Upgrade Python to 3.9.1, pip to 20.3.3 #30589

mkoeppe · 2020-09-17T16:57:10Z

This contains the upgrade to Python 3.9.1

To test, use

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

Depends on #31050

CC: @slel @jhpalmieri @fchapoton @dimpase @vbraun @kiwifb

Component: packages: standard

Author: Matthias Koeppe

Branch/Commit: 41d7e7a

Reviewer: John Palmieri, Samuel Lelièvre

Issue created by migration from https://trac.sagemath.org/ticket/30589

The text was updated successfully, but these errors were encountered:

mkoeppe · 2020-09-17T16:57:34Z

Dependencies: #30184

mkoeppe · 2020-09-17T18:05:07Z

Branch: u/mkoeppe/upgrade-python-3.9

sagetrac-git · 2020-09-17T22:29:10Z

Commit: e188c5e

sagetrac-git · 2020-09-17T22:29:10Z

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

`e188c5e`	`src/sage/cpython/debugimpl.c: Disable _type_debug for Python 3.9`

sagetrac-git · 2020-09-18T00:56:34Z

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`

sagetrac-git · 2020-09-18T00:56:34Z

Changed commit from e188c5e to 5e89ab2

sagetrac-git · 2020-09-24T18:47:49Z

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`

sagetrac-git · 2020-09-24T18:47:49Z

Changed commit from 5e89ab2 to 316ae6d

sagetrac-git · 2020-09-24T18:59:17Z

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`

sagetrac-git · 2020-09-24T18:59:17Z

Changed commit from 316ae6d to 5cf1baf

sagetrac-git · 2020-09-25T01:54:09Z

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`

sagetrac-git · 2020-09-25T01:54:09Z

Changed commit from 5cf1baf to b3c1dc1

sagetrac-git · 2020-10-06T00:02:47Z

Changed commit from b3c1dc1 to 6d3a0fa

sagetrac-git · 2020-10-06T00:02:47Z

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 · 2020-10-06T00:08:30Z

Changed dependencies from #30184 to none

mkoeppe · 2020-10-06T00:20:32Z

Reviewer: https://github.com/mkoeppe/sage/actions/runs/290402434

mkoeppe · 2020-12-15T17:20:30Z

comment:13

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 · 2020-12-15T17:22:26Z

comment:14

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)

sagetrac-git · 2020-12-16T01:51:14Z

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`

sagetrac-git · 2020-12-16T01:51:14Z

Changed commit from 6d3a0fa to f8bb56d

mkoeppe · 2020-12-16T01:55:48Z

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/290402434 to https://github.com/mkoeppe/sage/actions/runs/424627107

jhpalmieri · 2020-12-17T19:31:14Z

comment:28

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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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 · 2020-12-18T22:08:48Z

comment:29

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 · 2020-12-18T23:02:59Z

comment:30

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 · 2020-12-19T04:47:20Z

comment:31

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/[email protected]/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/[email protected]/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 · 2020-12-21T09:51:39Z

comment:32

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/[email protected]/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/[email protected]/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:
scipy/scipy#13102 (comment)

jhpalmieri · 2020-12-22T04:03:44Z

comment:33

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 · 2020-12-22T06:17:26Z

comment:34

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

mkoeppe · 2020-12-27T19:45:09Z

comment:35

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.

slel · 2021-01-03T10:15:42Z

comment:38

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 · 2021-01-06T03:05:49Z

comment:39

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 · 2021-01-07T21:40:52Z

comment:40

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 · 2021-01-07T21:44:10Z

comment:41

This is now #31204

mkoeppe · 2021-01-07T21:44:52Z

comment:42

Replying to @slel:

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 · 2021-01-11T03:10:47Z

comment:43

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

Let's get this in please.

jhpalmieri · 2021-01-11T19:00:41Z

comment:44

Sure, let's proceed.

jhpalmieri · 2021-01-11T19:00:41Z

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/426748847 to John Palmieri, Samuel Lelièvre

vbraun · 2021-01-24T10:38:12Z

Changed branch from u/mkoeppe/upgrade-python-3.9 to 41d7e7a

mkoeppe added c: packages: standard pending labels Sep 17, 2020

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mkoeppe changed the title ~~Test ticket: Python 3.9.0rc2~~ Test ticket: Python 3.9.0 Oct 6, 2020

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mkoeppe added p: critical / 2 and removed p: major / 3 labels Dec 27, 2020

jhpalmieri added s: positive review and removed s: needs review labels Jan 11, 2021

vbraun removed the s: positive review label Jan 24, 2021

vbraun closed this as completed in a549452 Jan 24, 2021

slel mentioned this issue Oct 20, 2020

Support Python 3.9 #30184

Closed

jhpalmieri mentioned this issue Dec 28, 2020

Meta-ticket: support macOS 11 Big Sur #30651

Closed

slel mentioned this issue Mar 9, 2022

Update Python to 3.10.x #30767

Closed

This was referenced Dec 28, 2020

build/pkgs/python3: Remove libpng from dependencies, SAGE_SPKG_DEPCHECK #31009

Closed

homebrew: Unused packages (singular, pari, ...) in /usr/local leak into build when using homebrew's python3 #31132

Closed

jhpalmieri mentioned this issue Jan 31, 2021

Update setuptools and setuptools_scm #31134

Closed

mkoeppe mentioned this issue Mar 18, 2021

doctests: Filter out linker warning messages #31204

Closed

Upgrade Python to 3.9.1, pip to 20.3.3 #30589

Upgrade Python to 3.9.1, pip to 20.3.3 #30589

Comments

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