<commit_before>class Gubbins < Formula
  desc "Detect recombinations in Bacteria"
  homepage "https://github.com/sanger-pathogens/gubbins"
  url "https://github.com/sanger-pathogens/gubbins/archive/v2.1.0.tar.gz"
  sha256 "27d9d26febf8858e038d91d32ec8736d61644e13069c1cc81b8315eb7b32318f"
  head "https://github.com/sanger-pathogens/gubbins.git"
  # tag "bioinformatics"
  # doi "10.1093/nar/gku1196"

  bottle do
    cellar :any
    sha256 "1914a61d01d27b72cbe0f5d1f05530c0e8fbc4fa373fdeb4850fc3bdf5c382c4" => :el_capitan
    sha256 "b5c3f146aaca4145359a2a699702e91d1688cd0c99eee838b3f83a09a0c8f650" => :yosemite
    sha256 "5014f75893a38e50638c039d034e664f7843c8aad89e111fdcc3791bed8504df" => :mavericks
  end

  depends_on "autoconf"  => :build
  depends_on "automake"  => :build
  depends_on "libtool"   => :build
  depends_on "check"     => :build
  depends_on :python3
  depends_on "homebrew/python/numpy" => ["with-python3"]
  depends_on "homebrew/python/pillow" => ["with-python3"]
  depends_on "zlib" unless OS.mac?
  depends_on "raxml"
  depends_on "fasttree" => ["with-double", :recommended]

  resource "biopython" do
    url "https://pypi.python.org/packages/f4/35/67d779f52870770c228f9edd0c9d1d1b9bc11afad794e220295d7b88a804/biopython-1.67.tar.gz"
    sha256 "1ab322fe4d2f79d2d999c9d8faf8b4e0b4c41c4e8b5f0a97912dfa0e3aa249e6"
  end

  resource "dendropy" do
    url "https://pypi.python.org/packages/65/3a/19556a58c560de488dffbf3c7fe7c9ed34c1a6223f0dfe971224a42aaf39/DendroPy-4.1.0.tar.gz"
    sha256 "c3d4b2780b84fb6ad64a8350855b2d762cabe45ecffbc04318f07214ee3bdfc9"
  end

  resource "nose" do
    url "https://pypi.python.org/packages/58/a5/0dc93c3ec33f4e281849523a5a913fa1eea9a3068acfa754d44d88107a44/nose-1.3.7.tar.gz"
    sha256 "f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98"
  end

  resource "reportlab" do<commit_msg>gubbins: builds deps without python2 support<commit_after>class Gubbins < Formula
  desc "Detect recombinations in Bacteria"
  homepage "https://github.com/sanger-pathogens/gubbins"
  url "https://github.com/sanger-pathogens/gubbins/archive/v2.1.0.tar.gz"
  sha256 "27d9d26febf8858e038d91d32ec8736d61644e13069c1cc81b8315eb7b32318f"
  revision 1

  head "https://github.com/sanger-pathogens/gubbins.git"
  # tag "bioinformatics"
  # doi "10.1093/nar/gku1196"

  bottle do
    cellar :any
    sha256 "1914a61d01d27b72cbe0f5d1f05530c0e8fbc4fa373fdeb4850fc3bdf5c382c4" => :el_capitan
    sha256 "b5c3f146aaca4145359a2a699702e91d1688cd0c99eee838b3f83a09a0c8f650" => :yosemite
    sha256 "5014f75893a38e50638c039d034e664f7843c8aad89e111fdcc3791bed8504df" => :mavericks
  end

  depends_on "autoconf"  => :build
  depends_on "automake"  => :build
  depends_on "libtool"   => :build
  depends_on "check"     => :build
  depends_on :python3
  depends_on "homebrew/python/numpy" => ["with-python3", "without-python"]
  depends_on "homebrew/python/pillow" => ["with-python3", "without-python"]
  depends_on "zlib" unless OS.mac?
  depends_on "raxml"
  depends_on "fasttree" => ["with-double", :recommended]

  resource "biopython" do
    url "https://pypi.python.org/packages/f4/35/67d779f52870770c228f9edd0c9d1d1b9bc11afad794e220295d7b88a804/biopython-1.67.tar.gz"
    sha256 "1ab322fe4d2f79d2d999c9d8faf8b4e0b4c41c4e8b5f0a97912dfa0e3aa249e6"
  end

  resource "dendropy" do
    url "https://pypi.python.org/packages/65/3a/19556a58c560de488dffbf3c7fe7c9ed34c1a6223f0dfe971224a42aaf39/DendroPy-4.1.0.tar.gz"
    sha256 "c3d4b2780b84fb6ad64a8350855b2d762cabe45ecffbc04318f07214ee3bdfc9"
  end

  resource "nose" do
    url "https://pypi.python.org/packages/58/a5/0dc93c3ec33f4e281849523a5a913fa1eea9a3068acfa754d44d88107a44/nose-1.3.7.tar.gz"
    sha256 "f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98"
  end

  resource "reportlab" do
{'fraction_non_alphanumeric': 0.102867666403578, 'fraction_numerical': 0.22888713496448304, 'mean_word_length': 5.477001703577513, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 23, 'https://': 12, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, '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': '1290553', 'n_tokens_mistral': 2242, 'n_tokens_neox': 1819, 'n_words': 190}