Sphinx build is failing with extension error (pydata_sphinx_theme)

[tomwhite]

E.g. from https://github.com/pystatgen/sgkit/actions/runs/4293787906/jobs/7481927063:

Running Sphinx v4.2.0
python exec: /opt/hostedtoolcache/Python/3.[9](https://github.com/pystatgen/sgkit/actions/runs/4293787906/jobs/7481927063#step:6:10).16/x64/bin/python
sys.path: ['/home/runner/work/sgkit/sgkit', '/opt/hostedtoolcache/Python/3.9.16/x64/bin', '/home/runner/work/sgkit/sgkit', '/opt/hostedtoolcache/Python/3.9.16/x64/lib/python39.zip', '/opt/hostedtoolcache/Python/3.9.16/x64/lib/python3.9', '/opt/hostedtoolcache/Python/3.9.16/x64/lib/python3.9/lib-dynload', '/opt/hostedtoolcache/Python/3.9.16/x64/lib/python3.9/site-packages']
making output directory... done
[autosummary] generating autosummary for: about.rst, api.rst, changelog.rst, contributing.rst, examples/gwas_tutorial.ipynb, examples/index.rst, getting_started.rst, how_do_i.rst, index.rst, news.rst, news/introducing_sgkit.md, user_guide.rst, vcf.rst
[autosummary] generating autosummary for: /home/runner/work/sgkit/sgkit/docs/generated/sgkit.Fst.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.Garud_H.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.Tajimas_D.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.Weir_Goudet_beta.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.call_allele_frequencies.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.cohort_allele_frequencies.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.convert_probability_to_call.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.count_call_alleles.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.count_cohort_alleles.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.count_variant_alleles.rst, ..., /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variables.variant_position_spec.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variables.variant_score_spec.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variables.window_contig_spec.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variables.window_start_spec.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variables.window_stop_spec.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.variant_stats.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.window_by_genome.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.window_by_interval.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.window_by_position.rst, /home/runner/work/sgkit/sgkit/docs/generated/sgkit.window_by_variant.rst
loading intersphinx inventory from https://docs.dask.org/en/stable/objects.inv...
loading intersphinx inventory from https://xarray.pydata.org/en/stable/objects.inv...
loading intersphinx inventory from https://zarr.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
intersphinx inventory has moved: https://xarray.pydata.org/en/stable/objects.inv -> https://docs.xarray.dev/en/stable/objects.inv
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
myst-nb v0.17.1: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='auto', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/runner/work/sgkit/sgkit/docs/_build/.jupyter_cache

Extension error (pydata_sphinx_theme):
Handler <function update_config at 0x7f89d55e5[16](https://github.com/pystatgen/sgkit/actions/runs/4293787906/jobs/7481927063#step:6:17)0> for event 'builder-inited' threw an exception (exception: 'icon_links')
make: *** [Makefile:[27](https://github.com/pystatgen/sgkit/actions/runs/4293787906/jobs/7481927063#step:6:28): html] Error 2
Error: Process completed with exit code 2.

Looks like it's due to https://github.com/pydata/pydata-sphinx-theme/releases/tag/v0.13.0

[tomwhite]

See pydata/pydata-sphinx-theme#1220

[jeromekelleher]

Is this fixed now?

[tomwhite]

Yes, fixed in #1041