dependency bug ??

[ChrisBarker-NOAA]

Installing the latest version of Sphinx with conda into an existing environment results in a dependency bug:

Running Sphinx v4.1.2

Extension error:
Could not import extension sphinx.builders.epub3 (exception: cannot import name 'RemovedInSphinx40Warning' from 'sphinx.deprecation' (/Users/chris.barker/miniconda3/envs/adios_db/lib/python3.9/site-packages/sphinx/deprecation.py))

This was identified in this Sphinx Issue:

sphinx-doc/sphinx#9434

and fixed in the PR:

https://github.com/sphinx-doc/sphinx/pull/9448

Which was in release 4.1.2.

I've looked at the dependencies in this recipe, and they were updated to match the updated pinning in the Sphinx release.

And, indeed, if I start with a fresh environment, and instal Sphinx, it does work.

However: if I install into an existing environment, I get the error.

So I'm guessing there is a missing pin somewhere deeping the dependency stack.

The existing environment is kinda big, but I wrote a nifty script for comparing conda environments, I see this:

sphinxcontrib-serializinghtml :
    adios_db       1.1.4     py_0                conda-forge         
    sphinx-conda   1.1.5     pyhd8ed1ab_0        conda-forge 

sphinxcontrib-htmlhelp :
    adios_db       1.0.3     py_0                conda-forge         
    sphinx-conda   2.0.0     pyhd8ed1ab_0        conda-forge

Those are both older than the current sphinx requirements.

If I hand update those two, it all works:

conda update sphinxcontrib-serializinghtml sphinxcontrib-htmlhelp

adios_db is my big ol' environment, built a few months ago, probably. sphinx was just added with:

conda install sphinx

sphinx-conda is a brand new environment, built with:

conda create -n sphinx-conda python=3.9 sphinx sphinx_rtd_theme

So the question is -- when I installed sphinx, why didn't it update sphinxcontrib-serializinghtml and sphinxcontrib-htmlhelp ?

Here's the full list of packages they both share, but have different versions:

Packages in both, with different versions:
pygments :
    adios_db       2.8.0     pyhd8ed1ab_0        conda-forge         
    sphinx-conda   2.9.0     pyhd8ed1ab_0        conda-forge         
python_abi :
    adios_db       3.9       1_cp39              conda-forge         
    sphinx-conda   3.9       2_cp39              conda-forge         
sphinx :
    adios_db       4.1.2     pyh6c4a22f_0        conda-forge         
    sphinx-conda   4.1.2     pyh6c4a22f_1        conda-forge         
sphinx_rtd_theme :
    adios_db       0.5.2     pyhd8ed1ab_0        conda-forge         
    sphinx-conda   0.5.2     pyhd8ed1ab_1        conda-forge         
requests :
    adios_db       2.25.1    pyhd3deb0d_0        conda-forge         
    sphinx-conda   2.26.0    pyhd8ed1ab_0        conda-forge         
idna :
    adios_db       2.10      pyh9f0ad1d_0        conda-forge         
    sphinx-conda   3.1       pyhd3deb0d_0        conda-forge         
packaging :
    adios_db       20.9      pyh44b312d_0        conda-forge         
    sphinx-conda   21.0      pyhd8ed1ab_0        conda-forge         
sqlite :
    adios_db       3.34.0    h17101e1_0          conda-forge         
    sphinx-conda   3.36.0    h23a322b_0          conda-forge         
six :
    adios_db       1.15.0    pyh9f0ad1d_0        conda-forge         
    sphinx-conda   1.16.0    pyh6c4a22f_0        conda-forge         
cffi :
    adios_db       1.14.5    py39h319c39b_0      conda-forge         
    sphinx-conda   1.14.6    py39hb71fe58_0      conda-forge         
readline :
    adios_db       8.0       h0678c8f_2          conda-forge         
    sphinx-conda   8.1       h05e3726_0          conda-forge         
brotlipy :
    adios_db       0.7.0     py39hcbf5805_1001   conda-forge         
    sphinx-conda   0.7.0     py39h89e85a6_1001   conda-forge         
sphinxcontrib-serializinghtml :
    adios_db       1.1.4     py_0                conda-forge         
    sphinx-conda   1.1.5     pyhd8ed1ab_0        conda-forge         
urllib3 :
    adios_db       1.26.3    pyhd8ed1ab_0        conda-forge         
    sphinx-conda   1.26.6    pyhd8ed1ab_0        conda-forge         
pip :
    adios_db       21.0.1    pyhd8ed1ab_0        conda-forge         
    sphinx-conda   21.2.1    pyhd8ed1ab_0        conda-forge         
tzdata :
    adios_db       2021a     he74cb21_0          conda-forge         
    sphinx-conda   2021a     he74cb21_1          conda-forge         
libcxx :
    adios_db       11.1.0    habf9029_0          conda-forge         
    sphinx-conda   12.0.1    habf9029_0          conda-forge         
cryptography :
    adios_db       3.4.4     py39h36ea649_0      conda-forge         
    sphinx-conda   3.4.7     py39ha2c9959_0      conda-forge         
sphinxcontrib-htmlhelp :
    adios_db       1.0.3     py_0                conda-forge         
    sphinx-conda   2.0.0     pyhd8ed1ab_0        conda-forge         
babel :
    adios_db       2.9.0     pyhd3deb0d_0        conda-forge         
    sphinx-conda   2.9.1     pyh44b312d_0        conda-forge         
markupsafe :
    adios_db       1.1.1     py39hcbf5805_3      conda-forge         
    sphinx-conda   2.0.1     py39h89e85a6_0      conda-forge         
jinja2 :
    adios_db       2.11.3    pyh44b312d_0        conda-forge         
    sphinx-conda   3.0.1     pyhd8ed1ab_0        conda-forge         
docutils :
    adios_db       0.17.1    py39h6e9494a_0      conda-forge         
    sphinx-conda   0.16      py39h6e9494a_3      conda-forge         
python :
    adios_db       3.9.2     h2502468_0_cpython  conda-forge         
    sphinx-conda   3.9.6     hd187cdc_1_cpython  conda-forge     

[chohner]

I think you actually installed two subtly different versions of sphinx (notice the _1 in the working sphinx-conda env)

sphinx :
    adios_db       4.1.2     pyh6c4a22f_0        conda-forge         
    sphinx-conda   4.1.2     pyh6c4a22f_1        conda-forge         

This recipe version bump introduces the following pins, as per #106

sphinxcontrib-htmlhelp >=2.0.0
sphinxcontrib-serializinghtml >=1.1.5

Have you tried whether updating sphinx to pyh6c4a22f_1 in the broken adios_db env bumps the dependencies?

[jakirkham]

Is this still an issue @ChrisBarker-NOAA?

[ChrisBarker-NOAA]

I don't think so -- sphinx is now at 4.4 so not using this older version anyway.

Oddly just yesterday we got another mysterious error with sphinx in our CI -- but I haven't figured out what it is yet.

So closing this

[jakirkham]

Thanks for following up here Chris! 😄

Oddly just yesterday we got another mysterious error with sphinx in our CI -- but I haven't figured out what it is yet.

We just got this report ( #114 ). Maybe related?

If not, please let us know once the issue is isolated 🙂

[ChrisBarker-NOAA]

Yup, that was it.