make -C bin make[1]: Entering directory '/home/jonathanb/software/cryptosite/bin' make[1]: 'cryptosite' is up to date. make[1]: Leaving directory '/home/jonathanb/software/cryptosite/bin' pytest --flake8 -v . ============================= test session starts ============================== platform linux -- Python 3.6.13, pytest-6.2.2, py-1.10.0, pluggy-0.13.1 -- /home/jonathanb/anaconda3/envs/bowman/bin/python cachedir: .pytest_cache rootdir: /home/jonathanb/software/cryptosite, configfile: pytest.ini plugins: flake8-1.0.7, anyio-2.2.0 collecting ... collected 86 items lib/cryptosite/__init__.py::FLAKE8 SKIPPED (file(s) previously passe...) [ 1%] lib/cryptosite/am_bmi.py::FLAKE8 SKIPPED (file(s) previously passed ...) [ 2%] lib/cryptosite/analysis.py::FLAKE8 SKIPPED (file(s) previously passe...) [ 3%] lib/cryptosite/bmi_feature_parser.py::FLAKE8 SKIPPED (file(s) previo...) [ 4%] lib/cryptosite/chimera.py::FLAKE8 SKIPPED (file(s) previously passed...) [ 5%] lib/cryptosite/cleaning.py::FLAKE8 SKIPPED (file(s) previously passe...) [ 6%] lib/cryptosite/gather.py::FLAKE8 SKIPPED (file(s) previously passed ...) [ 8%] lib/cryptosite/hyd_chr_sse.py::FLAKE8 SKIPPED (file(s) previously pa...) [ 9%] lib/cryptosite/patch_mapper.py::FLAKE8 SKIPPED (file(s) previously p...) [ 10%] lib/cryptosite/pockets.py::FLAKE8 SKIPPED (file(s) previously passed...) [ 11%] lib/cryptosite/predict.py::FLAKE8 SKIPPED (file(s) previously passed...) [ 12%] lib/cryptosite/res_parser_bmi.py::FLAKE8 SKIPPED (file(s) previously...) [ 13%] lib/cryptosite/seq_conservation.py::FLAKE8 SKIPPED (file(s) previous...) [ 15%] lib/cryptosite/setup.py::FLAKE8 SKIPPED (file(s) previously passed F...) [ 16%] lib/cryptosite/soap.py::FLAKE8 SKIPPED (file(s) previously passed FL...) [ 17%] lib/cryptosite/config/__init__.py::FLAKE8 SKIPPED (file(s) previousl...) [ 18%] test/test_HydChrSSE.py::FLAKE8 SKIPPED (file(s) previously passed FL...) [ 19%] test/test_HydChrSSE.py::Tests::test_HydChrSSE PASSED [ 20%] test/test_am_bmi.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE...) [ 22%] test/test_am_bmi.py::Tests::test_bad PASSED [ 23%] test/test_am_bmi.py::Tests::test_get_sas PASSED [ 24%] test/test_am_bmi.py::Tests::test_main PASSED [ 25%] test/test_analysis.py::FLAKE8 SKIPPED (file(s) previously passed FLA...) [ 26%] test/test_analysis.py::Tests::test_bad PASSED [ 27%] test/test_analysis.py::Tests::test_get_coordinates_sc PASSED [ 29%] test/test_analysis.py::Tests::test_get_distance PASSED [ 30%] test/test_analysis.py::Tests::test_get_energy PASSED [ 31%] test/test_analysis.py::Tests::test_get_qi_bad_num_res PASSED [ 32%] test/test_analysis.py::Tests::test_get_qioft PASSED [ 33%] test/test_bmi_feature_parser.py::FLAKE8 SKIPPED (file(s) previously ...) [ 34%] test/test_bmi_feature_parser.py::Tests::test_gather_features PASSED [ 36%] test/test_bmi_feature_parser.py::Tests::test_get_cnc PASSED [ 37%] test/test_bmi_feature_parser.py::Tests::test_get_cnc_pockets PASSED [ 38%] test/test_chimera.py::FLAKE8 SKIPPED (file(s) previously passed FLAK...) [ 39%] test/test_chimera.py::Tests::test_bad PASSED [ 40%] test/test_chimera.py::Tests::test_make_chimera_file PASSED [ 41%] test/test_cleaning.py::FLAKE8 SKIPPED (file(s) previously passed FLA...) [ 43%] test/test_cleaning.py::Tests::test_build_model_gaps PASSED [ 44%] test/test_cleaning.py::Tests::test_build_model_no_gaps PASSED [ 45%] test/test_cleaning.py::Tests::test_detect_invalid_residue_types_bad PASSED [ 46%] test/test_cleaning.py::Tests::test_detect_invalid_residue_types_ok PASSED [ 47%] test/test_cleaning.py::Tests::test_get_gaps_multiple PASSED [ 48%] test/test_cleaning.py::Tests::test_get_gaps_single PASSED [ 50%] test/test_cleaning.py::Tests::test_get_pdb_seq PASSED [ 51%] test/test_cleaning.py::Tests::test_muscle_align PASSED [ 52%] test/test_cryptosite.py::FLAKE8 SKIPPED (file(s) previously passed F...) [ 53%] test/test_cryptosite.py::Tests::test_help PASSED [ 54%] test/test_cryptosite.py::Tests::test_help_command PASSED [ 55%] test/test_cryptosite.py::Tests::test_no_args PASSED [ 56%] test/test_cryptosite.py::Tests::test_unknown_command PASSED [ 58%] test/test_gather.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE...) [ 59%] test/test_gather.py::Tests::test_bad PASSED [ 60%] test/test_gather.py::Tests::test_process_directory PASSED [ 61%] test/test_patch_mapper.py::FLAKE8 SKIPPED (file(s) previously passed...) [ 62%] test/test_patch_mapper.py::Tests::test_get_ligand_mol2 PASSED [ 63%] test/test_patch_mapper.py::Tests::test_make_ligand_file PASSED [ 65%] test/test_patch_mapper.py::Tests::test_modify_patch_dock_params PASSED [ 66%] test/test_patch_mapper.py::Tests::test_patchmap_feature PASSED [ 67%] test/test_patch_mapper.py::Tests::test_read_ligand_data PASSED [ 68%] test/test_pockets.py::FLAKE8 SKIPPED (file(s) previously passed FLAK...) [ 69%] test/test_pockets.py::Tests::test_bad PASSED [ 70%] test/test_pockets.py::Tests::test_get_cnc PASSED [ 72%] test/test_pockets.py::Tests::test_main FAILED [ 73%] test/test_predict.py::FLAKE8 SKIPPED (file(s) previously passed FLAK...) [ 74%] test/test_predict.py::Tests::test_bad PASSED [ 75%] test/test_predict.py::Tests::test_get_matrix PASSED [ 76%] test/test_predict.py::Tests::test_main PASSED [ 77%] test/test_res_parser_bmi.py::FLAKE8 SKIPPED (file(s) previously pass...) [ 79%] test/test_res_parser_bmi.py::Tests::test_res_parser PASSED [ 80%] test/test_seq_conservation.py::FLAKE8 SKIPPED (file(s) previously pa...) [ 81%] test/test_seq_conservation.py::Tests::test_parse_blast PASSED [ 82%] test/test_seq_conservation.py::Tests::test_run_blast PASSED [ 83%] test/test_seq_conservation.py::Tests::test_ucluster PASSED [ 84%] test/test_setup.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE8...) [ 86%] test/test_setup.py::Tests::test_bad PASSED [ 87%] test/test_setup.py::Tests::test_extract_chains PASSED [ 88%] test/test_setup.py::Tests::test_extract_chains_missing PASSED [ 89%] test/test_setup.py::Tests::test_main PASSED [ 90%] test/test_soap.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE8 ...) [ 91%] test/test_soap.py::Tests::test_bad PASSED [ 93%] test/test_soap.py::Tests::test_soap_module PASSED [ 94%] test/test_soap.py::Tests::test_soap_subproc PASSED [ 95%] test/utils.py::FLAKE8 SKIPPED (file(s) previously passed FLAKE8 checks) [ 96%] test/mock/modeller/__init__.py::FLAKE8 SKIPPED (file(s) previously p...) [ 97%] test/mock/modeller/scripts.py::FLAKE8 SKIPPED (file(s) previously pa...) [ 98%] test/mock/modeller/soap_protein_od.py::FLAKE8 SKIPPED (file(s) previ...) [100%] =================================== FAILURES =================================== _______________________________ Tests.test_main ________________________________ self = def test_main(self): """Test simple complete run of pockets""" with utils.temporary_working_directory(): shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'pm.pdb.B10010001.pdb'), '.') with open('SnapList.txt', 'w') as fh: fh.write("pm.pdb.B10010001.pdb -100.0\n") fh.write("high-energy.pdb -10.0\n") subprocess.check_call(['cryptosite', 'pockets']) with open('pockets.out') as fh: lines = fh.readlines() self.assertEqual(len(lines), 13) > self.assertEqual(lines[1], 'ALA\t1\tA\t0.0\n') E AssertionError: 'ALA\t1\tA\t0.196\n' != 'ALA\t1\tA\t0.0\n' E - ALA 1 A 0.196 E ? ^^^ E + ALA 1 A 0.0 E ? ^ test/test_pockets.py:43: AssertionError ----------------------------- Captured stdout call ----------------------------- ***** POCKET HUNTING BEGINS ***** ***** POCKET HUNTING ENDS ***** DRS: ['pm.pdb.B10010001.pdb'] ['pm.pdb.B10010001_out/pm.pdb.B10010001_out.pdb'] pm.pdb.B10010001_out/pm.pdb.B10010001_out.pdb pm.pdb.B10010001_out/pm.pdb.B10010001_info.txt =========================== short test summary info ============================ FAILED test/test_pockets.py::Tests::test_main - AssertionError: 'ALA\t1\tA\t0... ================== 1 failed, 50 passed, 35 skipped in 11.27s =================== Makefile:19: recipe for target 'test' failed