A brew formula for installing E-Cell version 4. Put the formula in /usr/local/Library/formula, run "brew install ecell4", and add /usr/local/lib/python2.7/site-packages to the $PYTHONPATH variable. Uncomment the lines in the "targets" array to install the module of choice. Note that some of these modules depend on other Python modules (e.g. SciPy)

ecell4.rb

require 'formula'

# Contact celery [at] g-language.org for questions

# Or should I call this formula plain ecell...?
class Ecell4 < Formula
  homepage 'http://www.e-cell.org/'
  url 'https://github.com/ecell/ecell4/tarball/master'
  sha1 '2b1bdf70b0bdfd09e091943eb110b1aab03db6c6'
  version '4'

  # Bad practice for finding path to "cython"
  tmp = `mdfind -name cython | grep /bin/ | head -n 1`.split("/")
  tmp.pop
  CYTHONPATH = tmp.join("/")

  # Define some constants for environment variables
  PATH = String.new(ENV['PATH']) + ":" + CYTHONPATH
  PREFIX = "/usr/local/Cellar/ecell4/4"
  tmp = /\d\.\d\.\d/.match(`python --version 2>&1`).to_s.split(".")
  tmp.pop
  PYTHONVERSION = tmp.join(".")
  PYTHONPATH = PREFIX + "/lib/python" + PYTHONVERSION + "/site-packages"
  NEWPATH = "/usr/local/lib/python" + PYTHONVERSION + "/site-packages"
  CPATH = PREFIX + "/include"
  LIBRARY_PATH = PREFIX + "/lib"
  tmp = `echo $SHELL`.split("/")
  SHELL = tmp.pop.chomp

  # Dependencies
  depends_on 'pkg-config'
  depends_on 'gsl'
  depends_on 'boost'
  depends_on 'hdf5' => '--enable-cxx'

  # This will automatically build the target module
  def waf(target)
    puts "Building " + target + "..."

    tmp = `mdfind -name cython | grep /bin/ | head -n 1`.split("/")
    tmp.pop
    tmp = tmp.join("/")

    ENV['PATH'] = PATH + ":" + tmp
    ENV['CPATH'] = CPATH
    ENV['LIBRARY_PATH'] = LIBRARY_PATH
    ENV['PYTHONPATH'] = PYTHONPATH

    # Process the waf stuff
    Dir.chdir(target)
    system "../waf configure --prefix=" + PREFIX
    system "../waf build"
    system "../waf install"
    Dir.chdir("../")
  end

  def install
    ENV['PATH'] = PATH

    # Install pip if not present
    print "Looking for pip..."
    unless `which pip`.length > 1
      puts " not found"
      puts "\n\e[31mWarning:\e[0m"
      puts "We are trying to install \e[32mpip\e[0m into your environment"
      puts "If you do not wish for homebrew to perform this task, exit"
      puts "and install pip by performing"
      puts "\n  $ sudo easy_install pip"
      puts "\nIf you wish to proceed, enter root password"
      system "sudo easy_install pip"
    else
      puts " found"
    end

    # Install cython if not present
    print "Looking for cython..."
    if `pip freeze | grep -ic cython`.chomp.to_i == 0
      puts " not found"
      puts "\n\e[31mWarning:\e[0m"
      puts "We are trying to install \e[32mcython\e[0m into your environment"
      puts "If you do not wish for homebrew to perform this task, exit"
      puts "and install cython by performing"
      puts "\n  $ sudo pip install cython"
      puts "\nor if you are not root"
      puts "\n  $ pip install cython --user"
      puts "\nIf you wish to proceed, enter root password"
      system "sudo pip install cython"
    else
      puts " found"
    end

    # Install scipy if not present
    print "Looking for scipy..."
    puts " skipped" # Under development
    # if `pip freeze | grep -ic scipy`.chomp.to_i == 0
    #   puts " not found"
    #   system "sudo pip install scipy"
    # else
    #   puts " found"
    # end

    # Uncomment lines to include in installation
    # NOTE - Some of these modules may require additional Python modules
    targets = ["core",       "core_python",
               # "egfrd",      "egfrd_python", # Requires SciPy
               "gillespie",  "gillespie_python",
               "ode",        "ode_python",
               # "spatiocyte", "spatiocyte_python", # Requires ecs
               "reaction_reader"]

    targets.each {
      |target|
      waf(target)
    }

    if SHELL == "tcsh" || SHELL == "csh"
      puts "Remember to add"
      puts "'setenv PYTHONPATH $PYTHONPATH:#{NEWPATH}'"
      puts "into your .#{SHELL}rc"
    else
      puts "Remember to add"
      puts "'export PYTHONPATH=$PYTHONPATH:#{NEWPATH}'"
      puts "into your .#{SHELL}rc"
    end
  end

  test do
    # `test do` will create, run in and delete a temporary directory.
    #
    # This test will fail and we won't accept that! It's enough to just replace
    # "false" with the main program this formula installs, but it'd be nice if you
    # were more thorough. Run the test with `brew test ecell4`.
    system "false"
  end
end