homebrew-core/Formula/snakemake.rb

class Snakemake < Formula
  include Language::Python::Virtualenv

  desc "Pythonic workflow system"
  homepage "https://snakemake.readthedocs.io/"
  url "https://files.pythonhosted.org/packages/57/ae/2b4d5b1799823096809bd51f7f50dbdca1c5b65bf874763cb0f1716cd606/snakemake-6.15.5.tar.gz"
  sha256 "e3297898f96c358b2c1a883aeb0f3540f983943cd564511510b9112a37fcf1f4"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git", branch: "main"

  bottle do
    sha256 cellar: :any_skip_relocation, arm64_monterey: "0994631394b39ff32d7ce0caacef5c8ac5f8e99bdb65a51f038151514cc08c3a"
    sha256 cellar: :any_skip_relocation, arm64_big_sur:  "bcb1469e6847eae1538f6b3c402dcf1fc72acf02a7be6e841f4ccd76d26a462b"
    sha256 cellar: :any_skip_relocation, monterey:       "347dd3590b05076ab9d3643de2ea823043ca59b1b182aa4f2209717b4201fa04"
    sha256 cellar: :any_skip_relocation, big_sur:        "8d0fee5d24a064cdb1bf7174c89d3cbecdd1bcd2eca044dd9860d6c11f16413d"
    sha256 cellar: :any_skip_relocation, catalina:       "a8c6b8a2017aa5da3e7a4ea55268a81a68b922ef519e9b8e99e5b4834e59cd3d"
    sha256 cellar: :any_skip_relocation, x86_64_linux:   "cc7a21b4600b360a1ac73658ef1866077bdf4f6b6d91313291e873139ebc980c"
  end

  depends_on "cbc"
  depends_on "python@3.10"

  resource "appdirs" do
    url "https://files.pythonhosted.org/packages/d7/d8/05696357e0311f5b5c316d7b95f46c669dd9c15aaeecbb48c7d0aeb88c40/appdirs-1.4.4.tar.gz"
    sha256 "7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"
  end

  resource "attrs" do
    url "https://files.pythonhosted.org/packages/d7/77/ebb15fc26d0f815839ecd897b919ed6d85c050feeb83e100e020df9153d2/attrs-21.4.0.tar.gz"
    sha256 "626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/6c/ae/d26450834f0acc9e3d1f74508da6df1551ceab6c2ce0766a593362d6d57f/certifi-2021.10.8.tar.gz"
    sha256 "78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"
  end

  resource "charset-normalizer" do
    url "https://files.pythonhosted.org/packages/e8/e8/b6cfd28fb430b2ec9923ad0147025bf8bbdf304b1eb3039b69f1ce44ed6e/charset-normalizer-2.0.11.tar.gz"
    sha256 "98398a9d69ee80548c762ba991a4728bfc3836768ed226b3945908d1a688371c"
  end

  resource "ConfigArgParse" do
    url "https://files.pythonhosted.org/packages/16/05/385451bc8d20a3aa1d8934b32bd65847c100849ebba397dbf6c74566b237/ConfigArgParse-1.5.3.tar.gz"
    sha256 "1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f"
  end

  resource "connection_pool" do
    url "https://files.pythonhosted.org/packages/bd/df/c9b4e25dce00f6349fd28aadba7b6c3f7431cc8bd4308a158fbe57b6a22e/connection_pool-0.0.3.tar.gz"
    sha256 "bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc"
  end

  resource "datrie" do
    url "https://files.pythonhosted.org/packages/9d/fe/db74bd405d515f06657f11ad529878fd389576dca4812bea6f98d9b31574/datrie-0.8.2.tar.gz"
    sha256 "525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d"
  end

  resource "docutils" do
    url "https://files.pythonhosted.org/packages/57/b1/b880503681ea1b64df05106fc7e3c4e3801736cf63deffc6fa7fc5404cf5/docutils-0.18.1.tar.gz"
    sha256 "679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06"
  end

  resource "filelock" do
    url "https://files.pythonhosted.org/packages/11/d1/22318a1b5bb06c9be4c065ad6a09cb7bfade737758dc08235c99cd6cf216/filelock-3.4.2.tar.gz"
    sha256 "38b4f4c989f9d06d44524df1b24bd19e167d851f19b50bf3e3559952dddc5b80"
  end

  resource "gitdb" do
    url "https://files.pythonhosted.org/packages/fc/44/64e02ef96f20b347385f0e9c03098659cb5a1285d36c3d17c56e534d80cf/gitdb-4.0.9.tar.gz"
    sha256 "bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa"
  end

  resource "GitPython" do
    url "https://files.pythonhosted.org/packages/70/b0/23e3245248f63eac75335828527016c7636c1780e7ad934a341970b47a78/GitPython-3.1.26.tar.gz"
    sha256 "fc8868f63a2e6d268fb25f481995ba185a85a66fcad126f039323ff6635669ee"
  end

  resource "idna" do
    url "https://files.pythonhosted.org/packages/62/08/e3fc7c8161090f742f504f40b1bccbfc544d4a4e09eb774bf40aafce5436/idna-3.3.tar.gz"
    sha256 "9d643ff0a55b762d5cdb124b8eaa99c66322e2157b69160bc32796e824360e6d"
  end

  resource "ipython_genutils" do
    url "https://files.pythonhosted.org/packages/e8/69/fbeffffc05236398ebfcfb512b6d2511c622871dca1746361006da310399/ipython_genutils-0.2.0.tar.gz"
    sha256 "eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"
  end

  resource "jsonschema" do
    url "https://files.pythonhosted.org/packages/26/67/36cfd516f7b3560bbf7183d7a0f82bb9514d2a5f4e1d682a8a1d55d8031d/jsonschema-4.4.0.tar.gz"
    sha256 "636694eb41b3535ed608fe04129f26542b59ed99808b4f688aa32dcf55317a83"
  end

  resource "jupyter-core" do
    url "https://files.pythonhosted.org/packages/78/fa/a949d1f0d2aaaef1890c2ab7fee9e58ed7cc6301ebc26c0afbffff4ea6e3/jupyter_core-4.9.1.tar.gz"
    sha256 "dce8a7499da5a53ae3afd5a9f4b02e5df1d57250cf48f3ad79da23b4778cd6fa"
  end

  resource "nbformat" do
    url "https://files.pythonhosted.org/packages/e5/bd/847367dcc514b198936a3de8bfaeda1935e67ce369bf0b3e7f3ed4616ae8/nbformat-5.1.3.tar.gz"
    sha256 "b516788ad70771c6250977c1374fcca6edebe6126fd2adb5a69aa5c2356fd1c8"
  end

  resource "psutil" do
    url "https://files.pythonhosted.org/packages/47/b6/ea8a7728f096a597f0032564e8013b705aa992a0990becd773dcc4d7b4a7/psutil-5.9.0.tar.gz"
    sha256 "869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25"
  end

  resource "PuLP" do
    url "https://files.pythonhosted.org/packages/3a/74/0d6744ac87cbe9773be70917381d1834ac44015af7b6fa5cbc07b61abf03/PuLP-2.6.0.tar.gz"
    sha256 "4b4f7e1e954453e1b233720be23aea2f10ff068a835ac10c090a93d8e2eb2e8d"
  end

  resource "pyrsistent" do
    url "https://files.pythonhosted.org/packages/42/ac/455fdc7294acc4d4154b904e80d964cc9aae75b087bbf486be04df9f2abd/pyrsistent-0.18.1.tar.gz"
    sha256 "d4d61f8b993a7255ba714df3aca52700f8125289f84f704cf80916517c46eb96"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/36/2b/61d51a2c4f25ef062ae3f74576b01638bebad5e045f747ff12643df63844/PyYAML-6.0.tar.gz"
    sha256 "68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2"
  end

  resource "ratelimiter" do
    url "https://files.pythonhosted.org/packages/5b/e0/b36010bddcf91444ff51179c076e4a09c513674a56758d7cfea4f6520e29/ratelimiter-1.2.0.post0.tar.gz"
    sha256 "5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7"
  end

  resource "requests" do
    url "https://files.pythonhosted.org/packages/60/f3/26ff3767f099b73e0efa138a9998da67890793bfa475d8278f84a30fec77/requests-2.27.1.tar.gz"
    sha256 "68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61"
  end

  resource "smart-open" do
    url "https://files.pythonhosted.org/packages/53/9e/7a25cefbe4b51ea9bf883999c359dd761d32dcd2f764b70805278bb20bde/smart_open-5.2.1.tar.gz"
    sha256 "75abf758717a92a8f53aa96953f0c245c8cedf8e1e4184903db3659b419d4c17"
  end

  resource "smmap" do
    url "https://files.pythonhosted.org/packages/21/2d/39c6c57032f786f1965022563eec60623bb3e1409ade6ad834ff703724f3/smmap-5.0.0.tar.gz"
    sha256 "c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936"
  end

  resource "stopit" do
    url "https://files.pythonhosted.org/packages/35/58/e8bb0b0fb05baf07bbac1450c447d753da65f9701f551dca79823ce15d50/stopit-1.1.2.tar.gz"
    sha256 "f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d"
  end

  resource "tabulate" do
    url "https://files.pythonhosted.org/packages/ae/3d/9d7576d94007eaf3bb685acbaaec66ff4cdeb0b18f1bf1f17edbeebffb0a/tabulate-0.8.9.tar.gz"
    sha256 "eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7"
  end

  resource "toposort" do
    url "https://files.pythonhosted.org/packages/b2/be/67bec9a73041616dd359f06e997d56c9c99d252460a3f035411d97c96c48/toposort-1.7.tar.gz"
    sha256 "ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125"
  end

  resource "traitlets" do
    url "https://files.pythonhosted.org/packages/db/cf/e6cbf07ce2d21a17c8379f3f2f12db413a38da5ee20809638226b1490e48/traitlets-5.1.1.tar.gz"
    sha256 "059f456c5a7c1c82b98c2e8c799f39c9b8128f6d0d46941ee118daace9eb70c7"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/b0/b1/7bbf5181f8e3258efae31702f5eab87d8a74a72a0aa78bc8c08c1466e243/urllib3-1.26.8.tar.gz"
    sha256 "0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
  end

  resource "wrapt" do
    url "https://files.pythonhosted.org/packages/eb/f6/d81ccf43ac2a3c80ddb6647653ac8b53ce2d65796029369923be06b815b8/wrapt-1.13.3.tar.gz"
    sha256 "1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185"
  end

  def install
    virtualenv_install_with_resources
  end

  test do
    (testpath/"Snakefile").write <<~EOS
      rule testme:
          output:
               "test.out"
          shell:
               "touch {output}"
    EOS
    test_output = shell_output("#{bin}/snakemake --cores 1 -s #{testpath}/Snakefile 2>&1")
    assert_predicate testpath/"test.out", :exist?
    assert_match "Building DAG of jobs...", test_output
  end
end