Add installation scripts + update documentation with Zensical

[stuitje]

Description

This PR introduces a more complete installation and documentation workflow for SPIDER.

1. Add installer scripts for SPIDER and PETSc

This PR adds the scripts get_spider.sh and get_petsc.sh to provide a more consistent installation path for SPIDER. It aligns the standalone SPIDER installation process with the workflow already documented in PROTEUS. The scripts:

• support building SPIDER either as a standalone checkout or within a PROTEUS/SPIDER repository layout
• reduce manual setup for users by automatically installing PETSc (3.19) when needed, so that the user only has to run ./tools/get_spider.sh.
• provide clearer error handling and logging during installation and build steps.

Specifically, most of the output (i.e. warnings due to deprecation issues, etc) during installation are now logged in a file to keep the terminal clean. On the long term these deprecation issues should probably be fixed.

This closes #3.

2. Add Zensical support and expand the documentation

This PR also implements Zensical and significantly expands the SPIDER documentation.

New and updated files:

• How-to/installation.md has been updated with the new scripts
• How-to/quadruple_installation.md is a new file with the quadruple precision installation
• How-to/external_mesh_input explains how to use an external mesh file as explained in the README
• How-to/test.md explains how to test SPIDER
• 'Tutorials/first_run.md` is a small first-run tutorial mostly taken from the README
• getting_started.md is a new getting started page with a quick path and options
• proteus_framework.md contains info about PROTEUS and is the landing page for other modules
• Explanations/ contains many new files so that the model overview, directly converted from the LaTeX files in the notes/, is complete. Could use updates in the future, of course

mkdocs.yml and .github/workflows/docs.yaml have been updated accordingly, and there is a new css extra to configure the style.

Finally I have added a new job in CI.yml to test the new installation script alongside the normal build.

Validation

I have installed SPIDER and PETSc myself using these scripts and tested everything. In my case, everything worked (Linux on the Habrok cluster).

[nichollsh]

Thanks for this, @stuitje. The doc pages look much better and the scripts work. SPIDER and PETSc run fine on my Linux laptop with Python 3.12.

Minor comment below.

[timlichtenberg]

A few comments, looks great otherwise. I will give the explanations part and how-to another look once i update it for further Zalmoxis coupling

[timlichtenberg]

I also tested the install scripts on macos; all works well for me. Good new logic, much improved from the PROTEUS one; I will see if I can take some of this over into PROTEUS at the next PR.

[stuitje]

A few comments, looks great otherwise. I will give the explanations part and how-to another look once i update it for further Zalmoxis coupling

Thanks!

I'll incorporate your suggestions by tomorrow (and will try to fix the suddenly failing check 😢)

[stuitje]

@nichollsh @timlichtenberg I believe everything is covered now :)

[timlichtenberg]

👍 Let's go!