LBC-LNBio · jvsguerra · Sep 25, 2024 · Sep 12, 2024 · Sep 13, 2024 · Sep 13, 2024
diff --git a/.github/workflows/integration-testing.yml b/.github/workflows/integration-testing.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4

diff --git a/.github/workflows/unit-testing.yml b/.github/workflows/unit-testing.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4

diff --git a/README.md b/README.md
@@ -48,6 +48,10 @@ S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular
 Cages. Journal of chemical information and modeling, 63(12), 3772-3785.
 <https://doi.org/10.1021/acs.jcim.3c00328>.
 
+If you use *PyMOL pyKVFinder Tools*, please also cite:
+
+Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., & Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. https://doi.org/10.1016/j.softx.2020.100606.
+
 ## License
 
 The software is licensed under the terms of the GNU General Public

diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5e67e5b08739af2cbadbbffeab3c7d4f
+config: ff86b850e3cd6fe0e32862d27a6322e8
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/_about/index.doctree b/docs/.doctrees/_about/index.doctree
diff --git a/docs/.doctrees/_api_reference/Molecule.doctree b/docs/.doctrees/_api_reference/Molecule.doctree
diff --git a/docs/.doctrees/_api_reference/index.doctree b/docs/.doctrees/_api_reference/index.doctree
diff --git a/docs/.doctrees/_cli/index.doctree b/docs/.doctrees/_cli/index.doctree
diff --git a/docs/.doctrees/_installation/index.doctree b/docs/.doctrees/_installation/index.doctree
diff --git a/docs/.doctrees/_tutorial/index.doctree b/docs/.doctrees/_tutorial/index.doctree
diff --git a/docs/.doctrees/about/index.doctree b/docs/.doctrees/about/index.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/package/api_reference/Molecule.doctree b/docs/.doctrees/package/api_reference/Molecule.doctree
diff --git a/...rees/_cfg_files/box_file_template.doctree → ...e/api_reference/box_file_template.doctree b/...rees/_cfg_files/box_file_template.doctree → ...e/api_reference/box_file_template.doctree
diff --git a/...i_reference/calculate_frequencies.doctree → ...i_reference/calculate_frequencies.doctree b/...i_reference/calculate_frequencies.doctree → ...i_reference/calculate_frequencies.doctree
diff --git a/...ees/_api_reference/constitutional.doctree → ...kage/api_reference/constitutional.doctree b/...ees/_api_reference/constitutional.doctree → ...kage/api_reference/constitutional.doctree
diff --git a/docs/.doctrees/_api_reference/depth.doctree → ...trees/package/api_reference/depth.doctree b/docs/.doctrees/_api_reference/depth.doctree → ...trees/package/api_reference/depth.doctree
diff --git a/docs/.doctrees/_api_reference/detect.doctree → ...rees/package/api_reference/detect.doctree b/docs/.doctrees/_api_reference/detect.doctree → ...rees/package/api_reference/detect.doctree
diff --git a/docs/.doctrees/_api_reference/export.doctree → ...rees/package/api_reference/export.doctree b/docs/.doctrees/_api_reference/export.doctree → ...rees/package/api_reference/export.doctree
diff --git a/...es/_api_reference/export_openings.doctree → ...age/api_reference/export_openings.doctree b/...es/_api_reference/export_openings.doctree → ...age/api_reference/export_openings.doctree
diff --git a/...trees/_api_reference/get_vertices.doctree → ...ackage/api_reference/get_vertices.doctree b/...trees/_api_reference/get_vertices.doctree → ...ackage/api_reference/get_vertices.doctree
diff --git a/..._reference/get_vertices_from_file.doctree → ..._reference/get_vertices_from_file.doctree b/..._reference/get_vertices_from_file.doctree → ..._reference/get_vertices_from_file.doctree
diff --git a/...octrees/_api_reference/hydropathy.doctree → .../package/api_reference/hydropathy.doctree b/...octrees/_api_reference/hydropathy.doctree → .../package/api_reference/hydropathy.doctree
diff --git a/...ydrophobicity_scale_file_template.doctree → ...ydrophobicity_scale_file_template.doctree b/...ydrophobicity_scale_file_template.doctree → ...ydrophobicity_scale_file_template.doctree
diff --git a/docs/.doctrees/package/api_reference/index.doctree b/docs/.doctrees/package/api_reference/index.doctree
diff --git a/....doctrees/_api_reference/openings.doctree → ...es/package/api_reference/openings.doctree b/....doctrees/_api_reference/openings.doctree → ...es/package/api_reference/openings.doctree
diff --git a/...s/_api_reference/plot_frequencies.doctree → ...ge/api_reference/plot_frequencies.doctree b/...s/_api_reference/plot_frequencies.doctree → ...ge/api_reference/plot_frequencies.doctree
diff --git a/.../_api_reference/pyKVFinderResults.doctree → ...e/api_reference/pyKVFinderResults.doctree b/.../_api_reference/pyKVFinderResults.doctree → ...e/api_reference/pyKVFinderResults.doctree
diff --git a/...ctrees/_api_reference/read_cavity.doctree → ...package/api_reference/read_cavity.doctree b/...ctrees/_api_reference/read_cavity.doctree → ...package/api_reference/read_cavity.doctree
diff --git a/....doctrees/_api_reference/read_pdb.doctree → ...es/package/api_reference/read_pdb.doctree b/....doctrees/_api_reference/read_pdb.doctree → ...es/package/api_reference/read_pdb.doctree
diff --git a/....doctrees/_api_reference/read_vdw.doctree → ...es/package/api_reference/read_vdw.doctree b/....doctrees/_api_reference/read_vdw.doctree → ...es/package/api_reference/read_vdw.doctree
diff --git a/....doctrees/_api_reference/read_xyz.doctree → ...es/package/api_reference/read_xyz.doctree b/....doctrees/_api_reference/read_xyz.doctree → ...es/package/api_reference/read_xyz.doctree
diff --git a/...trees/_api_reference/run_workflow.doctree → ...ackage/api_reference/run_workflow.doctree b/...trees/_api_reference/run_workflow.doctree → ...ackage/api_reference/run_workflow.doctree
diff --git a/.../.doctrees/_api_reference/spatial.doctree → ...ees/package/api_reference/spatial.doctree b/.../.doctrees/_api_reference/spatial.doctree → ...ees/package/api_reference/spatial.doctree
diff --git a/...rees/_cfg_files/vdw_file_template.doctree → ...e/api_reference/vdw_file_template.doctree b/...rees/_cfg_files/vdw_file_template.doctree → ...e/api_reference/vdw_file_template.doctree
diff --git a/...rees/_api_reference/write_results.doctree → ...ckage/api_reference/write_results.doctree b/...rees/_api_reference/write_results.doctree → ...ckage/api_reference/write_results.doctree
diff --git a/docs/.doctrees/package/examples/index.doctree b/docs/.doctrees/package/examples/index.doctree
diff --git a/docs/.doctrees/package/installation/index.doctree b/docs/.doctrees/package/installation/index.doctree
diff --git a/docs/.doctrees/package/tutorial/index.doctree b/docs/.doctrees/package/tutorial/index.doctree
diff --git a/docs/.doctrees/plugins/cli/index.doctree b/docs/.doctrees/plugins/cli/index.doctree
diff --git a/docs/.doctrees/plugins/pymol/index.doctree b/docs/.doctrees/plugins/pymol/index.doctree
diff --git a/docs/INSTRUCTIONS.rst b/docs/INSTRUCTIONS.rst
@@ -8,3 +8,4 @@ To create pyKVFinder documentation as a GitHub page, run:
 .. code-block:: bash
 
     make html
+
diff --git a/docs/_api_reference/index.html b/docs/_api_reference/index.html
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,3 +8,4 @@ To create pyKVFinder documentation as a GitHub page, run:
		.. code-block:: bash

		make html