Coverage report: 67%

Files Functions Classes

coverage.py v7.13.0, created at 2025-12-15 15:57 +0000

File function   statements missing excluded   coverage
biobb_amber / __init__.py (no function)   4 0 0   100%
biobb_amber / ambpdb / __init__.py (no function)   3 0 0   100%
biobb_amber / ambpdb / amber_to_pdb.py AmberToPDB.__init__   8 0 0   100%
biobb_amber / ambpdb / amber_to_pdb.py AmberToPDB.check_data_params   3 0 0   100%
biobb_amber / ambpdb / amber_to_pdb.py AmberToPDB.launch   10 1 0   90%
biobb_amber / ambpdb / amber_to_pdb.py amber_to_pdb   1 0 0   100%
biobb_amber / ambpdb / amber_to_pdb.py (no function)   14 1 0   93%
biobb_amber / ambpdb / common.py check_input_path   10 5 0   50%
biobb_amber / ambpdb / common.py check_output_path   10 5 0   50%
biobb_amber / ambpdb / common.py is_valid_file   2 0 0   100%
biobb_amber / ambpdb / common.py (no function)   5 0 0   100%
biobb_amber / cphstats / __init__.py (no function)   4 0 0   100%
biobb_amber / cphstats / cestats_run.py CestatsRun.__init__   19 0 0   100%
biobb_amber / cphstats / cestats_run.py CestatsRun.check_data_params   8 0 0   100%
biobb_amber / cphstats / cestats_run.py CestatsRun.launch   52 23 0   56%
biobb_amber / cphstats / cestats_run.py cestats_run   1 0 0   100%
biobb_amber / cphstats / cestats_run.py (no function)   14 1 0   93%
biobb_amber / cphstats / common.py check_input_path   10 5 0   50%
biobb_amber / cphstats / common.py check_output_path   10 4 0   60%
biobb_amber / cphstats / common.py is_valid_file   2 0 0   100%
biobb_amber / cphstats / common.py (no function)   5 0 0   100%
biobb_amber / cphstats / cphstats_run.py CphstatsRun.__init__   19 0 0   100%
biobb_amber / cphstats / cphstats_run.py CphstatsRun.check_data_params   8 0 0   100%
biobb_amber / cphstats / cphstats_run.py CphstatsRun.launch   52 23 0   56%
biobb_amber / cphstats / cphstats_run.py cphstats_run   1 0 0   100%
biobb_amber / cphstats / cphstats_run.py (no function)   14 1 0   93%
biobb_amber / cpptraj / __init__.py (no function)   3 0 0   100%
biobb_amber / cpptraj / common.py check_input_path   10 5 0   50%
biobb_amber / cpptraj / common.py check_output_path   10 5 0   50%
biobb_amber / cpptraj / common.py is_valid_file   2 0 0   100%
biobb_amber / cpptraj / common.py (no function)   5 0 0   100%
biobb_amber / cpptraj / cpptraj_randomize_ions.py CpptrajRandomizeIons.__init__   12 0 0   100%
biobb_amber / cpptraj / cpptraj_randomize_ions.py CpptrajRandomizeIons.check_data_params   4 0 0   100%
biobb_amber / cpptraj / cpptraj_randomize_ions.py CpptrajRandomizeIons.launch   24 3 0   88%
biobb_amber / cpptraj / cpptraj_randomize_ions.py cpptraj_randomize_ions   1 0 0   100%
biobb_amber / cpptraj / cpptraj_randomize_ions.py (no function)   16 1 0   94%
biobb_amber / leap / __init__.py (no function)   6 0 0   100%
biobb_amber / leap / common.py check_input_path   10 10 0   0%
biobb_amber / leap / common.py check_output_path   10 5 0   50%
biobb_amber / leap / common.py is_valid_file   2 0 0   100%
biobb_amber / leap / common.py _from_string_to_list   8 5 0   38%
biobb_amber / leap / common.py (no function)   7 0 0   100%
biobb_amber / leap / leap_add_ions.py LeapAddIons.__init__   29 2 0   93%
biobb_amber / leap / leap_add_ions.py LeapAddIons.find_leaprc_paths   26 17 0   35%
biobb_amber / leap / leap_add_ions.py LeapAddIons.find_out_number_of_ions   9 0 0   100%
biobb_amber / leap / leap_add_ions.py LeapAddIons.launch   133 69 0   48%
biobb_amber / leap / leap_add_ions.py leap_add_ions   1 0 0   100%
biobb_amber / leap / leap_add_ions.py (no function)   21 1 0   95%
biobb_amber / leap / leap_build_linear_structure.py LeapBuildLinearStructure.__init__   16 0 0   100%
biobb_amber / leap / leap_build_linear_structure.py LeapBuildLinearStructure.check_data_params   1 0 0   100%
biobb_amber / leap / leap_build_linear_structure.py LeapBuildLinearStructure.find_leaprc_paths   26 17 0   35%
biobb_amber / leap / leap_build_linear_structure.py LeapBuildLinearStructure.launch   25 4 0   84%
biobb_amber / leap / leap_build_linear_structure.py leap_build_linear_structure   1 0 0   100%
biobb_amber / leap / leap_build_linear_structure.py (no function)   18 1 0   94%
biobb_amber / leap / leap_gen_top.py LeapGenTop.__init__   14 0 0   100%
biobb_amber / leap / leap_gen_top.py LeapGenTop.find_leaprc_paths   26 17 0   35%
biobb_amber / leap / leap_gen_top.py LeapGenTop.launch   61 24 0   61%
biobb_amber / leap / leap_gen_top.py leap_gen_top   1 0 0   100%
biobb_amber / leap / leap_gen_top.py (no function)   17 1 0   94%
biobb_amber / leap / leap_solvate.py LeapSolvate.__init__   25 0 0   100%
biobb_amber / leap / leap_solvate.py LeapSolvate.find_leaprc_paths   26 17 0   35%
biobb_amber / leap / leap_solvate.py LeapSolvate.launch   94 33 0   65%
biobb_amber / leap / leap_solvate.py leap_solvate   1 0 0   100%
biobb_amber / leap / leap_solvate.py (no function)   18 1 0   94%
biobb_amber / parmed / __init__.py (no function)   4 0 0   100%
biobb_amber / parmed / common.py check_input_path   10 5 0   50%
biobb_amber / parmed / common.py check_output_path   10 4 0   60%
biobb_amber / parmed / common.py is_valid_file   2 0 0   100%
biobb_amber / parmed / common.py (no function)   5 0 0   100%
biobb_amber / parmed / parmed_cpinutil.py ParmedCpinUtil.__init__   11 0 0   100%
biobb_amber / parmed / parmed_cpinutil.py ParmedCpinUtil.check_data_params   3 0 0   100%
biobb_amber / parmed / parmed_cpinutil.py ParmedCpinUtil.launch   26 3 0   88%
biobb_amber / parmed / parmed_cpinutil.py parmed_cpinutil   1 0 0   100%
biobb_amber / parmed / parmed_cpinutil.py (no function)   15 1 0   93%
biobb_amber / parmed / parmed_hmassrepartition.py ParmedHMassRepartition.__init__   8 0 0   100%
biobb_amber / parmed / parmed_hmassrepartition.py ParmedHMassRepartition.check_data_params   2 0 0   100%
biobb_amber / parmed / parmed_hmassrepartition.py ParmedHMassRepartition.launch   22 4 0   82%
biobb_amber / parmed / parmed_hmassrepartition.py parmed_hmassrepartition   1 0 0   100%
biobb_amber / parmed / parmed_hmassrepartition.py (no function)   16 1 0   94%
biobb_amber / pdb4amber / __init__.py (no function)   3 0 0   100%
biobb_amber / pdb4amber / common.py check_input_path   10 5 0   50%
biobb_amber / pdb4amber / common.py check_output_path   10 5 0   50%
biobb_amber / pdb4amber / common.py is_valid_file   2 0 0   100%
biobb_amber / pdb4amber / common.py (no function)   5 0 0   100%
biobb_amber / pdb4amber / pdb4amber_run.py Pdb4amberRun.__init__   12 0 0   100%
biobb_amber / pdb4amber / pdb4amber_run.py Pdb4amberRun.check_data_params   2 0 0   100%
biobb_amber / pdb4amber / pdb4amber_run.py Pdb4amberRun.launch   21 5 0   76%
biobb_amber / pdb4amber / pdb4amber_run.py pdb4amber_run   1 0 0   100%
biobb_amber / pdb4amber / pdb4amber_run.py (no function)   15 1 0   93%
biobb_amber / pmemd / __init__.py (no function)   3 0 0   100%
biobb_amber / pmemd / common.py check_input_path   10 10 0   0%
biobb_amber / pmemd / common.py check_output_path   10 10 0   0%
biobb_amber / pmemd / common.py is_valid_file   2 2 0   0%
biobb_amber / pmemd / common.py (no function)   5 0 0   100%
biobb_amber / pmemd / pmemd_mdrun.py PmemdMDRun.__init__   13 13 0   0%
biobb_amber / pmemd / pmemd_mdrun.py PmemdMDRun.check_data_params   11 11 0   0%
biobb_amber / pmemd / pmemd_mdrun.py PmemdMDRun.create_mdin   100 100 0   0%
biobb_amber / pmemd / pmemd_mdrun.py PmemdMDRun.launch   37 37 0   0%
biobb_amber / pmemd / pmemd_mdrun.py pmemd_mdrun   1 1 0   0%
biobb_amber / pmemd / pmemd_mdrun.py (no function)   18 1 0   94%
biobb_amber / process / __init__.py (no function)   4 0 0   100%
biobb_amber / process / common.py check_input_path   10 5 0   50%
biobb_amber / process / common.py check_output_path   10 5 0   50%
biobb_amber / process / common.py is_valid_file   2 0 0   100%
biobb_amber / process / common.py _from_string_to_list   8 5 0   38%
biobb_amber / process / common.py (no function)   7 0 0   100%
biobb_amber / process / process_mdout.py ProcessMDOut.__init__   9 0 0   100%
biobb_amber / process / process_mdout.py ProcessMDOut.check_data_params   2 0 0   100%
biobb_amber / process / process_mdout.py ProcessMDOut.launch   42 7 0   83%
biobb_amber / process / process_mdout.py process_mdout   1 0 0   100%
biobb_amber / process / process_mdout.py (no function)   17 1 0   94%
biobb_amber / process / process_minout.py ProcessMinOut.__init__   9 0 0   100%
biobb_amber / process / process_minout.py ProcessMinOut.check_data_params   2 0 0   100%
biobb_amber / process / process_minout.py ProcessMinOut.launch   42 26 0   38%
biobb_amber / process / process_minout.py process_minout   1 0 0   100%
biobb_amber / process / process_minout.py (no function)   17 1 0   94%
biobb_amber / sander / __init__.py (no function)   3 0 0   100%
biobb_amber / sander / common.py check_input_path   11 5 0   55%
biobb_amber / sander / common.py check_output_path   10 4 0   60%
biobb_amber / sander / common.py is_valid_file   2 0 0   100%
biobb_amber / sander / common.py (no function)   5 0 0   100%
biobb_amber / sander / sander_mdrun.py SanderMDRun.__init__   16 1 0   94%
biobb_amber / sander / sander_mdrun.py SanderMDRun.check_data_params   11 0 0   100%
biobb_amber / sander / sander_mdrun.py SanderMDRun.create_mdin   103 64 0   38%
biobb_amber / sander / sander_mdrun.py SanderMDRun.launch   41 21 0   49%
biobb_amber / sander / sander_mdrun.py sander_mdrun   1 0 0   100%
biobb_amber / sander / sander_mdrun.py (no function)   19 1 0   95%
biobb_amber / test / unitests / test_ambpdb / test_ambpdb_amber_to_pdb.py TestAmberToPDB.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_ambpdb / test_ambpdb_amber_to_pdb.py TestAmberToPDB.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_ambpdb / test_ambpdb_amber_to_pdb.py TestAmberToPDB.test_amber_to_pdb   3 0 0   100%
biobb_amber / test / unitests / test_ambpdb / test_ambpdb_amber_to_pdb.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cestats_run.py TestCestatsRun.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cestats_run.py TestCestatsRun.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cestats_run.py TestCestatsRun.test_cestats_run   3 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cestats_run.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cphstats_run.py TestCphstatsRun.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cphstats_run.py TestCphstatsRun.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cphstats_run.py TestCphstatsRun.test_cphstats_run   3 0 0   100%
biobb_amber / test / unitests / test_cphstats / test_cphstats_run.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_cpptraj / test_cpptraj_randomize_ions.py TestCpptrajRandomizeIons.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_cpptraj / test_cpptraj_randomize_ions.py TestCpptrajRandomizeIons.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_cpptraj / test_cpptraj_randomize_ions.py TestCpptrajRandomizeIons.test_cpptraj_randomize_ions   3 0 0   100%
biobb_amber / test / unitests / test_cpptraj / test_cpptraj_randomize_ions.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_add_ions.py TestLeapAddIons.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_add_ions.py TestLeapAddIons.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_add_ions.py TestLeapAddIons.test_leap_add_ions   4 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_add_ions.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_build_linear_structure.py TestLeapBuildLinearStructure.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_build_linear_structure.py TestLeapBuildLinearStructure.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_build_linear_structure.py TestLeapBuildLinearStructure.test_leap_build_linear_structure   3 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_build_linear_structure.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_gen_top.py TestLeapGenTop.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_gen_top.py TestLeapGenTop.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_gen_top.py TestLeapGenTop.test_leap_gen_top   7 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_gen_top.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_solvate.py TestLeapSolvate.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_solvate.py TestLeapSolvate.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_solvate.py TestLeapSolvate.test_leap_solvate   6 0 0   100%
biobb_amber / test / unitests / test_leap / test_leap_solvate.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_cpinutil.py TestParmedCpinUtil.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_cpinutil.py TestParmedCpinUtil.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_cpinutil.py TestParmedCpinUtil.test_parmed_cpinutil   3 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_cpinutil.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_hmassrepartition.py TestParmedHMassRepartition.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_hmassrepartition.py TestParmedHMassRepartition.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_hmassrepartition.py TestParmedHMassRepartition.test_parmed_hmassrepartition   3 0 0   100%
biobb_amber / test / unitests / test_parmed / test_parmed_hmassrepartition.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_pdb4amber / test_pdb4amber_pdb4amber.py TestPdb4amberRun.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_pdb4amber / test_pdb4amber_pdb4amber.py TestPdb4amberRun.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_pdb4amber / test_pdb4amber_pdb4amber.py TestPdb4amberRun.test_pdb4amber_run   3 0 0   100%
biobb_amber / test / unitests / test_pdb4amber / test_pdb4amber_pdb4amber.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_process / test_process_mdout.py TestProcessMDOut.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_process / test_process_mdout.py TestProcessMDOut.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_process / test_process_mdout.py TestProcessMDOut.test_process_mdout   3 0 0   100%
biobb_amber / test / unitests / test_process / test_process_mdout.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_process / test_process_minout.py TestProcessMinOut.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_process / test_process_minout.py TestProcessMinOut.teardown_class   2 0 0   100%
biobb_amber / test / unitests / test_process / test_process_minout.py TestProcessMinOut.test_process_minout   3 0 0   100%
biobb_amber / test / unitests / test_process / test_process_minout.py (no function)   6 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRun.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRun.teardown_class   1 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRun.test_sander_mdrun   4 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRunDirectMDin.setup_class   1 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRunDirectMDin.teardown_class   1 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py TestSanderMDRunDirectMDin.test_sander_mdrun   4 0 0   100%
biobb_amber / test / unitests / test_sander / test_sander_mdrun.py (no function)   10 0 0   100%
Total     2026 672 0   67%

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