Preparing 1.4.3

[Didou09]

What's new in 1.4.3

Main changes:

• Python 2 not supported anymore
• Several changes to try and make installation cleaner / easier
• More robust IMAS interface Issue218 plasma2d extraction iter #280, Issue316 common idd for all id sget #317, Issue318 add synth diag ids #319, [Issue335] description_2d propagated and set to 1 by default #336, Issue341 indchauto #343, Issue349 new imas reflectometer profile #350
• Better documentation, more ressources
• More informative error messages
• Better PEP8 compliance

New features:

• New bash commands tofuplot, tofucalc and tofu-custom Issue344 deploybin #345, Issue346 tofucalc mat #352, Issue #351 tofu-custom #353, Issue #359 tofu-custom allow customization of script parameters #360
• New AUG configuration available! Issue281 new default configs - AUG #333
• More complete CrystalBragg class Issue202 spectro x2 d crystal #320

Detailed changes:

Installation / portability:

• travis test matrix New travis matrix #328
• Skipped deployment if package already detected, deploy bdist for Mac [quick fix] took out wheel deployment and add skip if already in pypi #293
• Bug corrected Cython vs cython #Issue272 Cythonvscython #274
• pip install working, cleaned up setup.py, requirements.txt included Updates in setup.py for pypi installation #283 [Issue292] Hotfix: both solutions #299 Preparing tofu 1.4.2-a5 #302
• More general path delimiters, corrected path in update_version Fix issue295 #296 Quick fix: wrong path in update version #315
• Bug fixed on Mac (due to wrong modulo operation) [ #314 ] fixed bug on mac coming from modulo with negative values #323
• Debugged deployment and updating of version number Deploy test #348

scripts:

• Introduction of bash command line tools: tofuplot (for plotting IMAS data)
  tofucalc (for calculating synthetic signal) and tofu-custom for user-specific
  customization of tofu default parameters Issue344 deploybin #345
• tofucalc also handles input_file and output_file in .mat format Issue346 tofucalc mat #352
• tofu-custom allows for cutomization of IMAS shortcuts Issue #351 tofu-custom #353
• tofu-custom allows for cutomization of script parameters Issue #359 tofu-custom allow customization of script parameters #360

Exception / warnings:

• More details exception msg when loading wrong Config #301 List of available config accessible for end-users #327
• Better warning when a sub-package is not available Less verbose warnings for missing sub-packages #269 [enhancement] took out the word error from warning #270
• Warning added when gcc compiler < 8 used on Mac [doc] added warning for mac and gcc compiler #268
• Better (more concise) warnings when unable to load data from IMAS Issue218 plasma2d extraction iter #280
• Now warns if IMAS version loaded is not the latest available on the system [Issue287] IMAS version check operational in imas2tofu.__init__, made… #289
• Exception raised when poly ill-defined [bf #331] raising exceptions when poly ill defined #332

Default configurations:

• Asdex Upgrade added (AUG) Issue281 new default configs - AUG #333

Geom classes (Struct, Config, CamLOS1D, CamLOS2D...):

• Reformatted _GG.Poly_Order by _GG.format_poly [Issue #337] replaced Poly_Order by format_poly #338
• get_summary() routine implemented for Struct and CamLOS2D [Issue304] get_summary() added to Struct and CamLOS2D #305
• Faster synthetic signal cmputation (calc_signal()) using method='sum' Faster los calc signal sum calls for newcalc=False #308 Faster LOS calc signal with new_calc = True #322

Plasma2D:

• Bug fixed in interpolation routine [Issue215] fixed #279
• Now handles rectangular meshes Issue218 plasma2d extraction iter #280
• Can now save/load Config to/from IMAS and indch_auto propagated Issue321 rectangular grid metis #325

2D XRay spectrometer:

• CrystalBragg ow has several geometry and data plotting methods useful for geometrical adjustments and spectrum visualization Issue202 spectro x2 d crystal #320

IMAS interfacing:

• More robust MultiIDSLoader vs one-time-step signal Issue218 plasma2d extraction iter #280
• Now loads rectangular meshes Issue218 plasma2d extraction iter #280
• add_ids() now also works with idd handle Issue316 common idd for all id sget #317
• It is now possible to add the ids corresponding to the synthetic diagnostics of an ids, and optionally to add them from a diffrent idd Issue318 add synth diag ids #319
• description_2d input argument propagated [Issue335] description_2d propagated and set to 1 by default #336
• Automated selection of valiud channels (indch_auto=True) now more robust Issue341 indchauto #343
• Updated signal for relectometer_profile Issue349 new imas reflectometer profile #350

Documentation:

• New tutorials and link to release notes Update in online documentation #273 New tutorial on builtin configs #297 New doc #300 [doc] updated gallery tuto: bf #329 #330
• Better badges on Github [Issue277] Fixed badges and added gitter badge #278
• Better release notes [doc] updated format for text modificators in release_notes #284
• Documentation page on bash command lines

Miscellaneous:

• Better PEP8 compliance PEP8 compliances #285
• Removed useless files [Issue288] Files removed #290 Delete TFG_CrystalBragg_…453d6a3.npz #324
• Minutes from meeting on 27.11.2019 added November meeting summary #291
• allow_pickle available to users Issue #357 Made allow_pickle available to user #358

Contributors:

Many thanks to all developpers:

• Didier Vezinet (@Didou09)
• Laura Mendoza (@lasofivec)
• Florian Le Bourdais (@flothesof)
• Jack Hare (@harej)

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 class 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 PR merged into this release:

• PR: [doc] added warning for mac and gcc compiler #268, Less verbose warnings for missing sub-packages #269, [enhancement] took out the word error from warning #270, Update in online documentation #273, #Issue272 Cythonvscython #274, [Issue277] Fixed badges and added gitter badge #278, [Issue215] fixed #279, Issue218 plasma2d extraction iter #280, Issue281 new default configs #282, Updates in setup.py for pypi installation #283, [doc] updated format for text modificators in release_notes #284, PEP8 compliances #285,
  [Issue287] IMAS version check operational in imas2tofu.__init__, made… #289, [Issue288] Files removed #290, November meeting summary #291, [quick fix] took out wheel deployment and add skip if already in pypi #293, Fix issue295 #296, New tutorial on builtin configs #297, [Issue292] Hotfix: both solutions #299, New doc #300, Preparing tofu 1.4.2-a5 #302, [Issue304] get_summary() added to Struct and CamLOS2D #305, Faster los calc signal sum calls for newcalc=False #308, Feature nstx #309, Quick fix: wrong path in update version #315,
  Issue316 common idd for all id sget #317, Issue318 add synth diag ids #319, Issue202 spectro x2 d crystal #320, Faster LOS calc signal with new_calc = True #322, [ #314 ] fixed bug on mac coming from modulo with negative values #323, Delete TFG_CrystalBragg_…453d6a3.npz #324, Issue321 rectangular grid metis #325, #301 List of available config accessible for end-users #327, New travis matrix #328, [doc] updated gallery tuto: bf #329 #330, [bf #331] raising exceptions when poly ill defined #332, Issue281 new default configs - AUG #333, [Issue335] description_2d propagated and set to 1 by default #336,
  [Issue #337] replaced Poly_Order by format_poly #338, Issue341 indchauto #343, Issue344 deploybin #345, Deploy test #348, Issue346 tofucalc mat #352, Issue #351 tofu-custom #353, Issue #357 Made allow_pickle available to user #358, Issue #359 tofu-custom allow customization of script parameters #360

[pep8speaks]

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

• In the file tofu/openadas2tofu/__init__.py:

Line 2:1: E265 block comment should start with '# '

[codecov-io]

Codecov Report

Merging #364 into master will not change coverage by %.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #364   +/-   ##
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  Coverage   38.58%   38.58%           
=======================================
  Files          88       88           
  Lines       25162    25162           
=======================================
  Hits         9709     9709           
  Misses      15453    15453           

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