mrtrix3_0rc3.rb

# typed: false
# frozen_string_literal: true

run_test_patch = <<~EOS
  diff --git a/run_tests b/run_tests
  index a9dd80320..bd5fb9133 100755
  --- a/run_tests
  +++ b/run_tests
  @@ -10,6 +10,10 @@ cat > $LOGFILE <<EOD

   EOD

  +no_fetch=${1:-do_fetch}
  +no_build=${2:-do_build}
  +
  +if [ $no_fetch != no_fetch ]; then
   echo -n "fetching test data... "
   git submodule update --init >> $LOGFILE 2>&1

  @@ -19,9 +23,12 @@ if [ $? != 0 ]; then
   else
     echo OK
   fi
  +else
  +  shift
  +fi


  -
  +if [ $no_build != no_build ]; then
   echo -n "building testing commands... "
   cat >> $LOGFILE <<EOD

  @@ -30,9 +37,10 @@ cat >> $LOGFILE <<EOD
   ## building test commands...

   EOD
  +
   (
     cd testing
  -  ../build
  +  ../build -nopaginate
   ) >> $LOGFILE 2>&1
   if [ $? != 0 ]; then
     echo ERROR!
  @@ -40,6 +48,9 @@ if [ $? != 0 ]; then
   else
     echo OK
   fi
  +else
  +  shift
  +fi


   # generate list of tests to run:
EOS

class Mrtrix30rc3 < Formula
  desc "MRtrix3: tools to perform various types of diffusion MRI analyses"

  homepage "http://mrtrix.org"

  url "https://github.com/MRtrix3/mrtrix3.git"

  version  "3.0_RC3-0-g57e351eb"
  revision 1

  bottle do
    root_url "https://github.com/MRtrix3/mrtrix3/releases/download/3.0_RC3"
    rebuild 0
    sha256 cellar: :any, high_sierra: "5483cefd60aa12fe2039997588b055e811863c65b75577e96da06a8b0ea96edd"
  end

  option "test", "Run tests after installation."
  option "assert", "Build with assert statements (executables are slower)."
  option "debug", "Build with debug statements (executables are slower)."
  option "mrconvert", "Build mrconvert, no other binaries unless stated"
  option "mrinfo", "Build mrinfo, no other binaries unless stated"
  option "mrview", "Build mrview, no other binaries unless stated"
  option "without-multithreaded_build",
         "This is useful if your computer has many cores but not enough RAM to build MRtrix using multiple threads."
  option "without-matlab", "Do not add MRtrix scripts to matlab path."
  option "with-copy_src_from_home",
         "Use MRtrix3 source code from ~/mrtrix3. This settting is for developers and testing purposes!"

  depends_on "eigen" => :build
  depends_on "fftw"
  depends_on "libtiff"
  depends_on "pkg-config"
  depends_on "qt5"
  depends_on "python" => :recommended

  conflicts_with "mrtrix3", because: "tagged version (this) conflicts with non-tagged version of mrtrix3"

  def execute(cmd)
    # verbose alternative to: system cmd
    require "pty"
    raw = ""
    PTY.spawn(cmd) do |stdout_err, _stdin, pid|
      while (char = stdout_err.getc)
        raw << char
        print char
      end
    rescue Errno::EIO # always raised when PTY runs out of input
    ensure
      Process.waitpid pid # Wait for PTY to complete before continuing
    end
    raw
  end

  def set_matlab_path
    matlab_add = <<~EOS
      import os, glob, sys, subprocess

      # Trick out homebrew's overwrite of USER
      p = subprocess.Popen('whoami', shell = True, stdout=subprocess.PIPE)
      me = p.stdout.readline().rstrip()
      p.wait()

      comment='% MRtrix3 PATH automatically generated by homebrew installation formula - do NOT modify:'
      set_path = "addpath('#{prefix}/matlab')" + os.linesep

      def path_has_been_set(startup):
          if not os.path.isfile(startup):
              return False
          with open (startup, "r") as inp:
              for iline, line in enumerate(inp):
                  if comment in line:
                      nl = next(inp)
                      if not 'mrtrix' in nl.lower():
                          raise Exception ('matlab startup file ' + startup + ' has been modified. aborting. ' + nl)
                      return iline + 1
          return 0

      matlab_bins = glob.glob("/Applications/MATLAB_R20*/bin/matlab")
      if not len(matlab_bins):
          print ("WARNING: no Matlab binary found. Not adding MRtrix to Matlab startup path")
          sys.exit(0)

      startup_locations = []
      for bin in matlab_bins:
          matlab_root = os.path.split(os.path.split(bin)[0])[0]
          startup_locations.append(os.path.join(matlab_root, "toolbox", "local", "startup.m"))

      userdir = os.path.join('/Users',me,'Documents','MATLAB')
      if os.path.isdir(userdir):
          startup_locations.append(os.path.join(userdir,"startup.m"))
      else:
        print userdir + " not found"

      is_set = 0
      for startup in startup_locations:
          try:
              pline = path_has_been_set(startup)
              if pline:
                  with open (startup, "r") as inp:
                      sf = inp.readlines()
                      sf[pline] = set_path + os.linesep
                  with open (startup, "w") as inp:
                      inp.write(''.join(sf))
                  print ("updated mrtrix path in " + startup)
              else:
                  with open (startup, "a") as inp:
                      inp.write(comment + os.linesep + set_path + os.linesep)
                  print ("added mrtrix path to " + startup)
              is_set += 1
          except:
              print "WARNING: could not set mrtrix path in Matlab startup file: " + startup
      if not (is_set):
          raise Exception('could not set mrtrix path in any Matlab startup file')
    EOS
    open("#{pkgshare}/matlab_add.py", "w") do |f|
      f.puts matlab_add
    end
    system "python", "#{pkgshare}/matlab_add.py"
    rm "#{pkgshare}/matlab_add.py"
  end

  def install
    puts "PATH:"
    puts ENV["PATH"]
    if ENV["PATH"].downcase.include? "anaconda"
      puts "warning: anaconda found in PATH. You might want to exclude those directories from you PATH."
    end
    xcodeerror=`xcodebuild 2>&1`
    # puts xcodeerror
    if xcodeerror.include? "tool 'xcodebuild' requires Xcode"
      puts "\nxcodebuild failed with the error message:"
      puts xcodeerror
      puts "If the command line tools were installed before Xcode, you can fix this with:"
      puts "sudo xcode-select -s /Applications/Xcode.app/Contents/Developer"
      raise "command line tools failure"
    end

    system "git", "fetch", "--unshallow"
    system "git", "reset", "--hard", "origin/master"
    system "git", "checkout", version.to_s

    if build.without? "multithreaded_build"
      ENV["NUMBER_OF_PROCESSORS"] = "1"
      print "NUMBER_OF_PROCESSORS = 1"
    end

    conf = ["./configure"]
    # if build.without? "qt5"
    #   conf.push("-nogui")
    # end
    conf.push("-assert") if build.include? "assert"
    conf.push("-debug") if build.include? "debug"

    if build.with? "copy_src_from_home"
      me = `whoami`.strip
      external_mrtrix_src_dir = "/Users/#{me}/mrtrix3"
      unless File.directory?(external_mrtrix_src_dir.to_s)
        raise "not found: #{external_mrtrix_src_dir}. --with-copy_src_from_home is intended for developers only"
      end

      execute("rm -r *")
      execute("cp -r #{external_mrtrix_src_dir}/* ./")
    end

    execute(conf.join(" "))
    bin.mkpath
    pkgshare.mkpath
    cp "LICENCE.txt", "#{prefix}/"
    cp "LICENCE.txt", "#{pkgshare}/"
    system "git", "reset", "head"
    system "git", "log", "-1"
    system "git", "describe", "--always", "--dirty"

    env = `env`
    puts "shared path: #{pkgshare}"
    File.open("#{pkgshare}/env", "w") { |file| file.write(env) }

    if File.directory?("release") # pre tag 0.3.16

      system "mkdir", "#{prefix}/lib"
      system "mkdir", "#{prefix}/release"
      system "ln", "-s", "#{prefix}/bin", "#{prefix}/release/bin"

      system "mkdir", "#{prefix}/matlab"
      cp_r "matlab/.", "#{prefix}/matlab/"

      system "mkdir", "#{prefix}/icons"
      cp_r "icons/.", "#{prefix}/icons/"

      # copy and link scripts
      system "mkdir", "#{prefix}/scripts"
      cp_r "scripts/.", "#{prefix}/scripts/"
      # find scripts that have lib.app.initParser and add others manually
      scripts = `find "#{prefix}/scripts" -type f ! -name "*.*" -maxdepth 1`
      scripts = scripts.split
      scripts = scripts.uniq.sort
      scripts.each do |scrpt|
        print "linking #{Pathname(scrpt).each_filename.to_a[-1]}\n"
        # bin.install_symlink prefix/"scripts/"Pathname(scrpt).each_filename.to_a[-1]
        system "ln", "-s", scrpt, "#{prefix}/bin/"+Pathname(scrpt).each_filename.to_a[-1]
      end

      bld = ["./build"]
      bld.push("release/bin/mrconvert") if build.include? "mrconvert"
      bld.push("release/bin/mrinfo") if build.include? "mrinfo"
      bld.push("release/bin/mrview") if build.include? "mrview"
      execute(bld.join(" "))

      # This has to be before bin.install or else binaries are not in place.
      if build.include? "test"
        tst = ["./run_tests"]
        tst.push("mrconvert") if build.include? "mrconvert"
        execute(tst.join(" "))
        cp "testing.log", pkgshare
        print "Testing done. Testlog is in #{pkgshare}\n"
      end

      execute("git rev-parse HEAD > #{pkgshare}/git_hash")
      bin.install Dir["release/bin/*"]
      cp_r "release/lib/.", "#{prefix}/lib/"
      cp "release/config", pkgshare

    else # >= tag_0.3.16
      cp "config", pkgshare
      cp "configure.log", pkgshare

      system "mkdir", "#{prefix}/matlab"
      cp_r "matlab/.", "#{prefix}/matlab/"

      system "mkdir", "#{prefix}/icons"
      cp_r "icons/.", "#{prefix}/icons/"

      bld = ["./build"]
      bld.push("bin/mrconvert") if build.include? "mrconvert"
      bld.push("bin/mrinfo") if build.include? "mrinfo"
      bld.push("bin/mrview") if build.include? "mrview"
      execute(bld.join(" "))

      # This has to be before bin.install or else binaries are not in place.
      if build.include? "test"
        tst = ["./run_tests"]
        tst.push("mrconvert") if build.include? "mrconvert"
        execute(tst.join(" "))
        system "mkdir", "#{prefix}/testing"
        cp_r "testing/.", "#{prefix}/testing/"

        # patch run_tests tests to not fetch the data and not build
        open("run_test_patch.diff", "w") do |f|
          f.puts un_test_patch
        end
        system "python", "matlab_add.py"
        execute("git apply run_test_patch.diff")
        rm "run_test_patch.diff"

        cp_r "run_tests", prefix.to_s
        cp "testing.log", prefix.to_s
        print "Testing done. Testlog is in #{pkgshare}\n"
      end

      execute("git rev-parse HEAD > #{pkgshare}/git_hash")
      bin.install Dir["bin/*"]
      system "mkdir", "#{prefix}/lib"
      cp_r "lib/.", "#{prefix}/lib/"
      cp "config", pkgshare

    end

    # TODO: mrtrix_bash_completion
  end

  def post_install
    if build.without? "matlab"
      print "ignoring Matlab"
    else
      begin
        set_matlab_path
      rescue Exception => e
        print "Warning: unable to set Matlab path: #{e}\n"
        print "You can add it manually to your startup.m: addpath('#{prefix}/matlab')\n"
      end
    end
    print "Installation done. The MRtrix3 binaries are in #{prefix}/bin\n"
    print "\n"
    print "⚠️: If you have an existing version of MRtrix3 in your PATH\n"
    print "and want to use this version without prepending '$(brew --prefix)/bin' to your commands,\n"
    print "make sure to remove the previous version from your PATH.\n"
    print "You can find out with 'ls -l $(which mrinfo)'\n"
    print "\n"
    # print "Alternatively, rename its folder or prepend your PATH with #{prefix}/bin\n"
    print "For more information go to http://mrtrix.readthedocs.io\n"
  end

  test do
    if build.include? "test"
      puts prefix.to_s
      puts testpath
      cp_r "#{prefix}/.", testpath # mrtrix directory is not writable, testpath is
      cd testpath
      system("./run_tests", "no_fetch", "no_build")
    end
  end
end