[spossann]

Addresses #203

Auto-generates PRs into struphy-parameter-files and struphy-tutorials on push to main in case changes exist in the new folders examples/ or tutorials/.

Moreover:

• New PR-test of examples: test all *.py files in new examples/ folder
• Tests use the new option Simulation.run(one_time_step=True) for performing just one time step.
• New folder tutorials/, used in build of the sphinx doc
• New PR-test of tutorials in tutorials/
• use def main(): in pproc and regression scripts
• Auto-generate tag in the two repos when pushing to struphy main
• temporarily add the bound jax-finufft<=1.2.0 until desc has a new release

Example of PR: struphy-hub/struphy-examples#14
Example of tag: https://github.com/struphy-hub/struphy-parameter-files/tags

[spossann]

We have to wait for desc update, see #181 (comment)

[Copilot]

Pull request overview

This PR removes the struphy-tutorials and struphy-parameter-files git submodules by moving their contents into this repository, adds CI coverage to execute examples/tutorials, and updates docs/build tooling to include the notebooks in the Sphinx documentation.

Changes:

• Remove the two submodules and add tutorials/ notebooks plus examples/ parameter files directly in-repo.
• Add CI workflows to execute tutorial notebooks and to run each examples/**/params_*.py (with one time step) plus optional pproc_*/regress_* scripts.
• Extend Simulation.run() with a one_time_step option and update Sphinx config to include notebook collections.

Reviewed changes

Copilot reviewed 33 out of 34 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
tutorials/tutorial_01_struphy_simulations.ipynb	Adds/relocates tutorial notebook into repo.
tutorials/tutorial_02_parameter_files.ipynb	Adds/relocates tutorial notebook; documents launch/parameter files.
tutorials/tutorial_03_test_particles.ipynb	Adds/relocates tutorial notebook; particle examples.
tutorials/tutorial_04_smoothed_particle_hydrodynamics.ipynb	Adds/relocates tutorial notebook; SPH examples.
tutorials/tutorial_05_vlasov_maxwell.ipynb	Adds/relocates tutorial notebook; Vlasov-Ampère example walkthrough.
tutorials/tutorial_06_mapped_domains.ipynb	Adds/relocates tutorial notebook; mapped domains.
tutorials/tutorial_07_mhd_equilibria.ipynb	Adds/relocates tutorial notebook; MHD equilibria interface examples.
struphy-tutorials	Removes the struphy-tutorials submodule pointer.
struphy-parameter-files	Removes the struphy-parameter-files submodule pointer.
.gitmodules	Drops removed submodules from git submodule configuration.
src/struphy/simulation/sim.py	Adds one_time_step option to Simulation.run().
src/struphy/models/tests/test_examples.py	New pytest that discovers/runs examples/**/params_*.py and companion scripts.
src/struphy/io/setup.py	Allows importing parameter scripts under a configurable module name.
pyproject.toml	Adds sphinx-collections to doc extras.
examples/VlasovMaxwellOneSpecies/weibel_instability/params_weibel_instability.py	Adds example parameter file previously managed externally.
examples/VlasovMaxwellOneSpecies/weibel_instability/pproc_weibel_instability.py	Adds example post-processing script.
examples/VlasovAmpereOneSpecies/weak_Landau_damping/params_weak_Landau_damping.py	Adds example parameter file.
examples/VlasovAmpereOneSpecies/weak_Landau_damping/pproc_weak_Landau_damping.py	Adds example post-processing script.
examples/VlasovAmpereOneSpecies/strong_Landau_damping/params_strong_Landau_damping.py	Adds example parameter file.
examples/VlasovAmpereOneSpecies/strong_Landau_damping/pproc_strong_Landau_damping.py	Adds example post-processing script.
examples/VlasovAmpereOneSpecies/two_stream/params_two_stream.py	Adds example parameter file.
examples/VlasovAmpereOneSpecies/two_stream/pproc_two_stream.py	Adds example post-processing script.
examples/VlasovAmpereOneSpecies/bump_on/params_bump_on.py	Adds example parameter file.
examples/VlasovAmpereOneSpecies/bump_on/pproc_bump_on.py	Adds example post-processing script.
doc/conf.py	Enables sphinx_collections and configures notebook collection copying.
doc/index.rst	Adds tutorials section to documentation index.
doc/sections/tutorials.rst	New tutorials page with toctree entries for notebooks.
.gitignore	Ignores Sphinx notebook collection outputs and generated params_* files.
.github/workflows/test-PR-examples.yml	New CI workflow to run example tests (serial + MPI).
.github/workflows/test-PR-tutorials.yml	New CI workflow to execute tutorial notebooks via nbconvert.
.github/workflows/submod-struphy-tutorials.yml	Removes old submodule-based CI workflow.
.github/workflows/submod-struphy-params.yml	Removes old submodule-based CI workflow.
.github/workflows/create-PR-tutorials.yml	New workflow to sync tutorials/ changes into external tutorials repo.
.github/workflows/create-PR-parameters.yml	New workflow to sync examples/ changes into external parameter-files repo.

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[spossann]

@max-models this is now ready for final review

[max-models]

Maybe try this:

export PYVISTA_OFF_SCREEN=true
export DISPLAY=
export LIBGL_ALWAYS_SOFTWARE=1