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ENH: Bump sphinx version, add pandoc version, bump RTD python version.
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Old sphinx version spec is very old.  Both RTD and CI interpret sphinx>=2.0.0 as
5.0.3, so it seems reasonable that requiring this for developers would only
serve to prevent doc build mistakes.

Also, added pandoc as a dev requirement, because it is a requirement for
building docs.  It has an external binary requirement (pandoc) which can't be
accomodated in a requirements file.  So I added info to the readme.rst

Bump python version to 3.8 in RTD since 3.7 is approaching EOL

FWIW, was confused about pandoc so added an issue to RTFD:
readthedocs/readthedocs.org#10229
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Jacob-Stevens-Haas committed Apr 7, 2023
1 parent e19ea64 commit 2b2a767
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2 changes: 1 addition & 1 deletion .readthedocs.yml
Expand Up @@ -4,6 +4,6 @@ sphinx:
configuration: docs/conf.py

python:
version: 3.7
version: 3.8
install:
- requirements: requirements-dev.txt
8 changes: 8 additions & 0 deletions README.rst
Expand Up @@ -204,6 +204,14 @@ you can run the following to automatically reformat your staged code
Note that you will then need to re-stage any changes ``pre-commit`` made to your code.

Building documentation requires [pandoc](https://pandoc.org/installing.html) as a separate install. Once installed, run

.. code-block:: bash
python -m sphinx -TEb html -d _build/doctrees -D language=en . ./build
Or check the build step in the most recent CI run or [RTD build](https://readthedocs.org/projects/pysindy/builds/).

There are a number of SINDy variants and advanced functionality that would be great to implement in future releases:

1. Bayesian SINDy, for instance that from Hirsh, Seth M., David A. Barajas-Solano, and J. Nathan Kutz. "Sparsifying Priors for Bayesian Uncertainty Quantification in Model Discovery." arXiv preprint arXiv:2107.02107 (2021).
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3 changes: 2 additions & 1 deletion requirements-dev.txt
Expand Up @@ -12,14 +12,15 @@ setuptools_scm_git_archive
jupyter
jupytext
notebook
sphinx >= 2
sphinx==5.3.0
sphinxcontrib-apidoc
sphinx_rtd_theme
pre-commit
hypothesis
nbsphinx
jupyter_contrib_nbextensions
pandas
pandoc
seaborn
ipython
gurobipy>=9.5.1,<10.0

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