Release v2.0

What's Changed

• Purge all legacy fenics content ready for new fenicsx by @jhdark in #583
• HydrogenTransportProblem class, Mesh and 1Dmesh class by @jhdark in #584
• Fix readthedocs by @RemDelaporteMathurin in #586
• GitHub actions CI workflow by @jhdark in #589
• Species class by @RemDelaporteMathurin in #585
• Formulation by @RemDelaporteMathurin in #587
• Fix docs build by @RemDelaporteMathurin in #592
• Permeation test case modification by @jhdark in #591
• new docker workflow by @jhdark in #595
• Subdomain classes by @jhdark in #593
• Materials class and temperature processing by @jhdark in #596
• Mesh properties fdim and vdim by @jhdark in #599
• Check borders by @jhdark in #601
• Implement simple run method by @RemDelaporteMathurin in #604
• VTX export capability by @RemDelaporteMathurin in #603
• Remove conda workflow temporarily by @jhdark in #608
• Mesh normal as property of F.Mesh by @jhdark in #605
• Fix conda workflow, new badges by @jhdark in #610
• benchmarking script by @jhdark in #607
• Dirichlet BC attempt 3 by @RemDelaporteMathurin in #609
• added the export stage in .run() by @RemDelaporteMathurin in #612
• Support for XDMF export by @RemDelaporteMathurin in #613
• Fix ufl cell vs basix cell by @RemDelaporteMathurin in #615
• Reactions by @RemDelaporteMathurin in #614
• Settings and Stepsize classes by @jhdark in #616
• Multispecies support by @jhdark in #617
• Iterate method by @RemDelaporteMathurin in #621
• Time dependent temperature by @jhdark in #620
• Fix vtx outputs zero by @RemDelaporteMathurin in #624
• Better error message when users use conditional for functions of t only by @RemDelaporteMathurin in #627
• Surface Quantities: Surface Flux by @jhdark in #629
• Update time dependent bcs by @jhdark in #619
• Henry's boundary conditions by @gabriele-ferrero in #637
• support sources by @jhdark in #636
• Tests for reactions 2 by @jhdark in #639
• Reactions in formulation by @RemDelaporteMathurin in #633
• typo in F.Source by @jhdark in #645
• Steady state by @RemDelaporteMathurin in #642
• Mesh from XDMF files by @jhdark in #641
• Use dolfinx v0.7.0 in CI by @jhdark in #658
• Formulation well defined by @jhdark in #646
• H transport initialisation refactoring by @jhdark in #661
• Adaptive stepsize by @RemDelaporteMathurin in #654
• Trap convenience class by @jhdark in #657
• Initial Conditions by @jhdark in #640
• Mesh1D vertices to accept list by @JonathanGSDUFOUR in #665
• Custom fenics mesh by @jhdark in #677
• Reduce number of warnings by @RemDelaporteMathurin in #683
• Patch derived quantity overwriting csv file by @RemDelaporteMathurin in #706
• Total volume quantity by @RemDelaporteMathurin in #703
• Reaction.product now accepts a list of Species by @RemDelaporteMathurin in #704
• MMS testing by @jhdark in #721
• Heat transfer class by @RemDelaporteMathurin in #686
• Remove Source for ParticleSource by @RemDelaporteMathurin in #732
• fenicsx: Flux BC support by @jhdark in #737
• Fix codecov checks by @RemDelaporteMathurin in #756
• Adds init to boundary conditions file by @RemDelaporteMathurin in #758
• Surface Flux fix by @jhdark in #747
• tqdm.auto instead of tqdm.autonotebook + refresh by @RemDelaporteMathurin in #759
• Refactor create_value_fenics for source and fluxes by @RemDelaporteMathurin in #750
• Robin boundary conditions for ParticleFlux by @RemDelaporteMathurin in #752
• Arbitrary reaction by @Allentro in #730
• Pin version in benchmark by @RemDelaporteMathurin in #784
• Simplify custom tagging of meshes by @RemDelaporteMathurin in #755
• DerivedQuantities for fenicsx by @JonathanGSDUFOUR in #735
• created shared Problem class for HeatTransferProblem and HTransportProblem by @rekomodo in #857
• Update dolfinx 0.8 by @RemDelaporteMathurin in #764
• added possibility to not display the progress bar by @RemDelaporteMathurin in #879
• New default PETSC parameters by @RemDelaporteMathurin in #899
• Interface concentration discontinuities (fenicsx) by @RemDelaporteMathurin in #878
• Fix API docs by @RemDelaporteMathurin in #905
• Fix solver options by @RemDelaporteMathurin in #909
• Surface reactions by @RemDelaporteMathurin in #753
• Various fixes by @kaelyndunnell in #894
• Reset derived quantity objects data and t at the beginning of a simulation by @Allentro in #733
• Adaptive timestepping by @kaelyndunnell in #916
• Penalty method for interfaces by @RemDelaporteMathurin in #918
• Always CI on different docker versions by @RemDelaporteMathurin in #923
• Fix timestep bug by @kaelyndunnell in #922
• Update docs on fenicsx by @RemDelaporteMathurin in #931
• ImplicitSpecies.n can be space and time dependent by @RemDelaporteMathurin in #886
• Change of variable method for interface discontinuities by @RemDelaporteMathurin in #904
• added scifem as conda dependency by @RemDelaporteMathurin in #943
• Support nightly by @RemDelaporteMathurin in #955
• New method to handle and convert user inputs to FEniCS objects by @jhdark in #940
• Conda install 2.0 by @RemDelaporteMathurin in #960
• Coupled transient heat transfer and hydrogen transport models by @jhdark in #948
• Find max value in parallel safely by @jhdark in #953
• Checkpointing by @RemDelaporteMathurin in #952
• Allows tolerances to be callable by @kaelyndunnell in #958
• use temporary directory for exports by @jhdark in #968
• 1D mesh parallelisation by @jhdark in #964
• Advection term support by @jhdark in #965
• Add VTX Temperature Export (with rebased branch) by @kaelyndunnell in #957
• Subdomains documentation by @jhdark in #971
• Refactoring by @RemDelaporteMathurin in #963
• Remove velocity field export from test by @jhdark in #977
• API documentation for fenicsx branch by @jhdark in #976
• allow Value for SourceBase by @RemDelaporteMathurin in #979
• nmm_interpolation function options by @jhdark in #984
• Fix locate entities by @RemDelaporteMathurin in #981
• Fix temperature parent mesh by @RemDelaporteMathurin in #987
• Allow functions to given as diffusion coefficient by @jhdark in #989
• Derived quantities for mixed domain by @RemDelaporteMathurin in #982
• Export at specific times by @jhdark in #990
• Fix transient csv writing for VolumeQuantity by @RemDelaporteMathurin in #994
• Added adaptive timestepping by @RemDelaporteMathurin in #993
• Parrallel assemble with scifem by @RemDelaporteMathurin in #995
• Added functionality to specify degree element order by @ck768 in #997
• test fixes by @jorgensd in #1008
• Delete options once they have been applied by @RemDelaporteMathurin in #1009
• New SNES newton solver for dolfinx 0.10 by @RemDelaporteMathurin in #1006
• Simplify SurfaceSubdomain by @RemDelaporteMathurin in #1005
• Multiple mobile species in mixed domain problem by @RemDelaporteMathurin in #1014
• Profile 1d export by @RemDelaporteMathurin in #1013
• Profile 1d 1 species by @RemDelaporteMathurin in #1015
• Locator for VolumeSubdomain by @RemDelaporteMathurin in #1016
• Add times argument to ProfileExport by @RemDelaporteMathurin in #1017
• Initial condition for mixed domain by @jhdark in #1019
• Fixes for DOLFINx v0.10 by @jhdark in #1020
• Cylindrical and Spherical coordinate support by @jhdark in #1011
• Dont output on tests by @jhdark in #1024
• [BUG FIX] Initial condition bug by @jhdark in #1025
• Documentation for BC's in v2.0 by @jhdark in #974
• [BUG] Fix for exports with Change of Variable method by @jhdark in #1028
• Add enums and remove python implementation of transfer meshtags to submesh by @jorgensd in #1029
• fix repo branch in docs for suggested edits by @hhy2022 in #1032
• Fixed broken link for HTM by @hhy2022 in #1033
• Fix del problem by @RemDelaporteMathurin in #1034
• Only get diffusion coeff if mobile by @jhdark in #1037
• Fix to allow D as Function in discontinuous case by @RemDelaporteMathurin in #1040
• Update post-processing solution in multispecies cases by @jhdark in #1038
• Update to use dolfinx v0.10 by @jhdark in #1039
• Only used mixed function spaces by @jhdark in #1042
• removed old TODO comment by @hhy2022 in #1048
• Non convergence error + SNES div tol unlimited by @RemDelaporteMathurin in #1049
• Boundary condition handling by @jhdark in #1044
• Fix badges in README by @jhdark in #1050
• Fixed bug with advection fields + mixed domains by @RemDelaporteMathurin in #1051
• fixed two more links + updated citation by @RemDelaporteMathurin in #1052
• Fix Surface Reaction BC in Discontinuous Case by @kaelyndunnell in #1056
• Fix surface exports by @jhdark in #1058
• removed sphinx-contrib by @RemDelaporteMathurin in #1065
• Add URL checker to doctest workflow by @RemDelaporteMathurin in #1068
• Subdomain temperature fields by @jhdark in #1060
• Initial conditions in mixed-domain cases by @jhdark in #1066
• Logger by @RemDelaporteMathurin in #1070
• Fix: prevent duplicate exports by popping matched time in is_it_time_… by @AdriaLlealS in #1073
• Hotfix for Total Volume bug by @RemDelaporteMathurin in #1083
• Fellowship docs by @jhdark in #1085
• Add apply button to fellowship page by @jhdark in #1087
• New name attribute for subdomains by @tez-orr123 in #1089
• Patch implicit species bug by @tez-orr123 in #1090
• Fixes & minor improvements by @RemDelaporteMathurin in #1091
• Improved default PETSc options behaviour by @RemDelaporteMathurin in #1077
• fellowship page updates by @RemDelaporteMathurin in #1095
• Various fixes in IO by @jorgensd in #1078
• Update fellowship page by @jhdark in #1096
• Refactoring interfaces by @RemDelaporteMathurin in #1098
• FESTIM2 merge by @RemDelaporteMathurin in #1102
• Bump conda-incubator/setup-miniconda from 2 to 3 by @dependabot[bot] in #1103
• Bump codecov/codecov-action from 4 to 6 by @dependabot[bot] in #1104
• Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.14.0 by @dependabot[bot] in #1105
• Bump actions/setup-python from 2 to 6 by @dependabot[bot] in #1106
• Bump actions/checkout from 2 to 6 by @dependabot[bot] in #1107
• Nightly conda build by @RemDelaporteMathurin in #1110
• updated url by @RemDelaporteMathurin in #1111
• Conda nightly by @RemDelaporteMathurin in #1112
• improved installation instructions by @RemDelaporteMathurin in #1113
• Bump actions/checkout from 4 to 6 by @dependabot[bot] in #1116
• Give name to post processing functions by @RemDelaporteMathurin in #1124
• Qol unmarked cells by @RemDelaporteMathurin in #1118
• Qol auto detect surface to volume by @RemDelaporteMathurin in #1122
• Custom Field export by @RemDelaporteMathurin in #1126
• Bump conda-incubator/setup-miniconda from 3 to 4 by @dependabot[bot] in #1129
• Ruff fixes by @RemDelaporteMathurin in #1119
• Update .sub_T when temperature is time dependent by @RemDelaporteMathurin in #1128
• Workflow for adding institutions by @RemDelaporteMathurin in #1132
• Export reaction rate by @RemDelaporteMathurin in #1127
• Landing page makeover by @RemDelaporteMathurin in #1131
• Publications page by @RemDelaporteMathurin in #1139
• Add base env to install build tools (nightly conda) by @RemDelaporteMathurin in #1142
• Bump actions/checkout from 4 to 6 by @dependabot[bot] in #1145
• Bump peter-evans/create-pull-request from 6 to 8 by @dependabot[bot] in #1146
• Bump peter-evans/create-or-update-comment from 4 to 5 by @dependabot[bot] in #1147
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #1144
• Fix conda nightly 2 by @RemDelaporteMathurin in #1148
• Tez fellowship testimonial by @RemDelaporteMathurin in #1143
• New FESTIM paper by @RemDelaporteMathurin in #1149
• Support VTXTemperatureExport in mixed domain case by @RemDelaporteMathurin in #1140
• Add GenF Systems to landing page by @github-actions[bot] in #1151
• Custom derived quantity by @RemDelaporteMathurin in #1138
• remove duplicate by @RemDelaporteMathurin in #1152

New Contributors

• @ck768 made their first contribution in #997
• @jorgensd made their first contribution in #1008
• @AdriaLlealS made their first contribution in #1073
• @tez-orr123 made their first contribution in #1089
• @dependabot[bot] made their first contribution in #1103
• @github-actions[bot] made their first contribution in #1151

Full Changelog: v1.4.2...v2.0