numpy-1.25 compatibility #36255
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numpy-1.25 compatibility #36255
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Some numpy.random signatures changed in numpy-1.25.x, and pythran normally wants to warn about those. It's not clear, however, whether or not the numpy changes will be reverted. Until we know, pythran-0.14.0 has a special case to ignore the warnings for numpy.random. Here we ignore those warnings in the doctest parser as well, allowing older versions of pythran to be used with numpy-1.25.x.
One of the tests for the "Computational Math..." book is plotting lines on a vector field by calling scipy.integrate.odeint repeatedly. This test runs, y = integrate.odeint(f, k, t) p += line(zip(t, flatten(y))) in an attempt to flatten y, which is returned as a numpy array of 1-dimensional numpy arrays. However, flatten() isn't smart enough to handle that: it returns a list of 1-dimensional numpy arrays rather than a list of floating point numbers. And numpy-1.25.x now warns about casting 1-dimensional arrays to float deep in our plotting infrastructure. Instead, we now call y.tolist() before passing it to flatten(), and this does the right thing.
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sagemathgh-36123: Upgrade numpy to 1.26.0, setuptools to 68.2.2 <!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes sagemath#1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility. 1.26.0 was released 2023-09-16. As NumPy has changed its build system from setuptools-pinned-to-an- ancient-version to meson_python, we get rid of our ancient version of `setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the same (current) version. - [x] Check portability run: https://github.com/mkoeppe/sage/actions/runs/5959239800 - [ ] Check SAGE_FAT_BINARY <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes sagemath#12345". --> Resolves sagemath#34816 <!-- If your change requires a documentation PR, please link it appropriately. --> ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - Depends on sagemath#36112 (for the `meson_python` upgrades, merged here) - Depends on sagemath#35404 (merged here as part of above) - Depends on sagemath#35810 (merged here as part of above) - Depends on sagemath#36110 (merged here) - Depends on sagemath#36263 (merged here) - Depends on sagemath#36238 (merged here) - Depends on sagemath#36255 (merged here) <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36123 Reported by: Matthias Köppe Reviewer(s):
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gh-36123: Upgrade numpy to 1.26.0, setuptools to 68.2.2 <!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility. 1.26.0 was released 2023-09-16. As NumPy has changed its build system from setuptools-pinned-to-an- ancient-version to meson_python, we get rid of our ancient version of `setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the same (current) version. - [x] Check portability run: https://github.com/mkoeppe/sage/actions/runs/5959239800 - [ ] Check SAGE_FAT_BINARY <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". --> Resolves #34816 <!-- If your change requires a documentation PR, please link it appropriately. --> ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - Depends on #36112 (for the `meson_python` upgrades, merged here) - Depends on #35404 (merged here as part of above) - Depends on #35810 (merged here as part of above) - Depends on #36110 (merged here) - Depends on #36263 (merged here) - Depends on #36238 (merged here) - Depends on #36255 (merged here) <!-- List all open PRs that this PR logically depends on - #12345: short description why this is a dependency - #34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: #36123 Reported by: Matthias Köppe Reviewer(s):
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Fixes two doctest failures with numpy-1.25.x. One is a warning from pythran that needs to be hidden (to avoid requiring a bleeding-edge version of pythran), and the other is a buggy doctest that now triggers a numpy warning.