4_possible_issues_for_building_html_using_jupyter-book

[shlff]

Hi @mmcky , when I use the command jupyter-book build ctmc_lectures/ to build html files from the original files, I come across 4 issues:

1. 970 : WARNING: duplicate citation,
2. OSError: [Errno 24] Too many open files,
3. ValueError,
4. AttributeError: '_UnixSelectorEventLoop' object has no attribute '_ssock'

Please find the screenshot for the execution and those issues with red labels below:

However, when I use the command jupyter-book page path/xx.md to build HTML files for those md-myst files separately, it works well.

Do you think how I should improve those issues? I look forward to your comments.

[mmcky]

thanks @shlff. Just a few preliminary points.

1. jupyter-book is technically supported for sphinx < 3.0 but looks like it is working on the most part for you. You may want to create a new environment using conda and install jupyter-book. It should bring in sphinx version 2+ but <3.

Issue [1]: This is likely an issue in the source bib file. Is there a duplicate tag?

Issue [2]: This is a limitation of os x when running many jupyter notebooks in parallel. You can try and run ulimit -S -n 2048 in the terminal to see if that is the issue. This command allows for more open sockets.

Issue [3] and Issue [4] may be as a result of Issue [2] so let's iterate on those first to see if they resolve these.

[mmcky]

hey @shlff I can't replicate these issues on my mac.

I would recommend you do the following:

conda create -n jupyterbook python=3.7 anaconda

then activate the conda environment

conda activate jupyterbook

then install jupyter-book

pip install jupyter-book

you should see this install downgrades sphinx=2.4.4

Installing collected packages: libsass, sphinx, pydata-sphinx-theme, sphinx-book-theme, nest-asyncio, async-generator, nbclient, sphinx-thebe, sphinx-togglebutton, jupyter-sphinx, markdown-it-py, myst-parser, smmap, gitdb, GitPython, nbdime, jupyter-cache, myst-nb, latexcodec, pybtex, pybtex-docutils, oset, sphinxcontrib-bibtex, sphinx-copybutton, jupyter-book
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 3.1.2
    Uninstalling Sphinx-3.1.2:
      Successfully uninstalled Sphinx-3.1.2
Successfully installed GitPython-3.1.7 async-generator-1.10 gitdb-4.0.5 jupyter-book-0.7.4 jupyter-cache-0.2.2 jupyter-sphinx-0.2.4 latexcodec-2.0.1 libsass-0.20.0 markdown-it-py-0.4.8 myst-nb-0.8.4 myst-parser-0.10.0 nbclient-0.4.1 nbdime-2.0.0 nest-asyncio-1.4.0 oset-0.1.3 pybtex-0.22.2 pybtex-docutils-0.2.2 pydata-sphinx-theme-0.3.1 smmap-3.0.4 sphinx-2.4.4 sphinx-book-theme-0.0.34 sphinx-copybutton-0.3.0 sphinx-thebe-0.0.7 sphinx-togglebutton-0.2.1 sphinxcontrib-bibtex-1.0.0

Install dependencies:

pip install quantecon

Then run the build

jb build ctmc_lectures

then we will be working to the same software environment.

I get the following issues showing up

▶ jb build ctmc_lectures
Running Sphinx v2.4.4
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 9 source files that are out of date
updating environment: [new config] 9 added, 9 changed, 0 removed
Executing: ergodicity11%] ergodicity                                                                                                                   
Executing: infinitesimals infinitesimals                                                                                                               
Executing: kolmogorov_bwd kolmogorov_bwd                                                                                                               
checking for continuous_time_mcs/ctmc_lectures/references.bib in bibtex cache... not found
parsing bibtex file continuous_time_mcs/ctmc_lectures/references.bib... parsed 6 entries
Executing: kolmogorov_fwd kolmogorov_fwd                                                                                                               
Executing: markov_prop6%] markov_prop                                                                                                                  
checking for continuous_time_mcs/ctmc_lectures/references.bib in bibtex cache... up to date
Executing: memoryless77%] memoryless                                                                                                                   
Executing: poisson [ 88%] poisson                                                                                                                      
checking for continuous_time_mcs/ctmc_lectures/references.bib in bibtex cache... up to date
Executing: prob_view100%] prob_view                                                                                                                    

continuous_time_mcs/ctmc_lectures/markov_prop.md:969: WARNING: duplicate citation stroock2013introduction, other instance in /Users/matthewmckay/repos-collab/continuous_time_mcs/ctmc_lectures/kolmogorov_bwd.md
continuous_time_mcs/ctmc_lectures/poisson.md:524: WARNING: duplicate citation le2016brownian, other instance in continuous_time_mcs/ctmc_lectures/markov_prop.md
continuous_time_mcs/ctmc_lectures/poisson.md:524: WARNING: duplicate citation stroock2013introduction, other instance in continuous_time_mcs/ctmc_lectures/markov_prop.md
continuous_time_mcs/ctmc_lectures/poisson.md:524: WARNING: duplicate citation walsh2012knowing, other instance in continuous_time_mcs/ctmc_lectures/markov_prop.md
WARNING: duplicate label for keys stroock2013introduction and stroock2013introduction
WARNING: duplicate label for keys le2016brownian and le2016brownian
WARNING: duplicate label for keys stroock2013introduction and stroock2013introduction
WARNING: duplicate label for keys walsh2012knowing and walsh2012knowing
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] prob_view                                                                                                                     
continuous_time_mcs/ctmc_lectures/markov_prop.md:389: WARNING: undefined label: exp_unique (if the link has no caption the label must precede a section header)
generating indices...  genindexdone
writing additional pages...  searchdone
copying images... [100%] _build/jupyter_execute/poisson_11_0.png                                                                                       
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 9 warnings.

[mmcky]

@jstac and @shlff

The warnings I am getting are due to multiple instances of bibliography. Generating local bibliographies in each file with sphinxcontrob-bibtex (used under the hood of jupyter-book) is a bit clunky but can be done with filters.

I don't have write access to submit a PR but these are the changes required.

diff --git a/ctmc_lectures/kolmogorov_bwd.md b/ctmc_lectures/kolmogorov_bwd.md
index 6822ac4..eee1f82 100644
--- a/ctmc_lectures/kolmogorov_bwd.md
+++ b/ctmc_lectures/kolmogorov_bwd.md
@@ -488,4 +488,5 @@ which is identical to {eq}`kolbackeq`.
 ## References
 
 ```{bibliography} references.bib
+:filter: docname in docnames
 ```
diff --git a/ctmc_lectures/markov_prop.md b/ctmc_lectures/markov_prop.md
index 34c16ee..a989d38 100644
--- a/ctmc_lectures/markov_prop.md
+++ b/ctmc_lectures/markov_prop.md
@@ -969,4 +969,5 @@ The last expression equals $\mathbf P_\psi^n$, which concludes the proof.
 ## References
 
 ```{bibliography} references.bib
+:filter: docname in docnames
 ```
diff --git a/ctmc_lectures/poisson.md b/ctmc_lectures/poisson.md
index efdafb5..d532e54 100644
--- a/ctmc_lectures/poisson.md
+++ b/ctmc_lectures/poisson.md
@@ -526,4 +526,5 @@ plt.show()
 ## References
 
 ```{bibliography} references.bib
+:filter: docname in docnames
```

[mmcky]

I will update https://jupyterbook.org/content/citations.html?highlight=bibliography#citations-and-bibliographies to document this. See jupyter-book/jupyter-book#863

[shlff]

Thanks a lot, @mmcky .

As you instructed, I added :filter: docname in docnames in those files and the building works correctly immediately.

Please find the screenshot attached.