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

[Martin Losch]

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
> 
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> MITgcm-devel at mitgcm.org
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