Preparing 1.4.2 by Didou09 · Pull Request #266 · ToFuProject/tofu

Didou09 · 2019-11-20T13:28:45Z

Main changes:

Python 2.7 is not supported anymore
Python 3.6 and 3.7 are supported
Several changes to try and make installation easier (on clusters, windows, mac....) and less verbose for users
More explicit names for default saved configurations
Major bug fix in one of the methods for computing synthetic signal
Minor bug fixes in interactive figures
Minor bug fixes in Plasma2D interpolation
New configuration (ITER) available
First version of a class handling 2D XRay bragg spectrometers
First tools for magnetic field line tracing available on WEST
Better documentation, more ressources
More informative error messages
extra tools for computing LOS length, closest point to magnetic axis...
Better PEP8 compliance

Detailed changes:

Installation / portability:

Bug fixes for installation on ITER and Gateway clusters pip install dependencies missing #250
Easier installation on Mac Mac OSX - OpenMP - reduction #183 (requirements.txt)
Removed explicit compiler specification in setup.py for more flexibility
When sub-packages imas2tofu or mag are missing, the warning is much more concise, but the error traceback is still accessible in a hidden dictionnary for developpers Less verbose warnings for missing sub-packages #243
python setup.py clean now doesn't cythonize
Dropped python 2 support: Change default separator in to_dict() from '_' to '.' #228
- merged _GG02 and _GG03 into the _GG file
- no longer being tested in travis
- no longer packaged in conda
- updated README file accordingly
- dropped funcsigs dependency
- made necessary changes in setup.py
- benchmarks/calc_signal_benchmark.py: now working with python 3

Bug fixes:

Major bug fix in LOS_calc_signal() for computing the synthetic signal of a LOS camera using a particular algortihm : method='sum', minimize='hybrid', ani=True, Bug in _GG_LOS_calc_signal() #247 Possible bug / inconsistency in _GG.LOS_calc_signal() #255
Major bug fix in LOS_get_sample() when minimize='hybrid' and minimize='memory' the limits were not set correctly
in some cases the formula for sampling a LOS was wrong (los_get_sample_core_var_res).
Minor bug fixes in interactive figures when t=None was used (the interactivity was lost due to wrong formatting of the time array)
Minor bug fixed in Plasma 2D interpolation (interp_t was not being set), imporved error messages Plasma2D interpolation failing #209
Removed unused variable in _Ves_get_sampleS (_GG), in _core.py In _core.py: set of variables related issues #190
Gave more explicit names to some variables in _core.py to avoid bugs/typos (eg. I to current) In _core.py: unused variable #186
Removed a secondary init function for the class tf.geom.CoilsPF Two init functions for CoilPF #187
_checkformat_inputs_dgeom now is a function of Rays class
Change default separator in to_dict() from '_' to '.', Change default separator in to_dict() from '_' to '.' #228
Rays.calc_kInOut_IsoFlux() is now more flexible (accepts 3d np.arrays as well as lists of np.ndarrays), Make Rays.calc_kInOut_IsoFlux() more robust vs lPoly arg #188
repr() is now overloaded in a more robust way so it falls back to printing the class if get_summary() fails to avoid crashing in debug mode Bug was not there, but __repr__() now more robust in debug #242

Documentation:

Updated information about support of python version
Added slides of talk given at PyConFR 2019 conference
Added a gallery in our documentation with 3 different tutorials:
- 5 minutes tutorial to show to create a geometry and 1D/2D cameras
- Guide on how to create your own Geometry from scratch (vacuum vessel, structures, etc.)
- How to compute the signal received by a camera using a synthetic signal.
  For all of these tutorials, you can see directly the codes and the
  resulting images, and you can get the source code or download it as a
  Jupyter notebook!
Minor changes to the web doc: updated install instructions to be "cleaner"
now in rST and not HTML), small changes in the navigation bar.
Guide on how to contribute to ToFu.

New features:

First version of magnetic field line tracing (for WEST only so far, to be improved) magfieldlines : add argument to choose start point #213 magfieldline should plot config with reversed x axis #235
First version of 2D XRay Bragg spectrometers for synthetic diagnostics, modelling the diagnotics geometry and providing 2d spectral fitting routines (to be improved) Issue202 spectro x2 d crystal #267
When computing a signal LOS_calc_signal emissivity function can now return
a 1D array if t=None Plotting signal with t=None #217 Re-format output of user-defined signal function when t=None #252
Three functions added to tf.geom.Rays: Tools for CamLOS closest points #211
- calc_length_in_isoflux(): compute the length inside a set of isoflux surfaces of each LOS
- calc_min_geom_radius(): compute the minimal geometrical radius (impact parameter) of each LOS
- calc_min_rho_from_Plasma2D(): compute the minimum normalized radius (or any field with a minimum on the axis) for each LOS
New ITER configuration available! Integrate ITER new config #220 Wrong naming of PFC files for B4 configuration #227
More explicit names for default configurations Harmonize default Config names #264

Contributors:

Many thanks to all developpers:

Didier Vezinet (@Didou09)
Laura Mendoza (@lasofivec)
Florian Le Bourdais (@flothesof)
Jorge Morales (@jmoralesFusion)
Koyo Munechika (@munechika-koyo)
Louwrens Van Dellen (@Louwrensth)

What's next (indicative):

Migrating from nosetests (ongoing for @lasofivec : issues nosetests not running on windows #95 and Moving on from nosetests... #232 )
Easier binary and source installs from pip and conda for all platforms, including unit tests on alla platforms (ongoing for @lasofivec and @flothesof : issue pip wheel : make sure wheel creation works out-of-the box #92 and Travis build on MacOS and Windows (for unit tests, conda packages and pip wheels) #259 )
Solid angles for Volume-Of-Sight and radiative heat loads computation (ongoing for @lasofivec : Issues Solid angles particle - NxM points vectorized version without unit vector - exact and approx #71, Solid angles particle - NxM points vectorized version with unit vector - exact and approx #72, Solid angles particle - M points no unit vector - cython for large plasma sub-domain toroidal integral #73, Solid angles polygon- 1 polygon 1 points inlined without unit vector #74, Solid angles polygon- 1 polygon 1 points inlined with unit vector #75, Solid angles polygon - N polygons M points without unit vector #76, Solid angles polygon - N polygons M points with unit vector #77, Solid angles polygon - N polygons plasma sub-domain integrated toroidally, no unit vector #78 )
Tools and classes to handle 2D Bragg X-Ray crystal spectrometer (ongoing for @Didou09 : Issues Spectro X 2D - crystal #202 and Spectro X 2D - Te and Ti fitting #263)
Generic data classe to incorporate plateau-finding, data analysis and 1d Bayesian fitting routines and classes (ongoing for @Didou09 and @jmoralesFusion and @MohammadKozeiha: issues DataHolder class #208, Plateau finding into data class #260 and GPR fits of 1d profiles into data class #262)
More general magnetic field line tracing workflow
Better unit tests coverage
More complete documentation

List of issues and PR closed:

…_min_geom_radius()

[Issue211] Added calc_LOS_length_in_isoflux()

…ne for spectral fits (Notes_Upgrades)

…tes) => try with crystal method

…cluding local plot from geom to ellipses, to be continued

…ansform => to be tested and validated in code

…> reveals probable errors in analytical calculations in Notes/SpectroX2D... to be recalculated with an alternative method

…directions, successfull but need to check bragg vs theta and ang_param vs epsilon (axis vs center), to test and validate

…s.py

…irections with proper parameters (bragg,angle) vs (xi, xj), tested and validated => optimize numerically or start testing on real data

… moved later to units tests

…annotated), for computing default geom parameters from bragg and curve radius, operational but results from calc_braggangle_from_xixj() not consistent: to be checked and then tested with experimental data

…be finished and tested

…onal => need to test with lambda => need to test crystal instanciation

… tested, surface computed, add rotation axis in dgeom and angle, add other crystals, try plotting fitted data

Issue #264 config names

Update in documentation

pep8speaks · 2019-11-20T13:31:20Z

Hello @Didou09! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file examples/tutorials/tuto_plot_custom_emissivity.py:

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Line 1316:17: E116 unexpected indentation (comment)
Line 1317:17: E116 unexpected indentation (comment)
Line 1318:47: E114 indentation is not a multiple of four (comment)
Line 1318:47: E116 unexpected indentation (comment)
Line 1319:47: E114 indentation is not a multiple of four (comment)
Line 1319:47: E116 unexpected indentation (comment)
Line 1320:47: E114 indentation is not a multiple of four (comment)
Line 1320:47: E116 unexpected indentation (comment)
Line 1321:47: E114 indentation is not a multiple of four (comment)
Line 1321:47: E116 unexpected indentation (comment)
Line 1322:47: E114 indentation is not a multiple of four (comment)
Line 1322:47: E116 unexpected indentation (comment)
Line 1323:17: E116 unexpected indentation (comment)
Line 1324:17: E116 unexpected indentation (comment)
Line 1325:47: E114 indentation is not a multiple of four (comment)
Line 1325:47: E116 unexpected indentation (comment)
Line 1326:47: E114 indentation is not a multiple of four (comment)
Line 1326:47: E116 unexpected indentation (comment)
Line 1327:47: E114 indentation is not a multiple of four (comment)
Line 1327:47: E116 unexpected indentation (comment)
Line 1328:47: E114 indentation is not a multiple of four (comment)
Line 1328:47: E116 unexpected indentation (comment)
Line 1329:47: E114 indentation is not a multiple of four (comment)
Line 1329:47: E116 unexpected indentation (comment)
Line 1330:17: E116 unexpected indentation (comment)
Line 1331:13: E116 unexpected indentation (comment)
Line 1332:17: E116 unexpected indentation (comment)
Line 1333:17: E116 unexpected indentation (comment)
Line 1334:17: E116 unexpected indentation (comment)
Line 1335:17: E116 unexpected indentation (comment)
Line 1338:9: E116 unexpected indentation (comment)
Line 1338:9: E303 too many blank lines (2)
Line 1339:9: E116 unexpected indentation (comment)
Line 1340:9: E116 unexpected indentation (comment)
Line 1341:9: E116 unexpected indentation (comment)
Line 1343:9: E116 unexpected indentation (comment)
Line 1344:9: E116 unexpected indentation (comment)
Line 1345:9: E116 unexpected indentation (comment)
Line 1346:9: E116 unexpected indentation (comment)
Line 1347:9: E116 unexpected indentation (comment)
Line 1348:9: E116 unexpected indentation (comment)
Line 1350:9: E116 unexpected indentation (comment)
Line 1352:9: E116 unexpected indentation (comment)
Line 1353:13: E116 unexpected indentation (comment)
Line 1355:13: E116 unexpected indentation (comment)
Line 1356:13: E116 unexpected indentation (comment)
Line 1357:13: E116 unexpected indentation (comment)
Line 1358:13: E116 unexpected indentation (comment)
Line 1359:22: E114 indentation is not a multiple of four (comment)
Line 1359:22: E116 unexpected indentation (comment)
Line 1360:13: E116 unexpected indentation (comment)
Line 1366:1: E303 too many blank lines (3)
Line 1367:22: E114 indentation is not a multiple of four (comment)
Line 1367:22: E116 unexpected indentation (comment)
Line 1372:9: E116 unexpected indentation (comment)
Line 1373:9: E116 unexpected indentation (comment)
Line 1374:13: E116 unexpected indentation (comment)
Line 1375:9: E116 unexpected indentation (comment)
Line 1376:9: E116 unexpected indentation (comment)
Line 1377:9: E116 unexpected indentation (comment)
Line 1378:13: E116 unexpected indentation (comment)
Line 1379:17: E116 unexpected indentation (comment)
Line 1379:80: E501 line too long (81 > 79 characters)
Line 1381:9: E116 unexpected indentation (comment)
Line 1382:9: E116 unexpected indentation (comment)
Line 1385:5: E303 too many blank lines (2)
Line 1390:56: E114 indentation is not a multiple of four (comment)
Line 1390:56: E116 unexpected indentation (comment)
Line 1390:80: E501 line too long (84 > 79 characters)
Line 1391:56: E114 indentation is not a multiple of four (comment)
Line 1391:56: E116 unexpected indentation (comment)
Line 1407:9: E116 unexpected indentation (comment)
Line 1410:9: E116 unexpected indentation (comment)
Line 1411:9: E116 unexpected indentation (comment)
Line 1412:9: E116 unexpected indentation (comment)
Line 1413:9: E116 unexpected indentation (comment)
Line 1414:9: E116 unexpected indentation (comment)
Line 1420:1: E303 too many blank lines (3)
Line 1427:21: E116 unexpected indentation (comment)
Line 1457:16: E114 indentation is not a multiple of four (comment)
Line 1457:16: E116 unexpected indentation (comment)
Line 1458:16: E114 indentation is not a multiple of four (comment)
Line 1458:16: E116 unexpected indentation (comment)
Line 1459:16: E114 indentation is not a multiple of four (comment)
Line 1459:16: E116 unexpected indentation (comment)
Line 1466:9: E116 unexpected indentation (comment)
Line 1467:19: E114 indentation is not a multiple of four (comment)
Line 1467:19: E116 unexpected indentation (comment)
Line 1468:9: E116 unexpected indentation (comment)
Line 1469:13: E116 unexpected indentation (comment)
Line 1470:13: E116 unexpected indentation (comment)
Line 1471:13: E116 unexpected indentation (comment)
Line 1472:31: E114 indentation is not a multiple of four (comment)
Line 1472:31: E116 unexpected indentation (comment)
Line 1473:31: E114 indentation is not a multiple of four (comment)
Line 1473:31: E116 unexpected indentation (comment)
Line 1474:31: E114 indentation is not a multiple of four (comment)
Line 1474:31: E116 unexpected indentation (comment)
Line 1475:13: E116 unexpected indentation (comment)
Line 1476:17: E116 unexpected indentation (comment)
Line 1477:17: E116 unexpected indentation (comment)
Line 1478:17: E116 unexpected indentation (comment)
Line 1479:17: E116 unexpected indentation (comment)
Line 1480:17: E116 unexpected indentation (comment)
Line 1481:17: E116 unexpected indentation (comment)

In the file tofu/geom/_comp.py:

Line 885:28: E203 whitespace before ':'

In the file tofu/geom/_comp_optics.py:

Line 15:1: E302 expected 2 blank lines, found 1
Line 28:1: E302 expected 2 blank lines, found 1
Line 34:80: E501 line too long (86 > 79 characters)
Line 42:1: E302 expected 2 blank lines, found 1
Line 55:1: E302 expected 2 blank lines, found 1
Line 92:10: E225 missing whitespace around operator
Line 98:1: E302 expected 2 blank lines, found 1
Line 119:1: E302 expected 2 blank lines, found 1
Line 124:17: E127 continuation line over-indented for visual indent
Line 147:1: E302 expected 2 blank lines, found 1
Line 158:1: E302 expected 2 blank lines, found 1
Line 171:1: E302 expected 2 blank lines, found 1
Line 188:5: E303 too many blank lines (2)
Line 197:1: E302 expected 2 blank lines, found 1
Line 199:27: E225 missing whitespace around operator

In the file tofu/geom/_core.py:

Line 3089:5: E303 too many blank lines (2)
Line 4095:80: E501 line too long (81 > 79 characters)
Line 4986:5: E129 visually indented line with same indent as next logical line

In the file tofu/geom/_core_optics.py:

Line 4:80: E501 line too long (81 > 79 characters)
Line 37:1: E303 too many blank lines (3)
Line 41:1: E303 too many blank lines (3)
Line 53:1: E303 too many blank lines (3)
Line 81:18: E231 missing whitespace after ':'
Line 82:29: E231 missing whitespace after ':'
Line 84:21: E231 missing whitespace after ':'
Line 85:20: E231 missing whitespace after ':'
Line 86:22: E231 missing whitespace after ':'
Line 87:21: E231 missing whitespace after ':'
Line 87:30: E231 missing whitespace after ':'
Line 88:22: E231 missing whitespace after ':'
Line 88:29: E231 missing whitespace after ':'
Line 89:28: E231 missing whitespace after ':'
Line 89:37: E231 missing whitespace after ':'
Line 89:41: E231 missing whitespace after ','
Line 89:46: E231 missing whitespace after ':'
Line 90:28: E231 missing whitespace after ':'
Line 90:37: E231 missing whitespace after ':'
Line 90:41: E231 missing whitespace after ','
Line 90:46: E231 missing whitespace after ':'
Line 90:51: E231 missing whitespace after ','
Line 90:60: E231 missing whitespace after ':'
Line 90:64: E231 missing whitespace after ','
Line 90:69: E231 missing whitespace after ':'
Line 90:71: E231 missing whitespace after ','
Line 90:77: E231 missing whitespace after ':'
Line 90:80: E501 line too long (80 > 79 characters)
Line 91:29: E231 missing whitespace after ':'
Line 91:38: E231 missing whitespace after ':'
Line 91:42: E231 missing whitespace after ','
Line 91:47: E231 missing whitespace after ':'
Line 91:52: E231 missing whitespace after ','
Line 91:61: E231 missing whitespace after ':'
Line 91:65: E231 missing whitespace after ','
Line 91:70: E231 missing whitespace after ':'
Line 91:72: E231 missing whitespace after ','
Line 91:78: E231 missing whitespace after ':'
Line 91:80: E501 line too long (81 > 79 characters)
Line 92:29: E231 missing whitespace after ':'
Line 92:38: E231 missing whitespace after ':'
Line 92:42: E231 missing whitespace after ','
Line 92:47: E231 missing whitespace after ':'
Line 92:52: E231 missing whitespace after ','
Line 92:61: E231 missing whitespace after ':'
Line 92:65: E231 missing whitespace after ','
Line 92:70: E231 missing whitespace after ':'
Line 92:72: E231 missing whitespace after ','
Line 92:78: E231 missing whitespace after ':'
Line 92:80: E501 line too long (81 > 79 characters)
Line 93:31: E231 missing whitespace after ':'
Line 93:40: E231 missing whitespace after ':'
Line 93:44: E231 missing whitespace after ','
Line 93:52: E231 missing whitespace after ':'
Line 94:20: E231 missing whitespace after ':'
Line 94:27: E231 missing whitespace after ':'
Line 95:26: E231 missing whitespace after ':'
Line 95:35: E231 missing whitespace after ':'
Line 95:39: E231 missing whitespace after ','
Line 95:44: E231 missing whitespace after ':'
Line 96:26: E231 missing whitespace after ':'
Line 96:35: E231 missing whitespace after ':'
Line 96:39: E231 missing whitespace after ','
Line 96:44: E231 missing whitespace after ':'
Line 97:27: E231 missing whitespace after ':'
Line 97:36: E231 missing whitespace after ':'
Line 97:40: E231 missing whitespace after ','
Line 97:45: E231 missing whitespace after ':'
Line 98:27: E231 missing whitespace after ':'
Line 98:36: E231 missing whitespace after ':'
Line 98:40: E231 missing whitespace after ','
Line 98:45: E231 missing whitespace after ':'
Line 99:29: E231 missing whitespace after ':'
Line 100:19: E231 missing whitespace after ':'
Line 107:5: E303 too many blank lines (2)
Line 108:5: E301 expected 1 blank line, found 0
Line 110:27: E231 missing whitespace after ','
Line 112:9: E265 block comment should start with '# '
Line 128:26: E225 missing whitespace around operator
Line 138:27: E231 missing whitespace after ','
Line 142:27: E231 missing whitespace after ','
Line 147:9: E265 block comment should start with '# '
Line 155:33: E231 missing whitespace after ','
Line 168:23: E231 missing whitespace after ':'
Line 168:30: E231 missing whitespace after ':'
Line 168:42: E231 missing whitespace after ':'
Line 169:30: E231 missing whitespace after ':'
Line 169:41: E231 missing whitespace after ':'
Line 170:31: E231 missing whitespace after ':'
Line 170:43: E231 missing whitespace after ':'
Line 171:31: E231 missing whitespace after ':'
Line 171:43: E231 missing whitespace after ':'
Line 172:31: E231 missing whitespace after ':'
Line 172:42: E231 missing whitespace after ':'
Line 173:26: E231 missing whitespace after ':'
Line 173:33: E231 missing whitespace after ':'
Line 173:51: E231 missing whitespace after ':'
Line 178:31: E231 missing whitespace after ':'
Line 178:44: E231 missing whitespace after ':'
Line 179:30: E231 missing whitespace after ':'
Line 179:42: E231 missing whitespace after ':'
Line 179:55: E231 missing whitespace after ':'
Line 180:34: E231 missing whitespace after ':'
Line 271:20: E231 missing whitespace after ','
Line 271:33: E231 missing whitespace after ','
Line 271:61: E231 missing whitespace after ','
Line 391:80: E501 line too long (80 > 79 characters)
Line 393:80: E501 line too long (81 > 79 characters)
Line 481:36: E231 missing whitespace after ','
Line 485:60: E231 missing whitespace after ','
Line 486:26: E225 missing whitespace around operator
Line 496:17: E225 missing whitespace around operator
Line 508:24: E231 missing whitespace after ':'
Line 508:32: E231 missing whitespace after ':'
Line 508:55: E231 missing whitespace after ':'
Line 509:23: E231 missing whitespace after ':'
Line 509:31: E231 missing whitespace after ':'
Line 509:53: E231 missing whitespace after ':'
Line 510:25: E231 missing whitespace after ':'
Line 510:33: E231 missing whitespace after ':'
Line 510:57: E231 missing whitespace after ':'
Line 511:24: E231 missing whitespace after ':'
Line 511:32: E231 missing whitespace after ':'
Line 511:55: E231 missing whitespace after ':'
Line 512:24: E231 missing whitespace after ':'
Line 512:32: E231 missing whitespace after ':'
Line 512:55: E231 missing whitespace after ':'
Line 594:45: E228 missing whitespace around modulo operator
Line 623:34: E712 comparison to False should be 'if cond is not False:' or 'if cond:'
Line 629:80: E501 line too long (80 > 79 characters)
Line 633:35: E127 continuation line over-indented for visual indent
Line 634:35: E127 continuation line over-indented for visual indent
Line 648:5: E303 too many blank lines (2)
Line 655:58: E228 missing whitespace around modulo operator
Line 657:54: E228 missing whitespace around modulo operator
Line 682:55: E231 missing whitespace after ':'
Line 683:49: E231 missing whitespace after ':'
Line 687:34: E712 comparison to False should be 'if cond is False:' or 'if not cond:'
Line 705:80: E501 line too long (80 > 79 characters)
Line 726:5: E303 too many blank lines (3)
Line 730:5: E301 expected 1 blank line, found 0
Line 753:51: E228 missing whitespace around modulo operator
Line 754:51: E228 missing whitespace around modulo operator
Line 819:5: E303 too many blank lines (3)
Line 823:5: E301 expected 1 blank line, found 0
Line 881:38: E231 missing whitespace after ','
Line 908:5: E303 too many blank lines (2)
Line 1005:17: E712 comparison to False should be 'if cond is not False:' or 'if cond:'
Line 1018:29: E128 continuation line under-indented for visual indent
Line 1019:29: E128 continuation line under-indented for visual indent
Line 1020:29: E128 continuation line under-indented for visual indent
Line 1021:29: E128 continuation line under-indented for visual indent
Line 1040:48: E225 missing whitespace around operator
Line 1040:80: E501 line too long (80 > 79 characters)
Line 1077:48: E225 missing whitespace around operator
Line 1077:80: E501 line too long (80 > 79 characters)
Line 1096:42: E231 missing whitespace after ','
Line 1099:9: E303 too many blank lines (2)
Line 1103:80: E501 line too long (80 > 79 characters)
Line 1112:9: E303 too many blank lines (2)

In the file tofu/geom/_plot_optics.py:

Line 16:58: E228 missing whitespace around modulo operator
Line 16:80: E501 line too long (80 > 79 characters)
Line 57:37: E228 missing whitespace around modulo operator
Line 58:36: E228 missing whitespace around modulo operator
Line 71:80: E501 line too long (140 > 79 characters)
Line 78:54: E127 continuation line over-indented for visual indent
Line 79:26: E272 multiple spaces before keyword
Line 81:53: E128 continuation line under-indented for visual indent
Line 88:1: E303 too many blank lines (3)
Line 94:1: E302 expected 2 blank lines, found 3
Line 111:10: E111 indentation is not a multiple of four
Line 111:10: E117 over-indented
Line 121:80: E501 line too long (94 > 79 characters)
Line 136:12: E712 comparison to False should be 'if cond is not False:' or 'if cond:'
Line 142:1: E302 expected 2 blank lines, found 1
Line 142:80: E501 line too long (83 > 79 characters)
Line 143:80: E501 line too long (87 > 79 characters)
Line 154:80: E501 line too long (95 > 79 characters)
Line 195:46: E231 missing whitespace after ','
Line 195:57: E231 missing whitespace after ','
Line 195:69: E231 missing whitespace after ','
Line 199:35: E231 missing whitespace after ','
Line 199:46: E231 missing whitespace after ','
Line 222:45: E231 missing whitespace after ','
Line 222:55: E231 missing whitespace after ','
Line 222:66: E231 missing whitespace after ','
Line 226:34: E231 missing whitespace after ','
Line 226:44: E231 missing whitespace after ','
Line 232:30: E231 missing whitespace after ','
Line 235:46: E231 missing whitespace after ','
Line 235:55: E231 missing whitespace after ','
Line 235:65: E231 missing whitespace after ','
Line 236:45: E231 missing whitespace after ','
Line 236:53: E231 missing whitespace after ','
Line 236:62: E231 missing whitespace after ','
Line 241:35: E231 missing whitespace after ','
Line 241:44: E231 missing whitespace after ','
Line 242:34: E231 missing whitespace after ','
Line 242:42: E231 missing whitespace after ','
Line 265:27: E231 missing whitespace after ','
Line 265:31: E231 missing whitespace after ','
Line 265:35: E231 missing whitespace after ','
Line 270:37: E231 missing whitespace after ','
Line 270:39: E231 missing whitespace after ','
Line 271:36: E231 missing whitespace after ','
Line 271:38: E231 missing whitespace after ','
Line 288:31: E231 missing whitespace after ','
Line 288:35: E231 missing whitespace after ','
Line 288:39: E231 missing whitespace after ','
Line 291:14: E225 missing whitespace around operator
Line 292:21: E231 missing whitespace after ','
Line 292:31: E231 missing whitespace after ','
Line 292:58: E228 missing whitespace around modulo operator
Line 302:1: E303 too many blank lines (4)
Line 340:48: E228 missing whitespace around modulo operator
Line 341:37: E228 missing whitespace around modulo operator
Line 355:17: E231 missing whitespace after ','
Line 359:26: E231 missing whitespace after ':'
Line 359:40: E231 missing whitespace after ':'
Line 360:28: E231 missing whitespace after ':'
Line 360:40: E231 missing whitespace after ':'
Line 361:28: E231 missing whitespace after ':'
Line 361:43: E231 missing whitespace after ':'
Line 369:5: E303 too many blank lines (2)
Line 425:26: E231 missing whitespace after ':'
Line 425:40: E231 missing whitespace after ':'
Line 426:28: E231 missing whitespace after ':'
Line 426:40: E231 missing whitespace after ':'
Line 427:28: E231 missing whitespace after ':'
Line 427:43: E231 missing whitespace after ':'
Line 435:5: E303 too many blank lines (2)
Line 445:19: E225 missing whitespace around operator
Line 461:49: E261 at least two spaces before inline comment
Line 461:49: E262 inline comment should start with '# '
Line 463:49: E261 at least two spaces before inline comment
Line 463:49: E262 inline comment should start with '# '
Line 473:24: E228 missing whitespace around modulo operator
Line 507:25: E127 continuation line over-indented for visual indent
Line 510:66: E231 missing whitespace after ','
Line 510:80: E501 line too long (92 > 79 characters)
Line 511:66: E231 missing whitespace after ','
Line 511:80: E501 line too long (92 > 79 characters)
Line 518:80: E501 line too long (82 > 79 characters)
Line 520:66: E231 missing whitespace after ','
Line 520:80: E501 line too long (92 > 79 characters)
Line 521:80: E501 line too long (80 > 79 characters)
Line 522:41: E128 continuation line under-indented for visual indent

In the file tofu/mag/test_equimap.py:

Line 15:5: E265 block comment should start with '# '
Line 16:80: E501 line too long (86 > 79 characters)
Line 17:5: E265 block comment should start with '# '
Line 31:62: E502 the backslash is redundant between brackets
Line 32:13: E128 continuation line under-indented for visual indent
Line 32:80: E501 line too long (80 > 79 characters)
Line 32:80: E502 the backslash is redundant between brackets
Line 39:80: E501 line too long (80 > 79 characters)
Line 59:29: E127 continuation line over-indented for visual indent
Line 63:65: E502 the backslash is redundant between brackets
Line 68:69: E502 the backslash is redundant between brackets
Line 69:55: E502 the backslash is redundant between brackets
Line 72:80: E501 line too long (84 > 79 characters)
Line 73:80: E501 line too long (84 > 79 characters)
Line 79:44: E502 the backslash is redundant between brackets
Line 80:13: E128 continuation line under-indented for visual indent
Line 80:70: E502 the backslash is redundant between brackets
Line 81:13: E128 continuation line under-indented for visual indent
Line 90:5: E265 block comment should start with '# '
Line 93:5: E265 block comment should start with '# '
Line 94:5: E265 block comment should start with '# '
Line 97:5: E265 block comment should start with '# '
Line 98:80: E501 line too long (80 > 79 characters)
Line 101:5: E265 block comment should start with '# '
Line 103:5: E265 block comment should start with '# '
Line 103:80: E501 line too long (81 > 79 characters)
Line 104:5: E265 block comment should start with '# '
Line 104:80: E501 line too long (80 > 79 characters)
Line 105:5: E265 block comment should start with '# '
Line 105:80: E501 line too long (86 > 79 characters)
Line 106:5: E265 block comment should start with '# '
Line 107:5: E265 block comment should start with '# '
Line 108:5: E265 block comment should start with '# '
Line 109:5: E265 block comment should start with '# '
Line 109:80: E501 line too long (88 > 79 characters)
Line 110:5: E265 block comment should start with '# '
Line 112:5: E265 block comment should start with '# '
Line 113:5: E265 block comment should start with '# '
Line 114:5: E265 block comment should start with '# '
Line 115:5: E265 block comment should start with '# '
Line 117:5: E265 block comment should start with '# '
Line 118:5: E265 block comment should start with '# '
Line 119:5: E265 block comment should start with '# '
Line 120:5: E265 block comment should start with '# '
Line 124:71: E502 the backslash is redundant between brackets
Line 125:71: E502 the backslash is redundant between brackets
Line 127:74: E502 the backslash is redundant between brackets
Line 128:74: E502 the backslash is redundant between brackets
Line 136:5: E265 block comment should start with '# '
Line 137:5: E265 block comment should start with '# '
Line 138:5: E265 block comment should start with '# '
Line 139:5: E265 block comment should start with '# '
Line 140:5: E265 block comment should start with '# '
Line 141:5: E265 block comment should start with '# '
Line 143:5: E265 block comment should start with '# '
Line 144:5: E265 block comment should start with '# '
Line 146:5: E265 block comment should start with '# '
Line 147:5: E265 block comment should start with '# '
Line 149:5: E265 block comment should start with '# '
Line 150:5: E265 block comment should start with '# '
Line 152:5: E265 block comment should start with '# '
Line 153:5: E265 block comment should start with '# '
Line 154:5: E265 block comment should start with '# '
Line 155:5: E265 block comment should start with '# '
Line 156:5: E265 block comment should start with '# '
Line 157:80: E501 line too long (83 > 79 characters)
Line 161:56: E502 the backslash is redundant between brackets
Line 162:13: E128 continuation line under-indented for visual indent
Line 162:70: E502 the backslash is redundant between brackets
Line 163:13: E128 continuation line under-indented for visual indent
Line 167:5: E265 block comment should start with '# '
Line 171:80: E501 line too long (81 > 79 characters)
Line 174:71: E502 the backslash is redundant between brackets
Line 175:71: E502 the backslash is redundant between brackets
Line 177:74: E502 the backslash is redundant between brackets
Line 178:74: E502 the backslash is redundant between brackets
Line 185:56: E502 the backslash is redundant between brackets
Line 186:13: E128 continuation line under-indented for visual indent
Line 186:70: E502 the backslash is redundant between brackets
Line 187:13: E128 continuation line under-indented for visual indent
Line 190:5: E265 block comment should start with '# '
Line 193:80: E501 line too long (81 > 79 characters)
Line 197:71: E502 the backslash is redundant between brackets
Line 198:71: E502 the backslash is redundant between brackets
Line 200:74: E502 the backslash is redundant between brackets
Line 201:74: E502 the backslash is redundant between brackets
Line 208:51: E502 the backslash is redundant between brackets
Line 209:13: E128 continuation line under-indented for visual indent
Line 209:70: E502 the backslash is redundant between brackets
Line 210:13: E128 continuation line under-indented for visual indent
Line 214:5: E265 block comment should start with '# '
Line 221:71: E502 the backslash is redundant between brackets
Line 222:71: E502 the backslash is redundant between brackets
Line 224:74: E502 the backslash is redundant between brackets
Line 225:74: E502 the backslash is redundant between brackets
Line 232:80: E501 line too long (100 > 79 characters)
Line 236:5: E265 block comment should start with '# '
Line 237:5: E265 block comment should start with '# '
Line 240:5: E265 block comment should start with '# '
Line 243:5: E265 block comment should start with '# '
Line 246:5: E265 block comment should start with '# '
Line 247:5: E265 block comment should start with '# '
Line 248:5: E265 block comment should start with '# '
Line 249:5: E265 block comment should start with '# '
Line 252:50: E502 the backslash is redundant between brackets
Line 253:13: E128 continuation line under-indented for visual indent
Line 253:70: E502 the backslash is redundant between brackets
Line 254:13: E128 continuation line under-indented for visual indent
Line 258:5: E265 block comment should start with '# '
Line 265:71: E502 the backslash is redundant between brackets
Line 266:71: E502 the backslash is redundant between brackets
Line 268:74: E502 the backslash is redundant between brackets
Line 269:74: E502 the backslash is redundant between brackets
Line 276:49: E502 the backslash is redundant between brackets
Line 277:13: E128 continuation line under-indented for visual indent
Line 277:70: E502 the backslash is redundant between brackets
Line 278:13: E128 continuation line under-indented for visual indent
Line 289:71: E502 the backslash is redundant between brackets
Line 290:71: E502 the backslash is redundant between brackets
Line 292:74: E502 the backslash is redundant between brackets
Line 293:74: E502 the backslash is redundant between brackets

In the file tofu/mag/test_magFieldLines.py:

Line 7:61: E502 the backslash is redundant between brackets
Line 14:5: E265 block comment should start with '# '
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In the file tofu/mag/test_ripple.py:

Line 17:5: E265 block comment should start with '# '
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Line 382:13: E128 continuation line under-indented for visual indent
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Line 442:74: E502 the backslash is redundant between brackets

In the file tofu/tests/tests09_tutorials/tests01_runall.py:

Line 158:39: E713 test for membership should be 'not in'

In the file tofu/utils.py:

Line 548:62: E231 missing whitespace after ','

Comment last updated at 2019-11-20 15:15:41 UTC

codecov-io · 2019-11-20T13:41:02Z

Codecov Report

Merging #266 into master will decrease coverage by 3.68%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #266      +/-   ##
==========================================
- Coverage   45.16%   41.47%   -3.69%     
==========================================
  Files          70       79       +9     
  Lines       20608    23217    +2609     
==========================================
+ Hits         9307     9629     +322     
- Misses      11301    13588    +2287

Impacted Files	Coverage Δ
tofu/imas2tofu/_core.py	`0.74% <ø> (-0.01%)`	⬇️
tofu/tests/tests01_geom/tests03_core.py	`90.08% <ø> (+0.45%)`	⬆️
tofu/tests/tests02_data/tests03_core.py	`99.08% <ø> (ø)`	⬆️
tofu/mag/test_magFieldLines.py	`0% <ø> (ø)`
tofu/utils.py	`47.99% <ø> (-0.87%)`	⬇️
tofu/data/__init__.py	`100% <ø> (ø)`	⬆️
tofu/geom/utils.py	`43.08% <ø> (-0.64%)`	⬇️
tofu/data/_plot.py	`91.15% <ø> (ø)`	⬆️
tofu/mag/test_ripple.py	`0% <ø> (ø)`	⬆️
tofu/mag/mag_ripple/__init__.py	`0% <ø> (ø)`	⬆️
... and 47 more

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…d branch into devel for release 1.4.2

…s correspondence

… Features and typo correction

[doc] added warning for mac and gcc compiler

Issue202 spectro x2 d crystal

VEZINET Didier and others added 30 commits October 8, 2019 10:58

[Issue211] Added calc_LOS_length_in_isoflux()

df8cd98

[Issue211] Rename Rays.calc_lenght_in_isoflux() and created Rays.calc…

55184b4

…_min_geom_radius()

[Issue211] Added Rays.calc_min_rho_from_Plasma2D()

be0525a

[Issue211] PEP8 compliance in tofu/geom/_core.py 1

e5ffef4

[Issue211] PEP8 compliance in tofu/geom/_core.py 2

13190fa

Merge pull request #212 from ToFuProject/Issue211_ToolsPtsCamLOS

93ae5c5

[Issue211] Added calc_LOS_length_in_isoflux()

update example for nicer plots

fe9a7bd

[Issue203] Advanced a bit herratically spectral fits...

ee04449

[Issue203] Started latex / pdf notes on ellipse intersection with pla…

c4146ac

…ne for spectral fits (Notes_Upgrades)

[Issue203] Moved notes to Notes_Upgrades/SpectroX2D

54d77e7

[Issue203] Ellipses coordinates transform ok until direct problem (No…

a6825f5

…tes) => try with crystal method

[Issue202] Advanced CrystalBragg class up to public class methods, in…

7177f0c

…cluding local plot from geom to ellipses, to be continued

[Issue202] Tested, about to merge with Issue203

59bec07

[Issue202] Advanced reverse coordinates transform in Notes

27e5416

[Issue202] Completed Notes on SpectroX2D up to reverse coordinates tr…

78e1ec3

…ansform => to be tested and validated in code

[Issue202] First version of CrystalBragg.get_braggangle_from_xixj() =…

65155bb

…> reveals probable errors in analytical calculations in Notes/SpectroX2D... to be recalculated with an alternative method

[Issue202] CrystalBragg now performing coordinates tranforms in both …

6c3b689

…directions, successfull but need to check bragg vs theta and ang_param vs epsilon (axis vs center), to test and validate

[Issue202] Renamed tofu/geom/_core_Optics.py to tofu/geom/_core_optic…

6dedc3a

…s.py

[Issue202] Added l = f(\beta) in Notes_Upgrades/SpectroX2D

d60d835

[Issue202] CrystalBragg now performs coordinates transforms in both d…

38727e8

…irections with proper parameters (bragg,angle) vs (xi, xj), tested and validated => optimize numerically or start testing on real data

[Issue202] Preparing CrystalBragg for tests with experimental data

346b58a

[Issue202] Creating tofu/geom/inputs/test_data/ for SpectroX2D (to be…

c4ff052

… moved later to units tests

[Issue202] CrystalBragg has helper routine for simple 2d plot (to be …

7396ca9

…annotated), for computing default geom parameters from bragg and curve radius, operational but results from calc_braggangle_from_xixj() not consistent: to be checked and then tested with experimental data

[Issue202] Advanced plot for fit and fitting 2d spectra function, to …

4c9be5f

…be finished and tested

[bf] return type of emissivity should always be 2D

7030392

[Issue202] plot of coords tranform and 2d spectral fit almost operati…

ce4650d

…onal => need to test with lambda => need to test crystal instanciation

[Issue202] Save crystal for further testing

5942ef3

[Issue202] CyrstalBragg instanciation ok up to dgeom and dmat, ArXVII…

1db9b01

… tested, surface computed, add rotation axis in dgeom and angle, add other crystals, try plotting fitted data

[Issue202] Advanced plotting

c758bad

[Issue202] Advanced CrystalBragg.plot(), to be checked

88dc5e9

Merge pull request #265 from ToFuProject/Issue264_ConfigNames

561d6ef

Issue #264 config names

Didou09 added the enhancement label Nov 20, 2019

Didou09 requested review from flothesof, jmoralesFusion and lasofivec November 20, 2019 13:28

Didou09 self-assigned this Nov 20, 2019

Merge pull request #261 from ToFuProject/new-doc

c430b67

Update in documentation

[Preparing release 1.4.2] PEP8 compliance for release notes

f30384d

VEZINET Didier and others added 15 commits November 20, 2019 14:46

Merge branch 'devel' into Issue202_SpectroX2DCrystal

9d8e582

[Issue202] Just making sure tofu is stable to merge this non-finalize…

806dbc9

…d branch into devel for release 1.4.2

[release] update contributors

4c17ca3

[doc] added warning for mac and gcc compiler

3c70bc3

[Issue202] PEP8 Compliance 1

0dd876b

[release] added info from almost all issues

62ea2c9

[Release Notes 1.4.2] Updated release notes with SpectroX2D and issue…

36acddd

…s correspondence

[release] added info from all PR

8b588ed

Merge branch 'devel' into Issue202_SpectroX2DCrystal

43c9b29

[release] merged with didier's changes

a146ee8

[Release notes 1.4.2] Emphasizing 2d Xray Crystal Spectrometer in new…

fb342b7

… Features and typo correction

Merge pull request #268 from ToFuProject/new-doc

526535c

[doc] added warning for mac and gcc compiler

Merge branch 'devel' into Issue202_SpectroX2DCrystal

8ad363d

Merge pull request #267 from ToFuProject/Issue202_SpectroX2DCrystal

4c43aed

Issue202 spectro x2 d crystal

Update release_notes_142.rst

314b7bc

lasofivec approved these changes Nov 20, 2019

View reviewed changes

Didou09 requested review from lasofivec and removed request for flothesof and jmoralesFusion November 20, 2019 15:31

Didou09 merged commit 92523ae into master Nov 20, 2019

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