sagemath · vbraun · Mar 22, 2025 · Oct 19, 2024 · Mar 8, 2025 · Mar 8, 2025
diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
@@ -275,7 +275,7 @@ cat <<EOF
 FROM with-system-packages AS bootstrapped
 #:bootstrapping:
 RUN rm -rf /new /sage/.git
-$ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap configure.ac sage .homebrew-build-env tox.ini .gitignore /new/
+$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/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
 $ADD src/bin /new/src/bin

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -311,6 +311,8 @@ jobs:
 
       - name: Generate Dockerfile
         # From docker.yml
+        # tox -e <environment name> command runs commands in `tox.ini`,
+        # in particular the script `.ci/write-dockerfile.sh`, to generate `Dockerfile`.
         run: |
           tox -e ${{ env.TOX_ENV }}
           cp .tox/${{ env.TOX_ENV }}/Dockerfile .

diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,7 @@
 /config.log
 /config.status
 /configure
+/real_configure
 /confdefs.h
 
 /m4/sage_spkg_configures.m4

diff --git a/bootstrap b/bootstrap
@@ -146,7 +146,9 @@ EOF
 
     st=$?
     case $st in
-        0) true;; # Success
+        0)  # Success
+            mv configure real_configure
+            cp configure_wrapper configure;;
 
         179|16|63|127)  # no m4 for pkg-config|autotools not installed|or version too old
             if [ $DOWNLOAD = yes ]; then
@@ -220,7 +222,7 @@ save () {
     fi
     mkdir -p upstream
     tar zcf "$NEWCONFBALL" \
-	configure \
+	configure real_configure configure_wrapper \
 	config/install-sh config/compile config/config.guess config/config.sub config/missing \
 	build/make/Makefile-auto.in \
 	src/doc/en/installation/*.txt \

diff --git a/build/pkgs/meson/spkg-configure.m4 b/build/pkgs/meson/spkg-configure.m4
@@ -1,16 +1,14 @@
 SAGE_SPKG_CONFIGURE([meson], [dnl
-    dnl scipy 1.11.2 needs meson >= 1.1.0
-    dnl contourpy needs meson >= 1.2.0
-    dnl meson_python needs meson >= 1.2.3 for Python >= 3.12
-    AC_CACHE_CHECK([for meson >= 1.2.3], [ac_cv_path_MESON], [dnl
+    dnl scipy 1.15.2 needs meson >= 1.5.0
+    AC_CACHE_CHECK([for meson >= 1.5.0], [ac_cv_path_MESON], [dnl
         dnl Do not accept meson installed in the default user scheme;
         dnl it will not work in our venv because we set PYTHONUSERBASE
         dnl in sage-env.
         WITH_SAGE_PYTHONUSERBASE([dnl
             AC_PATH_PROGS_FEATURE_CHECK([MESON], [meson], [dnl
                 AS_IF([meson_version=$($ac_path_MESON --version 2>&1)], [dnl
                     AS_IF([test -n "$meson_version"], [dnl
-                        AX_COMPARE_VERSION([$meson_version], [ge], [1.2.3], [dnl
+                        AX_COMPARE_VERSION([$meson_version], [ge], [1.5.0], [dnl
                             ac_cv_path_MESON="$ac_path_MESON"
                             ac_path_MESON_found=:
                         ])

diff --git a/build/pkgs/meson/version_requirements.txt b/build/pkgs/meson/version_requirements.txt
@@ -1 +1 @@
-meson
+meson >= 1.5.0
diff --git a/build/pkgs/ninja_build/checksums.ini b/build/pkgs/ninja_build/checksums.ini
@@ -1,4 +1,4 @@
 tarball=ninja_build-VERSION.tar.gz
-sha1=938723cdfc7a6f7c8f84c83b9a2cecdf1e5e1ad3
-sha256=31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea
+sha1=f3a1a28e0e427be58b4f2ff2e61b7a4a0e4f0c24
+sha256=821bdff48a3f683bc4bb3b6f0b5fe7b2d647cf65d52aeb63328c91a6c6df285a
 upstream_url=https://github.com/ninja-build/ninja/archive/refs/tags/vVERSION.tar.gz
diff --git a/build/pkgs/ninja_build/package-version.txt b/build/pkgs/ninja_build/package-version.txt
@@ -1 +1 @@
-1.11.1
+1.12.1
diff --git a/build/pkgs/numpy/checksums.ini b/build/pkgs/numpy/checksums.ini
@@ -1,4 +1,4 @@
 tarball=numpy-VERSION.tar.gz
-sha1=915414f1efabd7c183583154cf1a709bd2745828
-sha256=697df43e2b6310ecc9d95f05d5ef20eacc09c7c4ecc9da3f235d39e71b7da1e4
+sha1=f776e594fbd88e4a50639213b4c510b1588e2dd0
+sha256=dbdc15f0c81611925f382dfa97b3bd0bc2c1ce19d4fe50482cb0ddc12ba30020
 upstream_url=https://files.pythonhosted.org/packages/source/n/numpy/numpy-VERSION.tar.gz
diff --git a/build/pkgs/numpy/package-version.txt b/build/pkgs/numpy/package-version.txt
@@ -1 +1 @@
-1.26.3
+2.2.3
diff --git a/build/pkgs/pybind11/checksums.ini b/build/pkgs/pybind11/checksums.ini
@@ -1,4 +1,4 @@
-tarball=pybind11-VERSION.tar.gz
-sha1=3c75333a9056f0be18eb612803cd46a2bb0c87fc
-sha256=00cd59116a6e8155aecd9174f37ba299d1d397ed4a6b86ac1dfe01b3e40f2cc4
-upstream_url=https://files.pythonhosted.org/packages/source/p/pybind11/pybind11-VERSION.tar.gz
+tarball=pybind11-VERSION-py3-none-any.whl
+sha1=3d927e0ba37bd0af47cd14ec2b52eb796d412806
+sha256=237c41e29157b962835d356b370ededd57594a26d5894a795960f0047cb5caf5
+upstream_url=https://pypi.io/packages/py3/p/pybind11/pybind11-VERSION-py3-none-any.whl
diff --git a/build/pkgs/pybind11/package-version.txt b/build/pkgs/pybind11/package-version.txt
@@ -1 +1 @@
-2.11.1
+2.13.6
diff --git a/build/pkgs/pybind11/spkg-install.in b/build/pkgs/pybind11/spkg-install.in
diff --git a/build/pkgs/pybind11/version_requirements.txt b/build/pkgs/pybind11/version_requirements.txt
@@ -1 +1,2 @@
-pybind11 >=2.6
+pybind11>=2.13.2,<2.14.0
+# see https://github.com/scipy/scipy/blob/maintenance/1.15.x/pyproject.toml
diff --git a/build/pkgs/pythran/checksums.ini b/build/pkgs/pythran/checksums.ini
@@ -1,4 +1,4 @@
-tarball=pythran-VERSION.tar.gz
-sha1=dc8a6035c0c46d36630085003160a3aba4444add
-sha256=f9bc61bcb96df2cd4b578abc5a62dfb3fbb0b0ef02c264513dfb615c5f87871c
-upstream_url=https://files.pythonhosted.org/packages/source/p/pythran/pythran-VERSION.tar.gz
+tarball=pythran-VERSION-py3-none-any.whl
+sha1=2341d42c014f88318f447083c62e8d3953b04ac2
+sha256=be569cc2817b625ccd2c8f74fa3c93806f245c65fadc282c26a9f546ebd34cfa
+upstream_url=https://files.pythonhosted.org/packages/py3/p/pythran/pythran-VERSION-py3-none-any.whl
diff --git a/build/pkgs/pythran/package-version.txt b/build/pkgs/pythran/package-version.txt
@@ -1 +1 @@
-0.15.0
+0.17.0
diff --git a/build/pkgs/pythran/spkg-install.in b/build/pkgs/pythran/spkg-install.in
diff --git a/build/pkgs/pythran/version_requirements.txt b/build/pkgs/pythran/version_requirements.txt
@@ -1 +1,2 @@
-pythran >=0.12.1
+pythran>=0.14.0,<0.18.0
+# per https://github.com/scipy/scipy/blob/maintenance/1.15.x/pyproject.toml
diff --git a/build/pkgs/scipy/checksums.ini b/build/pkgs/scipy/checksums.ini
@@ -1,4 +1,4 @@
 tarball=scipy-VERSION.tar.gz
-sha1=0fd6e14972d8dd9b4a656686a40aed00ad0f1396
-sha256=4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3
+sha1=093c30bdd187fd5693a8d2fc9fcb961b96418a85
+sha256=cd58a314d92838f7e6f755c8a2167ead4f27e1fd5c1251fd54289569ef3495ec
 upstream_url=https://files.pythonhosted.org/packages/source/s/scipy/scipy-VERSION.tar.gz
diff --git a/build/pkgs/scipy/package-version.txt b/build/pkgs/scipy/package-version.txt
@@ -1 +1 @@
-1.12.0
+1.15.2
diff --git a/build/pkgs/scipy/version_requirements.txt b/build/pkgs/scipy/version_requirements.txt
@@ -4,4 +4,4 @@
 # deprecations cannot be introduced in micro releases.
 # SciPy devs wait "at least 6 months", "in practice two (minor) releases"
 # from deprecation to removal of a feature.
-scipy >=1.5
+scipy >=1.12
diff --git a/configure_wrapper b/configure_wrapper
@@ -0,0 +1,4 @@
+#! /bin/sh
+cp conftest.py bak_conftest.py
+./real_configure $@
+mv bak_conftest.py conftest.py
diff --git a/src/doc/en/developer/tools.rst b/src/doc/en/developer/tools.rst
@@ -382,7 +382,7 @@ package :mod:`sage.numerical.backends` and some modules in
 
 - 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>`__.
 
-*Configuration:* :sage_root:`src/conftest.py`
+*Configuration:* :sage_root:`conftest.py`
 
 *Documentation:* https://docs.pytest.org/en/stable/index.html
 

diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
@@ -16220,21 +16220,25 @@ def clustering_coeff(self,
             {0: 1/3, 1: 1/3, 2: 0, 3: 1/3, 4: 1/3, 5: 1/3,
              6: 1/3, 7: 1/3, 8: 0, 9: 1/3, 10: 1/3, 11: 0}
 
-            sage: (graphs.FruchtGraph()).clustering_coeff(weight=True)                  # needs networkx
+            sage: # needs networkx
+            sage: import numpy
+            sage: if int(numpy.version.short_version[0]) > 1:
+            ....:     numpy.set_printoptions(legacy="1.25")
+            sage: graphs.FruchtGraph().clustering_coeff(weight=True)
             {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0,
              3: 0.3333333333333333, 4: 0.3333333333333333,
              5: 0.3333333333333333, 6: 0.3333333333333333,
              7: 0.3333333333333333, 8: 0, 9: 0.3333333333333333,
              10: 0.3333333333333333, 11: 0}
 
-            sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2])
+            sage: graphs.FruchtGraph().clustering_coeff(nodes=[0,1,2])
             {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0.0}
 
-            sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2],                # needs networkx
+            sage: graphs.FruchtGraph().clustering_coeff(nodes=[0,1,2],                # needs networkx
             ....:                                         weight=True)
             {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0}
 
-            sage: (graphs.GridGraph([5,5])).clustering_coeff(nodes=[(0,0),(0,1),(2,2)])
+            sage: graphs.GridGraph([5,5]).clustering_coeff(nodes=[(0,0),(0,1),(2,2)])
             {(0, 0): 0.0, (0, 1): 0.0, (2, 2): 0.0}
 
         TESTS: