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How do we approach the linting checks

See original GitHub issue

I ran pylint on pymbar so we only get warnings and errors (omitted style lint and the output from old_mbar.py and tests).

pylint --disable=all --enable=W,E pymbar/ --disable=W0511

This is the output

************* Module pymbar
pymbar/__init__.py:31:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/__init__.py:40:0: W0702: No exception type(s) specified (bare-except)
pymbar/__init__.py:39:4: W0406: Module import itself (import-self)
************* Module pymbar.utils
pymbar/utils.py:26:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/utils.py:374:4: W0107: Unnecessary pass statement (unnecessary-pass)
pymbar/utils.py:383:4: W0107: Unnecessary pass statement (unnecessary-pass)
pymbar/utils.py:392:4: W0107: Unnecessary pass statement (unnecessary-pass)
pymbar/utils.py:401:4: W0107: Unnecessary pass statement (unnecessary-pass)
************* Module pymbar.mbar
pymbar/mbar.py:40:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/mbar.py:418:100: W1619: division w/o __future__ statement (old-division)
pymbar/mbar.py:467:20: W0612: Unused variable 'eigevec' (unused-variable)
pymbar/mbar.py:564:33: W0613: Unused argument 'warning_cutoff' (unused-argument)
pymbar/mbar.py:982:8: W0612: Unused variable 'N' (unused-variable)
pymbar/mbar.py:1093:8: W0612: Unused variable 'K' (unused-variable)
pymbar/mbar.py:1113:8: W0612: Unused variable 'expectations' (unused-variable)
pymbar/mbar.py:1113:22: W0612: Unused variable 'uncertainties' (unused-variable)
pymbar/mbar.py:1113:37: W0612: Unused variable 'covariances' (unused-variable)
pymbar/mbar.py:1190:8: W0612: Unused variable 'Deltaf_ij' (unused-variable)
pymbar/mbar.py:1190:19: W0612: Unused variable 'dDeltaf_ij' (unused-variable)
pymbar/mbar.py:1258:11: W0612: Unused variable 'N' (unused-variable)
pymbar/mbar.py:1455:13: W0612: Unused variable 'U' (unused-variable)
pymbar/mbar.py:40:0: W0611: Unused import math (unused-import)
pymbar/mbar.py:43:0: W0611: Unused import warnings (unused-import)
************* Module pymbar.utils_for_testing
pymbar/utils_for_testing.py:22:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/utils_for_testing.py:76:4: W0612: Unused variable 'x_n' (unused-variable)
pymbar/utils_for_testing.py:88:4: W0612: Unused variable 'x_n' (unused-variable)
************* Module pymbar.exp
pymbar/exp.py:47:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/exp.py:118:13: W1619: division w/o __future__ statement (old-division)
pymbar/exp.py:121:19: W1619: division w/o __future__ statement (old-division)
pymbar/exp.py:195:14: W1619: division w/o __future__ statement (old-division)
pymbar/exp.py:195:44: W1619: division w/o __future__ statement (old-division)
************* Module pymbar.confidenceintervals
pymbar/confidenceintervals.py:22:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/confidenceintervals.py:42:10: W1619: division w/o __future__ statement (old-division)
pymbar/confidenceintervals.py:92:4: W0622: Redefining built-in 'sum' (redefined-builtin)
pymbar/confidenceintervals.py:96:14: W1619: division w/o __future__ statement (old-division)
pymbar/confidenceintervals.py:108:33: W1619: division w/o __future__ statement (old-division)
pymbar/confidenceintervals.py:262:28: W1619: division w/o __future__ statement (old-division)
pymbar/confidenceintervals.py:265:43: W1619: division w/o __future__ statement (old-division)
pymbar/confidenceintervals.py:270:12: E1101: Module 'scipy.special' has no 'erf' member (no-member)
pymbar/confidenceintervals.py:311:4: W0612: Unused variable 'aveerr' (unused-variable)
************* Module pymbar.timeseries
pymbar/timeseries.py:58:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/timeseries.py:318:12: W1619: division w/o __future__ statement (old-division)
pymbar/timeseries.py:321:12: W1619: division w/o __future__ statement (old-division)
pymbar/timeseries.py:451:4: W0612: Unused variable 'g' (unused-variable)
pymbar/timeseries.py:611:12: W1619: division w/o __future__ statement (old-division)
pymbar/timeseries.py:713:18: W1638: range built-in referenced when not iterating (range-builtin-not-iterating)
pymbar/timeseries.py:718:18: W1633: round built-in referenced (round-builtin)
pymbar/timeseries.py:719:20: W1633: round built-in referenced (round-builtin)
pymbar/timeseries.py:797:20: W1619: division w/o __future__ statement (old-division)
pymbar/timeseries.py:910:28: W1619: division w/o __future__ statement (old-division)
************* Module pymbar.mbar_solvers
pymbar/mbar_solvers.py:2:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/mbar_solvers.py:316:18: E1307: Argument '.ndarray' does not match format type 'g' (bad-string-format-type)
pymbar/mbar_solvers.py:316:18: E1307: Argument '.ndarray' does not match format type 'g' (bad-string-format-type)
pymbar/mbar_solvers.py:521:8: W0612: Unused variable 'k' (unused-variable)
pymbar/mbar_solvers.py:554:21: W0612: Unused variable 'all_results' (unused-variable)
************* Module pymbar.bar
pymbar/bar.py:49:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/bar.py:121:4: W0702: No exception type(s) specified (bare-except)
pymbar/bar.py:138:4: W0702: No exception type(s) specified (bare-except)
pymbar/bar.py:262:19: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:281:62: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:294:21: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:310:34: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:451:-1: W0105: String statement has no effect (pointless-string-statement)
pymbar/bar.py:482:15: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:485:24: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:485:44: W1619: division w/o __future__ statement (old-division)
pymbar/bar.py:50:0: W0611: Unused import numpy.linalg (unused-import)
************* Module pymbar.pmf
pymbar/pmf.py:24:0: W1618: import missing `from __future__ import absolute_import` (no-absolute-import)
pymbar/pmf.py:367:27: E1101: Module 'numpy.random' has no 'RandomState' member (no-member)
pymbar/pmf.py:517:48: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:636:22: W0212: Access to a protected member _computeUnnormalizedLogWeights of a client class (protected-access)
pymbar/pmf.py:699:16: W0612: Unused variable 'df_i' (unused-variable)
pymbar/pmf.py:885:36: W0622: Redefining built-in 'type' (redefined-builtin)
pymbar/pmf.py:1022:30: W0212: Access to a protected member _computeUnnormalizedLogWeights of a client class (protected-access)
pymbar/pmf.py:1034:31: W0212: Access to a protected member _computeAsymptoticCovarianceMatrix of a client class (protected-access)
pymbar/pmf.py:1373:43: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1266:8: W0612: Unused variable 'K' (unused-variable)
pymbar/pmf.py:1350:24: W0612: Unused variable 'Neff' (unused-variable)
pymbar/pmf.py:1361:12: W0612: Unused variable 'maxgc' (unused-variable)
pymbar/pmf.py:1362:12: W0612: Unused variable 'meangc' (unused-variable)
pymbar/pmf.py:1481:38: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1482:38: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1529:12: W0612: Unused variable 'cold' (unused-variable)
pymbar/pmf.py:1626:26: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1633:36: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1579:12: W0613: Unused argument 'nspline' (unused-argument)
pymbar/pmf.py:1580:12: W0613: Unused argument 'kdegree' (unused-argument)
pymbar/pmf.py:1583:12: W0613: Unused argument 'xrangei' (unused-argument)
pymbar/pmf.py:1584:12: W0613: Unused argument 'xrangeij' (unused-argument)
pymbar/pmf.py:1586:12: W0613: Unused argument 'dlogprior' (unused-argument)
pymbar/pmf.py:1587:12: W0613: Unused argument 'ddlogprior' (unused-argument)
pymbar/pmf.py:1761:35: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1674:12: W0613: Unused argument 'kdegree' (unused-argument)
pymbar/pmf.py:1678:12: W0613: Unused argument 'xrangeij' (unused-argument)
pymbar/pmf.py:1679:12: W0613: Unused argument 'logprior' (unused-argument)
pymbar/pmf.py:1681:12: W0613: Unused argument 'ddlogprior' (unused-argument)
pymbar/pmf.py:1865:47: W0640: Cell variable i defined in loop (cell-var-from-loop)
pymbar/pmf.py:1865:64: W0640: Cell variable j defined in loop (cell-var-from-loop)
pymbar/pmf.py:1870:39: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1881:42: W1619: division w/o __future__ statement (old-division)
pymbar/pmf.py:1793:12: W0613: Unused argument 'w_n' (unused-argument)
pymbar/pmf.py:1794:12: W0613: Unused argument 'x_n' (unused-argument)
pymbar/pmf.py:1798:12: W0613: Unused argument 'xrange' (unused-argument)
pymbar/pmf.py:1799:12: W0613: Unused argument 'xrangei' (unused-argument)
pymbar/pmf.py:1801:12: W0613: Unused argument 'logprior' (unused-argument)
pymbar/pmf.py:1802:12: W0613: Unused argument 'dlogprior' (unused-argument)
pymbar/pmf.py:1893:25: W0613: Unused argument 'spline_parameters' (unused-argument)
pymbar/pmf.py:756:29: E0203: Access to member 'kde' before its definition line 762 (access-member-before-definition)
pymbar/pmf.py:355:8: W0201: Attribute 'pmf_type' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:363:8: W0201: Attribute 'u_n' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:373:8: W0201: Attribute 'nbootstraps' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:378:8: W0201: Attribute 'pmf_function' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:851:20: W0201: Attribute 'pmf_function' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:386:8: W0201: Attribute 'mc_data' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1315:8: W0201: Attribute 'mc_data' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:390:12: W0201: Attribute 'histogram_datas' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:401:12: W0201: Attribute 'dims' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:402:12: W0201: Attribute 'histogram_parameters' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:406:12: W0201: Attribute 'kdes' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:430:12: W0201: Attribute 'bspline' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:596:12: W0201: Attribute 'bspline' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:785:20: W0201: Attribute 'bspline' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:848:20: W0201: Attribute 'bspline' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:431:12: W0201: Attribute 'pmf_functions' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:433:12: W0201: Attribute 'spline_parameters' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:595:12: W0201: Attribute 'bspline_derivatives' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:597:12: W0201: Attribute 'fkbias' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:640:12: W0201: Attribute 'w_n' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:641:12: W0201: Attribute 'w_n' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:643:12: W0201: Attribute 'w_kn' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:743:20: W0201: Attribute 'histogram_data' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:762:20: W0201: Attribute 'kde' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:863:20: W0201: Attribute 'aic' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:868:20: W0201: Attribute 'bic' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1325:8: W0201: Attribute 'naccept' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1568:12: W0201: Attribute 'naccept' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1328:8: W0201: Attribute 'first_step' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1530:12: W0201: Attribute 'first_step' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1527:12: W0201: Attribute 'previous_logposterior' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1567:12: W0201: Attribute 'previous_logposterior' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1532:12: W0201: Attribute 'newspline' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1535:8: W0201: Attribute 'cold' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1566:12: W0201: Attribute 'cold' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1659:8: W0201: Attribute 'bspline_expf' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1660:8: W0201: Attribute 'bspline_pF' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1786:8: W0201: Attribute 'bspline_gkquad' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1787:8: W0201: Attribute 'bspline_pE' defined outside __init__ (attribute-defined-outside-init)
pymbar/pmf.py:1949:-1: W0105: String statement has no effect (pointless-string-statement)
pymbar/pmf.py:27:0: W0611: Unused numpy.linalg imported as linalg (unused-import)
pymbar/pmf.py:31:0: W0611: Unused kn_to_n imported from pymbar.utils (unused-import)
pymbar/pmf.py:31:0: W0611: Unused check_w_normalized imported from pymbar.utils (unused-import)
pymbar/pmf.py:42:0: W0611: Unused import pdb (unused-import)

I can get rid of most of that noise, but there are some non trivial changes that will require the intervention of somebody more familiar with the code. Should I proceed with the PR anyway?

Issue Analytics

State:
Created 4 years ago
Comments:5 (2 by maintainers)

Top GitHub Comments

1reaction

mrshirtscommented, Feb 28, 2020

Once I remove all from future import * lines, we should have significantly less noise there. We can also add linting to our CI in a non-blocking way.

OK, start a PR with these, rerun lint on that PR, and I will take a look the remaining ones this weekend.

0reactions

jaimergpcommented, Mar 19, 2020

Addressed by #367

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