from setuptools import setup, find_packages import versioneer # read the contents of your README file with open('README.md') as f: long_description = f.read() setup( name='rna_tools', version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), packages=find_packages(), test_suite="tests", url='https://github.com/mmagnus/rna-tools', scripts=['rna_tools/rna_pdb_toolsx.py', 'rna_tools/rna_calc_fenergy.py', 'rna_tools/rna_pdb_replace.py', 'rna_tools/tools/misc/rna_tools_which.py', 'rna_tools/tools/workflow/rna_workflow.py', 'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd.py', 'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_all_vs_all.py', 'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_biopython.py', 'rna_tools/tools/diffpdb/diffpdb.py', 'rna_tools/tools/clanstix/rna_clanstix.py', 'rna_tools/rna_dot2ct.py', 'rna_tools/rna_secondary_structure_prediction.py', 'rna_tools/tools/rna_prediction_significance/rna_prediction_significance.py', 'rna_tools/tools/rna_multimodels/rna_pdb_merge_into_one.py', 'rna_tools/tools/rna_calc_inf/rna_calc_inf.py', 'rna_tools/tools/rna_convert_pseudoknot_formats/rna_pk_simrna_to_one_line.py', 'rna_tools/tools/clarna_app/clarna_app.py', 'rna_tools/tools/rna_helix_vis/rna_helix_vis.py', 'rna_tools/tools/misc/rna_add_chain.py', 'rna_tools/tools/rna_sali2dotbracket/rna_sali2dotbracket.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_run.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_cluster.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_min.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_n.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_extract_lowscore_decoys.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_check_progress.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_head.py', 'rna_tools/tools/rna_rosetta/rna_rosetta_extract.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_lowest.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_extract.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_cluster.py', 'rna_tools/tools/plotting/rna_plot_hist.py', 'rna_tools/tools/plotting/rna_plot_density.py', 'rna_tools/tools/plotting/rna_plot_heatmap.py', 'rna_tools/tools/plotting/rna_plot_dendogram.py', 'rna_tools/tools/plotting/rna_plot_boxplotlike.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_lowest.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_extract.py', 'rna_tools/tools/simrna_trajectory/rna_simrna_cluster.py', 'rna_tools/tools/rna_filter/rna_filter.py', 'rna_tools/tools/rna_filter/rna_ec2x.py', 'rna_tools/tools/rna_filter/rna_pairs2SimRNArestrs.py', 'rna_tools/tools/rna_filter/rna_ss_get_bps.py', 'rna_tools/tools/rna_filter/rna_pairs_diff.py', 'rna_tools/tools/rna_alignment/rna_align_seq_to_alignment.py', 'rna_tools/tools/rna_alignment/rna_align_find_core.py', 'rna_tools/tools/rna_alignment/rna_align_get_ss_from_stk.py', 'rna_tools/tools/rna_alignment/rna_align_seq_to_alignment.py', 'rna_tools/tools/rna_alignment/utils/rna_alignment_get_species.py', 'rna_tools/tools/rna_alignment/utils/rna_alignment_process_id.py', 'rna_tools/tools/rna_alignment/utils/rna_alignment_r2r.py', 'rna_tools/tools/rna_alignment/rna_align_find_seq_in_alignment.py', 'rna_tools/tools/rna_alignment/rna_align_foldability.py', 'rna_tools/tools/rna_pdb_edit_occupancy_bfactor/rna_pdb_edit_occupancy_bfactor.py', 'rna_tools/tools/rna_refinement/rna_refinement.py', 'rna_tools/rna_simrnaweb_download_job.py', 'rna_tools/tools/rna_calc_evo_rmsd/rna_calc_evo_rmsd.py', 'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_multi_targets.py', 'rna_tools/tools/rna_calc_rmsd_trafl/rna_calc_rmsd_trafl.py', 'rna_tools/tools/rna_calc_rmsd_trafl/rna_cal_rmsd_trafl_plot.py', 'rna_tools/tools/rna_x3dna/rna_x3dna.py', 'rna_tools/tools/renum_pdb_to_aln/renum_pdb_to_aln.py', 'rna_tools/tools/pdbs_measure_atom_dists/pdbs_measure_atom_dists.py', 'rna_tools/tools/rna_alignment/random_assignment_of_nucleotides.py', 'rna_tools/tools/rna_seq_search_BLASTn_outfmt-6/select_seq_fromBLAStn_6outfm.py', 'rna_tools/tools/misc/translate.py', 'rna_tools/tools/misc/reverse.py', 'rna_tools/tools/misc/reverse.py', 'rna_tools/tools/rna_alignment/utils/rna_align_strip_stk.py', 'rna_tools/tools/pymol_color_by_conserv/pymol_color_by_conserv.py', 'rna_tools/tools/pymol_preview_generator/pymol_preview_generator.py', 'rna_tools/tools/pymol_preview_generator/pymol_preview_install.py', 'rna_tools/tools/rna_binding_affinity/rna_dG2kd.py', 'rna_tools/tools/rna_binding_affinity/rna_dG2kd.py', 'rna_tools/tools/rna_binding_affinity/rna_kd2dG.py', 'rna_tools/tools/rna_binding_affinity/rna_kd2pkd.py', 'rna_tools/tools/rna_binding_affinity/rna_pkd2dG.py', 'rna_tools/tools/rna_binding_affinity/rna_pkd2kd.py', 'rna_tools/tools/clarna_play/rna_clarna_compare.py', 'rna_tools/tools/clarna_play/rna_clarna_run.py', 'rna_tools/tools/clarna_play/ClaRNAlib/clarna.py', 'rna_tools/tools/mq/rna_mq_score.py', 'rna_tools/tools/mq/rna_mq_collect.py', 'rna_tools/tools/mq/rna_mq_exp.py', 'rna_tools/tools/mq/rna_mq_plot.py', 'rna_tools/tools/mq/rna_mq_remote.sh', 'rna_tools/tools/mq/rna_mq_wx_collect.py', 'rna_tools/tools/mq/RNA3DCNN/rna_mq_rna3dcnn.py', 'rna_tools/tools/mq/Dfire/rna_mq_dfire.py', 'rna_tools/tools/mq/ClashScore/rna_mq_clashscore.py', 'rna_tools/tools/mq/RNAkb/rna_mq_rnakb.py', 'rna_tools/tools/mq/rsRNASP/rna_mq_rsRNASP.py', 'rna_tools/tools/mq/eSCORE/rna_mq_eSCORE.py', 'rna_tools/tools/mq/FARNA/rna_mq_farna.py', 'rna_tools/tools/mq/FARFAR2/rna_mq_farfar2.py', 'rna_tools/tools/mq/SimRNA/rna_mq_simrna.py', 'rna_tools/tools/mq/RASP/rna_mq_rasp.py', 'rna_tools/tools/md/rna_gromacs_ready.py', 'rna_tools/tools/md/rna_md.py', 'rna_tools/tools/md/rna_minimize.py', 'rna_tools/tools/md/rna_traj_n.py', 'rna_tools/tools/md/rna_traj_range.py', 'rna_tools/tools/md/rna_traj_nohetm.py', 'rna_tools/tools/triplexibility/triplexibility.py', 'rna_tools/tools/triplexibility/triplexibility2.py', 'rna_tools/tools/triplexibility/trx_mutagen_allvsall.py', 'rna_tools/tools/triplexibility/trx_mutgen.py', 'rna_tools/tools/triplexibility/trx_score_allvsall.py', 'rna_tools/tools/triplexibility/trx_score.py', 'rna_tools/tools/misc/rna_merge_two_dfs.py', 'rna_tools/tools/misc/rna_merge_dfs.py', 'rna_tools/tools/misc/rna_csv_sort.py', 'rna_tools/tools/misc/rna_ok_mail.py', 'rna_tools/tools/misc/rna_ok', 'rna_tools/tools/PyMOL4RNA/rna_draw_edges.py', 'rna_tools/tools/rna_calc_hbonds/rna_calc_hbonds.py', 'rna_tools/tools/rna_pdb_merge_structure_with_fragments/rna_pdb_merge_structure_with_fragments.py', 'rna_tools/tools/clarna_app/rna_clarna2graph.py', ], license='GPLv3', author='Marcin Magnus', author_email='mag_dex@o2.pl', description='a toolbox to analyze structures and simulations of RNA', long_description=long_description, long_description_content_type="text/markdown", include_package_data=True, install_requires=[ 'numpy', 'biopython', 'progressbar2', 'csvsort', # keep pip minimal #'sphinx==1.6.7', #'sphinx-argparse==0.1.15', #'sphinx-rtd-theme', #'sphinxcontrib-napoleon', #'forgi', 'urllib3', #'pandas', #'matplotlib', #'scipy', #'python-Levenshtein', 'versioneer', 'configparser', 'icecream', ], )