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Change bibliography to footbibliography #13

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merged 5 commits into from
Sep 17, 2023
Merged

Change bibliography to footbibliography #13

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b05ae81
change bibliography to footbibliography
lilyminium Aug 23, 2023
980fbae
fix intersphinx mapping
orbeckst Sep 17, 2023
0a51b39
install mdanalysis-sphinx-theme from conda-forge
orbeckst Sep 17, 2023
b982ddd
Merge branch 'main' into fix-bib
orbeckst Sep 17, 2023
41e6699
change docs first sentence
lilyminium Sep 17, 2023
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3 changes: 2 additions & 1 deletion docs/requirements.yaml
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Expand Up @@ -8,11 +8,12 @@ dependencies:
- pip

- sphinxcontrib-bibtex=2.5.0
- mdanalysis-sphinx-theme
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I forgot to merge main into the branch before editing and had independently moved danalysis-sphinx-theme from pip to conda... and then I grouped it with other sphinx things.


- numpy
- scipy
- MDAnalysis
- cython
- MDAnalysisTests
- pytest
- mdanalysis-sphinx-theme

4 changes: 2 additions & 2 deletions docs/source/conf.py
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Expand Up @@ -181,6 +181,6 @@

# -- Extension configuration -------------------------------------------------
intersphinx_mapping = {
'python': ('https://docs.python.org/3/', None),
'mdanalysis': ('https://docs.mdanalysis.org/stable/', None),
"python": ('https://docs.python.org/3/', None),
"mdanalysis": ('https://docs.mdanalysis.org/stable/', None),
Comment on lines -184 to +185
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same here... doubled up on work that was already in main

}
25 changes: 12 additions & 13 deletions mdaencore/similarity.py
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Expand Up @@ -22,8 +22,12 @@
#
"""\
The module contains implementations of similarity measures between protein
ensembles described in :cite:p:`b-LindorffLarsen2009`. The implementation and
examples are described in :cite:p:`b-Tiberti2015`.
ensembles.

The similarity measure algorithms here are as described
in :footcite:p:`LindorffLarsen2009`.
The implementation and examples are also further
described in :footcite:p:`Tiberti2015`.

The module includes facilities for handling ensembles and trajectories through
the :class:`Universe` class, performing clustering or dimensionality reduction
Expand All @@ -44,7 +48,7 @@
+ **Clustering based convergence evaluation** : :func:`ces_convergence`
+ **Dimensionality-reduction based convergence evaluation** : :func:`dres_convergence`

When using this module in published work please cite :cite:p:`b-Tiberti2015`.
When using this module in published work please cite :footcite:p:`Tiberti2015`.

.. _Examples:
Examples
Expand Down Expand Up @@ -154,13 +158,8 @@

.. rubric:: References

.. bibliography::
:filter: False
:keyprefix: b-
:labelprefix: ᵇ
.. footbibliography::

Tiberti2015
LindorffLarsen2009
"""
import warnings
import logging
Expand Down Expand Up @@ -246,7 +245,7 @@ def harmonic_ensemble_similarity(sigma1,
x2):
"""
Calculate the harmonic ensemble similarity measure
as defined in :cite:p:`b-Tiberti2015`.
as defined in :footcite:p:`Tiberti2015`.

Parameters
----------
Expand Down Expand Up @@ -719,7 +718,7 @@ def hes(ensembles,
r"""Calculates the Harmonic Ensemble Similarity (HES) between ensembles.

The HES is calculated with the symmetrized version of Kullback-Leibler
divergence as described in :cite:p:`b-Tiberti2015`.
divergence as described in :footcite:p:`Tiberti2015`.

Parameters
----------
Expand Down Expand Up @@ -962,7 +961,7 @@ def ces(ensembles,

Calculates the Clustering Ensemble Similarity (CES) between ensembles
using the Jensen-Shannon divergence as described in
:cite:p:`b-Tiberti2015`.
:footcite:p:`Tiberti2015`.

Parameters
----------
Expand Down Expand Up @@ -1230,7 +1229,7 @@ def dres(ensembles,

Calculates the Dimensional Reduction Ensemble Similarity (DRES) between
ensembles using the Jensen-Shannon divergence as described in
:cite:p:`b-Tiberti2015`.
:footcite:p:`Tiberti2015`.


Parameters
Expand Down
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