Use pydata-sphinx-theme #523

tupui · 2022-08-18T12:54:47Z

Closes #520, closes #531

tupui · 2022-08-18T12:55:08Z

Work in progress with Abdullah. We need to update a few things, this is just so that we can work together on the same PR.

tupui · 2022-08-18T14:33:39Z

@ConnectedSystems these are the first steps towards using the new theme.

Now polishing could consist in adding a logo, changing the landing page (see SciPy or NumPy for examples) and deciding on which elements should be in the navbar. By default, Sphinx themes are using the toctree which is present in the index page. So I would suggest only keeping a few elements here (again see SciPy for an example).

I allowed edits by maintainers on this branch and showed @sahin-abdullah how to build the doc on his machine.

Happy to help more there.

willu47 · 2022-09-08T08:48:39Z

ReadTheDocs is failing with the following error:

Running Sphinx v5.1.1

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/overrides.py", line 6, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/conf.py", line 102, in <module>
    import SALib
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/__init__.py", line 1, in <module>
    from SALib.util import ProblemSpec
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/util/__init__.py", line 8, in <module>
    import numpy as np  # type: ignore
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/__init__.py", line 144, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/bin/python"
  * The NumPy version is: "1.22.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/cmd/build.py", line 272, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/config.py", line 169, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/config.py", line 360, in eval_config_file
    raise ConfigError(msg % traceback.format_exc()) from exc
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/overrides.py", line 6, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/conf.py", line 102, in <module>
    import SALib
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/__init__.py", line 1, in <module>
    from SALib.util import ProblemSpec
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/util/__init__.py", line 8, in <module>
    import numpy as np  # type: ignore
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/__init__.py", line 144, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/bin/python"
  * The NumPy version is: "1.22.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'



Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/overrides.py", line 6, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/conf.py", line 102, in <module>
    import SALib
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/__init__.py", line 1, in <module>
    from SALib.util import ProblemSpec
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/../src/SALib/util/__init__.py", line 8, in <module>
    import numpy as np  # type: ignore
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/__init__.py", line 144, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/lib/pypy3.9/site-packages/numpy/core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/home/docs/checkouts/readthedocs.org/user_builds/salib/conda/523/bin/python"
  * The NumPy version is: "1.22.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'


Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.analyze.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.plotting.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.sample.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.sample.morris.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.scripts.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.test_functions.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/SALib.util.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/salib/checkouts/523/docs/api/modules.rst.

tupui · 2022-09-08T08:49:49Z

Yes I am not sure what is going on here. I will dig more into that today.

[skip actions]

tupui · 2022-09-08T09:29:55Z

@willu47 I found the issue and fixed it, now it builds fine and it's also faster 😃

tupui · 2022-09-08T09:32:46Z

I think this is in a good shape and doc rewrite (and removing all existing build warnings) could happen in follow up work.

[skip actions]

[skip ci]

willu47 · 2022-09-08T10:33:08Z

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.

tupui force-pushed the pydata-sphinx-theme branch 2 times, most recently from 8105a03 to a1a1ed6 Compare August 18, 2022 14:29

willu47 added documentation clean up/maintenance Changes to clean up code or for maintenance labels Aug 29, 2022

tupui mentioned this pull request Aug 29, 2022

Migrate to hatchling and migrate CI to GitHub actions #527

Merged

tupui added 6 commits September 6, 2022 15:26

Change theme to pydata-sphinx-theme

9be8654

Fix RTD configuration

e7465dd

Update version switcher

0d82014

Update intersphinx links

70237cc

Fix some warnings

56d1888

Fic config, title and cleanup

d87e201

tupui force-pushed the pydata-sphinx-theme branch from a1a1ed6 to d87e201 Compare September 6, 2022 13:28

Add missing deps in pyproject.toml

871bb32

ConnectedSystems added this to the v1.5 milestone Sep 7, 2022

Fix linter

875e5ee

tupui force-pushed the pydata-sphinx-theme branch from 26533d4 to fc61d87 Compare September 7, 2022 16:36

tupui force-pushed the pydata-sphinx-theme branch from fc61d87 to 17994a0 Compare September 8, 2022 09:06

Use mamba and install project before building

250a9e8

tupui force-pushed the pydata-sphinx-theme branch from 17994a0 to 250a9e8 Compare September 8, 2022 09:19

Update ubuntu machine.

25fb8e4

[skip actions]

tupui marked this pull request as ready for review September 8, 2022 09:31

tupui added 3 commits September 8, 2022 11:34

Fix license extension

cd49ead

Minor quick start install update.

0586455

[skip actions]

Remove ref to setup.py in readme.

8188822

[skip ci]

tupui mentioned this pull request Sep 8, 2022

Readme installation instructions are out of data #531

Closed

willu47 self-requested a review September 8, 2022 10:33

willu47 approved these changes Sep 8, 2022

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willu47 mentioned this pull request Sep 8, 2022

Large number of Sphinx warnings/errors when building documentation #532

Open

willu47 merged commit 0760674 into SALib:main Sep 13, 2022

tupui deleted the pydata-sphinx-theme branch September 13, 2022 21:28

tupui mentioned this pull request Sep 13, 2022

Update version switcher #533

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