Simplify MeshGeometry initialisation

[connorjward]

This seems tractable now that mesh.init is gone. This is part of a wider refactor that I want to do but this seems like a good start.

[connorjward]

The only failures now are some quite inscrutable IO ones with errors like:

2	[0] DMPlexSectionLoad() at /__w/firedrake/firedrake/petsc/src/dm/impls/plex/plex.c:2660
2	[0] DMPlexSectionLoad_HDF5_Internal() at /__w/firedrake/firedrake/petsc/src/dm/impls/plex/hdf5/plexhdf5.c:2972
2	[0] ISLoad() at /__w/firedrake/firedrake/petsc/src/vec/is/is/interface/index.c:1673
2	[0] ISLoad_Default() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/isio.c:113
2	[0] ISLoad_HDF5() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/isio.c:50
2	[0] PetscViewerHDF5Load() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/hdf5/hdf5io.c:327
2	[0] PetscViewerHDF5Load_Internal() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/hdf5/hdf5io.c:246
2	[0] Unexpected data in file
2	[0] Object (dataset) "order" not stored in group /topologies/channel_topology/dms/firedrake_dm_1_0_0_False_2
2	FAILED firedrake-repo/tests/firedrake/output/test_io_timestepping.py::test_io_timestepping[P2-P1] - petsc4py.PETSc.Error: error code 79
2	[0] DMPlexSectionLoad() at /__w/firedrake/firedrake/petsc/src/dm/impls/plex/plex.c:2660
2	[0] DMPlexSectionLoad_HDF5_Internal() at /__w/firedrake/firedrake/petsc/src/dm/impls/plex/hdf5/plexhdf5.c:2972
2	[0] ISLoad() at /__w/firedrake/firedrake/petsc/src/vec/is/is/interface/index.c:1673
2	[0] ISLoad_Default() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/isio.c:113
2	[0] ISLoad_HDF5() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/isio.c:50
2	[0] PetscViewerHDF5Load() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/hdf5/hdf5io.c:327
2	[0] PetscViewerHDF5Load_Internal() at /__w/firedrake/firedrake/petsc/src/vec/is/utils/hdf5/hdf5io.c:246
2	[0] Unexpected data in file
2	[0] Object (dataset) "order" not stored in group /topologies/channel_topology/dms/firedrake_dm_1_0_0_False_2

@ksagiyam do you know what could be causing this?

[ksagiyam]

We just need ngsPETSc.

[connorjward]

Suggested change

	pip install --no-deps git+https://github.com/connorjward/ngsPETSc.git@connorjward/mesh-init-changes netgen-mesher netgen-occt
	pip install --no-deps git+https://github.com/NGSolve/ngsPETSc.git netgen-mesher netgen-occt