Upgrade Python to 3.9.1, pip to 20.3.3

[mkoeppe]

This contains the upgrade to Python 3.9.1

To test, use

./configure --without-system-python3 --enable-download-from-upstream-url

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​e188c5e

src/sage/cpython/debugimpl.c: Disable _type_debug for Python 3.9

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

​d3dd329	Merge branch 't/30595/remove_deprecated_sage_libs_ppl' into t/30184/support_python_3_9
​68ef4c5	src/sage/cpython/debugimpl.c: Disable _type_debug for Python 3.9
​f3cb571	src/sage/all.py: Filter out Python 3.9 deprecation warnings from ast
​e16ded2	src/sage/symbolic/ring.pyx (isidentifier): Remove py2-only code, use of deprecated parser module
​27a57bc	src/sage/misc/sageinspect.py: Adjust doctest for sage_getsourcelines for Python 3.9 - decorators are now part of the definition
​39416fb	src/sage/misc/sageinspect.py (SageArgSpecVisitor): Relax doctest pattern for python 3.9
​5548c0d	src/sage/misc/latex.py (has_latex_attr): Relax doctest pattern for python 3.9
​4a9362e	src/sage/combinat/root_system/pieri_factors.py: Use sorted in doctest for python 3.9
​49eccd9	src/sage/geometry/polyhedron/palp_database.py: Relax doctest pattern for python 3.9
​5e89ab2	Merge branch 't/30184/support_python_3_9' into t/30589/upgrade-python-3.9

[git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

​b21ed97	build/pkgs/python3/spkg-configure.m4: Ensure that PYTHON_FOR_VENV is a full path
​49aa061	Revert "build/pkgs/python3/spkg-configure.m4: Use 'python >= 3.7'; keep checking for 'python3.8, python3.7'"
​a8b77cd	Revert "only test python3, to be 3.7 or 3.8"
​9403629	build/bin/sage-system-python: Work around LC_ALL=C
​ff0dbc6	build/sage_bootstrap/uncompress/tar_file.py: Fix encoding to utf-8
​f05a110	Merge branch 't/30008/after__30053__sphinx_3_1_2_does_not_build_on_ubuntu__trusty_xenial_bionic___debian_jessie__centos_7__again_' into t/30576/public/30576
​945c8c5	build/bin/sage-site (--docbuild): Set an English locale suuch as C.utf-8, but not the C locale, to ensure correct operation on Python 3.6
​8906897	Merge branch 't/30576/public/30576' into t/30546/build/py3x_conf
​60137bc	Merge branch 't/30546/build/py3x_conf' into t/30184/support_python_3_9
​316ae6d	Merge branch 't/30184/support_python_3_9' into t/30589/upgrade-python-3.9

[git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

​ca58693	build/pkgs/pillow/spkg-install.in: Install via bdist_wheel
​5a747c4	build/bin/sage-pip-{install,uninstall}: Remove pip2 support
​9ee2110	build/bin/sage-dist-helpers: Also use $sudo for storing the wheel file
​d7aac84	src/doc/en/developer/packaging.rst: Update sdh_... documentation
​9b7c7a0	build/bin/sage-pip-{install,uninstall}: Fix typo in comment
​4135e8b	build/bin/sage-pip-install: Remove an outdated comment
​f2e7075	Merge tag '9.2.beta13' into t/29500/install_all_python_packages_via_pip_wheel__create_pep_503_simple_repository_for_wheels
​a2dbb8d	Merge branch 't/29500/install_all_python_packages_via_pip_wheel__create_pep_503_simple_repository_for_wheels' into t/30546/build/py3x_conf
​8c756ed	Merge branch 't/30546/build/py3x_conf' into t/30184/support_python_3_9
​5cf1baf	Merge branch 't/30184/support_python_3_9' into t/30589/upgrade-python-3.9

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​f19d9a4	allow absolute names as arguments to --with-python
​4f7d588	Merge branch 't/30546/build/py3x_conf' into t/30184/support_python_3_9
​b3c1dc1	Merge branch 't/30184/support_python_3_9' into t/30589/upgrade-python-3.9

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

​255d22b	build/pkgs/python3: Update to 3.9.0rc2
​6d3a0fa	build/pkgs/python3: Update to 3.9.0

[mkoeppe]

3.9.1 is out ​https://www.python.org/downloads/release/python-391/ Release Date: Dec. 7, 2020

"3.9.1 is the first version of Python to support macOS 11 Big Sur. With Xcode 11 and later it is now possible to build “Universal 2” binaries which work on Apple Silicon. We are providing such an installer as the macos11.0 variant. This installer can be deployed back to older versions, tested down to OS X 10.9. As we are waiting for an updated version of pip, please consider the macos11.0 installer experimental."

[mkoeppe]

Not sure which updated version of pip they are referring to. 20.3 (2020-11-30) lists "Add support for MacOS Big Sur compatibility tags. (#9138)" ​https://pip.pypa.io/en/stable/news/#id15

No new news items regarding Big Sur in 20.3.3 (2020-12-15)

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

​29aee87	build/pkgs/python3: Update to 3.9.0rc2
​e61d464	build/pkgs/python3: Update to 3.9.0
​f8bb56d	build/pkgs/python3: Update to 3.9.1

[jhpalmieri]

If this works (and I'll test it out soon), it should be a blocker, since I can't build Sage's Python 3.8 on Big Sur.

[jhpalmieri]

This builds for me on Big Sur. With the old version of wheel, I (not surprisingly) hit the problem fixed by #31050. With an updated wheel, gmpy2 still fails to build, with this error:

Successfully built gmpy2
Removed build tracker: '/private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-dw7p5f40'
Using pip 20.2.3 from /Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip (python 3.9)
Non-user install because site-packages writeable
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-ephem-wheel-cache-nd6d05pj
Created temporary directory: /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-d9f2exe4
Initialized build tracking at /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-d9f2exe4
Created build tracker: /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-d9f2exe4
Entered build tracker: /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-d9f2exe4
Created temporary directory: /private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-install-82a1edim
ERROR: gmpy2-2.1.0b5-cp39-cp39-macosx_10_9_x86_64.whl is not a supported wheel on this platform.
Exception information:
Traceback (most recent call last):
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 228, in _main
    status = self.run(options, args)
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper
    return func(self, options, args)
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 323, in run
    requirement_set = resolver.resolve(
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip/_internal/resolution/legacy/resolver.py", line 173, in resolve
    requirement_set.add_requirement(req)
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib/python3.9/site-packages/pip/_internal/req/req_set.py", line 104, in add_requirement
    raise InstallationError(
pip._internal.exceptions.InstallationError: gmpy2-2.1.0b5-cp39-cp39-macosx_10_9_x86_64.whl is not a supported wheel on this platform.
Removed build tracker: '/private/var/folders/z6/yjw_7s357yx3_mhh81__lplc0000gn/T/pip-req-tracker-d9f2exe4'
Error: installing with pip3 failed

Looks like a problem with MACOSX_DEPLOYMENT_TARGET.

[mkoeppe]

We should probably also update to latest pip

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​0e3513f	build/pkgs/pip: Update to 20.3.3
​6dc8e7c	trac 31050: upgrade wheel to 0.36.2
​41d7e7a	Merge branch 'u/jhpalmieri/new_wheel' of git://trac.sagemath.org/sage into t/30589/upgrade-python-3.9

[jhpalmieri]

Great, with the new pip and new wheel, everything works until I hit scipy. The error is not one I remember seeing before:

  /usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib build/temp.macosx-10.9-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.12_1/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib -Lbuild/temp.macosx-10.9-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so
  ld: library not found for -lSystem
  collect2: error: ld returned 1 exit status
  error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib build/temp.macosx-10.9-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.12_1/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib -Lbuild/temp.macosx-10.9-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so" failed with exit status 1
  Building wheel for scipy (PEP 517): finished with status 'error'
  ERROR: Failed building wheel for scipy

I'm guessing that this should be dealt with separately.

I would like to give this a positive review, but since I can't build Sage, I also can't build the documentation or run doctests. So for now I will have to leave the rest of the review to others.

[mkoeppe]

We can also try to throw in an upgrade of setuptools...

[mkoeppe]

Replying to jhpalmieri:

If this works (and I'll test it out soon), it should be a blocker, since I can't build Sage's Python 3.8 on Big Sur.

But doesn't the python3 from XCode work?

[jhpalmieri]

Right now homebrew's python3 is shadowing Xcode's, so I don't know. I would rather not uninstall homebrew's since it is used by other homebrew packages that I want to keep.

I have bigger issues right now: I can make almost no progress building Sage with 9.3.beta4. For example, with #31050 merged with beta4, gmpy2 fails to build:

  Compiling with an SDK that doesn't seem to exist: /Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk
  Please check your Xcode installation
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -O2 -g -I./src -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/include -I/usr/local/Cellar/python@3.9/3.9.1/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c src/gmpy2.c -o build/temp.macosx-11-x86_64-3.9/src/gmpy2.o -DSHARED=1
  clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk' [-Wmissing-sysroot]
  In file included from src/gmpy2.c:445:
  /usr/local/Cellar/python@3.9/3.9.1/Frameworks/Python.framework/Versions/3.9/include/python3.9/Python.h:25:10: fatal error: 'stdio.h' file not found
  #include <stdio.h>

Is my command-line tools installation broken? It is certainly true that the named sysroot directory does not exist, but instead it's .../MacOSX11.1.sdk. Where is that path stored? I've tried uninstalling and reinstalling the command-line tools, uninstalling and reinstalling homebrew and its packages, but no luck.

In contrast, with just #31050 (which was based on beta3), I see the following in the gmpy2 log file:

  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I./src -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/include -I/usr/local/Cellar/python@3.9/3.9.1/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c src/gmpy2.c -o build/temp.macosx-11-x86_64-3.9/src/gmpy2.o -DSHARED=1

(same wrong path given to -I) but gmpy2 builds successfully.

Separately, on a machine running Catalina, I'm having problems with cypari...

[dimpase]

In a (working) Homebrew installation on Catalina, I don't have these /Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk paths used by the tools - ie. gcc/clang is installed in InstalledDir: /Applications/Xcode-beta.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin and not in /Library/....

This can be seen in config.log

[jhpalmieri]

config.log is a good place to look. I see that gfortran -v prints that it is configured using --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk. I reinstalled homebrew's gcc but it didn't help. Any ideas how this is path determined? What does gfortran -v say for you?

(For gcc/clang, I see InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin.)

[jhpalmieri]

Well, this is probably not the right thing to do in the long term, but I created a symlink connecting MacOSX11.1.sdk to MacOSX11.0.sdk. The build still fails on scipy with

  /usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib build/temp.macosx-11-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.13/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -Lbuild/temp.macosx-11-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-11-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so
  gfortran: warning: couldn't understand version 11
  ld: library not found for -lgcc_s.10.4
  collect2: error: ld returned 1 exit status
  error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib build/temp.macosx-11-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.13/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -Lbuild/temp.macosx-11-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-11-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so" failed with exit status 1
  Building wheel for scipy (PEP 517): finished with status 'error'
  ERROR: Failed building wheel for scipy

but the other problems seem to be solved.

[dimpase]

Replying to jhpalmieri:

Well, this is probably not the right thing to do in the long term, but I created a symlink connecting MacOSX11.1.sdk to MacOSX11.0.sdk. The build still fails on scipy with

  /usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib build/temp.macosx-11-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.13/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -Lbuild/temp.macosx-11-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-11-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so
  gfortran: warning: couldn't understand version 11
  ld: library not found for -lgcc_s.10.4
  collect2: error: ld returned 1 exit status
  error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta4/local/lib build/temp.macosx-11-x86_64-3.9/scipy/integrate/_quadpackmodule.o -L/usr/local/Cellar/openblas/0.3.13/lib -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -Lbuild/temp.macosx-11-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-11-x86_64-3.9/scipy/integrate/_quadpack.cpython-39-darwin.so" failed with exit status 1
  Building wheel for scipy (PEP 517): finished with status 'error'
  ERROR: Failed building wheel for scipy

but the other problems seem to be solved.

scipy probably needs an update, and/or a hack: ​https://github.com/scipy/scipy/issues/13102#issuecomment-744473479

[jhpalmieri]

I'm not clever enough to figure out how to hack scipy so it builds. If I issue the command export SYSTEM_VERSION_COMPAT=1 globally before building Sage, then cython doesn't build. If I just issue it in the scipy spkg-install script, then scipy doesn't build with the same error as in comment:31.

Edit: the error with cython after executing export SYSTEM_VERSION_COMPAT=1:

ERROR: Cython-0.29.21-cp39-cp39-macosx_11_0_x86_64.whl is not a supported wheel on this platform.

This is with this ticket and an updated setuptools and setuptools_scm.

[jhpalmieri]

I guess we should move my derailment of the discussion to #30651.

[mkoeppe]

Does someone have time to review this ticket? The tests have already run successfully.

Note that an update to latest 3.8.x is not a good alternative:

​https://www.python.org/downloads/release/python-387/ Python 3.8.7 - Release Date: Dec. 21, 2020 macOS 11 Big Sur not fully supported

Python 3.8.7 is not yet fully supported on macOS 11 Big Sur. It will install on macOS 11 Big Sur and will run on Apple Silicon Macs using Rosetta 2 translation. However, a few features do not work correctly, most noticeably those involving searching for system libraries (vs user libraries) such as ctypes.util.find_library() and in Distutils. This limitation affects both Apple Silicon and Intel processors. We are looking into improving the situation for Python 3.8.8.

[slelievre]

On macOS 10.14.6 with lots of Homebrew packages, successfully ran

$ git trac checkout 30589
$ source .homebrew-build-env
$ ./bootstrap -q
$ ./configure --without-system-python3 --enable-download-from-upstream-url -q
$ make -s V=0

resulting in a build of Sage 9.3.beta4 based on Python 3.9.1.

But something that worked for another Sage install currently at 9.3.beta5:

$ V=0 sage -i pynormaliz

failed here while attempting to build e-antic.

[jhpalmieri]

On OS X Big Sur + various homebrew packages, if I use

% ./configure --with-system-python3=no --enable-download-from-upstream-url 

then Sage builds (if I also incorporate various other changes from #30651), but I get doctest failures of the form

File "src/sage/misc/sagedoc.py", line 646, in sage.misc.sagedoc.format
Failed example:
    cython('\n'.join(cython_code))
Expected nothing
Got:
    ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer macOS version (11.0) than being linked (10.9)

We could (a) not worry about these for now, (b) filter out these warnings, (c) tinker with MACOSX_DEPLOYMENT_TARGET, or (d) something else. I don't have an opinion about which way to go.

[mkoeppe]

These linker warnings are annoying and I think we should filter them out for the doctests. I think it should be a separate ticket. I think I have seen them on other platforms too.

[mkoeppe]

This is now #31204

[mkoeppe]

Replying to slelievre:

But something that worked for another Sage install currently at 9.3.beta5:

$ V=0 sage -i pynormaliz

failed here while attempting to build e-antic.

Is this on homebrew too?

[mkoeppe]

In any case, let's worry about optional packages like e-antic later.

Let's get this in please.

[jhpalmieri]

Sure, let's proceed.