gh-36123: Upgrade numpy to 1.26.0, setuptools to 68.2.2

    
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NumPy 1.26 provides Python 3.12 support and Cython 3 compatibility.

1.26.0 was released 2023-09-16.

As NumPy has changed its build system from setuptools-pinned-to-an-
ancient-version to meson_python, we get rid of our ancient version of
`setuptools`. The SPKGs `setuptools` and `setuptools_wheel` now ship the
same (current) version.

- [x] Check portability run:
https://github.com/mkoeppe/sage/actions/runs/5959239800
- [ ] Check SAGE_FAT_BINARY

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Resolves #34816
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### 📝 Checklist

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- [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
- Depends on #36112 (for the `meson_python` upgrades, merged here)
- Depends on #35404 (merged here as
part of above)
- Depends on #35810 (merged here as part of above)
- Depends on #36110 (merged here)
- Depends on #36263 (merged here)
- Depends on #36238 (merged here)
- Depends on #36255 (merged here)
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- #12345: short description why this is a dependency
- #34567: ...
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URL: #36123
Reported by: Matthias Köppe
Reviewer(s):

build/pkgs/numpy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=numpy-VERSION.tar.gz
-sha1=6c7f2278b4ddd113b30821e7e4d5f246dc3ee735
-md5=8b2692a511a3795f3af8af2cd7566a15
-cksum=3950457778
+sha1=a3f9d79d7852f5d35ff35693fc31d17ea270d2d0
+md5=69bd28f07afbeed2bb6ecd467afcd469
+cksum=3599108965
 upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.tar.gz

build/pkgs/numpy/dependencies

@@ -1,4 +1,4 @@
- $(BLAS) gfortran | $(PYTHON_TOOLCHAIN) pkgconfig cython $(PYTHON)
+$(BLAS) gfortran | $(PYTHON_TOOLCHAIN) pkgconfig cython meson_python $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.23.5
+1.26.0

build/pkgs/numpy/spkg-install.in

@@ -3,57 +3,33 @@ cd src
 
 set -e
 
-if [ `uname` = "Darwin" ]; then
-    unset ATLAS
-    unset BLAS
-    unset LAPACK
-    # https://github.com/sagemath/sage/issues/34110#comment:35
-    # The fix for "reciprocal" (affected by a clang compiler bug) in
-    # https://github.com/numpy/numpy/pull/19926 relies on -ftrapping-math
-    # being used when Apple clang v12+ is used.
-    # But numpy.distutils.ccompiler only sets this flag when
-    # $CC contains the string "clang" -- missing the case CC=/usr/bin/gcc.
-    # So we set it here explicitly if the compiler supports the flag.
-    export CFLAGS="$(testcflags.sh $CFLAGS -ftrapping-math)"
-else
-    export {ATLAS,PTATLAS,OPENBLAS,MKL,MKLROOT}=None
-    export LDFLAGS="${LDFLAGS} -shared"
-fi
+# https://github.com/scipy/scipy/issues/16536 - meson breaks when CXX="g++ -std=gnu++11"
+# -- this also affects numpy
+export CXX=$(echo "$CXX" | sed 's/-std=[a-z0-9+]*//g')
 
 if [ "$UNAME" = "CYGWIN" ]; then
     # Trac #30643
     export CPPFLAGS="${CPPFLAGS} -D_GNU_SOURCE"
 fi
 
-# Trac #32746: pkg-config omits -I and -L flags that refer to directories
-# that are already on CPATH, LIBRARY_PATH.
-# But our script tries to obtain the list of include_dirs and library_dirs
-# from pkg-config!
-(unset CPATH LIBRARY_PATH; python3 ../lapack_conf.py)
-
-# Make sure that the fortran objects are compiled with -fPIC
-export FFLAGS="$FFLAGS -fPIC"
-export FCFLAGS="$FCFLAGS -fPIC"
-
 if [ "$SAGE_FAT_BINARY" = "yes" ]; then
     export NUMPY_FCONFIG="--cpu-baseline=NONE"
 else
     export NUMPY_FCONFIG=""
 fi
 
-# Trac #32423: Fix 32-bit builds on x86_64
-ARCH=$($CC -dumpmachine 2>/dev/null || echo unknown)
-case "$ARCH" in
-    *x86_64*)
-        ;;
-    *)
-        export NPY_DISABLE_SVML=1
-        ;;
-esac
-
-################################################
-
-# Trac #33138: numpy is a PEP 517 package, so the crucial "--build-option"s would be ignored.
-eval sdh_pip_install --no-use-pep517 \
-     $(eval sdh_prefix_args "--build-option" build ${NUMPY_CONFIG} ${NUMPY_FCONFIG}) \
-     .
+### Per https://github.com/numpy/numpy/releases/tag/v1.26.0b1
+### "NumPy-specific build customization":
+###
+### The NPY_* environment variables which control BLAS/LAPACK, SIMD,
+### threading, and other such options are no longer supported, nor is
+### a site.cfg file to select BLAS and LAPACK. Instead, there are
+### command-line flags that can be passed to the build via pip/build's
+### config-settings interface.  These flags are all listed in
+### https://github.com/numpy/numpy/blob/main/meson_options.txt
+###
+### 1.26.0b1 temporarily vendors Meson and meson-python
+### http://scipy.github.io/devdocs/building/index.html
+
+
+sdh_pip_install .

build/pkgs/pip/checksums.ini

@@ -1,5 +1,5 @@
 tarball=pip-VERSION.tar.gz
-sha1=29167fffe19874a74247fe92f4fdba1bb1221c61
-md5=996f58a94fe0b8b82b6795c42bd171ba
-cksum=537001443
+sha1=4bdfd8e976b5122cf55f4f4740f7305f1ffa4310
+md5=e9b1226701a56ee3fcc81aba60d25d75
+cksum=1940746834
 upstream_url=https://pypi.io/packages/source/p/pip/pip-VERSION.tar.gz

build/pkgs/pip/package-version.txt

@@ -1 +1 @@
-22.3.1
+23.2.1

build/pkgs/setuptools/SPKG.rst

@@ -7,13 +7,6 @@ Description
 setuptools is the classical build system for Python packages,
 a collection of enhancements to the Python distutils.
 
-This package represents version 63.x of ``setuptools``.
-Sage installs this version to provide the build system
-for non-PEP 517 packages. In particular, Sage uses it
-for building ``numpy``, whose build system ``numpy.distutils`` 
-is not compatible with newer versions of ``setuptools``,
-see https://github.com/numpy/numpy/pull/22154
-
 License
 -------
 

build/pkgs/setuptools/checksums.ini

@@ -1,5 +1,5 @@
 tarball=setuptools-VERSION.tar.gz
-sha1=b14b8e2cf965fdb6870ebfccee50c751c056f757
-md5=02a0e4dc4fa13168904e8769a077aa26
-cksum=2734084418
+sha1=b0c9b16863c57d70adc22651906eea7eaee09803
+md5=d967ca2ba7f46db887daee2d5c9bd6a2
+cksum=2346145273
 upstream_url=https://pypi.io/packages/source/s/setuptools/setuptools-VERSION.tar.gz

build/pkgs/setuptools/install-requires.txt

@@ -1 +1,3 @@
-setuptools >=49.6.0, <64
+# 68.1.0 Promote pyproject.toml's [tool.setuptools] out of beta.
+# 68.1.1 Fix editable install finder handling of nested packages
+setuptools >= 68.1.1

build/pkgs/setuptools/package-version.txt

@@ -1 +1 @@
-63.4.3
+68.2.2

build/pkgs/setuptools_wheel/SPKG.rst

@@ -3,6 +3,3 @@ setuptools_wheel: Build the setuptools package as a wheel
 
 After installing setuptools and wheel, we build a wheel of setuptools
 to complete the set of wheels stored in our wheelhouse.
-
-This version of setuptools is suitable for PEP 517/518/660 builds,
-but it is not suitable for building ``numpy``.

build/pkgs/setuptools_wheel/checksums.ini

@@ -0,0 +1 @@
+../setuptools/checksums.ini

build/pkgs/setuptools_wheel/install-requires.txt

@@ -0,0 +1 @@
+../setuptools/install-requires.txt

build/pkgs/setuptools_wheel/package-version.txt

@@ -0,0 +1 @@
+../setuptools/package-version.txt

src/sage/repl/ipython_kernel/kernel.py

@@ -16,7 +16,18 @@
 # ***************************************************************************
 
 import sys
-from ipykernel.ipkernel import IPythonKernel
+import warnings
+with warnings.catch_warnings():
+    # When upstream pydevd (as opposed to the bundled version) is used
+    # with debugpy, a PEP 420 warning is emitted. Debugpy and/or
+    # pydevd will eventually work around this, but as of September
+    # 2023, hiding the warning gives us more flexibility in the
+    # versions of those packages that we can accept.
+    warnings.filterwarnings("ignore",
+                            message=r".*pkg_resources\.declare_namespace",
+                            category=DeprecationWarning)
+    from ipykernel.ipkernel import IPythonKernel
+
 from ipykernel.zmqshell import ZMQInteractiveShell
 from traitlets import Type