Easy Install and MISC Fix

[cindytsai]

Easy Install and MISC Fix

Enhancements

MISC

• Reorganize CMake and add minimum version requirement for Python.
• Fix the yt_rma_particle printing error msg when failing to read particle data from the particle_data dictionary even though the particle data isn't loaded. (These kind of particle data will be generated through user-defined C function)

Easy Install

• Make libyt fetches dependencies itself when -DJUPYTER_KERNEL=ON.
• The dependencies will be stored under libyt/vendor for reuse and linkage purpose.

APIs

• Remove uint (unsigned int), ulong (unsigned long). This is useless and unnecessary.
• Add velocity_unit to yt_param_yt. This is important in cosmology simulation. libyt now enforces user to set this parameter manually.
  • [x] Inform Fish.
  • [x] Need yt_libyt 0.0.8 releases

Test

• cmake-build-test.yml for making sure each option can compile successfully and independently.
• example-test-run.yml for running example/amr-example and make sure it can run.

Doc

• Add quick start page and example.
• Update document to make install page easier to follow (I hope)
• Add setting OMPI_MCA_osc=sm,pt2pt when running libyt in parallel.

Example

• Add quick start example.

Bug

• Fix the logic of identifying user not-done-yet error and real error. It now follows the rule:

  1. If the last line has valid '\' -> not-done-yet
  2. If err msg matches those from compound keywords (ex: if) and colon exist at last line and error lineno is at the last line -> not-done-yet
  3. If err msg matches those from bracket (ex: (, [, """) -> not-done-yet
  4. Else, it's a true error.

     It turns out the the identifying multi-line statement or so called distinguish what is not-done-yet code is more complicated then I initially thought, since each python version prints out different error messages and even defines error lineno differently. And some API (PyErr_Fetch and PyErr_Restore) are deprecated since python 3.12. These are the API that is deprecated, the others are stable API.

• [ ] ~Make sure exception hook is set before entering interactive mode or jupyter mode.~

  • The exception hook to avoid MPI abort if one of the process gets error can be overwritten by yt.enable_parallelism() or other stuff. I'm not sure if this is a bug or not. (Probably not, should ask Matt)

• [x] Fix yt_libyt when using mpi4py in Serial Mode.

  • [x] Push to PyPI

GitHub Action

• Runner image reference: https://github.com/actions/runner-images/tree/main/images/macos
• Some Python version is not supported in some macOS, check the reference.

TODOs

• [x] Publish jupyter_libyt on PyPI

Check

• [x] amr-example run
• [x] Enzo
• [x] Gamer

[cindytsai]

@hyschive Can you try compiling libyt on MacOS? Because macos-latest and macos-14 image in GitHub Actions failed to set up Python < 3.11. (Don't know why) Maybe follow the Install page generated by the PR, it wouldn't take long.

[cindytsai]

Thank you @ChunYen-Chen for going through the documents, and giving feedbacks.

[cindytsai]

Hi @hyschive,

I'm enforcing setting velocity_unit in libyt. Please update libyt and use yt_libyt >= 0.0.8.