Jupyterbook not building with sphinxcontrib-bibtex failure

[Rahuketu86]

I am unable to build a jupyter book with following error /home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/sphinxcontrib/bibtex/init.py

Steps taken :

1. Created a new conda environment
2. pip install -r requirements.txt

My requirements.txt

jupyter
jupyter-book
pyreadline
plotly
plotly-express
plotnine
ipympl
altair
vega_datasets
bqplot
seaborn

3. jb create tbook
4. jb build tbook
5. (Others) Tried adding bibtex_bibfiles in _config.yml with no success

(testjb) ubuntu@ip-10-134-194-166:/Landmark2/pdo/Code/ALDAOps/metis$ jb create tbook

===============================================================================

Your book template can be found at

tbook/

===============================================================================

(testjb) ubuntu@ip-10-134-194-166:/Landmark2/pdo/Code/ALDAOps/metis$ jb build tbook
Running Jupyter-Book v0.8.3
Source Folder: /Landmark2/pdo/Code/ALDAOps/metis/tbook
Config Path: /Landmark2/pdo/Code/ALDAOps/metis/tbook/_config.yml
Output Path: /Landmark2/pdo/Code/ALDAOps/metis/tbook/_build/html
Running Sphinx v3.3.1
making output directory... done
myst v0.12.10: MdParserConfig(renderer='sphinx', commonmark_only=False, dmath_enable=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, amsmath_enable=False, deflist_enable=False, update_mathjax=True, admonition_enable=False, figure_enable=False, disable_syntax=[], html_img_enable=False, url_schemes=['mailto', 'http', 'https'], heading_anchors=None)

Extension error:
You must configure the bibtex_bibfiles setting
Traceback (most recent call last):
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/jupyter_book/sphinx.py", line 110, in build_sphinx
app = Sphinx(
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/sphinx/application.py", line 278, in init
self._init_builder()
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/sphinx/application.py", line 337, in _init_builder
self.events.emit('builder-inited')
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/sphinx/events.py", line 110, in emit
results.append(listener.handler(self.app, *args))
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/sphinxcontrib/bibtex/init.py", line 45, in init_bibtex_cache
raise ExtensionError("You must configure the bibtex_bibfiles setting")
sphinx.errors.ExtensionError: You must configure the bibtex_bibfiles setting

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/ubuntu/anaconda3/envs/testjb/bin/jb", line 8, in
sys.exit(main())
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/jupyter_book/commands/init.py", line 259, in build
builder_specific_actions(
File "/home/ubuntu/anaconda3/envs/testjb/lib/python3.9/site-packages/jupyter_book/commands/init.py", line 500, in builder_specific_actions
raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError:

There was an error in building your book. Look above for the cause.

===============================================================================

(testjb) ubuntu@ip-10-134-194-166:/Landmark2/pdo/Code/ALDAOps/metis$

[spring-haru]

I encountered the same problem in running Github Actions to build my site today, though versions are different.

Running Jupyter-Book v0.8.3
7
Source Folder: /home/runner/work/py4etrics.github.io/py4etrics.github.io
8
Config Path: /home/runner/work/py4etrics.github.io/py4etrics.github.io/_config.yml
9
Output Path: /home/runner/work/py4etrics.github.io/py4etrics.github.io/_build/html
10
Running Sphinx v3.3.1
11
myst v0.12.10: MdParserConfig(renderer='sphinx', commonmark_only=False, dmath_enable=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, amsmath_enable=False, deflist_enable=False, update_mathjax=True, admonition_enable=False, figure_enable=False, disable_syntax=[], html_img_enable=False, url_schemes=['mailto', 'http', 'https'], heading_anchors=None)
12

13
Extension error:
14
You must configure the bibtex_bibfiles setting
15
Traceback (most recent call last):
16
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 124, in build_sphinx
17
    keep_going=keep_going,
18
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/sphinx/application.py", line 278, in __init__
19
    self._init_builder()
20
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/sphinx/application.py", line 337, in _init_builder
21
    self.events.emit('builder-inited')
22
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/sphinx/events.py", line 110, in emit
23
    results.append(listener.handler(self.app, *args))
24
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/sphinxcontrib/bibtex/__init__.py", line 45, in init_bibtex_cache
25
    raise ExtensionError("You must configure the bibtex_bibfiles setting")
26
sphinx.errors.ExtensionError: You must configure the bibtex_bibfiles setting
27

28
The above exception was the direct cause of the following exception:
29

30
Traceback (most recent call last):
31
  File "/opt/hostedtoolcache/Python/3.7.9/x64/bin/jupyter-book", line 8, in <module>
32
    sys.exit(main())
33
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/click/core.py", line 829, in __call__
34
    return self.main(*args, **kwargs)
35
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/click/core.py", line 782, in main
36
    rv = self.invoke(ctx)
37
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
38
    return _process_result(sub_ctx.command.invoke(sub_ctx))
39
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
40
    return ctx.invoke(self.callback, **ctx.params)
41
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/click/core.py", line 610, in invoke
42
    return callback(*args, **kwargs)
43
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/jupyter_book/commands/__init__.py", line 260, in build
44
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
45
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/jupyter_book/commands/__init__.py", line 500, in builder_specific_actions
46
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
47
RuntimeError: 
48
===============================================================================
49

50
There was an error in building your book. Look above for the cause.
51

52
===============================================================================
53

54
Error: Process completed with exit code 1.

[partmor]

Same as @spring-haru here:

I got the ExtensionError("You must configure the bibtex_bibfiles setting") in gh-actions, using ubuntu-latest and Python 3.7.9.

[choldgraf]

Argg - this is because sphinx-bibtex just released a major version that's incompatible. I've pinned sphinxcontrib-bibtex to the 1.0 version on the master branch, and we'll get that into the next JB release. In the meantime just ensure that you have sphinxcontrib-bibtex 1.0 👍

[partmor]

Argg - this is because sphinx-bibtex just released a major version that's incompatible. I've pinned sphinxcontrib-bibtex to the 1.0 version on the master branch, and we'll get that into the next JB release. In the meantime just ensure that you have sphinxcontrib-bibtex 1.0 👍

@choldgraf correct! I've just tried it, the sphinxcontrib-bibtex version 1.0 works, 2.0 doesn't (this is installed by default).

For the rest of people in the thread:

just add sphinxcontrib-bibtex==1.0.0 in your requirements.txt

Edit: sphinxcontrib-bibtex<2.0.0 probably more correct

[SimonBiggs]

just add sphinxcontrib-bibtex==1.0.0 in your requirements.txt

And for those of us using something like poetry, the following is key:

sphinxcontrib-bibtex = {version = "<2.0.0"} 

[g4brielvs]

I am having the same issue. Adding sphinxcontrib-bibtex<2.0.0 to requirements.txt should fix it for the moment.

[Rahuketu86]

Thank you for quick resolution. It seems to be working with pinning to version 1.0.0

[atantet]

I'm new to Jupyter Book, but maybe an entry could be added to the FAQ for new users who encounter this problem ? A simple quick and dirty fix without having to handle versions with pip is to add

sphinx:
  config:
    bibtex_bibfiles: "your_reference_file.bib"

in the _config.yml file.

[arnavs]

I'm new to Jupyter Book, but maybe an entry could be added to the FAQ for new users who encounter this problem ? A simple quick and dirty fix without having to handle versions with pip is to add

sphinx:
  config:
    bibtex_bibfiles: "your_reference_file.bib"

in the _config.yml file.

I second this.

[scottyhq]

just came across this and crawled open issues for a bit trying to figure things out.

it wasn't clear that the current (jbook 0.10.2) documented citations syntax requires sphinxcontrib-bibtex>2.0.0 https://jupyterbook.org/content/citations.html?highlight=citations#change-the-in-line-citation-style

if you're installing jupyterbook from conda-forge it will pull sphinxcontrib-bibtex<2 until conda-forge/sphinxcontrib-bibtex-feedstock#16 is merged.

My current workaround is to pip install sphinxcontrib-bibtex==2.2.0 and then have the following in _config.yml:

# Bibliography
bibtex_bibfiles:
  - references.bib
sphinx:
  config:
    bibtex_reference_style: author_year  # or label, super, \supercite