Refactor test setup with temporary directories

[cpaniaguam]

Introduce temporary directories for test artifacts and streamline the end-to-end test setup. This change enhances test isolation and reduces clutter in the main directory.

Summary by CodeRabbit

• Tests
  • Updated end-to-end test setup to use shared temporary folders for generated data and model artifacts.
  • Improved file-path handling for saved and loaded training state files.
  • Simplified test code by moving data-generation helpers into reusable fixtures.
  • Marked one end-to-end test as slow and documented how to exclude slow tests during test runs.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated no new comments.

[AlexanderFengler]

@cpaniaguam this test-tempdir refactor has conflicted with main since July. Rebase if it is still wanted, otherwise close; the test layout has moved on since. @digicosmos86 is requested as reviewer.

[digicosmos86]

LGTM! Easy fix for merge conflict. Otherwise merge away

[cpaniaguam]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Merged main, resolved the pyproject.toml marker conflict while retaining both markers, and addressed the workflow-permissions alert. Merge commit: 6ee01fc; permissions fix: dc4c3e8.

[Copilot]

🟡 Changes recommended

The JAX OPN parameterization incorrectly saves and reloads artifacts under the CPN network type.

1 open finding

• Use OPN identity when saving and reloading parameterized artifacts · New

🧠 Review effort: Balanced

[Copilot]

🔵 Needs a closer look

The JAX OPN case still saves and reloads its artifact under the incorrect CPN identity.

1 open finding

• Use OPN identity when saving and reloading parameterized artifacts

Previously missed (1)

In code that hasn't changed since last review

Pass parameterized network type to prevent OPN mislabeling

tests/​test_end_to_end_jax.py:150

The OPN case is still deliberately mapped to cpn, so this end-to-end test writes and reloads an OPN model under the wrong network identity. ModelTrainerJaxMLP.train_and_evaluate supports network_type specifically because logits cannot distinguish CPN from OPN, and tests/test_run_identity.py:311-322 documents that the fallback is the legacy mislabeling. Pass the parameterized type to the trainer and use it in the expected state filename.

🧠 Review effort: Balanced

[Copilot]

🟢 Approval recommended

The fixture refactor consistently isolates artifacts while preserving the tested training workflows.

0 open findings

1 resolved since last review

• Use OPN identity when saving and reloading parameterized artifacts

🧠 Review effort: Balanced

[digicosmos86]

LGTM!