From b05ae81801dab5b95e08b4347cd29381956d5e1e Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 24 Aug 2023 09:52:58 +1000 Subject: [PATCH 1/4] change bibliography to footbibliography --- mdaencore/similarity.py | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/mdaencore/similarity.py b/mdaencore/similarity.py index 3fbc0da..0e21f10 100644 --- a/mdaencore/similarity.py +++ b/mdaencore/similarity.py @@ -28,8 +28,8 @@ :Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen 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 described in :footcite:p:`LindorffLarsen2009`. The implementation and +examples are described in :footcite:p:`Tiberti2015`. The module includes facilities for handling ensembles and trajectories through the :class:`Universe` class, performing clustering or dimensionality reduction @@ -50,7 +50,7 @@ + **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 @@ -160,13 +160,8 @@ .. rubric:: References -.. bibliography:: - :filter: False - :keyprefix: b- - :labelprefix: ᵇ +.. footbibliography:: - Tiberti2015 - LindorffLarsen2009 """ import warnings import logging @@ -252,7 +247,7 @@ 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 ---------- @@ -725,7 +720,7 @@ 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 ---------- @@ -968,7 +963,7 @@ 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 ---------- @@ -1236,7 +1231,7 @@ 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 From 980fbaed56dae2f8a2e3e68948229518fb9f6d4a Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 16 Sep 2023 21:29:05 -0400 Subject: [PATCH 2/4] fix intersphinx mapping --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 4ae5d58..1dd5fac 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -182,6 +182,6 @@ # -- Extension configuration ------------------------------------------------- intersphinx_mapping = { - 'https://docs.python.org/3/': None, - 'https://docs.mdanalysis.org/stable/': None, + "python": ('https://docs.python.org/3/', None), + "mdanalysis": ('https://docs.mdanalysis.org/stable/', None), } From 0a51b39226422320349d31c11c3f906adfda1199 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 16 Sep 2023 21:29:27 -0400 Subject: [PATCH 3/4] install mdanalysis-sphinx-theme from conda-forge --- docs/requirements.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/requirements.yaml b/docs/requirements.yaml index aaa0c0f..33258b3 100644 --- a/docs/requirements.yaml +++ b/docs/requirements.yaml @@ -15,5 +15,4 @@ dependencies: - MDAnalysisTests - pytest - - pip: - - mdanalysis-sphinx-theme + - mdanalysis-sphinx-theme From 41e6699290bb3a0be99a1712e266ae4aa9fd7edc Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Sun, 17 Sep 2023 09:54:08 +0800 Subject: [PATCH 4/4] change docs first sentence --- mdaencore/similarity.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/mdaencore/similarity.py b/mdaencore/similarity.py index 847299b..bfc1765 100644 --- a/mdaencore/similarity.py +++ b/mdaencore/similarity.py @@ -22,8 +22,12 @@ # """\ The module contains implementations of similarity measures between protein -ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and -examples are described in :footcite:p:`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