ci: update pyo3 to 0.28

[jpopesculian]

Summary by CodeRabbit

• Chores
  • Bumped Python interop dependency to v0.28 and normalized manifest formatting.
  • Migrated Python runtime access/initialization to an attach-based model for more reliable Python integration.
  • Updated async/generator, serialization, and interop surfaces to use updated Python ownership/stream types, improving async Python compatibility and stability without changing user-facing behavior.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request upgrades PyO3 to 0.28, replaces PyObject with Py<PyAny> across public APIs and streams, moves Python GIL usage from Python::with_gil to Python::attach, and switches PyO3 initialization to Python::initialize().

Changes

Cohort / File(s)	Summary
Manifests / Dependencies Cargo.toml, runner/Cargo.toml	Bumped pyo3 and pyo3-async-runtimes 0.24 → 0.28; normalized dependency formatting and preserved feature sets.
Core interop & pipeline runner/src/pipeline.rs, runner/src/ipython.rs	Replaced PyObject with Py<PyAny> in structs, method signatures, stream item types, and getters; adjusted many public APIs accordingly.
Python runtime & async/generator glue runner/src/python.rs	Migrated async generators, iterator streams, serde_pickle bindings, and related helpers to Py<PyAny> ownership and Python::attach usage; updated trait bounds to FromPyObjectOwned.
CLI, commands & tests src/commands/*, src/commands/test.rs, src/commands/info.rs, src/commands/version.rs	Replaced with_gil → attach; updated pipeline/test signatures and introduced PipelineResult = Result<Option<Py<PyAny>>, EvaluationError>.
Evaluation & runtime flow src/evaluate.rs, src/main.rs, src/ipynb.rs	Evaluation inputs/streams use Py<PyAny>; GIL acquisition switched to attach; PyO3 init changed to Python::initialize().
Printing / output helpers src/print.rs	Changed progress-suspend func ownership to Py<PyAny>; updated __call__/__getattr__ return types; added __setattr__ and __delattr__; migrated GIL usage to attach.
Python client & module glue src/python_module.rs	Replaced with_gil → attach in client send/s3_get paths; response casting tightened and error propagation adjusted.
Small formatting-only edits Cargo.toml entries, misc runner manifests	Whitespace/formatting normalizations in Cargo manifests without semantic changes.

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Poem

🐇 I swapped my PyObjects for Py today,
I attach to Python, no with_gil in my way.
Versions hopped to 0.28, neat and spry,
Streams and generators now leap high.
Carrot cheers for tidy types — hop, hop, hi!

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 23.81% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The PR title accurately summarizes the primary change: updating the pyo3 dependency to version 0.28 across multiple Cargo.toml files and related code changes.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch ci-update-pyo3

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No actionable comments were generated in the recent review. 🎉

🧹 Recent nitpick comments

runner/src/pipeline.rs (1)

382-387: Redundant .clone_ref(py) on PyNone.

PyNone::get(py).unbind() already produces an owned Py<PyNone>. The subsequent .clone_ref(py) creates a second owned handle (extra refcount bump), after which the first is dropped. You can simplify to:

♻️ Suggested simplification

         let (original_input, mut context) = Python::attach(|py| {
             (
                 input.clone_ref(py),
-                PyNone::get(py).unbind().clone_ref(py).into_any(),
+                PyNone::get(py).unbind().into_any(),
             )
         });

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