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dependencies: Update to numpy<1.24.4 #2693

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merged 5 commits into from
Jun 9, 2023

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jvesely
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@jvesely jvesely commented Jun 7, 2023

Numpy 1.24 removes few deprecated features and introduces new deprecations;

  • construction of rugged arrays now throws ValueError.
    • Update safe_create_np_array to handle both the original DeprecationWarning and the new ValueError
    • Extract values of all mechanisms in test_save_state_before_simulations to avoid rugged array
  • Conversion from Python integer types warns on range overflow.
    • Switch representation of ctype integers to unsigned. Most uses expect unsigned results.

jvesely and others added 4 commits June 6, 2023 22:40
Numpy 1.24 removed the deprecated feature of creating dtype=object
arrays in:
189eb6e38e78a06d86292b5d503de12fe2bebe38
	("DEP: Finalize ragged array creation deprecation")

Signed-off-by: Jan Vesely <[email protected]>
… homogeneous array

Mechanism values are 2D so we need to index all three results to avoid
rugged array.

Signed-off-by: Jan Vesely <[email protected]>
Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.19.0...v1.24.3)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
numpy >=1.24 is more sensitive to casting Python integers to numpy ints
with restricted range (e.g. signed vs. unsigned).
Most of our uses expect unsigned integers so switch to respective ctypes
types.

Signed-off-by: Jan Vesely <[email protected]>
@jvesely jvesely added compiler Runtime Compiler deps Dependency update labels Jun 7, 2023
@jvesely jvesely requested a review from kmantel June 7, 2023 20:42
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github-actions bot commented Jun 7, 2023

This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

No differences!

...

See CI logs for the full diff.

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github-actions bot commented Jun 8, 2023

This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

No differences!

...

See CI logs for the full diff.

# numpy 1.24 removed the above deprecation and raises
# ValueError instead. Note that the below call can still
# raise other ValueErrors
if 'The requested array has an inhomogeneous shape' in str(e):
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Was this getting sent as an np.VisibleDeprecationWarning before? It seems to be what's referenced in https://numpy.org/doc/stable/release/1.24.0-notes.html for ragged arrays, but I don't remember seeing this message before, just the "Creating an ndarray from ragged nested sequences..." one.

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Though I see now I referenced this https://numpy.org/neps/nep-0034-infer-dtype-is-object.html in the comment. Maybe I just didn't take note of the message.

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I think the wording of the warning was different. the numpy commit (numpy/numpy@189eb6e, clumsily referenced in the commit that adds these lines)
shows that the removed warnings were: "Creating an ndarray from ragged nested sequences ... " and similar. while the remaining error messages are

"setting an array element with a sequence. The "
"requested array has an inhomogeneous shape after "
"%d dimensions. The detected shape was "

@jvesely jvesely merged commit 59b1b20 into PrincetonUniversity:devel Jun 9, 2023
@jvesely jvesely deleted the numpy branch June 9, 2023 01:45
@jvesely jvesely mentioned this pull request Jun 9, 2023
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