Hmm, we have this in conf.py, which ought to show the special methods:

# This requires Sphinx 1.8.0b1 or later:
autodoc_default_values = {
    "members": None,
    "undoc-members": None,
    "special-members": None,
    "show-inheritance": None,
    "member-order": "bysource",
    "exclude-members": "__dict__,__weakref__,__module__",
}

Might be down to the version of Sphinx...

Looking at the most recent master build,
https://travis-ci.org/biopython/biopython/jobs/633717043

Tox installed:

alabaster==0.7.12,Babel==2.8.0,certifi==2019.11.28,chardet==3.0.4,docutils==0.15.2,idna==2.8,imagesize==1.2.0,isodate==0.6.0,Jinja2==2.10.3,MarkupSafe==1.1.1,mmtf-python==1.1.2,msgpack==0.6.2,mysql-connector-python-rf==2.2.2,numpy==1.18.1,numpydoc==0.9.2,packaging==20.0,Pillow==7.0.0,Pygments==2.5.2,pyparsing==2.4.6,pytz==2019.3,rdflib==4.2.2,reportlab==3.5.32,requests==2.22.0,scipy==1.4.1,six==1.13.0,snowballstemmer==2.0.0,Sphinx==2.3.1,sphinx-rtd-theme==0.4.3,sphinxcontrib-applehelp==1.0.1,sphinxcontrib-devhelp==1.0.1,sphinxcontrib-htmlhelp==1.0.2,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.2,sphinxcontrib-serializinghtml==1.1.3,urllib3==1.25.7

And to be clear, it said:

Running Sphinx v2.3.1

Looking back, even https://biopython.org/docs/1.74/api/Bio.SeqRecord.html had this problem - perhaps the configuration used only worked with a specific 1.8.0b1 era version of Sphinx.

It looks like the variable name was changed to be autodoc_default_options after 1.8 - https://www.sphinx-doc.org/en/2.0/usage/extensions/autodoc.html - changing this in conf.py produces the expected results for me (sphinx v. 2.2.1). I can submit a pull request shortly.

That is simple but subtle - I'm glad someone spotted it. Thank you!

Here's where autodoc_default_options was added on the main branch, sphinx-doc/sphinx@3d9e2cf

I suppose the other form autodoc_default_values must have been specific to the branch the beta release was made from?

Confirming the fix worked, https://biopython.org/docs/dev/api/Bio.Seq.html etc look good. Thank you @chebizarro 👍