/langevin_dynamics/issues/31","id":282550954,"user":{"login":"pyup-bot","id":16239342,"avatar_url":"https://avatars.githubusercontent.com/u/16239342?v=3","gravatar_id":"","url":"https://api.github.com/users/pyup-bot","html_url":"https://github.com/pyup-bot","followers_url":"https://api.github.com/users/pyup-bot/followers","following_url":"https://api.github.com/users/pyup-bot/following{/other_user}","gists_url":"https://api.github.com/users/pyup-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/pyup-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pyup-bot/subscriptions","organizations_url":"https://api.github.com/users/pyup-bot/orgs","repos_url":"https://api.github.com/users/pyup-bot/repos","events_url":"https://api.github.com/users/pyup-bot/events{/privacy}","received_events_url":"https://api.github.com/users/pyup-bot/received_events","type":"User","site_admin":false},"created_at":"2017-02-26T11:57:36Z","updated_at":"2017-02-26T11:57:36Z","body":"Closing this in favor of #34"}}
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