Modularization of sagelib: Distributions sagemath-{brial,combinat,eclib,flint,gap,giac,glpk,graphs,groups,homfly,lcalc,libbraiding,libecm,linbox,modules,mpmath,ntl,pari,plot,polyhedra,schemes,singular,standard-no-symbolics,symbolics} #35095
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mkoeppe
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## develop #35095 +/- ##
===========================================
- Coverage 88.62% 87.40% -1.22%
===========================================
Files 2148 2180 +32
Lines 398855 399144 +289
===========================================
- Hits 353480 348878 -4602
- Misses 45375 50266 +4891
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I ran after full rebuild on macOS monterey, and got [37/54] gcc -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I./sage/cpython -I/private/var/folders/td/fw1q9ljs311ggyph77rs53_40000gn/T/pip-build-env-_on11jf5/overlay/lib/python3.11/site-packages/gmpy2 -I./sage/rings -I/private/var/folders/td/fw1q9ljs311ggyph77rs53_40000gn/T/pip-build-env-_on11jf5/overlay/lib/python3.11/site-packages -I/usr/local/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 -Ibuild/cythonized -I/Users/kwankyu/GitHub/sage-dev/pkgs/sagemath-polyhedra/.tox/.pkg/include -I/usr/local/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c build/cythonized/sage/structure/coerce.c -o build/temp.macosx-12-x86_64-cpython-311/build/cythonized/sage/structure/coerce.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1
build/cythonized/sage/structure/coerce.c:779:10: fatal error: 'gmp.h' file not found
#include "gmp.h"
^~~~~~~
1 error generated. |
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I've updated the instructions for testing. |
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Is this on macOS with homebrew? DId you run .homebrew-build-env? |
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Yes. My bash profile does I manually pasted the line and tried again. But I got the same. |
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I am trying again after deleting |
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I got the same failure. Part of the log |
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Have you tried the command |
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No. Shall I? |
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Yes, that's what I would recommend as the best way of testing |
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I ran |
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Could you try if |
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I ran |
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Could you check the contents of |
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The |
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Part of the log: |
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It says |
vbraun
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Apr 20, 2024
…arate jobs for pyright, build, modularized tests, long tests
<!-- ^^^^^
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 -->
<!-- Why is this change required? What problem does it solve? -->
Running the containers explicitly, instead of using the declarative
`container:` feature of GH Actions gives us more control:
- we can create more space on the host if necessary; we just scraped by
an out of space condition in sagemath#36473 /
sagemath#36469 (comment)
- we can run some operations outside of the container but in the same
job; this will make the separate "Get CI fixes" jobs unnecessary,
addressing the cosmetic concerns from
sagemath#36338 (comment),
sagemath#36349
- it enables caching between the various workflows (as first discussed
in sagemath#36446).
We split out static type checking with pyright into its separate
workflow:
- **pyright.yml**: As static checking does not need a build of the Sage
library, for PRs that do not make any changes to packages, there's
nothing to build, and the workflow gives a fast turnaround just after 10
minutes. For applying the CI fixes from blocker tickets, this workflow
uses the technique favored in sagemath#36349.
The workflow **build.yml** first launches a job:
- **test-new:** It builds incrementally (using a tox-generated
`Dockerfile` and https://github.com/marketplace/actions/build-and-push-
docker-images) and does the quick incremental test. This completes
within 10 to 20 minutes when there's no change.
After this is completed, more jobs are launched:
- **test-mod:** It again builds incrementally and tests a modularized
distribution. Later (with more from sagemath#35095), more jobs will be added to
this matrix job for other distributions.
- **test-long:** It again builds incrementally and runs the long test.
The workflows **doc-build.yml** and **doc-build-pdf.yml** again build
incrementally and then build the documentation. The diffing code for the
HTML documentation now runs in the host, not the container, which
simplifies things. (To show that diffing still works, we include a small
change to the Sage library.)
Splitting the workflow jobs implements @kwankyu's suggestion from:
- sagemath#35652 (comment)
(Fixes sagemath#35814)
The steps "again builds incrementally" actually use the GH Actions
cache, https://docs.docker.com/build/ci/github-actions/cache/#cache-
backend-api. When nothing is cached and the 3 workflows are launched in
parallel, they may each build the same thing. But when there's
congestion that leads to the workflows to be run serially, the 2nd and
3rd workflow will be able to use the cache from the 1st workflow. This
elasticity may be helpful in reducing congestion.
There is a rather small per-project limit of 10 GB for this cache, so
we'll have to see how effectively caching works in practice. See
https://github.com/sagemath/sage/actions/caches
<!-- 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.
- [ ] 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#36938 (merged here)
- Depends on sagemath#36951 (merged here)
- Depends on sagemath#37351 (merged here)
- Depends on sagemath#37750 (merged here)
<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
URL: sagemath#36498
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
vbraun
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37714 Reported by: Matthias Köppe Reviewer(s): Matthias Köppe, Sebastian A. Spindler
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… after sagemath#37022 <!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> - Cherry-picked updates of testing infrastructure from sagemath#35095. - Add upper version bounds to avoid a regression in 4.14.1 - Fixes sagemath#37734. - Also removes some unnecessary runs of the "CI Linux Incremental" workflow. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37750 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37714 Reported by: Matthias Köppe Reviewer(s): Matthias Köppe, Sebastian A. Spindler
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…able.txt.m4: Copy from sagemath#35095
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… after sagemath#37022 <!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> - Cherry-picked updates of testing infrastructure from sagemath#35095. - Add upper version bounds to avoid a regression in 4.14.1 - Fixes sagemath#37734. - Also removes some unnecessary runs of the "CI Linux Incremental" workflow. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37750 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee
vbraun
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…arate jobs for pyright, build, modularized tests, long tests
<!-- ^^^^^
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 -->
<!-- Why is this change required? What problem does it solve? -->
Running the containers explicitly, instead of using the declarative
`container:` feature of GH Actions gives us more control:
- we can create more space on the host if necessary; we just scraped by
an out of space condition in sagemath#36473 /
sagemath#36469 (comment)
- we can run some operations outside of the container but in the same
job; this will make the separate "Get CI fixes" jobs unnecessary,
addressing the cosmetic concerns from
sagemath#36338 (comment),
sagemath#36349
- it enables caching between the various workflows (as first discussed
in sagemath#36446).
We split out static type checking with pyright into its separate
workflow:
- **pyright.yml**: As static checking does not need a build of the Sage
library, for PRs that do not make any changes to packages, there's
nothing to build, and the workflow gives a fast turnaround just after 10
minutes. For applying the CI fixes from blocker tickets, this workflow
uses the technique favored in sagemath#36349.
The workflow **build.yml** first launches a job:
- **test-new:** It builds incrementally (using a tox-generated
`Dockerfile` and https://github.com/marketplace/actions/build-and-push-
docker-images) and does the quick incremental test. This completes
within 10 to 20 minutes when there's no change.
After this is completed, more jobs are launched:
- **test-mod:** It again builds incrementally and tests a modularized
distribution. Later (with more from sagemath#35095), more jobs will be added to
this matrix job for other distributions.
- **test-long:** It again builds incrementally and runs the long test.
The workflows **doc-build.yml** and **doc-build-pdf.yml** again build
incrementally and then build the documentation. The diffing code for the
HTML documentation now runs in the host, not the container, which
simplifies things. (To show that diffing still works, we include a small
change to the Sage library.)
Splitting the workflow jobs implements @kwankyu's suggestion from:
- sagemath#35652 (comment)
(Fixes sagemath#35814)
The steps "again builds incrementally" actually use the GH Actions
cache, https://docs.docker.com/build/ci/github-actions/cache/#cache-
backend-api. When nothing is cached and the 3 workflows are launched in
parallel, they may each build the same thing. But when there's
congestion that leads to the workflows to be run serially, the 2nd and
3rd workflow will be able to use the cache from the 1st workflow. This
elasticity may be helpful in reducing congestion.
There is a rather small per-project limit of 10 GB for this cache, so
we'll have to see how effectively caching works in practice. See
https://github.com/sagemath/sage/actions/caches
<!-- 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.
- [ ] 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#36938 (merged here)
- Depends on sagemath#36951 (merged here)
- Depends on sagemath#37351 (merged here)
- Depends on sagemath#37750 (merged here)
- Depends on sagemath#37277 (merged here)
<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
URL: sagemath#36498
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
vbraun
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…string/doctest cosmetics, `# needs`
<!-- ^ Please provide a concise and informative title. -->
<!-- ^ Don't put issue numbers in the title, do this in the PR
description below. -->
<!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method
to calculate 1 + 2". -->
<!-- v Describe your changes below in detail. -->
<!-- v Why is this change required? What problem does it solve? -->
<!-- v If this PR resolves an open issue, please link to it here. For
example, "Fixes sagemath#12345". -->
Cherry-picked from sagemath#35095.
### 📝 Checklist
<!-- Put an `x` in all the boxes that apply. -->
- [x] The title is concise and informative.
- [ ] 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. For example,
-->
<!-- - sagemath#12345: short description why this is a dependency -->
<!-- - sagemath#34567: ... -->
URL: sagemath#37715
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
vbraun
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… after sagemath#37022 <!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> - Cherry-picked updates of testing infrastructure from sagemath#35095. - Add upper version bounds to avoid a regression in 4.14.1 - Fixes sagemath#37734. - Also removes some unnecessary runs of the "CI Linux Incremental" workflow. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37750 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37716 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37713 Reported by: Matthias Köppe Reviewer(s): Martin Rubey
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37716 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee
Open
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37713 Reported by: Matthias Köppe Reviewer(s): Martin Rubey
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<!-- ^ Please provide a concise and informative title. --> <!-- ^ Don't put issue numbers in the title, do this in the PR description below. --> <!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method to calculate 1 + 2". --> <!-- v Describe your changes below in detail. --> <!-- v Why is this change required? What problem does it solve? --> <!-- v If this PR resolves an open issue, please link to it here. For example, "Fixes sagemath#12345". --> Cherry-picked from sagemath#35095. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [ ] 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. For example, --> <!-- - sagemath#12345: short description why this is a dependency --> <!-- - sagemath#34567: ... --> URL: sagemath#37713 Reported by: Matthias Köppe Reviewer(s): Martin Rubey
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📚 Description
📝 Checklist
⌛ Dependencies
fast_callableinterpreters #35774sage.functions: Decouple fromsage.symbolic.expressionandmpmath, update# needs#35716sage.calculus: Modularization fixes, doctest cosmetics,# needs#35717pkgs/sagemath-{objects,categories,standard}: Switch to meson-python build system #37012src/bin/sage-cython: Repurpose as PEP 420 fixer #37009sage-generate-mesonscript to sage-setup #37008# sage_setup: distributiondirectives to all files, remove remaining# coding: utf-8#36964pkgs/sagemath-standard: Move metadata fromsetup.cfgtopyproject.toml#36951pkgs/sagemath-{objects,categories}: Enlarge #36566pyproject.toml: Add 'external' section according to draft PEP 725 #37486pkgs/sage-conf: Move metadata fromsetup.cfgtopyproject.toml#36561pkgs/sagemath-*/setup.pythroughsage_setup.sage_setup#36649sage.*.allfor modularization, replace relative by absolute imports #36676This is part of: