diff --git a/build/pkgs/cmake/checksums.ini b/build/pkgs/cmake/checksums.ini
index 477a967711a..b0310e0489c 100644
--- a/build/pkgs/cmake/checksums.ini
+++ b/build/pkgs/cmake/checksums.ini
@@ -1,4 +1,4 @@
 tarball=cmake-VERSION.tar.gz
-sha1=05de9ac807fefeb2a36ed5e8fcea376a00dd3d57
-sha256=fece24563f697870fbb982ea8bf17482c9d5f855d8c9bf0b82463d76c9e8d0cc
+sha1=bab4725b65d45b3c86e7f1413b265b2d498b1abf
+sha256=9f55e1a40508f2f29b7e065fa08c29f82c402fa0402da839fffe64a25755a86d
 upstream_url=https://github.com/Kitware/CMake/releases/download/vVERSION/cmake-VERSION.tar.gz
diff --git a/build/pkgs/cmake/package-version.txt b/build/pkgs/cmake/package-version.txt
index f641ba7ef04..246dbdaf34a 100644
--- a/build/pkgs/cmake/package-version.txt
+++ b/build/pkgs/cmake/package-version.txt
@@ -1 +1 @@
-3.27.8
+3.30.5
diff --git a/build/pkgs/gsl/checksums.ini b/build/pkgs/gsl/checksums.ini
index bfa1139780a..a633f28eda3 100644
--- a/build/pkgs/gsl/checksums.ini
+++ b/build/pkgs/gsl/checksums.ini
@@ -1,4 +1,4 @@
 tarball=gsl-VERSION.tar.gz
-sha1=549e1105cd1198537be9707257161531e109bd94
-sha256=dcb0fbd43048832b757ff9942691a8dd70026d5da0ff85601e52687f6deeb34b
+sha1=5190579205ca2e8763ef83ee375f1da9b880461a
+sha256=6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190
 upstream_url=https://ftp.gnu.org/gnu/gsl/gsl-VERSION.tar.gz
diff --git a/build/pkgs/gsl/package-version.txt b/build/pkgs/gsl/package-version.txt
index 860487ca19c..a4412fa745d 100644
--- a/build/pkgs/gsl/package-version.txt
+++ b/build/pkgs/gsl/package-version.txt
@@ -1 +1 @@
-2.7.1
+2.8
diff --git a/build/pkgs/gsl/patches/configure-big_sur.patch b/build/pkgs/gsl/patches/configure-big_sur.patch
deleted file mode 100644
index aba05df4d8a..00000000000
--- a/build/pkgs/gsl/patches/configure-big_sur.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- a/configure.orig	2021-10-01 08:15:08.000000000 -0700
-+++ b/configure		2021-10-20 12:44:47.000000000 -0700
-@@ -8733,16 +8733,11 @@
-       _lt_dar_allow_undefined='$wl-undefined ${wl}suppress' ;;
-     darwin1.*)
-       _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
--    darwin*) # darwin 5.x on
--      # if running on 10.5 or later, the deployment target defaults
--      # to the OS version, if on x86, and 10.4, the deployment
--      # target defaults to 10.4. Don't you love it?
--      case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
--	10.0,*86*-darwin8*|10.0,*-darwin[91]*)
--	  _lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
--	10.[012][,.]*)
-+    darwin*)
-+      case ${MACOSX_DEPLOYMENT_TARGET},$host in
-+	10.[012],*|,*powerpc*)
- 	  _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
--	10.*)
-+	*)
- 	  _lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
-       esac
-     ;;
diff --git a/build/pkgs/meson/checksums.ini b/build/pkgs/meson/checksums.ini
index 00cf028db1e..a120118003d 100644
--- a/build/pkgs/meson/checksums.ini
+++ b/build/pkgs/meson/checksums.ini
@@ -1,4 +1,4 @@
 tarball=meson-VERSION-py3-none-any.whl
-sha1=baf5b9bc9ca97f18c7dc87cfaf0e1dc4d617a4cf
-sha256=d5223ecca9564d735d36daaba2571abc6c032c8c3a7ffa0674e803ef0c7e0219
+sha1=a4c3dec12cca725704605d96e378342103d7de67
+sha256=77706e2368a00d789c097632ccf4fc39251fba56d03e1e1b262559a3c7a08f5b
 upstream_url=https://pypi.io/packages/py3/m/meson/meson-VERSION-py3-none-any.whl
diff --git a/build/pkgs/meson/package-version.txt b/build/pkgs/meson/package-version.txt
index 3a3cd8cc8b0..4cda8f19edc 100644
--- a/build/pkgs/meson/package-version.txt
+++ b/build/pkgs/meson/package-version.txt
@@ -1 +1 @@
-1.3.1
+1.5.2
diff --git a/build/pkgs/meson_python/checksums.ini b/build/pkgs/meson_python/checksums.ini
index 7aa199d18fb..db1d0ecaf47 100644
--- a/build/pkgs/meson_python/checksums.ini
+++ b/build/pkgs/meson_python/checksums.ini
@@ -1,4 +1,4 @@
-tarball=meson_python-VERSION.tar.gz
-sha1=71bf382c2f2e76aada2f511a84bd59a99a6b1238
-sha256=fddb73eecd49e89c1c41c87937cd89c2d0b65a1c63ba28238681d4bd9484d26f
-upstream_url=https://pypi.io/packages/source/m/meson_python/meson_python-VERSION.tar.gz
+tarball=meson_python-VERSION-py3-none-any.whl
+sha1=acb6eba0ec6f5d2a6cfd719f254f3b9351fa99ac
+sha256=842dc9f5dc29e55fc769ff1b6fe328412fe6c870220fc321060a1d2d395e69e8
+upstream_url=https://pypi.io/packages/py3/m/meson_python/meson_python-VERSION-py3-none-any.whl
diff --git a/build/pkgs/meson_python/package-version.txt b/build/pkgs/meson_python/package-version.txt
index a5510516948..04a373efe6b 100644
--- a/build/pkgs/meson_python/package-version.txt
+++ b/build/pkgs/meson_python/package-version.txt
@@ -1 +1 @@
-0.15.0
+0.16.0
diff --git a/build/pkgs/meson_python/spkg-install.in b/build/pkgs/meson_python/spkg-install.in
deleted file mode 100644
index b3bbe7b8f3e..00000000000
--- a/build/pkgs/meson_python/spkg-install.in
+++ /dev/null
@@ -1,2 +0,0 @@
-cd src
-sdh_pip_install --no-build-isolation --no-deps .
diff --git a/build/pkgs/meson_python/version_requirements.txt b/build/pkgs/meson_python/version_requirements.txt
index 9705cab644e..76c5596aad1 100644
--- a/build/pkgs/meson_python/version_requirements.txt
+++ b/build/pkgs/meson_python/version_requirements.txt
@@ -1 +1,2 @@
-meson-python
+# per https://github.com/scipy/scipy/blob/maintenance/1.13.x/pyproject.toml
+meson-python >=0.15.0
diff --git a/build/pkgs/ninja_build/checksums.ini b/build/pkgs/ninja_build/checksums.ini
index d640d72d1fc..245170a1449 100644
--- 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
index 720c7384c61..f8f4f03b3dc 100644
--- 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
index fde72f78b6d..915ff31752e 100644
--- 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=9b40b5ab8dd014502141cf33e3415034085538f2
+sha256=883c987dee1880e2a864ab0dc9892292582510604156762362d9326444636e78
 upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.tar.gz
diff --git a/build/pkgs/numpy/package-version.txt b/build/pkgs/numpy/package-version.txt
index f8f73814096..e9307ca5751 100644
--- a/build/pkgs/numpy/package-version.txt
+++ b/build/pkgs/numpy/package-version.txt
@@ -1 +1 @@
-1.26.3
+2.0.2
diff --git a/build/pkgs/pybind11/checksums.ini b/build/pkgs/pybind11/checksums.ini
index c3112e54327..5b78db42c17 100644
--- 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://pypi.io/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/dependencies b/build/pkgs/pybind11/dependencies
index ca33204bd52..644ad35f773 100644
--- a/build/pkgs/pybind11/dependencies
+++ b/build/pkgs/pybind11/dependencies
@@ -1 +1,4 @@
- | $(PYTHON_TOOLCHAIN) $(PYTHON)
+ | pip $(PYTHON)
+
+----------
+All lines of this file are ignored except the first.
diff --git a/build/pkgs/pybind11/package-version.txt b/build/pkgs/pybind11/package-version.txt
index 6ceb272eecd..14239ef1586 100644
--- 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
deleted file mode 100644
index deba1bb42bb..00000000000
--- a/build/pkgs/pybind11/spkg-install.in
+++ /dev/null
@@ -1 +0,0 @@
-cd src && sdh_pip_install .
diff --git a/build/pkgs/pybind11/version_requirements.txt b/build/pkgs/pybind11/version_requirements.txt
index 6c44c4bd07e..b619603e47f 100644
--- a/build/pkgs/pybind11/version_requirements.txt
+++ b/build/pkgs/pybind11/version_requirements.txt
@@ -1 +1,2 @@
-pybind11 >=2.6
+# per https://github.com/scipy/scipy/blob/maintenance/1.13.x/pyproject.toml
+pybind11 >= 2.12.0
diff --git a/build/pkgs/pythran/checksums.ini b/build/pkgs/pythran/checksums.ini
index 03d21286397..1ec089593e4 100644
--- 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
+sha1=a19c84c9f3665a60da8c355aa954109f96e14562
+sha256=861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9
 upstream_url=https://pypi.io/packages/source/p/pythran/pythran-VERSION.tar.gz
diff --git a/build/pkgs/pythran/package-version.txt b/build/pkgs/pythran/package-version.txt
index a5510516948..2a0970ca757 100644
--- a/build/pkgs/pythran/package-version.txt
+++ b/build/pkgs/pythran/package-version.txt
@@ -1 +1 @@
-0.15.0
+0.16.1
diff --git a/build/pkgs/pythran/version_requirements.txt b/build/pkgs/pythran/version_requirements.txt
index f365e5f4971..ff8b5f24aa1 100644
--- a/build/pkgs/pythran/version_requirements.txt
+++ b/build/pkgs/pythran/version_requirements.txt
@@ -1 +1,2 @@
-pythran >=0.12.1
+# per https://github.com/scipy/scipy/blob/maintenance/1.13.x/pyproject.toml
+pythran >=0.14
diff --git a/build/pkgs/scipy/checksums.ini b/build/pkgs/scipy/checksums.ini
index 8871f77250b..9c18b5f7113 100644
--- 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=f131e427ce458d2d97664a48f18875e967333995
+sha256=095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c
 upstream_url=https://pypi.io/packages/source/s/scipy/scipy-VERSION.tar.gz
diff --git a/build/pkgs/scipy/package-version.txt b/build/pkgs/scipy/package-version.txt
index 0eed1a29efd..b50dd27dd92 100644
--- a/build/pkgs/scipy/package-version.txt
+++ b/build/pkgs/scipy/package-version.txt
@@ -1 +1 @@
-1.12.0
+1.13.1
diff --git a/src/pyproject.toml b/src/pyproject.toml
index 4b70dc133d1..9fc75dbaad9 100644
--- a/src/pyproject.toml
+++ b/src/pyproject.toml
@@ -8,11 +8,12 @@ requires = [
     'wheel >=0.36.2',
     'cypari2 >=2.1.1',
     'cysignals >=1.10.2',
-    # Exclude 3.0.3 because of https://github.com/cython/cython/issues/5748
-    'cython >=3.0, != 3.0.3, <4.0',
+    # per https://github.com/scipy/scipy/blob/maintenance/1.13.x/pyproject.toml
+    'cython >=3.0.8,<3.1.0',
     'gmpy2 ~=2.1.b999',
     'memory_allocator',
-    'numpy >=1.19',
+    # per https://github.com/scipy/scipy/blob/maintenance/1.13.x/pyproject.toml
+    'numpy >=1.22.4',
     'pkgconfig',
     'jinja2',
 ]
diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
index 3ae14de7877..7d9d6edb0c1 100644
--- a/src/sage/graphs/generic_graph.py
+++ b/src/sage/graphs/generic_graph.py
@@ -15999,7 +15999,11 @@ 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,
diff --git a/src/sage/libs/flint/flint_wrap.h b/src/sage/libs/flint/flint_wrap.h
index 1302973779e..2cd39eb1441 100644
--- a/src/sage/libs/flint/flint_wrap.h
+++ b/src/sage/libs/flint/flint_wrap.h
@@ -26,6 +26,10 @@
 #pragma push_macro("ulong")
 #undef ulong
 
+/* Reserved in C99, needed for FLINT without https://github.com/flintlib/flint/pull/2027 */
+#pragma push_macro("I")
+#define I Iv
+
 #include <flint/flint.h>
 
 /* If flint was already previously included via another header (e.g.
@@ -169,6 +173,7 @@
 #undef mp_bitcnt_t
 
 #pragma pop_macro("ulong")
+#pragma pop_macro("I")
 
 /* CPU_SIZE_1 and SIZE_RED_FAILURE_THRESH are defined as macros in flint/fmpz_lll.h
  * and as variables in fplll/defs.h, which breaks build if linbox is compiled with fplll */