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committedMar 21, 2025
gh-39655: update numpy to 2.2.3, scipy to 1.15.2 this is long overdue update. It needs building tools bumped, too, thus dependencies ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> - [x] The title is concise and informative. - [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 and checked the documentation preview. ### ⌛ Dependencies build tools need a bump - #39652 : pythran - #39653 : ninja - #39654: pybind11 <!-- List all open PRs that this PR logically depends on. For example, --> <!-- - #12345: short description why this is a dependency --> <!-- - #34567: ... --> URL: #39655 Reported by: Dima Pasechnik Reviewer(s): David Coudert
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10.7.beta010.6.rc0
2 parents 2b78201 + 07e6461 commit 943b1b4

14 files changed

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-21
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‎.ci/write-dockerfile.sh

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@@ -275,7 +275,7 @@ cat <<EOF
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FROM with-system-packages AS bootstrapped
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#:bootstrapping:
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RUN rm -rf /new /sage/.git
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$ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap configure.ac sage .homebrew-build-env tox.ini .gitignore /new/
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$ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap conftest.py configure_wrapper configure.ac sage .homebrew-build-env tox.ini .gitignore /new/
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$ADD config/config.rpath /new/config/config.rpath
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$ADD src/doc/bootstrap /new/src/doc/bootstrap
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$ADD src/bin /new/src/bin

‎.github/workflows/build.yml

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- name: Generate Dockerfile
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# From docker.yml
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# tox -e <environment name> command runs commands in `tox.ini`,
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# in particular the script `.ci/write-dockerfile.sh`, to generate `Dockerfile`.
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run: |
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tox -e ${{ env.TOX_ENV }}
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cp .tox/${{ env.TOX_ENV }}/Dockerfile .

‎.gitignore

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/config.log
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/config.status
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/configure
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/real_configure
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/confdefs.h
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/m4/sage_spkg_configures.m4

‎bootstrap

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st=$?
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case $st in
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0) true;; # Success
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0) # Success
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mv configure real_configure
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cp configure_wrapper configure;;
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179|16|63|127) # no m4 for pkg-config|autotools not installed|or version too old
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if [ $DOWNLOAD = yes ]; then
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fi
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mkdir -p upstream
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tar zcf "$NEWCONFBALL" \
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configure \
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configure real_configure configure_wrapper \
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config/install-sh config/compile config/config.guess config/config.sub config/missing \
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build/make/Makefile-auto.in \
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src/doc/en/installation/*.txt \

‎build/pkgs/meson/spkg-configure.m4

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SAGE_SPKG_CONFIGURE([meson], [dnl
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dnl scipy 1.11.2 needs meson >= 1.1.0
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dnl contourpy needs meson >= 1.2.0
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dnl meson_python needs meson >= 1.2.3 for Python >= 3.12
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AC_CACHE_CHECK([for meson >= 1.2.3], [ac_cv_path_MESON], [dnl
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dnl scipy 1.15.2 needs meson >= 1.5.0
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AC_CACHE_CHECK([for meson >= 1.5.0], [ac_cv_path_MESON], [dnl
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dnl Do not accept meson installed in the default user scheme;
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dnl it will not work in our venv because we set PYTHONUSERBASE
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dnl in sage-env.
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WITH_SAGE_PYTHONUSERBASE([dnl
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AC_PATH_PROGS_FEATURE_CHECK([MESON], [meson], [dnl
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AS_IF([meson_version=$($ac_path_MESON --version 2>&1)], [dnl
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AS_IF([test -n "$meson_version"], [dnl
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AX_COMPARE_VERSION([$meson_version], [ge], [1.2.3], [dnl
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AX_COMPARE_VERSION([$meson_version], [ge], [1.5.0], [dnl
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ac_cv_path_MESON="$ac_path_MESON"
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ac_path_MESON_found=:
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])

‎build/pkgs/meson/version_requirements.txt

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meson
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meson >= 1.5.0

‎build/pkgs/numpy/checksums.ini

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tarball=numpy-VERSION.tar.gz
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sha1=915414f1efabd7c183583154cf1a709bd2745828
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sha256=697df43e2b6310ecc9d95f05d5ef20eacc09c7c4ecc9da3f235d39e71b7da1e4
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sha1=f776e594fbd88e4a50639213b4c510b1588e2dd0
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sha256=dbdc15f0c81611925f382dfa97b3bd0bc2c1ce19d4fe50482cb0ddc12ba30020
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upstream_url=https://files.pythonhosted.org/packages/source/n/numpy/numpy-VERSION.tar.gz

‎build/pkgs/numpy/package-version.txt

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1.26.3
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2.2.3

‎build/pkgs/scipy/checksums.ini

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tarball=scipy-VERSION.tar.gz
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sha1=0fd6e14972d8dd9b4a656686a40aed00ad0f1396
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sha256=4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3
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sha1=093c30bdd187fd5693a8d2fc9fcb961b96418a85
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sha256=cd58a314d92838f7e6f755c8a2167ead4f27e1fd5c1251fd54289569ef3495ec
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upstream_url=https://files.pythonhosted.org/packages/source/s/scipy/scipy-VERSION.tar.gz

‎build/pkgs/scipy/package-version.txt

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1.12.0
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1.15.2

‎build/pkgs/scipy/version_requirements.txt

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# deprecations cannot be introduced in micro releases.
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# SciPy devs wait "at least 6 months", "in practice two (minor) releases"
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# from deprecation to removal of a feature.
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scipy >=1.5
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scipy >=1.12

‎configure_wrapper

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#! /bin/sh
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cp conftest.py bak_conftest.py
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./real_configure $@
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mv bak_conftest.py conftest.py

‎src/doc/en/developer/tools.rst

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- VS Code: Install the `Python extension <https://marketplace.visualstudio.com/items?itemName=ms-python.python>`_ and follow the `official VS Code documentation <https://code.visualstudio.com/docs/python/testing>`__.
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*Configuration:* :sage_root:`src/conftest.py`
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*Configuration:* :sage_root:`conftest.py`
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*Documentation:* https://docs.pytest.org/en/stable/index.html
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‎src/sage/graphs/generic_graph.py

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{0: 1/3, 1: 1/3, 2: 0, 3: 1/3, 4: 1/3, 5: 1/3,
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6: 1/3, 7: 1/3, 8: 0, 9: 1/3, 10: 1/3, 11: 0}
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sage: (graphs.FruchtGraph()).clustering_coeff(weight=True) # needs networkx
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sage: # needs networkx
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sage: import numpy
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sage: if int(numpy.version.short_version[0]) > 1:
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....: numpy.set_printoptions(legacy="1.25")
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sage: graphs.FruchtGraph().clustering_coeff(weight=True)
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{0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0,
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3: 0.3333333333333333, 4: 0.3333333333333333,
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5: 0.3333333333333333, 6: 0.3333333333333333,
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7: 0.3333333333333333, 8: 0, 9: 0.3333333333333333,
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10: 0.3333333333333333, 11: 0}
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sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2])
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sage: graphs.FruchtGraph().clustering_coeff(nodes=[0,1,2])
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{0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0.0}
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sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2], # needs networkx
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sage: graphs.FruchtGraph().clustering_coeff(nodes=[0,1,2], # needs networkx
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....: weight=True)
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{0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0}
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sage: (graphs.GridGraph([5,5])).clustering_coeff(nodes=[(0,0),(0,1),(2,2)])
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sage: graphs.GridGraph([5,5]).clustering_coeff(nodes=[(0,0),(0,1),(2,2)])
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{(0, 0): 0.0, (0, 1): 0.0, (2, 2): 0.0}
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TESTS:

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