Large number of Sphinx warnings/errors when building documentation

[willu47]

Okay, I reinstalled my conda environment, built the docs locally and had a brief scan through. The new theme looks great, and nice that we're joining the look-and-feel of the pydata stack.

conda env create -f environment.yml
conda activate salib
cd docs
make html
open _build/html/index.html

Sphinx itself spits out a lot of warnings and a few errors which we should slowly look into:

Running Sphinx v5.1.1
Creating file docs/api/SALib.rst.
Creating file docs/api/SALib.analyze.rst.
Creating file docs/api/SALib.plotting.rst.
Creating file docs/api/SALib.sample.rst.
Creating file docs/api/SALib.sample.morris.rst.
Creating file docs/api/SALib.scripts.rst.
Creating file docs/api/SALib.test_functions.rst.
Creating file docs/api/SALib.util.rst.
Creating file docs/api/modules.rst.
loading pickled environment... failed
failed: No module named 'myst_parser.main'
loading intersphinx inventory from https://www.sphinx-doc.org/en/master/objects.inv...
loading intersphinx inventory from https://docs.python.org/3.10/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://pyscaffold.org/en/stable/objects.inv...
[autosummary] generating autosummary for: advanced.rst, api.rst, api/SALib.analyze.rst, api/SALib.plotting.rst, api/SALib.rst, api/SALib.sample.morris.rst, api/SALib.sample.rst, api/SALib.scripts.rst, api/SALib.test_functions.rst, api/SALib.util.rst, api/modules.rst, authors.rst, basics.rst, changelog.md, citations.rst, getting-started.rst, index.rst, license.rst
myst v0.18.0: 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')
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 18 source files that are out of date
updating environment: [new config] 18 added, 0 changed, 0 removed
reading sources... [100%] license                                                                             
docs/advanced.rst:43: ERROR: Unexpected indentation.
docs/../src/SALib/analyze/fast.py:docstring of SALib.analyze.fast.analyze:27: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/fast.py:docstring of SALib.analyze.fast.analyze:33: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:16: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:22: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:29: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:34: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:38: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:71: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:76: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:78: ERROR: Unexpected indentation.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:79: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:82: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:84: ERROR: Unexpected indentation.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:86: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:60: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:63: WARNING: Definition list ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:66: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:69: WARNING: Definition list ends without a blank line; unexpected unindent.
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:49: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:55: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:61: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:66: WARNING: Duplicate explicit target name: "4".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:37: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:41: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:44: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:16: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:22: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/delta.py:docstring of SALib.analyze.delta.analyze:28: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/delta.py:docstring of SALib.analyze.delta.analyze:32: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/dgsm.py:docstring of SALib.analyze.dgsm.analyze:31: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/ff.py:docstring of SALib.sample.ff.sample:27: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/ff.py:docstring of SALib.analyze.ff.analyze:33: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:56: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:62: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:67: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:73: WARNING: Duplicate explicit target name: "4".
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:11: ERROR: Unexpected indentation.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:12: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:68: ERROR: Unexpected indentation.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:75: WARNING: Duplicate explicit target name: "1".
src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:73: WARNING: Footnote [5] is not referenced.
docs/../src/SALib/util/problem.py:docstring of SALib.util.problem.ProblemSpec.evaluate_distributed:5: ERROR: Unexpected indentation.
docs/../src/SALib/util/problem.py:docstring of SALib.util.problem.ProblemSpec.evaluate_distributed:6: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/dgsm.py:docstring of SALib.analyze.dgsm.analyze:31: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/fast.py:docstring of SALib.analyze.fast.analyze:27: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/fast.py:docstring of SALib.analyze.fast.analyze:33: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/ff.py:docstring of SALib.analyze.ff.analyze:33: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:11: ERROR: Unexpected indentation.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:12: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:68: ERROR: Unexpected indentation.
docs/../src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:75: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:60: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:63: WARNING: Definition list ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:66: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/morris.py:docstring of SALib.analyze.morris.analyze:69: WARNING: Definition list ends without a blank line; unexpected unindent.
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:56: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:62: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/pawn.py:docstring of SALib.analyze.pawn.analyze:67: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:29: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:34: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:38: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.analyze:43: WARNING: Duplicate explicit target name: "4".
docs/../src/SALib/analyze/rbd_fast.py:docstring of SALib.analyze.rbd_fast.permute_outputs:5: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:37: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:41: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.analyze:44: WARNING: Duplicate explicit target name: "3".
docs/../src/SALib/sample/ff.py:docstring of SALib.sample.ff.sample:27: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/finite_diff.py:docstring of SALib.sample.finite_diff.sample:21: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/finite_diff.py:docstring of SALib.sample.finite_diff.sample:27: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:16: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/latin.py:docstring of SALib.sample.latin.sample:22: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:49: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:55: WARNING: Duplicate explicit target name: "2".
src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:61: WARNING: Footnote [3] is not referenced.
src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:66: WARNING: Footnote [4] is not referenced.
src/SALib/sample/saltelli.py:docstring of SALib.sample.saltelli.sample:73: WARNING: Footnote [5] is not referenced.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:78: ERROR: Unexpected indentation.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:79: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:84: ERROR: Unexpected indentation.
docs/../src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:86: WARNING: Block quote ends without a blank line; unexpected unindent.
src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:71: WARNING: Footnote [1] is not referenced.
src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:76: WARNING: Footnote [2] is not referenced.
src/SALib/sample/morris/morris.py:docstring of SALib.sample.morris.morris.sample:82: WARNING: Footnote [3] is not referenced.
docs/../src/SALib/test_functions/Sobol_G.py:docstring of SALib.test_functions.Sobol_G.evaluate:5: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.evaluate_lake:5: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.evaluate_lake:7: ERROR: Unexpected indentation.
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.evaluate_lake:8: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.evaluate_lake:11: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.lake_problem:9: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.lake_problem:11: ERROR: Unexpected indentation.
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.lake_problem:12: WARNING: Block quote ends without a blank line; unexpected unindent.
docs/../src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.lake_problem:15: WARNING: Duplicate explicit target name: "2".
docs/../src/SALib/test_functions/linear_model_1.py:docstring of SALib.test_functions.linear_model_1.evaluate:10: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/test_functions/linear_model_2.py:docstring of SALib.test_functions.linear_model_2.evaluate:10: WARNING: Duplicate explicit target name: "1".
docs/../src/SALib/test_functions/oakley2004.py:docstring of SALib.test_functions.oakley2004.evaluate:6: WARNING: Duplicate explicit target name: "1".
src/SALib/test_functions/lake_problem.py:docstring of SALib.test_functions.lake_problem.lake_problem:21: WARNING: Footnote [3] is not referenced.
docs/../src/SALib/util/problem.py:docstring of SALib.util.problem.ProblemSpec.evaluate_distributed:5: ERROR: Unexpected indentation.
docs/../src/SALib/util/problem.py:docstring of SALib.util.problem.ProblemSpec.evaluate_distributed:6: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] license                                                                              
src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:: WARNING: more than one target found for cross-reference 'ResultDict': SALib.util.results.ResultDict, SALib.util.ResultDict
src/SALib/analyze/hdmr.py:docstring of SALib.analyze.hdmr.analyze:: WARNING: more than one target found for cross-reference 'ResultDict': SALib.util.results.ResultDict, SALib.util.ResultDict
src/SALib/analyze/sobol.py:docstring of SALib.analyze.sobol.Si_to_pandas_dict:: WARNING: more than one target found for cross-reference 'ResultDict': SALib.util.results.ResultDict, SALib.util.ResultDict
generating indices... genindex py-modindex done
highlighting module code... [100%] SALib.util.util_funcs                                                      
writing additional pages... search done
copying images... [100%] assets/example_parabola.svg                                                          
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 102 warnings.

The HTML pages are in _build/html.

Originally posted by @willu47 in #523 (comment)