Merge branch 'main' into maint/clean_up_ci

Author: atravitz

.gitignore

@@ -228,3 +228,29 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.toptal.com/developers/gitignore/api/osx,python,jupyternotebooks,windows,linux
+
+# Files generated by example notebooks
+*.zip*
+*.tsv
+*.graphml
+*.tar.gz
+abfe_tutorial/abfe_results/
+abfe_tutorial/abfe_json/
+ahfe_tutorial/ahfe_json/
+cookbook/assets/of3_output/temp_ligands/
+cookbook/assets/of3_output/p_aligned/
+cookbook/dg.png
+cookbook/queries.json
+networks/transformations/
+openmm_md/md_input/
+openmm_md/shared*
+openmm_septop/septop_results/
+openmm_septop/transformations/
+plotting_rbfes_with_cinnabar/cinnabar_input.csv
+plotting_rbfes_with_cinnabar/*.dat
+rbfe_tutorial/transformations/
+showcase/db.json
+showcase/hybrid_system.pdb
+showcase/results/
+showcase/tyk2_edge.png
+showcase/tyk2_json/