Development andres

[andreshyer]

qsardq_export.py

• New file that has a script to export out models in a way that complies with QsarDB structure (http://qsardb.org/)

• Also helps line out the ground to export our data in our own xml format is desired

storage.py

• Fixed minor bugs where storing and moving files behave differently on different os's

• Changed name "export_json" to "store", as not only json is being exported

features.py

• Changed how data is exported. Data_csv now contains which molecules are in test/train/val sets, lifting the need to store this in attributes.json, significantly reducing size.

main.py

• in single_model, example of how to use QsarDB_export

[pep8speaks]

Hello @andreshyer! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file core/analysis.py:

Line 6:80: E501 line too long (128 > 79 characters) Line 11:1: E302 expected 2 blank lines, found 1 Line 23:32: E127 continuation line over-indented for visual indent Line 29:80: E501 line too long (93 > 79 characters) Line 76:80: E501 line too long (86 > 79 characters) Line 137:80: E501 line too long (80 > 79 characters) Line 140:80: E501 line too long (115 > 79 characters) Line 164:80: E501 line too long (111 > 79 characters) Line 167:80: E501 line too long (97 > 79 characters) Line 172:80: E501 line too long (82 > 79 characters) Line 173:80: E501 line too long (85 > 79 characters) Line 178:80: E501 line too long (91 > 79 characters) Line 180:80: E501 line too long (99 > 79 characters) Line 198:80: E501 line too long (117 > 79 characters) Line 210:80: E501 line too long (94 > 79 characters) Line 211:1: W391 blank line at end of file

• In the file core/classifiers.py:

Line 5:1: E302 expected 2 blank lines, found 1 Line 17:80: E501 line too long (104 > 79 characters) Line 21:1: W391 blank line at end of file

• In the file core/compare.py:

Line 27:80: E501 line too long (90 > 79 characters) Line 32:35: E261 at least two spaces before inline comment Line 42:5: E265 block comment should start with '# ' Line 43:80: E501 line too long (151 > 79 characters) Line 44:80: E501 line too long (125 > 79 characters) Line 50:80: E501 line too long (80 > 79 characters) Line 55:55: E261 at least two spaces before inline comment Line 55:55: E262 inline comment should start with '# ' Line 79:1: E303 too many blank lines (3) Line 83:1: E302 expected 2 blank lines, found 3 Line 97:27: E203 whitespace before ':' Line 108:80: E501 line too long (101 > 79 characters) Line 110:80: E501 line too long (81 > 79 characters) Line 116:80: E501 line too long (120 > 79 characters) Line 133:80: E501 line too long (107 > 79 characters) Line 135:80: E501 line too long (89 > 79 characters) Line 139:27: E261 at least two spaces before inline comment Line 139:80: E501 line too long (83 > 79 characters) Line 143:80: E501 line too long (98 > 79 characters) Line 145:18: E222 multiple spaces after operator Line 150:80: E501 line too long (92 > 79 characters) Line 150:93: W291 trailing whitespace Line 151:80: E501 line too long (108 > 79 characters) Line 151:109: W291 trailing whitespace Line 152:80: E501 line too long (101 > 79 characters) Line 152:102: W291 trailing whitespace Line 154:1: W293 blank line contains whitespace Line 155:80: E501 line too long (113 > 79 characters) Line 156:80: E501 line too long (114 > 79 characters) Line 157:80: E501 line too long (111 > 79 characters) Line 157:112: W291 trailing whitespace Line 158:30: W291 trailing whitespace Line 160:80: E501 line too long (98 > 79 characters) Line 168:13: E303 too many blank lines (2) Line 168:28: E231 missing whitespace after ':' Line 170:80: E501 line too long (81 > 79 characters) Line 175:9: E303 too many blank lines (3) Line 184:80: E501 line too long (119 > 79 characters) Line 188:80: E501 line too long (87 > 79 characters) Line 202:80: E501 line too long (85 > 79 characters) Line 215:80: E501 line too long (86 > 79 characters) Line 224:17: E116 unexpected indentation (comment) Line 225:17: E116 unexpected indentation (comment) Line 226:80: E501 line too long (103 > 79 characters) Line 244:9: E303 too many blank lines (3) Line 256:5: E303 too many blank lines (2) Line 323:80: E501 line too long (84 > 79 characters) Line 328:1: E302 expected 2 blank lines, found 1 Line 331:80: E501 line too long (104 > 79 characters) Line 344:80: E501 line too long (92 > 79 characters) Line 345:80: E501 line too long (100 > 79 characters) Line 353:80: E501 line too long (95 > 79 characters) Line 354:80: E501 line too long (102 > 79 characters) Line 356:52: E261 at least two spaces before inline comment Line 356:80: E501 line too long (90 > 79 characters) Line 358:80: E501 line too long (104 > 79 characters) Line 360:80: E501 line too long (103 > 79 characters) Line 361:80: E501 line too long (92 > 79 characters) Line 364:80: E501 line too long (97 > 79 characters) Line 365:80: E501 line too long (85 > 79 characters) Line 367:80: E501 line too long (109 > 79 characters) Line 373:80: E501 line too long (89 > 79 characters) Line 374:80: E501 line too long (109 > 79 characters) Line 384:9: E303 too many blank lines (2) Line 388:9: E303 too many blank lines (2) Line 392:9: E303 too many blank lines (2) Line 393:80: E501 line too long (99 > 79 characters) Line 396:9: E303 too many blank lines (2) Line 396:80: E501 line too long (149 > 79 characters) Line 397:38: E231 missing whitespace after ',' Line 397:59: E231 missing whitespace after ',' Line 397:65: E231 missing whitespace after ',' Line 397:80: E501 line too long (147 > 79 characters) Line 399:80: E501 line too long (106 > 79 characters) Line 400:80: E501 line too long (91 > 79 characters) Line 404:9: E303 too many blank lines (2) Line 406:80: E501 line too long (93 > 79 characters) Line 410:80: E501 line too long (94 > 79 characters) Line 411:80: E501 line too long (97 > 79 characters) Line 412:20: E231 missing whitespace after ',' Line 417:46: E231 missing whitespace after ',' Line 420:37: E261 at least two spaces before inline comment Line 420:80: E501 line too long (92 > 79 characters) Line 423:5: E303 too many blank lines (2) Line 428:1: E303 too many blank lines (4) Line 440:23: E203 whitespace before ':' Line 444:1: E265 block comment should start with '# ' Line 445:80: E501 line too long (103 > 79 characters) Line 449:1: E303 too many blank lines (3) Line 460:19: W292 no newline at end of file Line 460:19: W292 no newline at end of file Line 460:19: W292 no newline at end of file

• In the file core/enrich.py:

Line 43:80: E501 line too long (92 > 79 characters) Line 46:1: W391 blank line at end of file

• In the file core/features.py:

Line 17:80: E501 line too long (97 > 79 characters) Line 28:76: E703 statement ends with a semicolon Line 30:80: E501 line too long (125 > 79 characters) Line 32:80: E501 line too long (84 > 79 characters) Line 79:80: E501 line too long (101 > 79 characters) Line 114:80: E501 line too long (100 > 79 characters) Line 115:80: E501 line too long (107 > 79 characters) Line 116:80: E501 line too long (106 > 79 characters) Line 117:80: E501 line too long (116 > 79 characters) Line 118:80: E501 line too long (118 > 79 characters) Line 120:80: E501 line too long (102 > 79 characters) Line 121:80: E501 line too long (104 > 79 characters) Line 122:80: E501 line too long (106 > 79 characters) Line 123:80: E501 line too long (116 > 79 characters) Line 124:80: E501 line too long (118 > 79 characters) Line 137:80: E501 line too long (102 > 79 characters) Line 138:80: E501 line too long (108 > 79 characters) Line 139:80: E501 line too long (106 > 79 characters) Line 140:80: E501 line too long (100 > 79 characters) Line 141:80: E501 line too long (118 > 79 characters) Line 143:80: E501 line too long (104 > 79 characters) Line 144:80: E501 line too long (109 > 79 characters) Line 145:80: E501 line too long (106 > 79 characters) Line 146:80: E501 line too long (100 > 79 characters) Line 147:80: E501 line too long (118 > 79 characters) Line 164:80: E501 line too long (125 > 79 characters) Line 184:80: E501 line too long (113 > 79 characters) Line 201:80: E501 line too long (83 > 79 characters)

• In the file core/grid.py:

Line 16:1: E402 module level import not at top of file Line 59:79: E261 at least two spaces before inline comment Line 59:80: E262 inline comment should start with '# ' Line 59:80: E501 line too long (95 > 79 characters) Line 61:61: E261 at least two spaces before inline comment Line 61:80: E501 line too long (95 > 79 characters) Line 62:80: E501 line too long (94 > 79 characters) Line 63:80: E501 line too long (97 > 79 characters) Line 95:80: E501 line too long (86 > 79 characters) Line 140:80: E501 line too long (83 > 79 characters) Line 143:80: E501 line too long (82 > 79 characters) Line 175:43: E203 whitespace before ',' Line 175:44: E231 missing whitespace after ',' Line 175:54: E231 missing whitespace after ',' Line 175:58: E231 missing whitespace after ',' Line 175:80: E501 line too long (116 > 79 characters) Line 175:86: E251 unexpected spaces around keyword / parameter equals Line 175:88: E251 unexpected spaces around keyword / parameter equals Line 175:97: E251 unexpected spaces around keyword / parameter equals Line 175:99: E251 unexpected spaces around keyword / parameter equals Line 175:109: E251 unexpected spaces around keyword / parameter equals Line 175:111: E251 unexpected spaces around keyword / parameter equals

• In the file core/ingest.py:

Line 26:1: E302 expected 2 blank lines, found 1 Line 26:19: E231 missing whitespace after ',' Line 26:80: E501 line too long (89 > 79 characters) Line 28:80: E501 line too long (90 > 79 characters) Line 56:32: E711 comparison to None should be 'if cond is None:' Line 67:15: W292 no newline at end of file

• In the file core/misc.py:

Line 40:1: W391 blank line at end of file

• In the file core/models.py:

Line 2:80: E501 line too long (94 > 79 characters) Line 4:80: E501 line too long (86 > 79 characters) Line 15:80: E501 line too long (95 > 79 characters) Line 23:80: E501 line too long (96 > 79 characters) Line 32:80: E501 line too long (106 > 79 characters) Line 34:80: E501 line too long (107 > 79 characters) Line 35:80: E501 line too long (94 > 79 characters) Line 48:80: E501 line too long (109 > 79 characters) Line 67:80: E501 line too long (91 > 79 characters) Line 74:80: E501 line too long (98 > 79 characters) Line 76:80: E501 line too long (111 > 79 characters) Line 80:43: E261 at least two spaces before inline comment Line 80:80: E501 line too long (81 > 79 characters)

• In the file core/mol_view.py:

Line 12:1: E302 expected 2 blank lines, found 1 Line 13:80: E501 line too long (98 > 79 characters) Line 15:8: E221 multiple spaces before operator Line 17:33: E231 missing whitespace after ',' Line 24:80: E501 line too long (87 > 79 characters) Line 30:60: E231 missing whitespace after ',' Line 39:80: E501 line too long (81 > 79 characters) Line 45:80: E501 line too long (101 > 79 characters)

• In the file core/name.py:

Line 6:80: E501 line too long (89 > 79 characters) Line 7:80: E501 line too long (105 > 79 characters) Line 14:80: E501 line too long (119 > 79 characters) Line 17:80: E501 line too long (121 > 79 characters) Line 22:80: E501 line too long (97 > 79 characters) Line 25:80: E501 line too long (95 > 79 characters) Line 27:80: E501 line too long (81 > 79 characters) Line 29:80: E501 line too long (81 > 79 characters) Line 40:80: E501 line too long (91 > 79 characters) Line 41:80: E501 line too long (97 > 79 characters) Line 45:80: E501 line too long (106 > 79 characters) Line 46:80: E501 line too long (89 > 79 characters) Line 47:80: E501 line too long (92 > 79 characters) Line 48:80: E501 line too long (118 > 79 characters) Line 49:80: E501 line too long (111 > 79 characters) Line 50:80: E501 line too long (111 > 79 characters) Line 53:80: E501 line too long (120 > 79 characters) Line 54:80: E501 line too long (110 > 79 characters) Line 56:80: E501 line too long (115 > 79 characters) Line 65:80: E501 line too long (119 > 79 characters) Line 68:80: E501 line too long (124 > 79 characters) Line 69:80: E501 line too long (114 > 79 characters) Line 71:80: E501 line too long (99 > 79 characters) Line 72:80: E501 line too long (92 > 79 characters) Line 76:80: E501 line too long (109 > 79 characters) Line 85:80: E501 line too long (105 > 79 characters) Line 86:80: E501 line too long (99 > 79 characters) Line 87:80: E501 line too long (81 > 79 characters) Line 88:80: E501 line too long (85 > 79 characters) Line 90:80: E501 line too long (113 > 79 characters) Line 96:80: E501 line too long (117 > 79 characters) Line 97:80: E501 line too long (95 > 79 characters) Line 100:80: E501 line too long (101 > 79 characters) Line 101:80: E501 line too long (90 > 79 characters) Line 109:80: E501 line too long (109 > 79 characters)

• In the file core/qsardq_export.py:

Line 12:80: E501 line too long (99 > 79 characters) Line 13:80: E501 line too long (88 > 79 characters) Line 59:80: E501 line too long (80 > 79 characters) Line 69:80: E501 line too long (85 > 79 characters) Line 113:80: E501 line too long (98 > 79 characters)

• In the file core/regressors.py:

Line 22:1: E402 module level import not at top of file Line 23:1: E402 module level import not at top of file Line 24:1: E402 module level import not at top of file Line 29:14: E201 whitespace after '(' Line 29:23: E251 unexpected spaces around keyword / parameter equals Line 29:25: E251 unexpected spaces around keyword / parameter equals Line 29:37: E251 unexpected spaces around keyword / parameter equals Line 29:39: E251 unexpected spaces around keyword / parameter equals Line 29:57: E251 unexpected spaces around keyword / parameter equals Line 29:59: E251 unexpected spaces around keyword / parameter equals Line 29:80: E501 line too long (89 > 79 characters) Line 31:80: E501 line too long (104 > 79 characters) Line 35:80: E501 line too long (112 > 79 characters) Line 36:80: E501 line too long (87 > 79 characters) Line 37:80: E501 line too long (86 > 79 characters) Line 38:80: E501 line too long (118 > 79 characters) Line 39:80: E501 line too long (117 > 79 characters) Line 40:80: E501 line too long (103 > 79 characters) Line 46:80: E501 line too long (105 > 79 characters) Line 47:80: E501 line too long (100 > 79 characters) Line 50:80: E501 line too long (93 > 79 characters) Line 54:80: E501 line too long (118 > 79 characters) Line 57:80: E501 line too long (95 > 79 characters) Line 64:80: E501 line too long (92 > 79 characters) Line 74:80: E501 line too long (112 > 79 characters) Line 75:80: E501 line too long (82 > 79 characters) Line 79:80: E501 line too long (112 > 79 characters) Line 114:80: E501 line too long (94 > 79 characters) Line 116:80: E501 line too long (101 > 79 characters) Line 122:80: E501 line too long (82 > 79 characters) Line 137:80: E501 line too long (95 > 79 characters) Line 138:30: E231 missing whitespace after ',' Line 167:80: E501 line too long (114 > 79 characters) Line 172:80: E501 line too long (108 > 79 characters) Line 174:80: E501 line too long (83 > 79 characters) Line 177:8: W291 trailing whitespace Line 178:80: E501 line too long (80 > 79 characters) Line 179:80: E501 line too long (109 > 79 characters) Line 180:80: E501 line too long (98 > 79 characters) Line 181:80: E501 line too long (107 > 79 characters) Line 184:80: E501 line too long (84 > 79 characters) Line 190:80: E501 line too long (108 > 79 characters) Line 197:80: E501 line too long (115 > 79 characters) Line 213:1: W391 blank line at end of file

• In the file core/storage.py:

Line 14:1: E302 expected 2 blank lines, found 1 Line 26:80: E501 line too long (100 > 79 characters) Line 42:80: E501 line too long (101 > 79 characters) Line 43:80: E501 line too long (100 > 79 characters) Line 44:80: E501 line too long (98 > 79 characters) Line 45:80: E501 line too long (102 > 79 characters) Line 51:80: E501 line too long (93 > 79 characters) Line 58:80: E501 line too long (90 > 79 characters) Line 67:80: E501 line too long (95 > 79 characters) Line 70:80: E501 line too long (85 > 79 characters) Line 76:80: E501 line too long (119 > 79 characters) Line 90:80: E501 line too long (84 > 79 characters) Line 101:80: E501 line too long (87 > 79 characters) Line 123:80: E501 line too long (84 > 79 characters) Line 139:80: E501 line too long (107 > 79 characters) Line 141:80: E501 line too long (101 > 79 characters) Line 142:80: E501 line too long (84 > 79 characters) Line 155:80: E501 line too long (91 > 79 characters)

• In the file core/train.py:

Line 5:80: E501 line too long (98 > 79 characters) Line 11:19: E231 missing whitespace after ',' Line 13:80: E501 line too long (83 > 79 characters) Line 19:80: E501 line too long (89 > 79 characters) Line 33:80: E501 line too long (81 > 79 characters) Line 34:80: E501 line too long (89 > 79 characters) Line 77:80: E501 line too long (83 > 79 characters) Line 84:80: E501 line too long (89 > 79 characters) Line 86:5: E265 block comment should start with '# ' Line 87:5: E265 block comment should start with '# ' Line 137:8: E131 continuation line unaligned for hanging indent

• In the file main.py:

Line 21:80: E501 line too long (90 > 79 characters) Line 32:80: E501 line too long (81 > 79 characters) Line 33:80: E501 line too long (105 > 79 characters) Line 35:80: E501 line too long (91 > 79 characters) Line 47:9: E303 too many blank lines (2) Line 48:80: E501 line too long (81 > 79 characters) Line 50:22: E261 at least two spaces before inline comment Line 50:22: E262 inline comment should start with '# ' Line 50:80: E501 line too long (111 > 79 characters) Line 52:80: E501 line too long (87 > 79 characters) Line 69:21: E303 too many blank lines (2) Line 69:80: E501 line too long (111 > 79 characters) Line 75:80: E501 line too long (81 > 79 characters) Line 76:80: E501 line too long (109 > 79 characters) Line 96:80: E501 line too long (81 > 79 characters) Line 102:80: E501 line too long (81 > 79 characters) Line 117:80: E501 line too long (96 > 79 characters) Line 118:80: E501 line too long (92 > 79 characters) Line 123:80: E501 line too long (95 > 79 characters) Line 127:80: E501 line too long (104 > 79 characters) Line 129:80: E501 line too long (102 > 79 characters) Line 153:80: E501 line too long (89 > 79 characters) Line 158:80: E501 line too long (83 > 79 characters)

• In the file tests/test_analysis.py:

Line 13:80: E501 line too long (80 > 79 characters) Line 23:80: E501 line too long (113 > 79 characters) Line 24:80: E501 line too long (89 > 79 characters) Line 34:80: E501 line too long (98 > 79 characters) Line 36:80: E501 line too long (114 > 79 characters) Line 44:80: E501 line too long (123 > 79 characters) Line 45:80: E501 line too long (94 > 79 characters) Line 51:80: E501 line too long (121 > 79 characters) Line 65:80: E501 line too long (118 > 79 characters) Line 67:80: E501 line too long (122 > 79 characters) Line 94:80: E501 line too long (116 > 79 characters) Line 95:80: E501 line too long (81 > 79 characters) Line 100:80: E501 line too long (113 > 79 characters) Line 115:80: E501 line too long (114 > 79 characters) Line 117:80: E501 line too long (122 > 79 characters) Line 118:80: E501 line too long (121 > 79 characters) Line 119:80: E501 line too long (89 > 79 characters) Line 124:80: E501 line too long (113 > 79 characters) Line 133:80: E501 line too long (113 > 79 characters) Line 135:80: E501 line too long (122 > 79 characters) Line 136:80: E501 line too long (121 > 79 characters) Line 137:80: E501 line too long (89 > 79 characters) Line 142:80: E501 line too long (121 > 79 characters)

• In the file tests/test_features.py:

Line 10:80: E501 line too long (80 > 79 characters) Line 17:80: E501 line too long (102 > 79 characters) Line 23:80: E501 line too long (111 > 79 characters) Line 27:80: E501 line too long (122 > 79 characters) Line 38:80: E501 line too long (106 > 79 characters) Line 47:80: E501 line too long (122 > 79 characters) Line 58:80: E501 line too long (82 > 79 characters) Line 60:80: E501 line too long (82 > 79 characters) Line 66:80: E501 line too long (92 > 79 characters) Line 76:80: E501 line too long (108 > 79 characters) Line 80:80: E501 line too long (116 > 79 characters) Line 82:80: E501 line too long (86 > 79 characters) Line 84:80: E501 line too long (86 > 79 characters) Line 86:80: E501 line too long (89 > 79 characters) Line 88:80: E501 line too long (86 > 79 characters) Line 90:80: E501 line too long (86 > 79 characters) Line 94:80: E501 line too long (99 > 79 characters) Line 107:80: E501 line too long (114 > 79 characters) Line 109:80: E501 line too long (86 > 79 characters) Line 111:80: E501 line too long (83 > 79 characters) Line 113:44: W292 no newline at end of file Line 113:44: W292 no newline at end of file Line 113:44: W292 no newline at end of file

• In the file tests/test_ingest.py:

Line 9:80: E501 line too long (80 > 79 characters) Line 21:80: E501 line too long (122 > 79 characters) Line 22:80: E501 line too long (120 > 79 characters) Line 30:80: E501 line too long (117 > 79 characters) Line 37:80: E501 line too long (84 > 79 characters) Line 45:80: E501 line too long (117 > 79 characters) Line 46:80: E501 line too long (95 > 79 characters) Line 47:80: E501 line too long (97 > 79 characters) Line 51:80: E501 line too long (83 > 79 characters) Line 59:80: E501 line too long (155 > 79 characters) Line 60:80: E501 line too long (95 > 79 characters) Line 61:80: E501 line too long (97 > 79 characters)

• In the file tests/test_models.py:

Line 7:80: E501 line too long (80 > 79 characters) Line 18:80: E501 line too long (117 > 79 characters) Line 20:80: E501 line too long (116 > 79 characters)

• In the file tests/test_regressors.py:

Line 10:80: E501 line too long (80 > 79 characters) Line 23:80: E501 line too long (113 > 79 characters) Line 24:80: E501 line too long (89 > 79 characters) Line 34:80: E501 line too long (98 > 79 characters) Line 36:80: E501 line too long (114 > 79 characters) Line 43:80: E501 line too long (106 > 79 characters) Line 44:80: E501 line too long (121 > 79 characters) Line 50:80: E501 line too long (83 > 79 characters) Line 51:80: E501 line too long (99 > 79 characters) Line 60:80: E501 line too long (109 > 79 characters) Line 65:80: E501 line too long (102 > 79 characters) Line 66:80: E501 line too long (99 > 79 characters)