Merge pull request #29 from JecaTosovic/improve_autodoc

Update missing docs
JecaTosovic · Sep 22, 2023 · 7d2c455 · 7d2c455
2 parents a6e9bf2 + 4255ed3
commit 7d2c455
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diff --git 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
@@ -17,7 +17,7 @@ ConservedWaterSearch is available through `conda-forge <https://conda-forge.org/
 Installation via PyPI
 =====================
 
-ConservedWaterSearch can be installed via :code:`pip` from `PyPI <https://pypi.org/project/ConservedWaterSearch>`_:
+ConservedWaterSearch can be installed via :code:`pip` from `PyPI <https://pypi.org/project/ConservedWaterSearch>`__:
 
 .. 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 <https://pypi.org/project/pytest>`_) (using :code:`pip`):
+Or via `PyPI <https://pypi.org/project/pytest>`__ (using :code:`pip`):
 
 .. code:: bash
 

diff --git 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},
 }