Felupe

Added
- Add optional output location for `FieldContainer.extract(out=None)`.
- Add `Mesh.update(callback=None)`. This is especially useful if the points array of a mesh is changed and an already existing instance of a region has to be reloaded: `Mesh.update(points=new_points, callback=region.reload)`.
- Add `ax = FieldContainer.imshow()` which acts as a wrapper on top of the `img = FieldContainer.screenshot(filename=None)` method. The image data is passed to a matplotlib figure and the `ax` object is returned.
- Add `ax = Mesh.imshow()` which acts as a wrapper on top of the `img = Mesh.screenshot(filename=None)` method. The image data is passed to a matplotlib figure and the `ax` object is returned.
- Add view-methods for `SolidBody` and `SolidBodyNearlyIncompressible` (same as already implemented for mesh and fields).
- Add lists with norms of values and norms of the objective function in `tools.NewtonResult(xnorms=None, fnorms=None)`.
- Add lists of norms of the objective function as attribute to `Job.fnorms`.
- Add new method to `Mesh` for getting point ids next to a given point coordinate `Mesh.get_point_ids(value)`.
- Add new method to `Mesh` for getting cells attached to a given point coordinate `Mesh.get_cell_ids(point_ids)`.
- Add new method to `Mesh` for getting neighbour cells `Mesh.get_cell_ids_neighbours(cell_ids)`.
- Add new method to `Mesh` for getting shared points between neighbour cells `Mesh.get_point_ids_shared(cell_ids_neighbours)`.
- Add new method to `Mesh` for getting points on regular grids which are located at corners `Mesh.get_point_ids_corners()`.
- Add new method to `Mesh` for modifying the cell connectivity at corners `Mesh.modify_corners(point_ids=None)`, supported for regular quad and hexahedron meshes.

Changed
- Pass optional keyword-arguments in `math.dot(**kwargs)` to the underlying einsum-calls.
- Enhance the performance of `math.cdya()` by reducing the number of (intermediate) arrays to be created from 4 to 2.
- Use fixed output locations for the extracted field-gradients and the integrated stiffness matrices in `SolidBody` and `SolidBodyNearlyIncompressible`. This enhances the performance.
- Change default filename in `Mesh.screenshot()` from `filename="field.png"` to `filename="mesh.png"`.
- Change the return value on job-evaluation from `None = Job.evaluate()` to `job = Job.evaluate()`.
- Change implementation of `LinearElasticLargeStrain` from `NeoHooke` to `NeoHookeCompressible`.
- Do not invoke `pyvista.start_xvfb()` on a posix-os. If required, run it manually.
- Rename `tools._newton.Result` to `tools._newton.NewtonResult` and add it to the public API as `tools.NewtonResult` because this class is returned as a result of Newton's method.
- Rename the `r`-arguments of `tools.force()` and `tools.moment()` to `forces`.
- Rename the `point`-argument of `tools.moment()` to `centerpoint`.
- Rename the `r`-argument in `tools.save()` to `forces`. Remove the unused argument `converged`.
- Change the default file-extension from `.vtk` to `.vtu` in `tools.save(filename="result.vtu")`.
- Change the default values of the gravity vector to zeros if ``gravity=None`` in `SolidBodyGravity(field, gravity=None, density=1.0)`.

Fixed
- Fix `tools.moment()`. Use `math.cross()`. The old implementation was completely wrong!

Added
- Add `NeoHookeCompressible` for compressible hyperelastic materials or even as a fast alternative for `NeoHooke` when used in `SolidBodyIncompressible`.

Changed
- Vectorize `mesh.expand()` which enhances the performance of quad/hex mesh-generators like `Rectangle()` and `Cube()`.

Fixed
- Fix logarithmic strain tensor evaluation in `Job.evaluate(filename="result.xdmf")` and in `field.plot("Logarithmic Strain", component=0)`.

Added
- Add plot- and screenshot-methods to `Region` and `Scheme` (base class for quadratures).
- Add `item = FormItem(bilinearform, linearform=None)` to be used as an item in a `Step(items=[item])`.
- Add a new method `Boundary.apply_mask(mask)`. This simplifies re-definitions of boundary conditions with a custom `mask`.
- Add support for two-dimensional dof-based masks in `Boundary(mask)` with `mask.shape` of `(mesh.npoints, field.dim)` in addition to point-based masks with `mask.size` of `mesh.npoints`.
- Add a bubble-multiplier argument for `RegionTriangleMINI(mesh, bubble_multiplier=0.1)` and `RegionTetraMINI(mesh, bubble_multiplier=0.1)`.
- Add `region.reload(mesh, element, quadrature)` to re-evaluate a region, already linked to a field, with a modified mesh or element class or quadrature.

Changed
- Refactor the assembly-submodule. Move the weak-form expression-related classes to the `assembly.expression` submodule.
- Move `Basis` to the new `assembly.expression` submodule.
- Make the `field`-submodule public.
- Always `import felupe as fem` in docs and tests.
- Change default optional (keyword) arguments of a weak-form expression decorator from `Form(args=(), kwargs={})` to `Form(args=None, kwargs=None)`.
- Change default value of the skip-argument `Boundary(skip=None)`. This will be set to `(False, False, False)` during initialization if `mask=None`.
- Change the default bubble-multiplier in `RegionTriangleMINI` and `RegionTetraMINI` from 1.0 to 0.1. This affects only the template regions and not the element formulations `TriangleMINI` and `TetraMINI`, which still default to a bubble-multiplier of 1.0.
- Pass optional keyword-arguments to `math.einsum(**kwargs)`. This enables support for the `out`-argument.
- Don't broadcast `math.identity()`.
- Rename `quadrature/_base.py` to `quadrature/_scheme.py`.

Fixed
- Fix `Boundary` and subsequently also `dof.symmetry()` for different dimensions of the mesh and the field.
- Fix negative cell-volumes error in `RegionTriangleMINI` for meshes like `Rectangle(n=11).triangulate().add_midpoints_faces()` by scaling down the (arbitrary) bubble-multiplier from 1.0 to 0.1.

Removed
- Don't import `Basis` to the global namespace (not necessary as it is used only internally by the weak-`Form` expression decorator).
- Remove unused internal assemble-methods from `assembly.expression._linear.LinearForm` and `assembly.expression._bilinear.BilinearForm`.
- Remove extra-index-url `https://wheels.vtk.org` as they are now available on PyPI for Python 3.12.

Added
- Add cell-type argument to `Mesh.add_midpoints_volumes(cell_type=None)` and its variants for edges and faces.
- Add `element.Element.view()`, `element.Element.plot()` and `element.Element.screenshot()`. This enables an interactive plot of the element in the reference configuration with its point ids, e.g. `Hexahedron().plot().show()`.

Changed
- Change function signature and enhance `dof.biaxial(field, lefts=(None, None), rights=(None, None), moves=(0.2, 0.2), axes=(0, 1), clampes=(False, False), sym=True)`. Now with a full-featured docstring including an example.
- Change function signature and enhance `dof.shear(field, bottom=None, top=None, moves=(0.2, 0.0, 0.0), axes=(0, 1), sym=True)`. Now with a full-featured docstring including an example.
- Merge keyword-arguments for the dual-regions with hard-coded arguments in `FieldsMixed(region, **kwargs)`.
- Replace `np.product()` (will be removed in NumPy 2.0) with the equivalent `np.prod()`.

Fixed
- Fix `FieldsMixed()` for regions with MINI-element formulations: Disable the disconnection of the dual mesh.
- Fix `dof.shear(sym=True)` which was previously ignored due to a wrong setup of the symmetry boundaries.
- Fix the install command on Python 3.12 by adding an extra-index-url for VTK wheels if they are not yet available on PyPI (the extra index is provided by Kitware).
- Fix a warning because the timings of the Newton-Rhapson solver are printed from a one-dimensional array. Take the first item of the runtime-array to resolve this warning.

Deprecated
- Deprecate the old-style argument `move` in `dof.biaxial()`, which defaults to `None`.
- Deprecate the old-style arguments `move`, `axis_compression`, `axis_shear` and `compression` in `dof.shear()`, which all default to `None`.

Removed
- Remove the undocumented `dof.planar()` because this is a special case of the biaxial load case `dof.biaxial(field, clampes=(True, False), moves=(0.2, 0), sym=False, axes=(0, 1))`.

Added
- Add `ViewField` as method to a field container `FieldContainer.view()`. Now a field container provides the view sub-methods directly, i.e. add `FieldContainer.plot()` and `FieldContainer.screenshot(filename="mesh.png")`.

Changed
- Hide the undeformed mesh in `Mesh.plot()` by default (also affects `Mesh.screenshot()`).

Fixed
- Fix taking screenshots of a mesh.

Added
- Add `ViewMesh` as method to a mesh `Mesh.view()`. Now a mesh provides the view sub-methods directly, i.e. add `Mesh.plot()` and `Mesh.screenshot(filename="mesh.png")`.