Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.8.0

New Release

Once again we have waited far too long for a new release so we should be doing this on a monthly basis or so I think

Big one here is the matching of linear outputs here (eigenvalues and eigenfunctions) as well as the addition of GX/updated STELLA.

What's Changed

• Add option to handle loading in adiabatic electrons in GS2/STELLA by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/404
• Add option for kwargs in load_local and test by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/408
• Bugfix in gs2.py for normalisations value (qref-->zref) by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/409
• IMAS ignore default values in R, Z, psi by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/411
• Bugfix/adiabatic electron cgyro local species by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/412
• Enhancements/imas kinetics fast ions by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/415
• Reset localgeometry/species record after each loadlocal by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/410
• Enhancements/stella update by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/413
• Add higher moments to CGYRO by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/417
• Addition of GX by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/416
• Allow for case without theta0 in MG sat and add legacy flux defn in GS2 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/418
• Update gs2.py to force fapar and fbpar to zero if beta is zero by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/421
• Update gs2.py to give shatinput a default of shat if present by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/422
• Update input.gs2 to remove diagnostics_config namelist by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/424
• Update gs2.in to remove diagnostics_config and merge parameters to knobs by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/423
• Direct matching of linear GKOutput between codes by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/364
• Force the sign of ky to be positive when loading gk_output by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/427
• Bugfix/gene mxh map by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/426
• changed np.isclose() to np.allclose() for calculating normed gradients by @rijudutta in https://github.com/pyro-kinetics/pyrokinetics/pull/392
• get_charge() method fix by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/435
• Bugfix/tglf pyroscan by @fcasson in https://github.com/pyro-kinetics/pyrokinetics/pull/434
• Stella namelist backward compatibility by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/428
• GENE set beta_prime correctly if amhd=-1 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/433
• Enhancements/flux surface volumes by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/436
• Fix to setting of omprimfac in gs2.py by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/438
• Bugfix to prevent AttributeError by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/440
• Possibly erroneous calculation of ntheta in gs2geometryterms by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/442
• CGYRO signs of Bt/Ip/q by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/430
• Add in splines for psitor and rhotor by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/439
• Bugfix/hydrogenic species by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/447
• Add check for LCFS a minor in case of divertor legs by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/444
• Bugfix/pfile divide by zero by @physycola in https://github.com/pyro-kinetics/pyrokinetics/pull/452
• Add units to PyroScan output by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/450
• Enforce quasineutrality when writing GK files by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/448

New Contributors

• @physycola made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/413
• @rijudutta made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/392

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.7.1...v0.8.0

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 8 months ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.7.1

What's Changed

• Add units to eigenfunctions when loaded manually by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/361
• Add check for box_size when no kx is set with a test. by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/362
• Add method to enforce quasineutrality in LocalSpecies by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/365
• Remove extra species namelist from inputs when removed by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/366
• Set default norm convention when reading IDS GKOutput and add test by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/371
• Enhancements/gene fourier reading by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/370
• Switch TGLF to use MillerTurnbull by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/373
• Update to loop over all wavenumber/eigenmode and get fluxes/field to … by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/374
• Adding documentation for synthetic highk/dbs by @juanruizruiz in https://github.com/pyro-kinetics/pyrokinetics/pull/351
• Add default in ky from tglf get_numerics by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/375
• Bugfix/gk output field coord by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/379
• Add check for new position of rhostar in cgyro output by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/380
• GENE IMAS fixes by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/382
• Numpy 2.0 Compatibility by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/372
• IMAS Equilibrium/Kinetics Reader by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/383
• Fix for FreeQDSK 0.5 breaking changes by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/387
• Enhancements/gene magn geometry reader by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/388
• Enhancements/add gk output data by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/390
• Check for GENE precision in output by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/394
• Add in deuterium mass if not in Kinetics object - Fast and Furious edition by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/393
• Pin numpy to <2.1 and remove some warnings with numpy>=2.0 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/396
• Bicoherence diagnostics by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/395
• Limit xarray version for time being. by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/401
• Minor/find gs2 species type without reading the input data by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/399
• Saturation rules - KBM MG rule by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/402
• Account for correct k_perp calc by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/407

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.7.0...v0.7.1

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 about 1 year ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.7.0

What's Changed

• Minor JOSS edits by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/248
• JOSS Paper by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/229
• Replace "parameters" with "knobs" in GS2 by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/297
• Fix beta setting when directly specifying code by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/299
• method to check quasi-neutrality on density gradients by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/302
• Update normalisation.py to allow for the conversion of original base … by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/303
• fix if statement by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/304
• Modified the kperp diagnostic to work on any nperiod by @whornsby82 in https://github.com/pyro-kinetics/pyrokinetics/pull/306
• Nl documentation by @dake0795 in https://github.com/pyro-kinetics/pyrokinetics/pull/223
• Enhancements/merge species by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/296
• Write bespoke GACODE reader to avoid pygacode import by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/307
• Make more useful missing file error JETTO kinetics by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/313
• Fix NaN check for arrays and normalise to final finite timeslice in f… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/309
• Set qref to pint elementary_charge and mref to scipy constant in uni… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/318
• Add tutorial for using Pyrokinetics on HPC systems by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/314
• Enhancements/auto detect normalisations by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/311
• Check if LocalGeometry has pressure and set accordingly. Remove unnec… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/323
• Load in tracer_efit as "circular" LocalGeometry with q and shat by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/319
• Cache file reads in tests by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/327
• Bugfix: Slow deepcopies in tests by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/328
• Enhancements/add gkw v2 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/325
• Bugfix/eigenvalues units by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/332
• Replace setuptools-scm with versioningit, store __commit__ alongside __version__ by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/331
• update how ions are named by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/315
• Enhancements/imas update v3.4 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/301
• Bugfix/gene dpdx pm sign by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/339
• Add MXH to GENE by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/329
• Definition of inverse_lp was reverted accidentally when adding GKW. T… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/342
• GK code stella input file conversion feature by @mrhardman in https://github.com/pyro-kinetics/pyrokinetics/pull/338
• Drop units in directory name when making Pyroscan with pint Quantity by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/347
• Update bunit calculation to use analytic solution by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/346
• Add in reader for nrg in h5 format by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/343
• Update publishing workflow by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/340
• Bugfix/eigenfunction amp by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/341
• Set up reading ky from n0 in gs2 input file by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/324
• Add correct mass factor in rhoref scaling by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/348
• Update README.md by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/350
• wip: highk/dbs synthetic diagnostic by @juanruizruiz in https://github.com/pyro-kinetics/pyrokinetics/pull/294
• Use correct variable for fast ion nucleon by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/355
• Bugfix: unit conversions using simulation units by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/357
• Bugfix: Pin idspy-dictionaries version by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/358
• Feature/gene trpeps geometry file by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/359
• Unpin scipy by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/345

New Contributors

• @whornsby82 made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/306
• @mrhardman made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/338
• @juanruizruiz made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/294

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.6.1...v0.7.0

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 over 1 year ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.6.1

What's Changed

• Bugfix/docker publishing issues by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/293

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.6.0...v0.6.1

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 about 2 years ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.6.0

What's Changed

• Modify/copyright coverage by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/253
• Fix to code coverage, minor test updates by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/259
• Add entry-points plugin system + update factories (again) by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/258
• Enhancements/gene moments by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/254
• Fix downsizing in CGYRO by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/260
• Handle rotation/rotation gradients better by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/261
• Document collisions by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/252
• Pin idspy-toolkit version to 0.4.3 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/267
• Better error messages from file readers by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/270
• Update GS2 reader for next by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/271
• Feature/write normalisations by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/263
• Feature/gacode reader by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/265
• Move slow imports within relevant functions by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/275
• Bugfix/multiple linear ky by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/277
• Correct gs2 range defaults by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/278
• Update pyloidal usage to 0.2.0 by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/279
• Bugfi/eigenfunction normalisations by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/280
• Enhancements/kperp example by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/281
• Update gacode.py to correct typo in docstring by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/282
• Update examples and add contributing guide by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/283
• Update gs2.py to fix calculation of eigenvalues in non-wstar_units runs by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/289
• Docker workflow by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/291
• Update gk_output.py to fix issue #287 by @d7919 in https://github.com/pyro-kinetics/pyrokinetics/pull/288
• Add Dockerfile by @fcasson in https://github.com/pyro-kinetics/pyrokinetics/pull/286
• Modify/remove transp template by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/284
• Enhancements/ideal ballooning solver + GS2 geometric terms by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/292

New Contributors

• @fcasson made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/286

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.5.0...v0.6.0

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 about 2 years ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.5.0

What's Changed

• Read appropriate flux file if ExB shear is included by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/121
• Fixed GENE error when paths contain numbers by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/122
• Normalisation refactor by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/97
• Improved getfluxsurface by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/123
• Feature/gene improvements by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/127
• Enhancements/jetto kinetics time choice by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/129
• Bugfix/name path pint by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/131
• Enable reading GENE omega text file by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/126
• Better method for converting simulation/physical units by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/133
• Bugfix/remove template beta by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/134
• Enhancements/LocalGeometry by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/112
• fix sign for poloidal field fit by @hgd511 in https://github.com/pyro-kinetics/pyrokinetics/pull/137
• Enhancements/add zeff by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/140
• Bugfix/normalisation gene by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/139
• Fix incorrect collisionality for ions when Z!=1 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/141
• Set squareness to zero when not specifeid in CGYRO input by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/142
• Upgrade to latest build system (PEP 517/518/621) by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/147
• Don't run black on removed setup.py by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/148
• Fix/gene fields ballooning by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/149
• Don't run flake on nonexistent setup.py by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/150
• Equilibrium refactor and enhancements by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/145
• flake8 fixes by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/151
• Fix/cgyro flux flow shear by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/153
• Switched out freegs._geqdsk for freeqdsk.geqdsk by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/154
• Use contourpy instead of scikit-image by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/155
• Handle case when electron is last species by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/156
• Increase tolerance on fourier test by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/157
• Create CITATION.cff by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/158
• Fixed error in reading beta_prime from TGLF input by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/162
• Enhancements/poincare map by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/160
• Relax matplotlib contraint to >=3.3.4 (for OMFIT compatibility) by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/169
• Adds automatic COCOS detection and conversion for equilibria by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/161
• Bugfix/nspecies gene by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/172
• Zeff bugfix by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/174
• Handle different types of geometries by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/167
• standardize input scripts under templates by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/173
• Contributions to 'Feature/p file reader' by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/180
• Add command line interface by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/168
• Multiple GENE fixes by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/177
• Refactor Numerics by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/184
• Bugfix/cocos negative ip bt by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/181
• Bugfix/tglf mxh geometry by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/189
• Added cli for generating input files by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/190
• Removed base object of LocalGeometry as cleverdict as it had odd impa… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/192
• Enhancements/kinetics units by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/185
• Bugfix/transp major radius by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/193
• S_ZETA mislabel gk input cgyro by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/194
• Check for OMEGA in TRANSP and use .m for quantity if no data by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/195
• Set GENE output time to index and scale by nrg/field istep by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/191
• Enhancements/ion normalsation inputs by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/196
• Example GKOutput Implementation by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/186
• Enhancement/metric terms by @hgd511 in https://github.com/pyro-kinetics/pyrokinetics/pull/165
• Feature/p file reader by @jfparisi in https://github.com/pyro-kinetics/pyrokinetics/pull/179
• Update input.gene by @dake0795 in https://github.com/pyro-kinetics/pyrokinetics/pull/201
• Pin scipy to 1.10.1 by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/211
• Tests: Run example in /tmp by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/209
• WIP: Enhancements/gk output normalisation tweaks by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/213
• Enhancements/gk output normalisation by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/182
• Removed dZ0dr/shift from LocalGeometryFourierGENE.py as they shouldnt… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/212
• Typo/wrong variable used for temp moment by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/215
• Switch to pyloidal from omas by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/216
• Great rename of modules by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/217
• How to read equilibrium and profiles to create a GK input file by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/219
• Docs structure normalisations by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/221
• Enhancements/pyroscan apply func by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/220
• Restrict IDSPy features to Python version >= 3.9 by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/222
• Add method to convert Pyro object to IMAS dict by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/113
• Enhancements/gamma exb by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/214
• Reorganise and expand documentation by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/203
• Add neighbours as kwargs for RBFinterp in transp eq by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/224
• Bugfix/gkoutput issues by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/226
• Change theta grid from original geometry to MXH geometry when loading… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/227
• Update CITATION.cff by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/230
• Bugfix: Prevent main.py running when importing by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/228
• Need |q| for balloon transform in CGYRO by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/231
• Jetto files by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/232
• Bugfix/tglf transport eigval by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/237
• Add check for newer gs2 netcdf plus fix eigenfunction attr error by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/238
• Factories and Readers refactor + documentation by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/225
• Shift in kx coord, not ky coord in GENE by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/240
• add linear output documentation files by @hgd511 in https://github.com/pyro-kinetics/pyrokinetics/pull/241
• Add lightweight linear CGYRO scan to templates by @tomneiser in https://github.com/pyro-kinetics/pyrokinetics/pull/242
• Enhancement/reduce memory usage by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/239
• Fix alpha temp by @arkabokshi in https://github.com/pyro-kinetics/pyrokinetics/pull/244
• Select fields to load from data coords by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/243
• Remove deprecated system_packages for RTD by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/250

New Contributors

• @hgd511 made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/137
• @arkabokshi made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/174
• @jfparisi made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/179
• @tomneiser made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/242

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.4.0...v0.5.0

Scientific Software - Peer-reviewed - Python
Published by bpatel2107 over 2 years ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.4.0

Breaking Changes

• Drop support for Python 3.7 by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/118

What's Changed

• Fix for checking wstar_units set in nonlinear GS2 inputs by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/114
• Minor fixes and tests for missing/default keys in GS2 inputs by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/115
• Fix GENE reader for missing geometry::minor_r input by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/117
• Fix/cgyro sign frequency by @mgiacomin in https://github.com/pyro-kinetics/pyrokinetics/pull/119
• Fix reading nonlinear input for GENE by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/120

New Contributors

• @mgiacomin made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/119

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.3.0...v0.4.0

Scientific Software - Peer-reviewed - Python
Published by ZedThree over 3 years ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis - v0.3.0

What's Changed

• Fix bug in default Miller object: typos in attribute names by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/31
• Small tidy of docs by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/34
• Bugfix/rtd module missing by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/35
• Added flag for linear vs nonlinear fluxes and fixed error in non-zona… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/36
• Write json file describing pyro object and read in tolerance and flux… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/37
• Pull some Miller methods out into free functions by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/38
• Made generator for outer product a class method by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/39
• Data in each Pyro in PyroScan now a deepcopy by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/41
• Switched CGYRO frequency sign to match pyrokinetics convention by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/44
• theta0 not set in CGYRO/GENE writer by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/43
• Re-scale beta_prime if using different Bref by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/45
• Do line integral of path in psi contour fit to find closed loop for s… by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/47
• Removed Rgeo from miller object and corrected normalisations by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/53
• Enhancement/name gk type by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/54
• Check len con.collections and set path correctly by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/52
• WIP: Read transp eq by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/48
• Kinetics plugin architecture by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/58
• Flake8 fixes from #58 by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/62
• Bugfix/miller float point error by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/63
• Equilibrium plugin architecture by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/61
• GKCode plugin architecture by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/65
• LocalGeometry plugin architecture by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/66
• Bugfix/jetto multiple impurities by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/68
• Pass kwargs to Equilibrium/Kinetics object by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/69
• Fixed file inference for GKCode by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/73
• Bugfix/cgyro gene writer by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/75
• Fixed how rho is calculated from the JETTO kinetic data by @dake0795 in https://github.com/pyro-kinetics/pyrokinetics/pull/76
• Enable recreating PyroScan instances by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/79
• Fix for f90nml v1.4 by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/82
• Feature/nearest z jetto by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/83
• Bugfix/update examples by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/84
• Pyro/GK refactor by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/67
• Bugfix/gene beta prime by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/92
• Add TGLF into pyrokinetics by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/91
• 'supported types' lists now properties, not class-level vars by @LiamPattinson in https://github.com/pyro-kinetics/pyrokinetics/pull/99
• GENE field file .h5 read capability added. Corrections to open last field and nrg entries - Test files updated. by @ajaycj1 in https://github.com/pyro-kinetics/pyrokinetics/pull/104
• GENE circular geometry read capability added by @ajaycj1 in https://github.com/pyro-kinetics/pyrokinetics/pull/107
• Enable reading more kinds of GS2 simulations by @ZedThree in https://github.com/pyro-kinetics/pyrokinetics/pull/98
• Bugfix/gene rho fix by @bpatel2107 in https://github.com/pyro-kinetics/pyrokinetics/pull/110

New Contributors

• @LiamPattinson made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/58
• @ajaycj1 made their first contribution in https://github.com/pyro-kinetics/pyrokinetics/pull/104

Full Changelog: https://github.com/pyro-kinetics/pyrokinetics/compare/v0.2.0-alpha...v0.3.0

Scientific Software - Peer-reviewed - Python
Published by ZedThree over 3 years ago

Pyrokinetics - A Python library to standardise gyrokinetic analysis -

Scientific Software - Peer-reviewed - Python
Published by ZedThree over 4 years ago