Upgrades: scipy 1.11 and dependencies #36112
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added 11 commits
August 21, 2023 19:55
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Portability tests running at https://github.com/mkoeppe/sage/actions/runs/5934767113 |
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Tests at https://github.com/mkoeppe/sage/actions/runs/5959239800 (with other updates, including numpy (#36123), see https://github.com/mkoeppe/sage/commits/ci-10.1%2Bupdates-4) |
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CI is failing, I see sagelib failed to build. Do you know why? |
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First time I see this failure; I think it can only be seen in incremental builds |
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Documentation preview for this PR (built with commit 5b11b9b; changes) is ready! 🎉 |
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OK, now 3 tests failing in CI. One maxima execution timing out - probably something unrelated. Two very strange results in sage/schemes/curves but I cannot reproduce them in sage-on-gentoo with scipy-1.11.1. I'll try 1.11.2 but it seems unlikely to be related. |
Unrelated and fixed in #35376 |
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Thank you! |
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<!-- ^^^^^ 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 --> This includes updates of `meson`, `meson_python`, `ninja_build`, `pybind11`, `pyproject_metadata`, `pythran`, `gast`. <!-- 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#35703 <!-- 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. - [ ] 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 <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> - Depends on sagemath#35404 (merged here) - Depends on sagemath#35810 (merged here) - Depends on sagemath#35084 (merged here) <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36112 Reported by: Matthias Köppe Reviewer(s): François Bissey
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<!-- ^^^^^ 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 --> This includes updates of `meson`, `meson_python`, `ninja_build`, `pybind11`, `pyproject_metadata`, `pythran`, `gast`. <!-- 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#35703 <!-- 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. - [ ] 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 <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> - Depends on sagemath#35404 (merged here) - Depends on sagemath#35810 (merged here) - Depends on sagemath#35084 (merged here) <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36112 Reported by: Matthias Köppe Reviewer(s): François Bissey
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<!-- ^^^^^ 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 --> This includes updates of `meson`, `meson_python`, `ninja_build`, `pybind11`, `pyproject_metadata`, `pythran`, `gast`. <!-- 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#35703 <!-- 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. - [ ] 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 <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> - Depends on sagemath#35404 (merged here) - Depends on sagemath#35810 (merged here) - Depends on sagemath#35084 (merged here) <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36112 Reported by: Matthias Köppe Reviewer(s): François Bissey
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Sep 27, 2023
<!-- ^^^^^ 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 --> This PR builds on sagemath#36109 and contains the rest of changes needed to update Cython to 3.0.0. The actual changes needed for building Sage are a632238 for the code, 67ad2e4 for the build system, and 7195b8f for the doctests. The rest of commits are either from sagemath#36109 or for patching dependencies. Closes sagemath#29863. Ideally we should wait until numpy and scipy are upgraded to 1.25 and 1.11 respectively before merging this, so we can drop the patches for them. <!-- 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". --> <!-- 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. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> - Depends on sagemath#36109 - Depends on sagemath#36112 (merged here) <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36110 Reported by: Yutao Yuan Reviewer(s): Gonzalo Tornaría, Kwankyu Lee, Matthias Köppe, Tobias Diez
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<!-- ^^^^^ 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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<!-- ^^^^^ 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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This includes updates of
meson,meson_python,ninja_build,pybind11,pyproject_metadata,pythran,gast.Resolves #35703
📝 Checklist
⌛ Dependencies
debian-busterandfedora-29#35810 (merged here)