Review and modernization of the package

[kshitij-maths]

This PR introduces several modernization improvements to the package, including:

• Migrated the build system from setup.py to a modern pyproject.toml–based configuration.
• Updated the package structure and metadata in accordance with current Python packaging standards
• Revised and refactored supporting files impacted by the migration.
• Updated tutorials and documentation to ensure compatibility with the current version and the new build system.
• Performed a general review of the package to align it with modern best practices.

[ndem0]

Thanks @kshitij-maths can you check why all the tests are failing? We should fix them to merge the changes!

[kshitij-maths]

@ndem0 checking.

[kshitij-maths]

Please approve the current workflow. Let's see if it works.

[kshitij-maths]

@ndem0 The macOS PR test is consistently failing because s-weigand/setup-conda does not install Conda correctly on newer macOS images; all other OSs pass. Attempts to use an older macOS version (macos-12) also cause failures on the other OSs.

[ndem0]

Ok thanks! Yes the action is not working for MacOS, they also have a warning on the main page https://github.com/s-weigand/setup-conda

I would change the action so! I tried to quick search on google and there is the official action developed by miniconda developers https://github.com/conda-incubator/setup-miniconda

Also please try to fix the Codacy issues, there are 64 new issues https://app.codacy.com/gh/mathLab/PyGeM/pull-requests/280/issues

[kshitij-maths]

I would change the action so!

Okay, thanks!

Also please try to fix the Codacy issues, there are 64 new issues https://app.codacy.com/gh/mathLab/PyGeM/pull-requests/280/issues

Okay.

[ndem0]

A huge amount of file are changed because of small formatting (double quotes instead signle one for example). Also, a lot of new file have been added, but I don't think are necessary (they should be the output of some tests).
Additionally, please try to keep few lines of changes for PR, around 100 is completely fine (here we have 6000 lines for 35 commits, definetely to large).

Please remove unnecessary file.
Please restore to the previous version all the file contined in pygem, tests and tutorials folders.

[ndem0]

Why? Please revert

[kshitij-maths]

I don't think we need to revert the complete README to its original version. We've simply reorganized it for better clarity. If you look at the rendered file rather than the raw code, you'll see that the content is essentially the same, perhaps more polished and structured. The overwhelming number of added and deleted lines you see here is likely because I rewrote the file completely, rather than making changes line by line.

[ndem0]

add vtk