pyrokinetics

• 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 get_flux_surface 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

• @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...v.0.5.0