citation examples

[jessdtate]

some working citation using autorestructify and the eval_rst functionality.

[akilnarayan]

I can't get the citations to appear. Here are some details:

• I do rm -rf _build/html from within UncertainSCI/docs
• Then make html, and inspect _build/html

Here is what I see:

The output from make html is:

$ make html
Running Sphinx v3.2.1
loading translations [python]... not available for built-in messages
making output directory... done
loading pickled environment... checking for /Users/akil/work/python/UncertainSCI/docs/references.bib in bibtex cache... out of date
parsing bibtex file /Users/akil/work/python/UncertainSCI/docs/references.bib... parsed 5 entries
failed
failed: No such config value: recommonmark_config
checking for /Users/akil/work/python/UncertainSCI/docs/references.bib in bibtex cache... not found
parsing bibtex file /Users/akil/work/python/UncertainSCI/docs/references.bib... parsed 5 entries
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 22 source files that are out of date
updating environment: [new config] 22 added, 0 changed, 0 removed
/opt/anaconda3/lib/python3.7/site-packages/recommonmark/parser.py:75: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/opt/anaconda3/lib/python3.7/site-packages/recommonmark/parser.py:75: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [100%] user_docs/support                                     
/Users/akil/work/python/UncertainSCI/UncertainSCI/pce.py:docstring of UncertainSCI.pce.PolynomialChaosExpansion:6: WARNING: Unexpected section title.

Attributes:
-----------
/Users/akil/work/python/UncertainSCI/UncertainSCI/pce.py:docstring of UncertainSCI.pce.PolynomialChaosExpansion:9: WARNING: Unexpected indentation.
/Users/akil/work/python/UncertainSCI/UncertainSCI/pce.py:docstring of UncertainSCI.pce.PolynomialChaosExpansion:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/akil/work/python/UncertainSCI/UncertainSCI/pce.py:docstring of UncertainSCI.pce.PolynomialChaosExpansion:12: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/akil/work/python/UncertainSCI/UncertainSCI/pce.py:docstring of UncertainSCI.pce.PolynomialChaosExpansion.augment_samples_idist:7: WARNING: Unexpected indentation.
/Users/akil/work/python/UncertainSCI/docs/dev_docs/HowToTutorial.md:1: WARNING: Unknown interpreted text role "cite:p".
/Users/akil/work/python/UncertainSCI/docs/dev_docs/HowToTutorial.md:1: WARNING: Unknown interpreted text role "cite:p".
/Users/akil/work/python/UncertainSCI/docs/index.rst:19: WARNING: Unknown interpreted text role "cite:p".
/Users/akil/work/python/UncertainSCI/docs/tutorials/demos/pce_statistics.rst:2: WARNING: Title underline too short.

PCE Statistics
=====
/Users/akil/work/python/UncertainSCI/docs/tutorials/template.md:1: WARNING: Unknown interpreted text role "cite:p".
/Users/akil/work/python/UncertainSCI/docs/tutorials/template.md:1: WARNING: Unknown interpreted text role "cite:p".
/Users/akil/work/python/UncertainSCI/docs/user_docs/faq.md:0: WARNING: Document or section may not begin with a transition.
/Users/akil/work/python/UncertainSCI/docs/user_docs/specs.md:0: WARNING: Document or section may not begin with a transition.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/akil/work/python/UncertainSCI/docs/about.md: WARNING: document isn't included in any toctree
/Users/akil/work/python/UncertainSCI/docs/dev_docs/contribute.md: WARNING: document isn't included in any toctree
/Users/akil/work/python/UncertainSCI/docs/user_docs/faq.md: WARNING: document isn't included in any toctree
/Users/akil/work/python/UncertainSCI/docs/user_docs/install.rst: WARNING: document isn't included in any toctree
/Users/akil/work/python/UncertainSCI/docs/user_docs/specs.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] user_docs/support                                      
/Users/akil/work/python/UncertainSCI/docs/dev_docs/HowToTutorial.md:26: WARNING: None:any reference target not found: 
/Users/akil/work/python/UncertainSCI/docs/dev_docs/HowToTutorial.md:313: WARNING: None:any reference target not found: contribute.html
/Users/akil/work/python/UncertainSCI/docs/dev_docs/contribute.md:5: WARNING: None:any reference target not found: HowToTutorial.html
/Users/akil/work/python/UncertainSCI/docs/tutorials/demos/simple_boxplots.md:39: WARNING: None:any reference target not found: ../parameters.html
/Users/akil/work/python/UncertainSCI/docs/user_docs/getting_started.md:17: WARNING: None:any reference target not found: ../tutorials/index.html
/Users/akil/work/python/UncertainSCI/docs/user_docs/getting_started.md:17: WARNING: None:any reference target not found: ../api_docs/index.html
generating indices...  genindex py-modindexdone
writing additional pages...  searchdone
copying images... [100%] tutorials/../_static/UncertainSCI.png                  
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 24 warnings.

The HTML pages are in _build/html.

Regarding the failed: No such config value: recommonmark_config line near the top, this may be useful:

$ python
Python 3.7.7 (default, Mar 23 2020, 17:31:31) 
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import recommonmark
>>> recommonmark.__version__
'0.7.1'

Any ideas what I did wrong?

[jessdtate]

My recommonmark is the same and it's building on RTD. We're both building on Python 3.7, but I hope that doesn't matter.

Did you make sure that you reinstalled the dependences for the docs? You might also need to do a fresh install (delete _build folder). If reinstalling doesn't work, maybe try in python

import recommonmark
from recommonmark.transform import AutoStructify

[akilnarayan]

Ah, I didn't update new requirements.txt dependencies. Now it works, thanks!