Update examples to support latest Psydac and Python 3.12

[kvrigor]

It might be a good idea to externally link the IGA Python docs from the Psydac API docs. As a first step I'm making sure that all examples in this repository work with the latest version of Psydac.

[kvrigor]

This PR is ready for review! Here are the summary of changes:

• Updates to deploy-book.yml:
  • Use the latest version of Psydac (devel branch).
  • Simplified Psydac installation.
  • Added macOS test.
• Removed duplicate keywords field in references.bib since jupyter-book complains about them.
• Removed author info on the .ipynb and .md files.
• Using nb-clean, all Jupyter notebooks in this repo have been scrubbed free of data (e.g. cell execution count, cell result, path to Python environment, etc.) which shouldn't be tracked in git. The Build Jupyter Book step already handles the execution and rendering of these notebooks online.
• Updated the Installation guide.

[kvrigor]

Tagging @ratnania and @yguclu --- I hope you can take a look at this PR.. thanks!

[yguclu]

Looks good! I have just a couple of comments

[campospinto]

Thanks @kvrigor ! I have a few questions:

• With these changes are all the notebooks tested in the CI ?

• should one use nb-clean before every commit of a notebook ?

• I tried to follow the installation instructions from install.md and I get an error (see below): is this because I am using a mac (for which the installation is not tested), or because the CI and the install.md do not agree ?

INFO: pip is looking at multiple versions of psydac to determine which version is compatible with other requirements. This could take a while.
ERROR: Could not find a version that satisfies the requirement sympde==0.19.0 (from psydac) (from versions: 0.9.5, 0.9.6, 0.9.7, 0.9.8, 0.9.9, 0.9.10, 0.10.0, 0.10.1, 0.10.2, 0.10.3, 0.10.4, 0.10.5, 0.10.6, 0.10.7, 0.10.8, 0.10.9, 0.10.10, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.17.0, 0.17.1)
ERROR: No matching distribution found for sympde==0.19.0

[yguclu]

• I tried to follow the installation instructions from install.md and I get an error (see below): is this because I am using a mac (for which the installation is not tested), or because the CI and the install.md do not agree ?

INFO: pip is looking at multiple versions of psydac to determine which version is compatible with other requirements. This could take a while.
ERROR: Could not find a version that satisfies the requirement sympde==0.19.0 (from psydac) (from versions: 0.9.5, 0.9.6, 0.9.7, 0.9.8, 0.9.9, 0.9.10, 0.10.0, 0.10.1, 0.10.2, 0.10.3, 0.10.4, 0.10.5, 0.10.6, 0.10.7, 0.10.8, 0.10.9, 0.10.10, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.17.0, 0.17.1)
ERROR: No matching distribution found for sympde==0.19.0

Good point @campospinto, the build of the Jupyter book should probably be tested on multiple platforms.

As for the error, I do not see a substantial difference between the instructions in deploy-book.yml and those in install.md. They both use a virtual environment (one provided automatically by GitHub, the other manually created by the user) and install Psydac as a dependency through our requirements.txt file. The CI updates pip before installing, though...

[campospinto]

Good point @campospinto, the build of the Jupyter book should probably be tested on multiple platforms.

As for the error, I do not see a substantial difference between the instructions in deploy-book.yml and those in install.md. They both use a virtual environment (one provided automatically by GitHub, the other manually created by the user) and install Psydac as a dependency through our requirements.txt file. The CI updates pip before installing, though...

alright, then can you add a macos test @kvrigor ? If it passes, I'll try again to install on my mac.

[kvrigor]

I've also updated the README file and can be viewed here: https://github.com/kvrigor/IGA-Python/tree/build-ci-update?tab=readme-ov-file

[yguclu]

I've also updated the README file and can be viewed here: https://github.com/kvrigor/IGA-Python/tree/build-ci-update?tab=readme-ov-file

Looks good!

[campospinto]

I've also updated the README file and can be viewed here: https://github.com/kvrigor/IGA-Python/tree/build-ci-update?tab=readme-ov-file

Thanks Paul!

I have another question: when installing the dependencies, do you know if psydac is (re)installed ?

In particular, Is there a simple way to be sure that you will be using your psydac version, if you previously had one installed?

[kvrigor]

I have another question: when installing the dependencies, do you know if psydac is (re)installed ?

@campospinto Since psydac is declared as a git repo in requirements.txt, I'd assume that it could be re-installed whenever psydac devel gets updated.

In particular, Is there a simple way to be sure that you will be using your psydac version, if you previously had one installed?

Yes--by editing requirements.txt and then pointing psydac to a git commit hash, e.g.:

psydac @ git+https://github.com/pyccel/psydac.git@5ff388417225f5fb7a6e1ec1c4490d2fb48233f5

[campospinto]

I have another question: when installing the dependencies, do you know if psydac is (re)installed ?

@campospinto Since psydac is declared as a git repo in requirements.txt, I'd assume that it could be re-installed whenever psydac devel gets updated.

In particular, Is there a simple way to be sure that you will be using your psydac version, if you previously had one installed?

Yes--by editing requirements.txt and then pointing psydac to a git commit hash, e.g.:

psydac @ git+https://github.com/pyccel/psydac.git@5ff388417225f5fb7a6e1ec1c4490d2fb48233f5

I see. And would it also work if one simply removes this line in his requirements.txt file ?

[kvrigor]

Yes--by editing requirements.txt and then pointing psydac to a git commit hash, e.g.:

psydac @ git+https://github.com/pyccel/psydac.git@5ff388417225f5fb7a6e1ec1c4490d2fb48233f5

I see. And would it also work if one simply removes this line in his requirements.txt file ?

Yes, that would be the simplest solution! In this case psydac has to be manually installed.

[campospinto]

Thanks Paul ! This looks good, I have a few questions -- essentially on the README for now.

[campospinto]

Thanks Paul for the changes!