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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_silent_file_sort_and_select.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/rna_rosetta/rna_rosetta_get_score.py',
'rna_tools/tools/rna_rosetta/rna_rosetta_silent_file_sort_and_select.py',
'rna_tools/tools/rna_rosetta/rna_rosetta_silent_random.py',
'rna_tools/tools/rna_rosetta/rna_rosetta_silent_split.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/df/rna_df_csv_sort.py',
'rna_tools/tools/df/rna_df_merge.py',
'rna_tools/tools/df/rna_df_merge_on.py',
'rna_tools/tools/df/rna_df_merge_two.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',
],
)