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 https://githu...

Patch 1.4.2

This is the last patch release on FESTIM1 before the big FESTIM2 merge!

What's Changed

• Hotfix by @RemDelaporteMathurin in #1027
• Fix broken link for HTM by @hhy2022 in #1031
• Docs improvement by @RemDelaporteMathurin in #1059
• Improved template by @RemDelaporteMathurin in #1061
• Add URL checker to doctest workflow (main) by @RemDelaporteMathurin in #1069
• Fellowship page on main docs by @jhdark in #1086
• Update fellowship page (main) by @jhdark in #1097

Full Changelog: v1.4.1...v1.5

Patch 2.0-beta2.2

What's Changed

• 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

New Contributors

• @AdriaLlealS made their first contribution in #1073

Full Changelog: v2.0-beta.2post1...v2.0b2.post2

v2.0-beta.2

This is a post release after v2.0-beta.2 was released on main by mistake...

What's Changed

• 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

Full Changelog: v2.0-beta.1...v2.0-beta.2post1

Release v2.0-beta.1

What's Changed

• 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

Full Changelog: v2.0-beta...v2.0-beta.1

Release v2.0-beta.0

What's Changed

• 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

Full Changelog: v2.0-alpha.8...v2.0-beta

Patch post 1.4.1

This is just a post release dropping support for python 3.9. No need to update

What's Changed

• Hotfix by @RemDelaporteMathurin in #1027

Full Changelog: v1.4.1...v1.4.1.post1

Release v2.0-alpha.8

What's Changed

• 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

Full Changelog: v2.0-alpha.7...v2.0-alpha.8

Release 2.0-alpha-7

What's Changed

• Profile 1d 1 species by @RemDelaporteMathurin in #1015
• Locator for VolumeSubdomain by @RemDelaporteMathurin in #1016
• Add times argument to ProfileExport by @RemDelaporteMathurin in #1017

Full Changelog: v2.0-alpha.6...v2.0-alpha.7

Release 2.0-a6

What's Changed

• 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

New Contributors

• @jorgensd made their first contribution in #1008

Full Changelog: v2.0-alpha.5...v2.0-alpha.6