Install Python 3.8.6 with pyenv on macOS Big Sur (11)

pyenv-python38-macos.sh

#!/bin/sh

# 1) Install Xcode 12
# 2) Install command line tools: `xcode-select --install`
# 3) Install Homebrew
# 4) brew install zlib bzip2 xz

CFLAGS="-I$(brew --prefix zlib)/include -I$(brew --prefix bzip2)/include -I$(brew --prefix xz)/include" \
LDFLAGS="-L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib -L$(brew --prefix xz)/lib" \
pyenv install 3.8.6

Check bzip2 is correctly installed.

$ ls $(brew --prefix bzip2)/lib
libbz2.a

libbz2.a is the library Python should link to. -devel package is not required in macOS/Homebrew.

Next, make sure the arguments -I$(brew --prefix bzip2)/include and -L$(brew --prefix bzip2)/lib (don't mix up -I and -L, include and lib).

pyenv install -v shows the compile log. You can check if bz2 module was successfully installed.

$ LDFLAGS="-L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib" pyenv install -v 3.8.5 2>&1 | grep bz2
building '_bz2' extension
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Wstrict-prototypes -Werror=implicit-function-declaration -I./Include/internal -I./Include -I. -I/opt/brew/opt/readline/include -I/opt/brew/opt/zlib/include -I/usr/local/include -I/private/var/folders/nb/dw5p3r0j17q4y5r5wkhpnr0r0000gn/T/python-build.20210104122251.50610/Python-3.8.5/Include -I/private/var/folders/nb/dw5p3r0j17q4y5r5wkhpnr0r0000gn/T/python-build.20210104122251.50610/Python-3.8.5 -c /private/var/folders/nb/dw5p3r0j17q4y5r5wkhpnr0r0000gn/T/python-build.20210104122251.50610/Python-3.8.5/Modules/_bz2module.c -o build/temp.macosx-11.1-x86_64-3.8/private/var/folders/nb/dw5p3r0j17q4y5r5wkhpnr0r0000gn/T/python-build.20210104122251.50610/Python-3.8.5/Modules/_bz2module.o
clang -bundle -undefined dynamic_lookup -L/opt/brew/opt/readline/lib -L/opt/brew/opt/readline/lib -L/Users/yatsu/.pyenv/versions/3.8.5/lib -L/opt/brew/opt/zlib/lib -L/opt/brew/opt/bzip2/lib -L/opt/brew/opt/readline/lib -L/opt/brew/opt/readline/lib -L/Users/yatsu/.pyenv/versions/3.8.5/lib -L/opt/brew/opt/zlib/lib -L/opt/brew/opt/bzip2/lib -L/opt/brew/opt/readline/lib -L/opt/brew/opt/readline/lib -L/Users/yatsu/.pyenv/versions/3.8.5/lib -L/opt/brew/opt/zlib/lib -L/opt/brew/opt/bzip2/lib -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -I/opt/brew/opt/readline/include -I/opt/brew/opt/readline/include -I/Users/yatsu/.pyenv/versions/3.8.5/include -I/opt/brew/opt/zlib/include build/temp.macosx-11.1-x86_64-3.8/private/var/folders/nb/dw5p3r0j17q4y5r5wkhpnr0r0000gn/T/python-build.20210104122251.50610/Python-3.8.5/Modules/_bz2module.o -L/opt/brew/opt/readline/lib -L/Users/yatsu/.pyenv/versions/3.8.5/lib -L/opt/brew/opt/zlib/lib -L/opt/brew/opt/bzip2/lib -L/usr/local/lib -lbz2 -o build/lib.macosx-11.1-x86_64-3.8/_bz2.cpython-38-darwin.so -Wl,-search_paths_first
/opt/brew/bin/ginstall -c -m 644 ./Lib/bz2.py /Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8
/opt/brew/bin/ginstall -c -m 644 ./Lib/test/test_bz2.py /Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/test
/opt/brew/bin/ginstall -c -m 644 ./Lib/encodings/bz2_codec.py /Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/encodings
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/test/test_bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/encodings/bz2_codec.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/test/test_bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/encodings/bz2_codec.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/test/test_bz2.py'...
Compiling '/Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/encodings/bz2_codec.py'...
copying build/lib.macosx-11.1-x86_64-3.8/_bz2.cpython-38-darwin.so -> /Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/lib-dynload
changing mode of /Users/yatsu/.pyenv/versions/3.8.5/lib/python3.8/lib-dynload/_bz2.cpython-38-darwin.so to 755

I took another way.

OS: Big Sur 11.1

What I tried

• Remove brew and its packages
• and reinstall brew, pyenv, its dependencies python3.8.5
• without brew install bzip2 or brew install openblas

Result

• no more Polyfit issue with numpy
• or no more _bz2 module issue with pandas

I have no idea what's changed, but it worked.

Thanks for your help anyway.