Add support for Python 3.13 in conda #39189

tobiasdiez · 2024-12-23T04:39:19Z

📝 Checklist

The title is concise and informative.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation and checked the documentation preview.

⌛ Dependencies

github-actions · 2024-12-23T06:15:49Z

Documentation preview for this PR (built with commit 59103d5; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

``` In file included from build/cythonized/sage/graphs/base/boost_graph.cpp:1278: build/cythonized/sage/graphs/base/boost_interface.cpp:119:34: error: non-constant-expression cannot be narrowed from type 'value_type' (aka 'unsigned long') to 'int' in initializer list [-Wc++11-narrowing-const-reference] 119 | to_return.push_back({index[boost::source(*ei, graph)], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/cythonized/sage/graphs/base/boost_graph.cpp:17503:29: note: in instantiation of member function 'BoostGraph<boost::vecS, boost::vecS, boost::directedS, boost::vecS, boost::property<boost::edge_weight_t, double>>::edge_list' requested here 17503 | __pyx_v_edges = __pyx_v_g.edge_list(); ^ ``` https://clang.llvm.org/docs/DiagnosticsReference.html#wc-11-narrowing-const-reference To silence the error assign to a v_index outside of the initializer list.

…into conda-python-13

tobiasdiez · 2025-09-08T04:16:50Z

FAILED: [code=1] src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/meson-generated_src_sage_libs_linbox_linbox_flint_interface.pyx.cpp.o
  ccache /usr/share/miniconda/envs/sage-dev/bin/x86_64-conda-linux-gnu-c++ -Isrc/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p -Isrc/sage/libs/linbox -I../src/sage/libs/linbox -Isrc/sage/libs/flint -I../src/sage/libs/flint -I/usr/share/miniconda/envs/sage-dev/include/python3.11 -I/usr/share/miniconda/envs/sage-dev/include -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++11 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -DDISABLE_COMMENTATOR -pthread -DFFLAS_COMPILED -DFFPACK_COMPILED -MD -MQ src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/meson-generated_src_sage_libs_linbox_linbox_flint_interface.pyx.cpp.o -MF src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/meson-generated_src_sage_libs_linbox_linbox_flint_interface.pyx.cpp.o.d -o src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/meson-generated_src_sage_libs_linbox_linbox_flint_interface.pyx.cpp.o -c src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp
  In file included from /usr/share/miniconda/envs/sage-dev/include/givaro/givinteger.h:24,
                   from /usr/share/miniconda/envs/sage-dev/include/givaro/givrational.h:22,
                   from src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp:1145:
  /usr/share/miniconda/envs/sage-dev/include/givaro/random-integer.h: In member function 'Givaro::RandomIntegerIterator<_Unsigned, _Exact_Size>& Givaro::RandomIntegerIterator<_Unsigned, _Exact_Size>::operator=(const Givaro::RandomIntegerIterator<_Unsigned, _Exact_Size>&)':
  /usr/share/miniconda/envs/sage-dev/include/givaro/random-integer.h:90:54: error: no match for 'operator=' (operand types are 'Givaro::RandomIntegerIterator<_Unsigned, _Exact_Size>::Integer_Domain' {aka 'Givaro::ZRing<Givaro::Integer>'} and 'const Givaro::RandomIntegerIterator<_Unsigned, _Exact_Size>::Integer_Domain' {aka 'const Givaro::ZRing<Givaro::Integer>'})
     90 |                 const_cast<Integer_Domain&>(_ring)=R._ring;
        |                                                      ^~~~~
  In file included from /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparse-matrix.h:76,
                   from src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp:1156:
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ell-matrix.h: In member function 'LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>& LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::operator=(const LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>&)':
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ell-matrix.h:1216:44: error: assignment of read-only location '((LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>*)this)->LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::_ld'
   1216 |                                 _ld        = iter._ld ;
        |                                 ~~~~~~~~~~~^~~~~~~~~~
  In file included from /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparse-matrix.h:77:
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ellr-matrix.h: In member function 'LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_Iterator<element_iterator, Field>& LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_Iterator<element_iterator, Field>::operator=(const LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_Iterator<element_iterator, Field>&)':
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ellr-matrix.h:1108:47: error: no match for 'operator=' (operand types are 'const std::vector<long unsigned int>' and 'const std::vector<long unsigned int>')
   1108 |                                 _rowid = iter._rowid;
        |                                               ^~~~~~
  In file included from /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/vector:72,
                   from /usr/share/miniconda/envs/sage-dev/include/gmp++/gmp++_int.h:20,
                   from /usr/share/miniconda/envs/sage-dev/include/gmp++/gmp++.h:57,
                   from src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp:1144:
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/vector.tcc:210:5: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = long unsigned int; _Alloc = std::allocator<long unsigned int>]' (near match)
    210 |     vector<_Tp, _Alloc>::
        |     ^~~~~~~~~~~~~~~~~~~
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/vector.tcc:210:5: note:   passing 'const std::vector<long unsigned int>*' as 'this' argument discards qualifiers
  In file included from /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/vector:66:
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/stl_vector.h:779:7: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = long unsigned int; _Alloc = std::allocator<long unsigned int>]' (near match)
    779 |       operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
        |       ^~~~~~~~
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/stl_vector.h:779:7: note:   conversion of argument 1 would be ill-formed:
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/stl_vector.h:801:7: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = long unsigned int; _Alloc = std::allocator<long unsigned int>]'
    801 |       operator=(initializer_list<value_type> __l)
        |       ^~~~~~~~
  /usr/share/miniconda/envs/sage-dev/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/bits/stl_vector.h:801:46: note:   no known conversion for argument 1 from 'const std::vector<long unsigned int>' to 'std::initializer_list<long unsigned int>'
    801 |       operator=(initializer_list<value_type> __l)
        |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ellr-matrix.h:1109:37: error: assignment of read-only location '((LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_Iterator<element_iterator, Field>*)this)->LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_Iterator<element_iterator, Field>::_ld'
   1109 |                                 _ld = iter._ld ;
        |                                 ~~~~^~~~~~~~~~
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ellr-matrix.h: In member function 'LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_IndexedIterator<index_iterator, element_iterator, Field>& LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_IndexedIterator<index_iterator, element_iterator, Field>::operator=(const LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_IndexedIterator<index_iterator, element_iterator, Field>&)':
  /usr/share/miniconda/envs/sage-dev/include/linbox/matrix/sparsematrix/sparse-ellr-matrix.h:1258:44: error: assignment of read-only location '((LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_IndexedIterator<index_iterator, element_iterator, Field>*)this)->LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL_R>::_IndexedIterator<index_iterator, element_iterator, Field>::_ld'
   1258 |                                 _ld        = iter._ld ;
        |                                 ~~~~~~~~~~~^~~~~~~~~~
  src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp: In function 'void __pyx_f_4sage_4libs_6linbox_22linbox_flint_interface_fmpz_mat_get_linbox(LinBox::DenseMatrix<Givaro::ZRing<Givaro::Integer> >&, fmpz_mat_struct*)':
  src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp:2228:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and '__pyx_t_4sage_4libs_5flint_5types_slong' {aka 'long int'} [-Wsign-compare]
   2228 |   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
        |                       ~~~~~~~~~~^~~~~~~~~~~
  src/sage/libs/linbox/linbox_flint_interface.cpython-311-x86_64-linux-gnu.so.p/src/sage/libs/linbox/linbox_flint_interface.pyx.cpp:2240:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and '__pyx_t_4sage_4libs_5flint_5types_slong' {aka 'long int'} [-Wsign-compare]
   2240 |     for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
        |                         ~~~~~~~~~~^~~~~~~~~~~

Comes from the update to gcc14. Fixed in linbox-team/givaro#226, which is in givaro 4.2.1 - already on Conda but until conda-forge/fflas-ffpack-feedstock#21 is fixed it pulls in older givaro.

tobiasdiez · 2025-09-24T12:29:58Z

Tests are mostly green (modulo the what appears to be the common background noise of randomly failing tests), so this is now finally ready for review.

whoami730 · 2025-09-30T10:27:55Z

@tobiasdiez can you please update the checklist for this PR? Thanks!

tobiasdiez · 2025-09-30T11:04:24Z

@tobiasdiez can you please update the checklist for this PR? Thanks!

You mean the one in the PR description? It's mostly there as a reminder for the person opening the PR - but well, I clicked a few checkboxes ;-)

whoami730 · 2025-09-30T11:28:13Z

You mean the one in the PR description? It's mostly there as a reminder for the person opening the PR - but well, I clicked a few checkboxes ;-)

I thought that was used by folks to review/merge PRs :D

tobiasdiez and others added 3 commits December 19, 2024 10:44

Update conda to use Python 3.12, drop 3.9 and 3.10

d5f1da0

Merge branch 'develop' into conda-python-upgrade

9ea715f

Add support for python 3.13 in conda

fce9681

tobiasdiez added 2 commits December 23, 2024 17:21

Merge branch 'pr/antonio-rojas/39188' into conda-python-13

1122dcf

src/sage/libs/flint/flint_wrap.h: Work around 'I' symbol clash

0bb2a1b

tobiasdiez force-pushed the conda-python-13 branch from 3fd6590 to 0bb2a1b Compare December 24, 2024 03:50

tobiasdiez and others added 11 commits December 24, 2024 12:00

temporarily allow cysignals 1.12

ac5a4ff

Merge remote-tracking branch 'upstream/develop' into conda-python-13

802e473

Update conda lock files

5d0d0be

Readd fpylll for python 3.13

d9ed2af

Merge branch 'pr/antonio-rojas/38749' into conda-python-13

21d287c

Merge remote-tracking branch 'upstream/develop' into conda-python-13

a895195

Merge branch 'develop' into conda-python-13

ec7170a

add 'python-build' as dev dependency

9647a82

Run conda env updates in parallel

ec48c2c

Update conda envs

20da9ad

vbraun force-pushed the develop branch from 8a8453f to b8f98e7 Compare March 31, 2025 22:55

tobiasdiez added 3 commits September 8, 2025 11:28

Merge remote-tracking branch 'upstream/develop' into conda-python-13

ceb56ac

Merge branch 'conda-python-13' of https://github.com/tobiasdiez/sage …

97a1378

…into conda-python-13

Improve CI test matrix

731caab

tobiasdiez mentioned this pull request Sep 12, 2025

Update conda-lock files #40805

Closed

5 tasks

tobiasdiez added 3 commits September 24, 2025 12:34

Force downgrade of maxima and gcc

02af978

Merge remote-tracking branch 'upstream/develop' into conda-python-13

2f6559b

Fix Win lock file

59103d5

tobiasdiez marked this pull request as ready for review September 24, 2025 12:30

github-actions bot added the s: needs review label Sep 24, 2025

Merge branch 'develop' into conda-python-13

7984dd9

tobiasdiez requested a review from dimpase September 30, 2025 08:24

tobiasdiez mentioned this pull request Sep 30, 2025

Remove gmpy2 2.1 pin #40923

Open

4 tasks

tobiasdiez added 2 commits October 5, 2025 13:57

Remove version constraints on c-compiler and cxx-compiler

ad44362

Update linbox

25d0a92

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