From ff3f5f1105d380e7d4160185058c33a69a3738cf Mon Sep 17 00:00:00 2001 From: Domagoj Fijan Date: Sun, 17 Sep 2023 19:18:43 -0400 Subject: [PATCH 1/2] update missing docs and fix some minor doc bugs --- docs/source/WaterClustering.rst | 3 ++- docs/source/installation.rst | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/source/WaterClustering.rst b/docs/source/WaterClustering.rst index 7a79f3b..2e693ac 100644 --- a/docs/source/WaterClustering.rst +++ b/docs/source/WaterClustering.rst @@ -13,6 +13,7 @@ Determination of conserved water positions based on clustering of oxygen atoms. ConservedWaterSearch.water_clustering.WaterClustering.__init__ ConservedWaterSearch.water_clustering.WaterClustering.create_from_file ConservedWaterSearch.water_clustering.WaterClustering.multi_stage_reclustering + ConservedWaterSearch.water_clustering.WaterClustering.quick_multi_stage_reclustering ConservedWaterSearch.water_clustering.WaterClustering.single_clustering ConservedWaterSearch.water_clustering.WaterClustering.read_class_options ConservedWaterSearch.water_clustering.WaterClustering.read_water_clust_options @@ -29,7 +30,7 @@ Determination of conserved water positions based on clustering of oxygen atoms. .. automodule:: ConservedWaterSearch.water_clustering.WaterClustering - :members: __init__, create_from_file, multi_stage_reclustering, single_clustering, restart_cluster, restore_default_options, read_class_options, read_water_clust_options, save_clustering_options, save_results, visualise_nglview, visualise_pymol + :members: __init__, create_from_file, quick_multi_stage_reclustering, multi_stage_reclustering, single_clustering, restart_cluster, restore_default_options, read_class_options, read_water_clust_options, save_clustering_options, save_results, visualise_nglview, visualise_pymol .. autoclass:: ConservedWaterSearch.water_clustering.WaterClustering :noindex: diff --git a/docs/source/installation.rst b/docs/source/installation.rst index cd8fb71..9dc1796 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -17,7 +17,7 @@ ConservedWaterSearch is available through `conda-forge `_: +ConservedWaterSearch can be installed via :code:`pip` from `PyPI `__: .. code:: bash @@ -82,7 +82,7 @@ ConservedWaterSearch (CWS) uses :code:`pytest` for running unit tests. It can be conda install -c conda-forge pytest -Or via PyPI (`see here `_) (using :code:`pip`): +Or via `PyPI `__ (using :code:`pip`): .. code:: bash From 4255ed30f99a78c81714df4cb84f58b8a70b8752 Mon Sep 17 00:00:00 2001 From: Domagoj Fijan Date: Sun, 17 Sep 2023 19:36:41 -0400 Subject: [PATCH 2/2] remove two urls on bibliography --- docs/source/references/references.bib | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source/references/references.bib b/docs/source/references/references.bib index 5189678..42e548f 100644 --- a/docs/source/references/references.bib +++ b/docs/source/references/references.bib @@ -7,5 +7,4 @@ @article{conservedwatersearch2022 pages = {6105-6117}, year = {2022}, doi = {10.1021/acs.jcim.2c00801}, -URL = {https://doi.org/10.1021/acs.jcim.2c00801}, }