Building Graphviz when installing PyGraphviz
Graphviz is software for graph visualization written in C. PyGraphviz provides a nice Python wrapper for it. The issue is that getting Python to know about the C headers changes every few months. I’ll try and keep this blog post updated every time there are some changes.
November 2024
These days, pip install graphviz seemed to work but uv pip install graphviz gave the following:
$ uv pip install pygraphviz
Using Python 3.12.7 environment at /Users/cthoyt/.virtualenvs/orcid
Resolved 1 package in 597ms
error: Failed to prepare distributions
Caused by: Failed to download and build `pygraphviz==1.14`
Caused by: Build backend failed to build wheel through `build_wheel` (exit status: 1)
[stdout]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/scraper.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/testing.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
creating build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_repr_mimebundle.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-14.0-arm64-cpython-312/pygraphviz
clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/Users/cthoyt/Library/Caches/uv/builds-v0/.tmpKw7zNP/include -I/opt/homebrew/opt/python@3.12/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-14.0-arm64-cpython-312/pygraphviz/graphviz_wrap.o
[stderr]
warning: no files found matching '*.swg'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.html' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
pygraphviz/graphviz_wrap.c:9:9: warning: 'SWIG_PYTHON_STRICT_BYTE_CHAR' macro redefined [-Wmacro-redefined]
#define SWIG_PYTHON_STRICT_BYTE_CHAR
^
<command line>:2:9: note: previous definition is here
#define SWIG_PYTHON_STRICT_BYTE_CHAR 1
^
pygraphviz/graphviz_wrap.c:3023:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
^~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
Caused by: This error likely indicates that you need to install a library that provides "graphviz/cgraph.h" for pygraphviz@1.14
Here’s one solution that work (of the many possible ones):
$ export CFLAGS="-I$(brew --prefix graphviz)/include"
$ export LDFLAGS="-L$(brew --prefix graphviz)/lib"
$ uv pip install pygraphviz
Using Python 3.12.7 environment at /Users/cthoyt/.virtualenvs/orcid
Resolved 1 package in 2ms
Built pygraphviz==1.14
Prepared 1 package in 908ms
Installed 1 package in 1ms
+ pygraphviz==1.14
There’s also talk of using --global-option to pass -I/opt/homebrew/opt/graphviz/include and
-L/opt/homebrew/opt/graphviz/lib, but I couldn’t figure this out for uv pip install.
2023 Era
I was on Python 3.10 on a M2 Mac with macOS 13. pygraphviz didn’t have a pre-built wheel for my
systen so python -m pip install pygraphviz gave the following error:
$ python -m pip install pygraphviz
...
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/Users/cthoyt/.virtualenvs/indra/include -I/usr/local/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-13-x86_64-cpython-310/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:3020:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
^~~~~~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
I figured out based on the Homebrew troubleshooting in the docs (https://pygraphviz.github.io/documentation/stable/install.html#homebrew) that the following works:
python -m pip install --use-pep517 \
--config-setting="--global-option=build_ext" \
--config-setting="--build-option=-I$(brew --prefix graphviz)/include/" \
--config-setting="--build-option=-L$(brew --prefix graphviz)/lib/" \
pygraphviz