skpkg: apply pre-commit hooks with no manual edits

[zmx27]

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[zmx27]

@sbillinge ready for review.
Here's the work that still needs to be done:

check yaml...........................................(no files to check)Skipped
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
check for case conflicts.................................................Passed
check for merge conflicts................................................Passed
check toml...............................................................Passed
check for added large files..............................................Passed
black....................................................................Passed
flake8...................................................................Failed
- hook id: flake8
- exit code: 1

<unknown>:116: SyntaxWarning: invalid escape sequence '\s'
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doc/manual/source/conf.py:7:80: E501 line too long (80 > 79 characters)
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doc/manual/source/conf.py:61:1: E402 module level import not at top of file
doc/manual/source/conf.py:88:80: E501 line too long (80 > 79 characters)
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doc/manual/source/conf.py:196:5: E265 block comment should start with '# '
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src/diffpy/confutils/__init__.py:17:1: F401 'diffpy.confutils.config.ConfigBase' imported but unused
src/diffpy/confutils/__init__.py:20:1: F401 'diffpy.srxplanar.version.__version__' imported but unused
src/diffpy/confutils/config.py:26:1: F401 're' imported but unused
src/diffpy/confutils/config.py:27:1: F401 'sys' imported but unused
src/diffpy/confutils/config.py:29:1: F401 'functools.partial' imported but unused
src/diffpy/confutils/config.py:33:1: E722 do not use bare 'except'
src/diffpy/confutils/config.py:36:1: F401 'diffpy.confutils.tools._configPropertyR' imported but unused
src/diffpy/confutils/config.py:36:1: F401 'diffpy.confutils.tools._configPropertyRad' imported but unused
src/diffpy/confutils/config.py:36:1: F401 'diffpy.confutils.tools._configPropertyRW' imported but unused
src/diffpy/confutils/config.py:36:1: F401 'diffpy.confutils.tools.str2bool' imported but unused
src/diffpy/confutils/config.py:52:80: E501 line too long (80 > 79 characters)
src/diffpy/confutils/config.py:132:80: E501 line too long (83 > 79 characters)
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src/diffpy/confutils/config.py:232:80: E501 line too long (109 > 79 characters)
src/diffpy/confutils/config.py:269:9: F841 local variable 'rv' is assigned to but never used
src/diffpy/confutils/config.py:296:21: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:298:17: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:320:15: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:322:52: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:503:21: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:525:21: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:579:21: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:611:21: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:613:17: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:619:23: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:620:24: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:646:61: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:649:69: E711 comparison to None should be 'if cond is not None:'
src/diffpy/confutils/config.py:715:55: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:760:21: E711 comparison to None should be 'if cond is None:'
src/diffpy/confutils/config.py:769:80: E501 line too long (82 > 79 characters)
src/diffpy/confutils/config.py:775:80: E501 line too long (80 > 79 characters)
src/diffpy/confutils/tools.py:52:48: F821 undefined name 'nm'
src/diffpy/confutils/tools.py:53:55: F821 undefined name 'nm'
src/diffpy/confutils/tools.py:54:41: F821 undefined name 'nm'
src/diffpy/confutils/tools.py:116:26: W605 invalid escape sequence '\s'
src/diffpy/confutils/tools.py:116:30: W605 invalid escape sequence '\s'
src/diffpy/confutils/tools.py:159:5: E722 do not use bare 'except'
src/diffpy/confutils/tools.py:178:5: E722 do not use bare 'except'
src/diffpy/srxplanar/__init__.py:17:1: F401 'diffpy.srxplanar.srxplanar.SrXplanar' imported but unused
src/diffpy/srxplanar/__init__.py:18:1: F401 'diffpy.srxplanar.srxplanarconfig.SrXplanarConfig' imported but unused
src/diffpy/srxplanar/__init__.py:21:1: F401 'diffpy.srxplanar.version.__version__' imported but unused
src/diffpy/srxplanar/calculate.py:18:1: F401 'scipy.ndimage.morphology as snm' imported but unused
src/diffpy/srxplanar/calculate.py:19:1: F401 'scipy.sparse as ssp' imported but unused
src/diffpy/srxplanar/calculate.py:56:80: E501 line too long (108 > 79 characters)
src/diffpy/srxplanar/calculate.py:109:17: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/calculate.py:117:9: F841 local variable 'maskedmatrix' is assigned to but never used
src/diffpy/srxplanar/calculate.py:118:80: E501 line too long (96 > 79 characters)
src/diffpy/srxplanar/calculate.py:162:16: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/calculate.py:254:80: E501 line too long (80 > 79 characters)
src/diffpy/srxplanar/calculate.py:280:80: E501 line too long (80 > 79 characters)
src/diffpy/srxplanar/calculate.py:325:80: E501 line too long (107 > 79 characters)
src/diffpy/srxplanar/loadimage.py:18:1: F401 'sys' imported but unused
src/diffpy/srxplanar/loadimage.py:22:1: F401 'tifffile.imsave as saveImage' imported but unused
src/diffpy/srxplanar/loadimage.py:33:1: E722 do not use bare 'except'
src/diffpy/srxplanar/loadimage.py:91:17: E722 do not use bare 'except'
src/diffpy/srxplanar/loadimage.py:152:49: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/loadimage.py:153:49: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/loadimage.py:155:51: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/loadimage.py:158:51: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:17:1: F401 'scipy.sparse as ssp' imported but unused
src/diffpy/srxplanar/mask.py:26:1: E722 do not use bare 'except'
src/diffpy/srxplanar/mask.py:34:9: E722 do not use bare 'except'
src/diffpy/srxplanar/mask.py:77:80: E501 line too long (100 > 79 characters)
src/diffpy/srxplanar/mask.py:78:80: E501 line too long (88 > 79 characters)
src/diffpy/srxplanar/mask.py:82:46: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:120:32: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:124:49: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:126:43: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:148:42: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:170:19: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:172:48: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:173:45: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:183:42: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:198:41: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:225:52: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:226:43: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/mask.py:269:56: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/mask.py:273:33: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/mask.py:276:28: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/saveresults.py:19:1: F401 'scipy.io' imported but unused
src/diffpy/srxplanar/saveresults.py:51:58: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/saveresults.py:102:34: F821 undefined name 'path'
src/diffpy/srxplanar/saveresults.py:110:34: F821 undefined name 'path'
src/diffpy/srxplanar/saveresults.py:127:16: F821 undefined name 'numpy'
src/diffpy/srxplanar/saveresults.py:127:28: F821 undefined name 'numpy'
src/diffpy/srxplanar/saveresults.py:127:55: F821 undefined name 'numpy'
src/diffpy/srxplanar/saveresults.py:142:12: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/saveresults.py:145:20: F821 undefined name 'numpy'
src/diffpy/srxplanar/saveresults.py:160:20: F821 undefined name 'numpy'
src/diffpy/srxplanar/selfcalibrate.py:1:1: F401 'os' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:5:1: F401 'scipy as sp' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.brent' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_bfgs' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_cg' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_l_bfgs_b' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_powell' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_slsqp' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.fmin_tnc' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.golden' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:7:1: F401 'scipy.optimize.minimize_scalar' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:23:5: F401 'PySide' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:29:1: E722 do not use bare 'except'
src/diffpy/srxplanar/selfcalibrate.py:32:9: F401 'PyQt4' imported but unused
src/diffpy/srxplanar/selfcalibrate.py:35:5: E722 do not use bare 'except'
src/diffpy/srxplanar/selfcalibrate.py:236:22: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/selfcalibrate.py:242:22: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/selfcalibrate.py:319:9: F841 local variable 'prv' is assigned to but never used
src/diffpy/srxplanar/selfcalibrate.py:398:42: E713 test for membership should be 'not in'
src/diffpy/srxplanar/srxplanar.py:21:1: F401 'scipy.sparse as ssp' imported but unused
src/diffpy/srxplanar/srxplanar.py:51:28: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:103:24: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:105:26: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:107:24: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:112:25: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:112:48: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:126:31: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:128:23: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:130:24: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanar.py:130:64: F821 undefined name 'unicode'
src/diffpy/srxplanar/srxplanar.py:139:80: E501 line too long (82 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:143:80: E501 line too long (80 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:146:80: E501 line too long (86 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:155:38: F821 undefined name 'unicode'
src/diffpy/srxplanar/srxplanar.py:157:27: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:157:49: E712 comparison to True should be 'if cond is True:' or 'if cond:'
src/diffpy/srxplanar/srxplanar.py:165:21: E712 comparison to True should be 'if cond is True:' or 'if cond:'
src/diffpy/srxplanar/srxplanar.py:167:27: E712 comparison to True should be 'if cond is True:' or 'if cond:'
src/diffpy/srxplanar/srxplanar.py:193:80: E501 line too long (96 > 79 characters)
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src/diffpy/srxplanar/srxplanar.py:236:80: E501 line too long (80 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:239:80: E501 line too long (86 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:242:80: E501 line too long (124 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:243:80: E501 line too long (99 > 79 characters)
src/diffpy/srxplanar/srxplanar.py:246:56: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:249:25: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:261:29: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:318:55: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:320:50: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:325:16: E711 comparison to None should be 'if cond is None:'
src/diffpy/srxplanar/srxplanar.py:328:29: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanarconfig.py:16:1: F401 'argparse' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:17:1: F401 'os' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:18:1: F401 're' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:19:1: F401 'sys' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:20:1: F401 'configparser.ConfigParser' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:21:1: F401 'functools.partial' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:26:1: F401 'diffpy.confutils.tools._configPropertyR' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:26:1: F401 'diffpy.confutils.tools._configPropertyRW' imported but unused
src/diffpy/srxplanar/srxplanarconfig.py:33:80: E501 line too long (85 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:59:80: E501 line too long (97 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:116:80: E501 line too long (104 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:127:80: E501 line too long (91 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:359:80: E501 line too long (158 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:388:80: E501 line too long (117 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:402:80: E501 line too long (99 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:404:80: E501 line too long (81 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:417:80: E501 line too long (112 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:464:80: E501 line too long (131 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:475:80: E501 line too long (130 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:511:80: E501 line too long (89 > 79 characters)
src/diffpy/srxplanar/srxplanarconfig.py:546:61: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/srxplanarconfig.py:548:69: E711 comparison to None should be 'if cond is not None:'
src/diffpy/srxplanar/tifffile.py:857:20: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1218:20: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1225:28: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1295:12: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1330:12: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1456:37: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1903:12: E713 test for membership should be 'not in'
src/diffpy/srxplanar/tifffile.py:1943:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1944:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1945:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1946:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1947:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1948:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:1949:40: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:2118:13: E741 ambiguous variable name 'l'
src/diffpy/srxplanar/tifffile.py:2618:5: E741 ambiguous variable name 'l'
src/diffpy/srxplanar/tifffile.py:2763:28: W605 invalid escape sequence '\d'
src/diffpy/srxplanar/tifffile.py:3853:5: E731 do not assign a lambda expression, use a def

isort....................................................................Passed
nbstripout...........................................(no files to check)Skipped
Prevent Commit to Main Branch............................................Passed
codespell................................................................Failed
- hook id: codespell
- exit code: 65

src/diffpy/srxplanar/calculate.py:126: hould ==> hold, should
src/diffpy/srxplanar/calculate.py:127: retrun ==> return
src/diffpy/srxplanar/calculate.py:174: retrun ==> return
src/diffpy/srxplanar/calculate.py:185: hould ==> hold, should
src/diffpy/srxplanar/calculate.py:186: retrun ==> return
src/diffpy/srxplanar/calculate.py:199: loacl ==> local
src/diffpy/srxplanar/calculate.py:201: hould ==> hold, should
src/diffpy/srxplanar/mask.py:51: dymanic ==> dynamic
src/diffpy/srxplanar/mask.py:107: parma ==> param
src/diffpy/srxplanar/mask.py:259: fliped ==> flipped
src/diffpy/confutils/tools.py:67: truned ==> turned
src/diffpy/confutils/tools.py:69: opitons ==> options
src/diffpy/confutils/tools.py:108: opitons ==> options
src/diffpy/confutils/config.py:209: filp ==> flip
src/diffpy/confutils/config.py:547: comming ==> coming
src/diffpy/confutils/config.py:644: specfied ==> specified
src/diffpy/confutils/config.py:655: compatiable ==> compatible
src/diffpy/confutils/config.py:666: wirte ==> write
src/diffpy/confutils/config.py:710: writen ==> written
src/diffpy/confutils/config.py:718: wirte ==> write
src/diffpy/srxplanar/selfcalibrate.py:373: automaticly ==> automatically
src/diffpy/srxplanar/tifffile.py:957: modul ==> module
src/diffpy/srxplanar/tifffile.py:958: modul ==> module
src/diffpy/srxplanar/tifffile.py:3424: aquire ==> acquire
doc/examples/KFe2As2-00838_twotheta.chi:1: configration ==> configuration
src/diffpy/srxplanar/saveresults.py:66: orginal ==> original
src/diffpy/srxplanar/srxplanarconfig.py:88: Expeiment ==> Experiment
src/diffpy/srxplanar/srxplanarconfig.py:88: gropu ==> group
src/diffpy/srxplanar/srxplanarconfig.py:240: filp ==> flip
src/diffpy/srxplanar/srxplanarconfig.py:250: filp ==> flip
src/diffpy/srxplanar/srxplanarconfig.py:417: automaticly ==> automatically
src/diffpy/srxplanar/srxplanarconfig.py:483: configration ==> configuration

prettier.................................................................Passed
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