Clean up Sphinx interpreted text in the default role.
commit55332916d5e2261ea805c3e759304b9f3e5b90c6
authorM. Eric Irrgang <ericirrgang@gmail.com>
Thu, 12 Dec 2019 12:58:40 +0000 (12 15:58 +0300)
committerEric Irrgang <ericirrgang@gmail.com>
Thu, 26 Dec 2019 11:49:39 +0000 (26 12:49 +0100)
treea681c026b43e2a5551936e014ae0ab5870cc1aa4
parent867dabd6d495ab07011c4a622bae8ff5e5d41895
Clean up Sphinx interpreted text in the default role.

* Fix typos or syntax for several text literals that Sphinx tries to
  process as interpreted text (in the default role).
* Use Google docstring conventions to guide adjustment of gmxapi
  docstrings.

Change-Id: If6eeede8dcc782c04fc4363005c38c746a8664ea
20 files changed:
docs/dev-manual/testutils.rst
docs/reference-manual/algorithms/energy-minimization.rst
docs/reference-manual/algorithms/molecular-dynamics.rst
docs/reference-manual/analysis/rmsd.rst
docs/reference-manual/averages.rst
docs/reference-manual/functions/interaction-methods.rst
docs/reference-manual/special/density-guided-simulation.rst
docs/reference-manual/special/remove-fast-dgf.rst
docs/reference-manual/special/viscosity-calculation.rst
docs/reference-manual/topologies/particle-type.rst
docs/release-notes/2018/2018.2.rst
docs/user-guide/environment-variables.rst
docs/user-guide/mdp-options.rst
docs/user-guide/mdrun-performance.rst
python_packaging/src/gmxapi/_logging.py
python_packaging/src/gmxapi/commandline.py
python_packaging/src/gmxapi/datamodel.py
python_packaging/src/gmxapi/export_tprfile.cpp
python_packaging/src/gmxapi/operation.py
python_packaging/src/gmxapi/version.py