Update PyO3 to 0.22

[IvanIsCoding]

Closes #1250

This depends on:

• rust-numpy releasing 0.22, which will happen soon. For the time being, we build from their Git main branch
• py-clone feature is enabled, if it is disabled too many things fail
• The update broke iterators.rs, I haven't had the time to fix so for this draft I just deleted support for slicing. Of course the final version will need to reintroduce it Slicing is now fixed
• We have 68 warnings! But hey it builds Warnings are fixed

I also profited from this PR to update ndarray and ndarray-stats.

For py-clone I think we should handle it in a future PR

[IvanIsCoding]

Ok, this is ready just pending PyO3/rust-numpy#453. Although #1292 might break it because there are some deprecated methods.

Update: it worked fine after #1292 without issues

[coveralls]

Pull Request Test Coverage Report for Build 11331133743

Details

• 10 of 10 (100.0%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.002%) to 95.82%

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Totals
Change from base Build 11284044701:	0.002%
Covered Lines:	18016
Relevant Lines:	18802

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💛 - Coveralls

[IvanIsCoding]

Ok this is ready to go

[IvanIsCoding]

I think there is a bug in PyO3 0.22.4 released today (https://github.com/PyO3/pyo3/blob/release-0.22/CHANGELOG.md). Our code compiles with 0.22.3 but fails with 0.22.4. We should probably merge this as is an open an issue?

error[E0605]: non-primitive cast: `for<'py> unsafe fn(pyo3::Python<'py>, *mut pyo3::ffi::PyObject) -> Result<*mut pyo3::ffi::PyObject, pyo3::PyErr> {PyDiGraph::__pymethod_clear__}` as `unsafe extern "C" fn(*mut pyo3::ffi::PyObject) -> i32`
   --> src/digraph.rs:295:1
    |
295 | #[pymethods]
    | ^^^^^^^^^^^^ invalid cast
    |
    = note: this error originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info)

error[E0605]: non-primitive cast: `for<'py> unsafe fn(pyo3::Python<'py>, *mut pyo3::ffi::PyObject) -> Result<*mut pyo3::ffi::PyObject, pyo3::PyErr> {PyGraph::__pymethod_clear__}` as `unsafe extern "C" fn(*mut pyo3::ffi::PyObject) -> i32`
   --> src/graph.rs:191:1
    |
191 | #[pymethods]
    | ^^^^^^^^^^^^ invalid cast
    |
    = note: this error originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info)

error[E0592]: duplicate definitions with name `__pymethod_clear__`
   --> src/digraph.rs:295:1
    |
295 | #[pymethods]
    | ^^^^^^^^^^^^
    | |
    | duplicate definitions for `__pymethod_clear__`
    | other definition for `__pymethod_clear__`
    |
    = note: this error originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info)

[IvanIsCoding]

It is confirmed 0.22.4 has a regression: PyO3/pyo3#4616

We can bump to 0.22.5 once it is released.

[mtreinish]

Looks good, except for one small stray comment inline which I'll apply and re-approve for. Thanks for doing this. I agree we should update to 0.22.5 and remove py-clone in a follow-up PR.