<commit_before>class Beagle < Formula
  desc "Evaluate the likelihood of sequence evolution on trees"
  homepage "https://github.com/beagle-dev/beagle-lib"
  url "https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz"
  sha256 "dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275"

  bottle do
    cellar :any
    sha256 "032c922981ee1707934cceb53318a26dab4a0ca6c392db63115f626a9f56b412" => :mojave
    sha256 "d7834048b8aabdedcc824daf474cefe0436fdd8515da4df3f6c52a87d01395ef" => :high_sierra
    sha256 "87e49bf8faeff280ba1211a7c0a0b1626750652b0498eef2ff01dfcff4290056" => :sierra
  end

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "doxygen" => :build
  depends_on :java => [:build, :test]
  depends_on "libtool" => :build

  def install
    system "./autogen.sh"
    system "./configure", "--disable-dependency-tracking",
                          "--disable-silent-rules",
                          "--prefix=#{prefix}",
                          "--without-cuda",
                          "--disable-libtool-dev"
    system "make", "install"
  end

  test do<commit_msg>beagle: update 3.1.2 bottle.<commit_after>class Beagle < Formula
  desc "Evaluate the likelihood of sequence evolution on trees"
  homepage "https://github.com/beagle-dev/beagle-lib"
  url "https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz"
  sha256 "dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275"

  bottle do
    cellar :any
    rebuild 1
    sha256 "e3a8d1dae20da88139fceb606df94812e293024b8108222f762867ea6a64aafe" => :catalina
    sha256 "9ee0e3619b1aa655a6a6daf9ee2fa3d7b37098eacfb6e50214062b8c1989420b" => :mojave
    sha256 "2fa7d02be8cf19fa4b0344e2d4c920ec49981c39c7a60938a5c124ce601080e6" => :high_sierra
  end

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "doxygen" => :build
  depends_on :java => [:build, :test]
  depends_on "libtool" => :build

  def install
    system "./autogen.sh"
    system "./configure", "--disable-dependency-tracking",
                          "--disable-silent-rules",
                          "--prefix=#{prefix}",
                          "--without-cuda",
                          "--disable-libtool-dev"
    system "make", "install"
  end

  test do
{'fraction_non_alphanumeric': 0.11309264897781644, 'fraction_numerical': 0.1535450195737277, 'mean_word_length': 3.0280210157618215, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 19, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4578877', 'n_tokens_mistral': 1062, 'n_tokens_neox': 885, 'n_words': 134}