[MITgcm-devel] error when building the doc (html)

[Jean-Michel Campin]

Hi Martin and other,

OK, I found the issue. I don't have a recent enough version of sphinxcontrib-bibtex
which is now needed (after checkoint68a, after PR #491 got merged in).

So it's why it was working before (last summer) but no longer works.

Cheers,
Jean-Michel

On Tue, Apr 05, 2022 at 10:43:20AM +0200, Martin Losch wrote:
> Hi Jean-Michel,
> 
> I tried on my Laptop (MacBook with latest OS X 12.3), and I don???t have any issues.
> I am attaching my python/conda environment (created following the instructions in the documentation https://mitgcm.readthedocs.io/en/latest/contributing/contributing.html#building-the-manual)
> 
> Martin
> 
> $ conda env export
> name: mitgcm_build_the_docs
> channels:
>   - conda-forge
>   - defaults
> dependencies:
>   - alabaster=0.7.12=py_0
>   - babel=2.9.1=pyh44b312d_0
>   - bzip2=1.0.8=h3422bc3_4
>   - ca-certificates=2021.10.8=h4653dfc_0
>   - charset-normalizer=2.0.12=pyhd8ed1ab_0
>   - colorama=0.4.4=pyh9f0ad1d_0
>   - dataclasses=0.8=pyhc8e2a94_3
>   - idna=3.3=pyhd8ed1ab_0
>   - imagesize=1.3.0=pyhd8ed1ab_0
>   - jinja2=3.0.3=pyhd8ed1ab_0
>   - latexcodec=2.0.1=pyh9f0ad1d_0
>   - libblas=3.9.0=13_osxarm64_openblas
>   - libcblas=3.9.0=13_osxarm64_openblas
>   - libcxx=13.0.1=h6a5c8ee_0
>   - libffi=3.4.2=h3422bc3_5
>   - libgfortran=5.0.0.dev0=11_0_1_hf114ba7_23
>   - libgfortran5=11.0.1.dev0=hf114ba7_23
>   - liblapack=3.9.0=13_osxarm64_openblas
>   - libopenblas=0.3.18=openmp_h5dd58f0_0
>   - libzlib=1.2.11=hee7b306_1013
>   - llvm-openmp=13.0.1=h455960f_1
>   - ncurses=6.3=hc470f4d_0
>   - openssl=1.1.1l=h3422bc3_0
>   - packaging=21.3=pyhd8ed1ab_0
>   - pip=22.0.4=pyhd8ed1ab_0
>   - pybtex=0.24.0=pyhd8ed1ab_2
>   - pycparser=2.21=pyhd8ed1ab_0
>   - pygments=2.11.2=pyhd8ed1ab_0
>   - pyopenssl=22.0.0=pyhd8ed1ab_0
>   - pyparsing=3.0.7=pyhd8ed1ab_0
>   - python=3.10.2=hd16f9c5_4_cpython
>   - python_abi=3.10=2_cp310
>   - pytz=2021.3=pyhd8ed1ab_0
>   - readline=8.1=hedafd6a_0
>   - requests=2.27.1=pyhd8ed1ab_0
>   - six=1.16.0=pyh6c4a22f_0
>   - snowballstemmer=2.2.0=pyhd8ed1ab_0
>   - sphinx=4.4.0=pyh6c4a22f_1
>   - sphinx_rtd_theme=1.0.0=pyhd8ed1ab_0
>   - sphinxcontrib-applehelp=1.0.2=py_0
>   - sphinxcontrib-bibtex=2.4.1=pyhd8ed1ab_0
>   - sphinxcontrib-devhelp=1.0.2=py_0
>   - sphinxcontrib-htmlhelp=2.0.0=pyhd8ed1ab_0
>   - sphinxcontrib-jsmath=1.0.1=py_0
>   - sphinxcontrib-programoutput=0.16=pyh9f0ad1d_0
>   - sphinxcontrib-qthelp=1.0.3=py_0
>   - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_1
>   - sqlite=3.37.1=h7e3ccbd_0
>   - tk=8.6.12=he1e0b03_0
>   - tzdata=2022a=h191b570_0
>   - urllib3=1.26.9=pyhd8ed1ab_0
>   - wheel=0.37.1=pyhd8ed1ab_0
>   - xz=5.2.5=h642e427_1
>   - yaml=0.2.5=h3422bc3_2
>   - zipp=3.7.0=pyhd8ed1ab_1
>   - zlib=1.2.11=hee7b306_1013
>   - pip:
>     - brotlipy==0.7.0
>     - certifi==2021.10.8
>     - cffi==1.15.0
>     - cryptography==36.0.1
>     - docutils==0.15.2
>     - importlib-metadata==4.11.3
>     - markupsafe==2.1.1
>     - numpy==1.22.3
>     - pybtex-docutils==1.0.1
>     - pysocks==1.7.1
>     - pyyaml==6.0
>     - setuptools==60.10.0
> prefix: /Users/mlosch/miniconda3/envs/mitgcm_build_the_docs
> 
> > On 5. Apr 2022, at 09:07, Jean-Michel Campin <jmc at mit.edu> wrote:
> > 
> > Hi,
> > 
> > I used to be able to build the html doc on my laptop (Ubuntu LTS 18.04) by
> > just doing "make html" in MITgcm/doc.
> > But when I tried today I got this first error:
> > 
> > reading sources... [100%] utilities/utilities                                                       
> > /home/jmc/mitgcm/gcm_git/doc/references.rst:10: WARNING: Error in "bibliography" directive:
> > 1 argument(s) required, 0 supplied.
> > 
> > .. bibliography::
> >   :all:
> > looking for now-outdated files... none found
> > 
> > and then I get plenty of "WARNING: citation not found:"
> > 
> > May be something has changed that I did not notice ?
> > 
> > Cheers,
> > Jean-Michel
> > 
> > _______________________________________________
> > MITgcm-devel mailing list
> > MITgcm-devel at mitgcm.org
> > http://mailman.mitgcm.org/mailman/listinfo/mitgcm-devel
> 

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