[pyproject] add notebooks, rename notebooks

pyproject.toml

@@ -81,4 +81,4 @@ script-files = [ "scripts/mdc_neighborhoods.py",
 # This is discouraged by
 # https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
 # but I don't want to change package structure ATM
-data-files = {'data_for_mdciao/examples' = ['tests/data/examples/gs-b2ar.noH.stride.5.xtc', 'tests/data/examples/gs-b2ar.noH.pdb'], 'data_for_mdciao/nomenclature' = ['tests/data/nomenclature/adrb2_human.xlsx', 'tests/data/nomenclature/gnas2_human.xlsx', 'tests/data/nomenclature/nomenclature.bib', 'tests/data/nomenclature/KLIFS_P31751.xlsx'], 'data_for_mdciao/json' = ['tests/data/json/tip.json'] , 'data_for_mdciao/RCSB_pdb' = ['tests/data/RCSB_pdb/3SN6.pdb.gz', 'tests/data/RCSB_pdb/3E8D.pdb.gz'], 'data_for_mdciao/notebooks' = ['mdciao/examples/Tutorial.ipynb', 'mdciao/examples/Missing_Contacts.ipynb', 'mdciao/examples/Manuscript.ipynb', 'mdciao/examples/Flareplot_Schemes.ipynb', 'mdciao/examples/EGFR_Kinase_Inhibitors.ipynb', 'mdciao/examples/Comparing_CGs_Bars.ipynb', 'mdciao/examples/Comparing_CGs_Flares.ipynb', 'mdciao/examples/MSA_via_Consensus_Labels.ipynb']}
+data-files = {'data_for_mdciao/examples' = ['tests/data/examples/gs-b2ar.noH.stride.5.xtc', 'tests/data/examples/gs-b2ar.noH.pdb'], 'data_for_mdciao/nomenclature' = ['tests/data/nomenclature/adrb2_human.xlsx', 'tests/data/nomenclature/gnas2_human.xlsx', 'tests/data/nomenclature/nomenclature.bib', 'tests/data/nomenclature/KLIFS_P31751.xlsx'], 'data_for_mdciao/json' = ['tests/data/json/tip.json'] , 'data_for_mdciao/RCSB_pdb' = ['tests/data/RCSB_pdb/3SN6.pdb.gz', 'tests/data/RCSB_pdb/3E8D.pdb.gz'], 'data_for_mdciao/notebooks' = ['mdciao/examples/01.Tutorial.ipynb', 'mdciao/examples/02.Missing_Contacts.ipynb', 'mdciao/examples/08.Manuscript.ipynb', 'mdciao/examples/05.Flareplot_Schemes.ipynb', 'mdciao/examples/07.EGFR_Kinase_Inhibitors.ipynb', 'mdciao/examples/03.Comparing_CGs_Bars.ipynb', 'mdciao/examples/04.Comparing_CGs_Flares.ipynb', 'mdciao/examples/09.Consensus_Labels.ipynb', 'mdciao/examples/06.MSA_via_Consensus_Labels.ipynb']}