.codecov.yml
.environment.yaml
.flake8
.git-blame-ignore-revs
.gitignore
.readthedocs.yaml
CHANGELOG.md
CITATION.cff
Dockerfile
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/black.yml
.github/workflows/docker_publish.yml
.github/workflows/draft-pdf.yml
.github/workflows/flake8.yml
.github/workflows/python_publish.yml
.github/workflows/tests.yml
docs/Makefile
docs/api.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/_templates/custom-class-template.rst
docs/_templates/custom-module-template.rst
docs/developer_guide/contributing_guide.rst
docs/developer_guide/writing_docs.rst
docs/examples/bicoherence.rst
docs/examples/example.py
docs/examples/example_JETTO.py
docs/examples/example_JETTO_1dscan.py
docs/examples/example_JETTO_1dscan_complicated.py
docs/examples/example_PFILE.py
docs/examples/example_SCENE.py
docs/examples/example_TRANSP.py
docs/examples/example_add_bespoke_gk_output_data.py
docs/examples/example_addflags.py
docs/examples/example_cgyro.py
docs/examples/example_cgyro_to_stella.py
docs/examples/example_create_pyroscan.py
docs/examples/example_enforce_pvg.py
docs/examples/example_gene.py
docs/examples/example_generate_global_profiles.py
docs/examples/example_geqdsk.py
docs/examples/example_gs2.py
docs/examples/example_gx.py
docs/examples/example_ideal_ballooning.py
docs/examples/example_imas.py
docs/examples/example_merge_species.py
docs/examples/example_modify_shear.py
docs/examples/example_neoclassical.py
docs/examples/example_nonlinear_cgyro.py
docs/examples/example_nonzonal.py
docs/examples/example_poincare.py
docs/examples/example_pyro.py
docs/examples/example_pyro_jetto_bootstrap_comparison.py
docs/examples/example_pyro_to_netcdf.py
docs/examples/example_pyroscan_to_netcdf.py
docs/examples/example_read_cgyro_output.py
docs/examples/example_read_gene_output.py
docs/examples/example_read_gs2_output.py
docs/examples/example_read_pyroscan_output.py
docs/examples/example_read_tglf_linear.py
docs/examples/example_read_tglf_transport.py
docs/examples/example_real_space_3d.py
docs/examples/example_real_space_moment.py
docs/examples/example_saturation.py
docs/examples/example_simdb_yaml.py
docs/examples/example_syn_hk_dbs.py
docs/examples/ideal_ballooning.rst
docs/examples/index.rst
docs/examples/load_jetto.rst
docs/examples/load_transp.rst
docs/examples/parameter_scan.rst
docs/examples/pyro_example.rst
docs/examples/read_output.rst
docs/examples/figures/.DS_Store
docs/examples/figures/ideal_ballooning.png
docs/howtos/convert.rst
docs/howtos/field_line.rst
docs/howtos/index.rst
docs/howtos/linear_outputs.rst
docs/howtos/merge_species.rst
docs/howtos/normalisations.rst
docs/howtos/parameter_scans.rst
docs/howtos/read_eq_prof.rst
docs/howtos/read_nonlinear_data.rst
docs/howtos/real_space_plotting.rst
docs/howtos/stella_input_versions.rst
docs/howtos/syn_hkdbs.rst
docs/howtos/figures/CGYRO_ky_flux_spectrum.png
docs/howtos/figures/CGYRO_phi_kxky.png
docs/howtos/figures/CGYRO_total_heat_timetrace.png
docs/howtos/figures/GS2_eigenfunction_plot.png
docs/howtos/figures/GS2_ion_linear_flux_plot.png
docs/howtos/figures/GS2_linear_phi_field_plot.png
docs/howtos/figures/GS2_mode_frequency_plot.png
docs/howtos/figures/jet_example_scatloc.png
docs/howtos/figures/poincare.png
docs/joss/paper.bib
docs/joss/paper.md
docs/tutorials/equilibrium.rst
docs/tutorials/file_readers.rst
docs/tutorials/index.rst
docs/tutorials/kinetics.rst
docs/tutorials/using_pyrokinetics_on_hpc_systems.rst
docs/tutorials/figures/equilibrium_composite_plot.png
docs/tutorials/figures/equilibrium_contour_plot.png
docs/tutorials/figures/equilibrium_q_plot.png
docs/tutorials/figures/flux_surface_b_poloidal_plot.png
docs/tutorials/figures/flux_surface_path_plot.png
docs/user_guide/analysis.rst
docs/user_guide/collisions.rst
docs/user_guide/getting_started.rst
docs/user_guide/index.rst
docs/user_guide/metric_terms.rst
docs/user_guide/miller.rst
docs/user_guide/modify_shear.rst
docs/user_guide/structure.rst
docs/user_guide/figures/equilibrium.png
docs/user_guide/figures/gk_code.png
docs/user_guide/figures/kinetics.png
docs/user_guide/figures/pyro_structure.png
src/pyrokinetics/__init__.py
src/pyrokinetics/__main__.py
src/pyrokinetics/_version.py
src/pyrokinetics/constants.py
src/pyrokinetics/dataset_wrapper.py
src/pyrokinetics/decorators.py
src/pyrokinetics/factory.py
src/pyrokinetics/file_utils.py
src/pyrokinetics/local_species.py
src/pyrokinetics/metadata.py
src/pyrokinetics/normalisation.py
src/pyrokinetics/numerics.py
src/pyrokinetics/plugins.py
src/pyrokinetics/pyro.py
src/pyrokinetics/pyroscan.py
src/pyrokinetics/species.py
src/pyrokinetics/templates.py
src/pyrokinetics/typing.py
src/pyrokinetics/units.py
src/pyrokinetics.egg-info/PKG-INFO
src/pyrokinetics.egg-info/SOURCES.txt
src/pyrokinetics.egg-info/dependency_links.txt
src/pyrokinetics.egg-info/entry_points.txt
src/pyrokinetics.egg-info/requires.txt
src/pyrokinetics.egg-info/top_level.txt
src/pyrokinetics/cli/__init__.py
src/pyrokinetics/cli/convert.py
src/pyrokinetics/cli/entrypoint.py
src/pyrokinetics/cli/generate.py
src/pyrokinetics/databases/__init__.py
src/pyrokinetics/databases/imas.py
src/pyrokinetics/databases/yaml.py
src/pyrokinetics/diagnostics/__init__.py
src/pyrokinetics/diagnostics/convergence.py
src/pyrokinetics/diagnostics/field_line.py
src/pyrokinetics/diagnostics/neoclassical.py
src/pyrokinetics/diagnostics/saturation_rules.py
src/pyrokinetics/diagnostics/synthetic_highk_dbs.py
src/pyrokinetics/equilibrium/__init__.py
src/pyrokinetics/equilibrium/eliteinp.py
src/pyrokinetics/equilibrium/equilibrium.py
src/pyrokinetics/equilibrium/flux_surface.py
src/pyrokinetics/equilibrium/gacode.py
src/pyrokinetics/equilibrium/geqdsk.py
src/pyrokinetics/equilibrium/imas.py
src/pyrokinetics/equilibrium/transp.py
src/pyrokinetics/equilibrium/utils.py
src/pyrokinetics/gk_code/__init__.py
src/pyrokinetics/gk_code/cgyro.py
src/pyrokinetics/gk_code/gene.py
src/pyrokinetics/gk_code/gk_input.py
src/pyrokinetics/gk_code/gk_output.py
src/pyrokinetics/gk_code/gkw.py
src/pyrokinetics/gk_code/gs2.py
src/pyrokinetics/gk_code/gx.py
src/pyrokinetics/gk_code/ids.py
src/pyrokinetics/gk_code/neo.py
src/pyrokinetics/gk_code/stella.py
src/pyrokinetics/gk_code/tglf.py
src/pyrokinetics/kinetics/__init__.py
src/pyrokinetics/kinetics/eliteinp.py
src/pyrokinetics/kinetics/gacode.py
src/pyrokinetics/kinetics/imas.py
src/pyrokinetics/kinetics/iterdb.py
src/pyrokinetics/kinetics/jetto.py
src/pyrokinetics/kinetics/kinetics.py
src/pyrokinetics/kinetics/pfile.py
src/pyrokinetics/kinetics/scene.py
src/pyrokinetics/kinetics/transp.py
src/pyrokinetics/local_geometry/__init__.py
src/pyrokinetics/local_geometry/fourier_cgyro.py
src/pyrokinetics/local_geometry/fourier_gene.py
src/pyrokinetics/local_geometry/local_geometry.py
src/pyrokinetics/local_geometry/metric.py
src/pyrokinetics/local_geometry/miller.py
src/pyrokinetics/local_geometry/miller_turnbull.py
src/pyrokinetics/local_geometry/mxh.py
src/pyrokinetics/templates/core_profiles.h5
src/pyrokinetics/templates/equilibrium.h5
src/pyrokinetics/templates/input.cgyro
src/pyrokinetics/templates/input.gacode
src/pyrokinetics/templates/input.gene
src/pyrokinetics/templates/input.gkw
src/pyrokinetics/templates/input.gs2
src/pyrokinetics/templates/input.gx
src/pyrokinetics/templates/input.neo
src/pyrokinetics/templates/input.stella
src/pyrokinetics/templates/input.stella_nl
src/pyrokinetics/templates/input.stella_pre_v1
src/pyrokinetics/templates/input.stella_pre_v1_nl
src/pyrokinetics/templates/input.tglf
src/pyrokinetics/templates/input_wunits.gene
src/pyrokinetics/templates/jetto.jsp
src/pyrokinetics/templates/jetto.jss
src/pyrokinetics/templates/pfile.txt
src/pyrokinetics/templates/reverse_ipbt.geqdsk
src/pyrokinetics/templates/scene.cdf
src/pyrokinetics/templates/step.geqdsk
src/pyrokinetics/templates/template.yaml
src/pyrokinetics/templates/test.eliteinp
src/pyrokinetics/templates/test.geqdsk
src/pyrokinetics/templates/test.iterdb
src/pyrokinetics/templates/transp.cdf
src/pyrokinetics/templates/transp_eq.geqdsk
tests/conftest.py
tests/test_decorators.py
tests/test_deepcopy.py
tests/test_file_utils.py
tests/test_local_species.py
tests/test_normalisation.py
tests/test_numerics.py
tests/test_plugins.py
tests/test_pyro.py
tests/test_pyroscan.py
tests/test_roundtrip.py
tests/test_species.py
tests/cli/test_convert.py
tests/databases/test_imas.py
tests/databases/golden_answers/Apa_kykxs00000135_imag_sp
tests/databases/golden_answers/Apa_kykxs00000135_real_sp
tests/databases/golden_answers/Bpa_kykxs00000135_imag_sp
tests/databases/golden_answers/Bpa_kykxs00000135_real_sp
tests/databases/golden_answers/Phi_kykxs00000135_imag_sp
tests/databases/golden_answers/Phi_kykxs00000135_real_sp
tests/databases/golden_answers/Tpar_kykxs01_000135_imag_sp
tests/databases/golden_answers/Tpar_kykxs01_000135_real_sp
tests/databases/golden_answers/Tpar_kykxs02_000135_imag_sp
tests/databases/golden_answers/Tpar_kykxs02_000135_real_sp
tests/databases/golden_answers/Tperp_kykxs01_000135_imag_sp
tests/databases/golden_answers/Tperp_kykxs01_000135_real_sp
tests/databases/golden_answers/Tperp_kykxs02_000135_imag_sp
tests/databases/golden_answers/Tperp_kykxs02_000135_real_sp
tests/databases/golden_answers/dens_kykxs01_000135_imag_sp
tests/databases/golden_answers/dens_kykxs01_000135_real_sp
tests/databases/golden_answers/dens_kykxs02_000135_imag_sp
tests/databases/golden_answers/dens_kykxs02_000135_real_sp
tests/databases/golden_answers/file_count
tests/databases/golden_answers/fluxes.dat
tests/databases/golden_answers/fluxes_bpar.dat
tests/databases/golden_answers/fluxes_em.dat
tests/databases/golden_answers/geom.dat
tests/databases/golden_answers/imas_example.h5
tests/databases/golden_answers/input.dat
tests/databases/golden_answers/input.out
tests/databases/golden_answers/krho
tests/databases/golden_answers/kxrh
tests/databases/golden_answers/parallel.dat
tests/databases/golden_answers/time.dat
tests/databases/golden_answers/vpar_kykxs01_000135_imag_sp
tests/databases/golden_answers/vpar_kykxs01_000135_real_sp
tests/databases/golden_answers/vpar_kykxs02_000135_imag_sp
tests/databases/golden_answers/vpar_kykxs02_000135_real_sp
tests/diagnostics/test_correlation.py
tests/diagnostics/test_displacement.py
tests/diagnostics/test_gs2_geometry.py
tests/diagnostics/test_ideal_ball.py
tests/diagnostics/test_neoclassical.py
tests/diagnostics/test_poincare.py
tests/diagnostics/golden_answers/correlation.npy
tests/diagnostics/golden_answers/displacement.npy
tests/diagnostics/golden_answers/ideal_ball.npy
tests/diagnostics/golden_answers/poincare.npy
tests/equilibrium/test_eliteinp.py
tests/equilibrium/test_equilibrium.py
tests/equilibrium/test_gacode.py
tests/equilibrium/test_geqdsk.py
tests/equilibrium/test_imas.py
tests/equilibrium/test_transp.py
tests/gk_code/__init__.py
tests/gk_code/test_gk_code_output.py
tests/gk_code/test_gk_input_cgyro.py
tests/gk_code/test_gk_input_gene.py
tests/gk_code/test_gk_input_gkw.py
tests/gk_code/test_gk_input_gs2.py
tests/gk_code/test_gk_input_gx.py
tests/gk_code/test_gk_input_stella.py
tests/gk_code/test_gk_input_tglf.py
tests/gk_code/test_gk_output.py
tests/gk_code/test_gk_output_reader_cgyro.py
tests/gk_code/test_gk_output_reader_gene.py
tests/gk_code/test_gk_output_reader_gkw.py
tests/gk_code/test_gk_output_reader_gs2.py
tests/gk_code/test_gk_output_reader_gx.py
tests/gk_code/test_gk_output_reader_stella.py
tests/gk_code/test_gk_output_reader_tglf.py
tests/gk_code/fixtures/input.stella_v1_from_pre_v1
tests/gk_code/golden_answers/cgyro_linear_output_899a2cb8.netcdf4
tests/gk_code/golden_answers/gene_linear_output_788f630f.netcdf4
tests/gk_code/golden_answers/gkw_linear_output_899a2cb8.netcdf4
tests/gk_code/golden_answers/gs2_linear_output_899a2cb8.netcdf4
tests/gk_code/golden_answers/gx_linear_output_899a2cb8.netcdf4
tests/gk_code/golden_answers/stella_linear_output_899a2cb8.netcdf4
tests/gk_code/golden_answers/tglf_linear_output_899a2cb8.netcdf4
tests/kinetics/test_kinetics.py
tests/kinetics/test_kinetics_reader_eliteinp.py
tests/kinetics/test_kinetics_reader_gacode.py
tests/kinetics/test_kinetics_reader_imas.py
tests/kinetics/test_kinetics_reader_iterdb.py
tests/kinetics/test_kinetics_reader_jetto.py
tests/kinetics/test_kinetics_reader_pfile.py
tests/kinetics/test_kinetics_reader_scene.py
tests/kinetics/test_kinetics_reader_transp.py
tests/local_geometry/test_fourier.py
tests/local_geometry/test_fourier_cgyro.py
tests/local_geometry/test_local_geometry.py
tests/local_geometry/test_local_geometry_factory.py
tests/local_geometry/test_metric_terms.py
tests/local_geometry/test_miller.py
tests/local_geometry/test_miller_turnbull.py
tests/local_geometry/test_mxh.py
tests/local_geometry/test_transp_cdf_vs_geqdsk.py