[pull] devel from deepmodeling:devel by pull[bot] · Pull Request #19 · njzjz/deepmd-kit

pull · 2019-08-10T14:04:38Z

See Commits and Changes for more details.

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when using TensorFlow >= 1.14

find libtensorflow_framework.so.1 for cpp

refactoring the Data and DataSystem

similar-code-searcher · 2019-08-10T14:04:41Z

Similar files are

GitHub
deepmodeling/deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics - deepmodeling/deepmd-kit

pep8speaks · 2019-08-10T14:04:48Z

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

In the file source/tests/common.py:

Line 9:43: E203 whitespace before ':'
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In the file source/tests/test_class_arg.py:

Line 28:29: E211 whitespace before '('
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In the file source/tests/test_data_requirement.py:

Line 1:14: E231 missing whitespace after ','
Line 1:14: E401 multiple imports on one line
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In the file source/tests/test_deepmd_data.py:

Line 1:10: E231 missing whitespace after ','
Line 1:10: E401 multiple imports on one line
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In the file source/tests/test_deepmd_data_sys.py:

Line 1:10: E231 missing whitespace after ','
Line 1:10: E401 multiple imports on one line
Line 1:14: E231 missing whitespace after ','
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In the file source/tests/test_descrpt_nonsmth.py:

Line 54:19: E221 multiple spaces before operator
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In the file source/tests/test_descrpt_se_ar.py:

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In the file source/tests/test_descrpt_se_r.py:

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In the file source/tests/test_descrpt_smooth.py:

Line 55:19: E221 multiple spaces before operator
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In the file source/tests/test_model_loc_frame.py:

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In the file source/tests/test_model_se_a.py:

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In the file source/tests/test_model_se_a_fparam.py:

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In the file source/tests/test_model_se_a_srtab.py:

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In the file source/tests/test_model_se_r.py:

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In the file source/train/Data.py:

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Line 284:36: E203 whitespace before ':'
Line 285:31: E211 whitespace before '('
Line 285:80: E501 line too long (92 > 79 characters)
Line 287:24: E211 whitespace before '('
Line 288:29: E211 whitespace before '('
Line 291:39: E203 whitespace before ':'
Line 293:33: E203 whitespace before ':'
Line 293:35: W291 trailing whitespace
Line 295:41: W291 trailing whitespace
Line 296:13: E203 whitespace before ':'

In the file source/train/DataSystem.py:

Line 10:1: E402 module level import not at top of file
Line 12:1: E302 expected 2 blank lines, found 1
Line 12:25: E203 whitespace before ':'
Line 13:17: E211 whitespace before '('
Line 14:27: W291 trailing whitespace
Line 18:29: E251 unexpected spaces around keyword / parameter equals
Line 18:31: E251 unexpected spaces around keyword / parameter equals
Line 19:31: E251 unexpected spaces around keyword / parameter equals
Line 19:33: E251 unexpected spaces around keyword / parameter equals
Line 20:26: E251 unexpected spaces around keyword / parameter equals
Line 20:28: E251 unexpected spaces around keyword / parameter equals
Line 20:34: E203 whitespace before ':'
Line 26:35: E203 whitespace before ':'
Line 27:52: W291 trailing whitespace
Line 28:71: W291 trailing whitespace
Line 33:44: E203 whitespace before ':'
Line 34:80: E501 line too long (81 > 79 characters)
Line 37:34: E203 whitespace before ':'
Line 39:35: E203 whitespace before ':'
Line 44:13: E203 whitespace before ':'
Line 45:53: W291 trailing whitespace
Line 46:49: E231 missing whitespace after ','
Line 51:36: E203 whitespace before ':'
Line 58:39: E203 whitespace before ':'
Line 60:80: E501 line too long (101 > 79 characters)
Line 61:80: E501 line too long (95 > 79 characters)
Line 66:31: E201 whitespace after '['
Line 66:80: E501 line too long (87 > 79 characters)
Line 66:88: W291 trailing whitespace
Line 70:39: E203 whitespace before ':'
Line 71:80: E501 line too long (81 > 79 characters)
Line 72:35: E203 whitespace before ':'
Line 73:35: E211 whitespace before '('
Line 73:80: E501 line too long (119 > 79 characters)
Line 73:119: E502 the backslash is redundant between brackets
Line 74:80: E501 line too long (104 > 79 characters)
Line 76:35: E203 whitespace before ':'
Line 77:80: E501 line too long (114 > 79 characters)
Line 77:114: E502 the backslash is redundant between brackets
Line 78:80: E501 line too long (80 > 79 characters)
Line 85:5: E303 too many blank lines (2)
Line 88:39: E203 whitespace before ':'
Line 89:62: E211 whitespace before '('
Line 92:31: E211 whitespace before '('
Line 93:33: E211 whitespace before '('
Line 93:64: E251 unexpected spaces around keyword / parameter equals
Line 93:66: E251 unexpected spaces around keyword / parameter equals
Line 94:33: E211 whitespace before '('
Line 94:46: E231 missing whitespace after ','
Line 95:53: E225 missing whitespace around operator
Line 95:80: E501 line too long (81 > 79 characters)
Line 97:36: E211 whitespace before '('
Line 97:46: E251 unexpected spaces around keyword / parameter equals
Line 97:48: E251 unexpected spaces around keyword / parameter equals
Line 102:5: E303 too many blank lines (2)
Line 102:41: E251 unexpected spaces around keyword / parameter equals
Line 102:43: E251 unexpected spaces around keyword / parameter equals
Line 102:53: E251 unexpected spaces around keyword / parameter equals
Line 102:55: E251 unexpected spaces around keyword / parameter equals
Line 102:65: E203 whitespace before ':'
Line 104:36: E203 whitespace before ':'
Line 106:54: E251 unexpected spaces around keyword / parameter equals
Line 106:56: E251 unexpected spaces around keyword / parameter equals
Line 107:61: E231 missing whitespace after ','
Line 108:36: E231 missing whitespace after ','
Line 109:21: E231 missing whitespace after ','
Line 109:26: E231 missing whitespace after ','
Line 109:31: E231 missing whitespace after ','
Line 110:59: E251 unexpected spaces around keyword / parameter equals
Line 110:61: E251 unexpected spaces around keyword / parameter equals
Line 114:5: E303 too many blank lines (2)
Line 114:30: E203 whitespace before ':'
Line 115:24: E203 whitespace before ':'
Line 116:25: W291 trailing whitespace
Line 117:40: W291 trailing whitespace
Line 118:49: W291 trailing whitespace
Line 119:45: W291 trailing whitespace
Line 120:55: W291 trailing whitespace
Line 123:18: W291 trailing whitespace
Line 124:17: W291 trailing whitespace
Line 125:18: W291 trailing whitespace
Line 126:19: E251 unexpected spaces around keyword / parameter equals
Line 126:21: E251 unexpected spaces around keyword / parameter equals
Line 126:28: W291 trailing whitespace
Line 127:17: E251 unexpected spaces around keyword / parameter equals
Line 127:19: E251 unexpected spaces around keyword / parameter equals
Line 127:26: W291 trailing whitespace
Line 128:22: E251 unexpected spaces around keyword / parameter equals
Line 128:24: E251 unexpected spaces around keyword / parameter equals
Line 129:19: E251 unexpected spaces around keyword / parameter equals
Line 129:21: E251 unexpected spaces around keyword / parameter equals
Line 129:24: E203 whitespace before ':'
Line 131:80: E501 line too long (91 > 79 characters)
Line 133:21: W291 trailing whitespace
Line 135:23: E203 whitespace before ':'
Line 139:28: E203 whitespace before ':'
Line 142:18: E211 whitespace before '('
Line 142:25: W291 trailing whitespace
Line 143:27: E251 unexpected spaces around keyword / parameter equals
Line 143:29: E251 unexpected spaces around keyword / parameter equals
Line 144:31: E251 unexpected spaces around keyword / parameter equals
Line 144:33: E251 unexpected spaces around keyword / parameter equals
Line 145:25: E251 unexpected spaces around keyword / parameter equals
Line 145:27: E251 unexpected spaces around keyword / parameter equals
Line 145:44: E203 whitespace before ':'
Line 146:45: E203 whitespace before ':'
Line 148:31: E203 whitespace before ':'
Line 150:13: E203 whitespace before ':'
Line 151:35: E203 whitespace before ':'
Line 152:44: E203 whitespace before ':'
Line 154:45: E203 whitespace before ':'
Line 156:21: E203 whitespace before ':'
Line 158:17: E203 whitespace before ':'
Line 160:73: E251 unexpected spaces around keyword / parameter equals
Line 160:75: E251 unexpected spaces around keyword / parameter equals
Line 160:80: E501 line too long (80 > 79 characters)
Line 161:80: E501 line too long (91 > 79 characters)
Line 166:17: E211 whitespace before '('
Line 166:24: W291 trailing whitespace
Line 167:26: E251 unexpected spaces around keyword / parameter equals
Line 167:28: E251 unexpected spaces around keyword / parameter equals
Line 167:34: E203 whitespace before ':'
Line 168:45: E203 whitespace before ':'
Line 170:31: E203 whitespace before ':'
Line 172:13: E203 whitespace before ':'
Line 181:1: W293 blank line contains whitespace
Line 182:5: E303 too many blank lines (2)
Line 185:21: E211 whitespace before '('
Line 185:28: E203 whitespace before ':'
Line 185:30: W291 trailing whitespace
Line 187:1: W293 blank line contains whitespace
Line 188:19: E211 whitespace before '('
Line 188:26: E203 whitespace before ':'
Line 191:21: E211 whitespace before '('
Line 191:28: E203 whitespace before ':'
Line 194:16: E211 whitespace before '('
Line 194:28: E203 whitespace before ':'
Line 197:29: E203 whitespace before ':'
Line 200:47: E203 whitespace before ':'
Line 203:13: E203 whitespace before ':'
Line 206:24: W291 trailing whitespace
Line 208:37: E203 whitespace before ':'
Line 212:80: E501 line too long (88 > 79 characters)
Line 216:39: E203 whitespace before ':'
Line 217:48: W291 trailing whitespace
Line 218:80: E501 line too long (83 > 79 characters)
Line 219:42: W291 trailing whitespace
Line 220:46: W291 trailing whitespace
Line 221:44: E202 whitespace before ')'
Line 222:80: E501 line too long (88 > 79 characters)
Line 225:1: W293 blank line contains whitespace
Line 226:5: E303 too many blank lines (2)
Line 226:34: E203 whitespace before ':'
Line 241:42: E203 whitespace before ':'
Line 242:43: E203 whitespace before ':'
Line 243:80: E501 line too long (96 > 79 characters)
Line 244:38: E203 whitespace before ':'
Line 248:48: E203 whitespace before ':'
Line 252:80: E501 line too long (94 > 79 characters)
Line 445:16: E211 whitespace before '('
Line 445:32: E203 whitespace before ':'

In the file source/train/DescrptLocFrame.py:

Line 93:21: W291 trailing whitespace
Line 122:12: E221 multiple spaces before operator
Line 122:27: E211 whitespace before '('

In the file source/train/DescrptSeA.py:

Line 113:21: W291 trailing whitespace
Line 143:12: E221 multiple spaces before operator
Line 143:27: E211 whitespace before '('

In the file source/train/DescrptSeR.py:

Line 97:21: W291 trailing whitespace
Line 126:12: E221 multiple spaces before operator
Line 126:27: E211 whitespace before '('

In the file source/train/Fitting.py:

Line 30:32: E203 whitespace before ':'
Line 31:80: E501 line too long (103 > 79 characters)
Line 31:104: W291 trailing whitespace

In the file source/train/Loss.py:

Line 12:1: E302 expected 2 blank lines, found 1
Line 12:21: E203 whitespace before ':'
Line 43:80: E501 line too long (83 > 79 characters)
Line 44:80: E501 line too long (84 > 79 characters)
Line 45:80: E501 line too long (84 > 79 characters)
Line 46:80: E501 line too long (86 > 79 characters)
Line 47:80: E501 line too long (96 > 79 characters)
Line 55:26: W291 trailing whitespace
Line 57:24: W291 trailing whitespace
Line 66:54: W291 trailing whitespace
Line 67:54: W291 trailing whitespace
Line 87:80: E501 line too long (163 > 79 characters)
Line 87:162: E202 whitespace before ')'
Line 88:80: E501 line too long (160 > 79 characters)
Line 88:159: E202 whitespace before ')'
Line 89:80: E501 line too long (161 > 79 characters)
Line 89:160: E202 whitespace before ')'
Line 90:16: E225 missing whitespace around operator
Line 90:76: E225 missing whitespace around operator
Line 90:80: E501 line too long (164 > 79 characters)
Line 90:163: E202 whitespace before ')'
Line 91:16: E225 missing whitespace around operator
Line 91:76: E225 missing whitespace around operator
Line 91:80: E501 line too long (164 > 79 characters)
Line 91:163: E202 whitespace before ')'

In the file source/train/Model.py:

Line 29:56: E251 unexpected spaces around keyword / parameter equals
Line 29:58: E251 unexpected spaces around keyword / parameter equals
Line 65:1: W293 blank line contains whitespace
Line 66:29: E211 whitespace before '('
Line 66:49: W291 trailing whitespace
Line 67:47: W291 trailing whitespace
Line 68:48: W291 trailing whitespace
Line 69:54: W291 trailing whitespace
Line 74:5: E303 too many blank lines (2)
Line 74:24: E211 whitespace before '('
Line 75:37: W291 trailing whitespace
Line 76:35: W291 trailing whitespace
Line 77:37: W291 trailing whitespace
Line 80:31: E251 unexpected spaces around keyword / parameter equals
Line 80:33: E251 unexpected spaces around keyword / parameter equals
Line 80:39: E203 whitespace before ':'
Line 80:41: W291 trailing whitespace
Line 82:80: E501 line too long (100 > 79 characters)
Line 121:38: E251 unexpected spaces around keyword / parameter equals
Line 121:40: E251 unexpected spaces around keyword / parameter equals
Line 122:38: E251 unexpected spaces around keyword / parameter equals
Line 122:40: E251 unexpected spaces around keyword / parameter equals
Line 133:52: W291 trailing whitespace
Line 135:52: E251 unexpected spaces around keyword / parameter equals
Line 135:54: E251 unexpected spaces around keyword / parameter equals
Line 135:72: W291 trailing whitespace

In the file source/train/Trainer.py:

Line 44:1: E402 module level import not at top of file
Line 44:80: E501 line too long (87 > 79 characters)
Line 142:38: E271 multiple spaces after keyword
Line 142:74: E203 whitespace before ':'
Line 144:13: E203 whitespace before ':'
Line 184:36: W291 trailing whitespace
Line 191:42: E203 whitespace before ':'
Line 193:71: E251 unexpected spaces around keyword / parameter equals
Line 193:73: E251 unexpected spaces around keyword / parameter equals
Line 193:80: E501 line too long (83 > 79 characters)
Line 194:77: E251 unexpected spaces around keyword / parameter equals
Line 194:79: E251 unexpected spaces around keyword / parameter equals
Line 194:80: E501 line too long (94 > 79 characters)
Line 196:35: E221 multiple spaces before operator
Line 196:80: E501 line too long (91 > 79 characters)
Line 197:41: E221 multiple spaces before operator
Line 197:80: E501 line too long (110 > 79 characters)
Line 198:43: E221 multiple spaces before operator
Line 198:80: E501 line too long (99 > 79 characters)
Line 199:42: E221 multiple spaces before operator
Line 202:31: E211 whitespace before '('
Line 202:61: W291 trailing whitespace
Line 203:60: W291 trailing whitespace
Line 204:66: W291 trailing whitespace
Line 205:59: W291 trailing whitespace
Line 213:65: W291 trailing whitespace
Line 348:53: E203 whitespace before ':'
Line 350:33: E203 whitespace before ':'
Line 353:80: E501 line too long (94 > 79 characters)
Line 354:31: E203 whitespace before ':'
Line 355:80: E501 line too long (90 > 79 characters)
Line 356:53: E203 whitespace before ':'
Line 420:49: E203 whitespace before ':'
Line 425:80: E501 line too long (105 > 79 characters)
Line 426:27: E203 whitespace before ':'
Line 427:80: E501 line too long (101 > 79 characters)
Line 427:102: W291 trailing whitespace
Line 428:49: E203 whitespace before ':'
Line 434:60: E502 the backslash is redundant between brackets
Line 435:61: E502 the backslash is redundant between brackets
Line 436:62: E502 the backslash is redundant between brackets
Line 437:64: E502 the backslash is redundant between brackets
Line 442:60: E502 the backslash is redundant between brackets
Line 443:61: E502 the backslash is redundant between brackets
Line 444:62: E502 the backslash is redundant between brackets
Line 445:64: E502 the backslash is redundant between brackets
Line 446:66: W291 trailing whitespace

In the file source/train/common.py:

Line 3:1: E302 expected 2 blank lines, found 1
Line 3:30: W291 trailing whitespace
Line 4:31: W291 trailing whitespace
Line 5:32: E251 unexpected spaces around keyword / parameter equals
Line 5:34: E251 unexpected spaces around keyword / parameter equals
Line 5:41: W291 trailing whitespace
Line 6:30: E251 unexpected spaces around keyword / parameter equals
Line 6:32: E251 unexpected spaces around keyword / parameter equals
Line 6:39: W291 trailing whitespace
Line 7:35: E251 unexpected spaces around keyword / parameter equals
Line 7:37: E251 unexpected spaces around keyword / parameter equals
Line 8:32: E251 unexpected spaces around keyword / parameter equals
Line 8:34: E251 unexpected spaces around keyword / parameter equals
Line 8:37: E203 whitespace before ':'
Line 9:43: W291 trailing whitespace
Line 11:43: W291 trailing whitespace
Line 14:5: E124 closing bracket does not match visual indentation
Line 15:1: W293 blank line contains whitespace
Line 30:13: E203 whitespace before ':'

In the file source/train/train.py:

Line 15:1: E402 module level import not at top of file
Line 17:1: E402 module level import not at top of file
Line 99:80: E501 line too long (102 > 79 characters)

always-be-closing · 2019-08-10T14:11:09Z

41882e8 Codacy/PR Quality Review — Codacy was unable to analyse your pull request. Details

api update from amcadmus

add LSF support and bugfix

Han Wang and others added 18 commits July 31, 2019 18:58

fix bug in parsing mulit types

bf24e0e

implement new data

f035dc5

implement get_batch, get_test. fix bugs.

62d919a

fix bug in shuffle data. get numb batches

2c52f56

shape should be list of length 2, fix bug in test

2dfaf4b

backup data system

15e0003

load test when get batch or test

7251d37

floating point prec control in tests

3274169

fix bugs

68b2617

replicate type in Data

cc5502e

find libtensorflow_framework.so.1 for cpp

e4ebd6a

when using TensorFlow >= 1.14

using new data interface

1ab6166

input box as a vector. rename input tensors: starting with t_

4ee3827

explicitly set the precision of floating point numbers in setup.py

dbf9522

explicitly set rcond. save the result of stat in Model

d6cecb6

fix bugs in tests.

8cc3b02

Merge pull request #60 from njzjz/patch-1

ddfe8b2

find libtensorflow_framework.so.1 for cpp

Merge pull request #61 from amcadmus/devel

41882e8

refactoring the Data and DataSystem

pull Bot added the ⤵️ pull label Aug 10, 2019

pr-triage Bot added the PR: unreviewed label Aug 10, 2019

pull Bot merged commit 41882e8 into njzjz:devel Aug 10, 2019

pr-triage Bot added the PR: merged label Aug 10, 2019

pull-request-size Bot added the size/XXL label Aug 10, 2019

njzjz pushed a commit that referenced this pull request Mar 22, 2021

Merge pull request #19 from amcadmus/api

71dc7a8

api update from amcadmus

njzjz pushed a commit that referenced this pull request Sep 21, 2023

Merge pull request #19 from njzjz/lsf

6f06104

add LSF support and bugfix

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[pull] devel from deepmodeling:devel#19

[pull] devel from deepmodeling:devel#19
pull[bot] merged 18 commits intonjzjz:develfrom
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