Linting of doc/

[ns-rse]

Currently linting of Markdown documents in docs/ reports errors, these need fixing.

See also maxgamill-sheffield/btr_docs (or related branch) for where these were detected.

[MaxGamill-Sheffield]

My bad, this no longer seems to be a linting problem, more a Sphinx build problem as I can pass the pre-commit hooks now.
The output from the maxgamill-sheffield/btr-docs sphinx build is below:

(topo_test) Max:TopoStats Maxgamill$ sphinx-build -M html ./docs ./docs
Running Sphinx v7.4.7
loading translations [en]... done
loading pickled environment... done
[AutoAPI] Reading files... [100%] /Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/topostats/measure/geometry.py
WARNING: Cannot resolve import of unknown module topostats.measure.geometry in topostats.tracing.nodestats
WARNING: Cannot resolve import of unknown module topostats.measure.geometry in topostats.tracing.nodestats
WARNING: Cannot resolve import of unknown module topostats.measure.geometry in topostats.tracing.nodestats
[AutoAPI] Mapping Data... [100%] /Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/topostats/measure/geometry.py
[AutoAPI] Rendering Data... [  3%] geometry
[AutoAPI] Rendering Data... [  6%] topostats
[AutoAPI] Rendering Data... [ 10%] topostats.io
[AutoAPI] Rendering Data... [ 13%] topostats.logs
[AutoAPI] Rendering Data... [ 16%] topostats.theme
[AutoAPI] Rendering Data... [ 19%] topostats.scars
[AutoAPI] Rendering Data... [ 23%] topostats.utils
[AutoAPI] Rendering Data... [ 26%] topostats.grains
[AutoAPI] Rendering Data... [ 29%] topostats.filters
[AutoAPI] Rendering Data... [ 32%] topostats.tracing
[AutoAPI] Rendering Data... [ 35%] topostats._version
[AutoAPI] Rendering Data... [ 39%] topostats.plotting
[AutoAPI] Rendering Data... [ 42%] topostats.__main__
[AutoAPI] Rendering Data... [ 45%] topostats.logs.logs
[AutoAPI] Rendering Data... [ 48%] topostats.thresholds
[AutoAPI] Rendering Data... [ 52%] topostats.grainstats
[AutoAPI] Rendering Data... [ 55%] topostats.statistics
[AutoAPI] Rendering Data... [ 58%] topostats.processing
[AutoAPI] Rendering Data... [ 61%] topostats.validation
[AutoAPI] Rendering Data... [ 65%] topostats.entry_point
[AutoAPI] Rendering Data... [ 68%] topostats.run_topostats
[AutoAPI] Rendering Data... [ 71%] topostats.plottingfuncs
[AutoAPI] Rendering Data... [ 74%] topostats.tracing.pruning
[AutoAPI] Rendering Data... [ 77%] topostats.tracing.splining
[AutoAPI] Rendering Data... [ 81%] topostats.tracing.nodestats
[AutoAPI] Rendering Data... [ 84%] topostats.tracing.dnatracing
[AutoAPI] Rendering Data... [ 87%] topostats.tracing.skeletonize
[AutoAPI] Rendering Data... [ 90%] topostats.tracing.tracingfuncs
[AutoAPI] Rendering Data... [ 94%] topostats.tracing.dnacurvature
[AutoAPI] Rendering Data... [ 97%] topostats.tracing.ordered_tracing
[AutoAPI] Rendering Data... [100%] topostats.tracing.disordered_tracing

[autosummary] generating autosummary for: advanced/disordered_tracing.md, advanced/nodestats.md, advanced/ordered_tracing.md, advanced/splining.md, autoapi/geometry/index.rst, autoapi/index.rst, autoapi/topostats/__main__/index.rst, autoapi/topostats/_version/index.rst, autoapi/topostats/entry_point/index.rst, autoapi/topostats/filters/index.rst, ..., html/_static/scripts/bootstrap.js.LICENSE.txt, html/_static/vendor/fontawesome/6.5.2/LICENSE.txt, html/_static/vendor/fontawesome/6.5.2/js/all.min.js.LICENSE.txt, index.rst, installation.md, introduction.md, notebooks.md, related_software.md, usage.md, workflow.md
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, 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', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 32 source files that are out of date
updating environment: 0 added, 37 changed, 0 removed
[AutoAPI] Adding AutoAPI TOCTree [autoapi/index] to index.rst

/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:137: WARNING: Bullet list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:141: WARNING: Bullet list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:144: WARNING: Bullet list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:191: ERROR: Unexpected indentation.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:186: WARNING: Inline literal start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:186: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:193: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:193: WARNING: Inline literal start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/geometry/index.rst:193: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/grains/index.rst:148: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/grains/index.rst:245: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/grains/index.rst:277: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/grains/index.rst:339: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/grains/index.rst:371: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/plotting/index.rst:427: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/thresholds/index.rst:117: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/thresholds/index.rst:152: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/thresholds/index.rst:187: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/thresholds/index.rst:222: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/thresholds/index.rst:257: WARNING: Inline strong start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:317: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:313: ERROR: Unexpected indentation.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:310: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:314: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:314: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:314: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:314: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:323: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:323: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:326: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:327: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:327: WARNING: Inline substitution_reference start-string without end-string.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:944: ERROR: Undefined substitution referenced: "a".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:944: ERROR: Undefined substitution referenced: "b".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:944: ERROR: Undefined substitution referenced: "a||b".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:42: ERROR: Unknown target name: "np.bool".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:649: ERROR: Unknown target name: "np.bool".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:729: ERROR: Unknown target name: "np.bool".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/nodestats/index.rst:781: ERROR: Unknown target name: "np.bool".
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/skeletonize/index.rst:447: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/skeletonize/index.rst:482: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/tracing/skeletonize/index.rst:679: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/autoapi/topostats/utils/index.rst:227: WARNING: Inline strong start-string without end-string.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/html/_static/scripts/bootstrap.js.LICENSE.txt: WARNING: document isn't included in any toctree
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/html/_static/vendor/fontawesome/6.5.2/LICENSE.txt: WARNING: document isn't included in any toctree
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/html/_static/vendor/fontawesome/6.5.2/js/all.min.js.LICENSE.txt: WARNING: document isn't included in any toctree
done
preparing documents... done
copying assets... 
copying static files... done
copying extra files... done
copying assets: done
writing output... [100%] index
/Users/Maxgamill/Desktop/Uni/PhD/topo_test/TopoStats/docs/advanced/ordered_tracing.md:86: WARNING: 'myst' cross-reference target not found: 'LINK'
generating indices... genindex py-modindex done
highlighting module code... [100%] topostats.validation
writing additional pages... search done
copying images... [100%] _static/images/splining/topostats_file.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 50 warnings.

The HTML pages are in docs/html.
(topo_test) Max:TopoStats Maxgamill$ 

Are these essential to fix for the release @ns-rse? Some of the nodestats complaints seem to surround how I've structured the dictionary returns, or equation labels i.e:

[MaxGamill-Sheffield]

How the above dict looks in the docs: