Merge MR !165, 'jrwrigh/plex_filter_fix', into 'main'

fix(upstream): Update DMPlexFilter with new arguments from petsc:!8876

See merge request phypid/honee!165

fix(upstream): PETSc changes to PetscCtxDestroyFn

Merge MR !161, 'jrwrigh/dm-utils-coords', into 'main'

feat(dm_utils): Add Coordinate-specific getter for CeedField values

See merge request phypid/honee!161

feat: Add dedicated mesh transform functionality

Mostly so that the mesh transformation can occur independently of the
coordinate scaling process.

Merge MR !157, 'jrwrigh/format_parentesis_break', into 'main'

style: Change clang-format to penalize newline after open ()

See merge request phypid/honee!157

style: Change clang-format to penalize newline after open ()

Merge MR !153, 'jrwrigh/checkbadSource', into 'main'

style: Add checkbadSource

See merge request phypid/honee!153

style: Corrections from make checkbadSource

Merge MR !148, 'jrwrigh/newt_fluid_properties', into 'main'

refactor: Extract Newtonian fluid properties from primary Newtonian context

Closes #38

See merge request phypid/honee!148

refactor: Extract NewtonianIGProperties from NewtonianIdealGasContext

Merge MR !146, 'jrwrigh/refactor', into 'main'

refactor: Use compound literals for struct initialization

See merge request phypid/honee!146

refactor: Use compound literals for struct setting

Using compound literals to initialize structs is often either easier to
read or more compact than setting struct members individually
one-by-one.

Merge MR !145, 'jrwrigh/refactor', into 'main'

refactor: Change default struct in Newtonian, change Calloc1() -> New(), DivFDiff changes

See merge request phypid/honee!145

style: Change PetscCalloc1(1, ...) into PetscNew(...)

Merge MR !133, 'Amin/units', into 'main'

Unify `Units` setup

See merge request phypid/honee!133

(!133) Unify `Units` setup

Merge MR !122, 'jrwrigh/honee_petscobject', into 'main'

feat: Convert Honee to PetscObject, remove auxillary structs

See merge request phypid/honee!122

feat: Move differential filtering into separate header

Merge MR !118, 'jrwrigh/rename_jac_data_size', into 'main'

style: jac_data_size -> num_comps_jac_data

See merge request phypid/honee!118

Merge MR !116, 'jrwrigh/update_jac_data_size_bc', into 'main'

feat(bc): Shrink jac_data_size to that being used

Closes #30

See merge request phypid/honee!116

Merge MR !67, 'jrwrigh/bc_QF_setup', into 'main'

Use BCDefinition for setting up boundary integral QFunctions

Closes #27

See merge request phypid/honee!67

style: jac_data_size -> num_comps_jac_data

Includes:
- jac_data_size_sur -> num_comps_jac_data
- jac_data_size_vol -> num_comps_jac_data
- jac_data_size -> num_comps_jac_data

feat(bc): Shrink jac_data_size to that being used

refactor: Delete SimpleBC struct

bc(inflow): Convert inflow bc to use BCDef functions