Port to Ubuntu 24.04

[MakisH]

Summary of the changes:

• Updates the base box to bento/ubuntu-24.04
• Updates some basic packages and various links
• Creates reusable Python virtual environments in the ~/python-venvs directory, since we can no longer use system- or user-wide installations with PIP.
• Installs deal.II from the Ubuntu packages instead of the PPA. We not have 9.5.1 instead of 9.3.0, but the adapter seems to build successfully.
• Applies the usual patch to the CalculiX 2.20 Makefile environment.

The current state is building successfully.

What is currently missing:

• code_aster: the current stable version (14.6) has several issues. I would not wait for this to merge and even release.
• FEniCS: there seems to be no package yet. This would be quite important for us. I assume that the developers mainly want to push towards FEniCS-X, given that I only see some *x packages for noble. @IshaanDesai @BenjaminRodenberg do you have any insight on this?
• ASTE: It depends on VTK, but the VTK package seems to conflict with other packages:

  python3-paraview : Conflicts: python3-vtk9 but 9.1.0+really9.1.0+dfsg2-7.1build3 is to be installed
  

  @davidscn have you already found any solution for this?
• Check Python dependencies for tutorials post-processing scripts, and specify them in a more fine-grained way in each tutorial. See also Python packages not installed automatically for all tutorials tutorials#526. In that sense, we also need to:
• Integrate the step of enabling the Python venvs in the run scripts of the respective tutorials.

Replaces and closes #45.

@fsimonis FYI

[fsimonis]

Is python3-paraview needed? Otherwise, we could just install paraview without it apt-get install -y --no-install-recommends paraview.

[MakisH]

Is python3-paraview needed? Otherwise, we could just install paraview without it apt-get install -y --no-install-recommends paraview.

Ah true. I already tried the opposite, but of course python3-paraview is a recommended package of paraview, not of libvtk9-dev 🙈

Works like this.

[fsimonis]

Disk space usage of this port:

We loose quite some space as cargo vendor vendors a lot of windows-related stuff.
I don't see a straight forward way of disabling them. Maybe rm -rf vendor/winapi* vendor/windows* would solve the majority of the issue.

Also some python venvs eat some space e.g. in the dune build.

Using kde-plasma-desktop instead of xubuntu requires 19GB of disk space, which is a pretty substantial overhead.

[fsimonis]

The micro-manager two-scale tutorial is compatible with pix installations since precice/tutorials#533