Instruction to install pygraphviz package in Pycharm in MacOs

Since I spend a lot of time to solve this problem, so make a rocord for future reuse.

Environment

• Mao os 12.4
• Macbook air(M1,2020)
• PyCharm 2022.1.4 (Community Edition)
  • Runtime version: 11.0.15+10-b2043.56 aarch64
• graphviz: stable 5.0.0
• pygraphviz: 1.9

Problem

• The problem is encounter after install graphviz
  • as to install pygraphviz you need
    • Python (version 3.8, 3.9, or 3.10)
    • Graphviz (version 2.42 or later)
    • C/C++ Compiler
• if you use normal command pip install graphviz to install graphviz first
  • then use pip install pygraphviz to install pygraphviz
  • you would encounter a fatal error

fatal error: 'graphviz/cgraph.h' file not found

• the file cgraph.h cannot be found
• even you may find the file in graphviz package file

Why this problem happen

• the installation wizard of pygraphviz cannot find cgraph.h in his default searching path
• So, you need to provide searching path when install pygraphviz

Solution that work for me

Step 1. use Homebrew to graphviz package first

• Install Homebrew from its official website
• type following command in Pycharm terminal

brew install graphviz

• it takes a long time to install
  • then you should be able to find graphviz file in the following path :(/opt/homebrew/Cellar/graphviz)

Some explanation

• Homebrew is a kind of package manager for MacOS (or Linux)
• and all package installed via Homebrew is stored its Homebrew file which is under an opt file
• the opt file is a directory for installing unbundled packages
• i.e. Homebrew in this case help you to install graphviz and provide an searching path for further installation for pygraphviz

Step 2. Provide searching path when install pygraphviz

• type following command in Pycharm terminal

pip3 install --global-option=build_ext --global-option="-I$(brew --prefix graphviz)/include" --global-option="-L$(brew --prefix graphviz)/lib" pygraphviz

• pip3 is just to make sure package is install for python 3
• the -I and -L flags tell the linker where to look for the required Graphviz libraries at build time and run time
• --prefix will let you specific where the directory to go for

Credit

• pygraphviz homepage
• pygraphviz github

Comments

[JoelBonetR 🥇]

Hi @mathewchan , please remove the #help tag if you don't need help to solve it.

It's better to add #pygraphviz #Pycharm #MacOs and #python as tags so other users can find this quickly.

Thank you! 😁