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/49/00/2f34497646848d86d39fdef61232fea5e402f29ff6b25ef94561270093fc/snakemake-6.4.0.tar.gz"
  sha256 "829df4f09352d6a79056e42ed6e89d5ba8f7d7fe1b341ba1ec065212447eeeef"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git"

  bottle do
    sha256 cellar: :any_skip_relocation, arm64_big_sur: "77509a25fc1fdcd8b5a0e42e3612163a15063e79626ba36530d4ef6628cc025f"
    sha256 cellar: :any_skip_relocation, big_sur:       "0277689996b0bf8371353f11933a734e4d9c8c9bfa13d7bb99ca4b0c2c9d03f6"
    sha256 cellar: :any_skip_relocation, catalina:      "e64c23d19965f45b6e3f8fc36497e3ab7f7b19127e444616208801b278587a97"
    sha256 cellar: :any_skip_relocation, mojave:        "ea3d34329843b4074cd853f9f56a05cd56c99f115e18df37fb701f55a93ae950"
  end

  depends_on "cbc"
  depends_on "python@3.9"

  resource "amply" do
    url "https://files.pythonhosted.org/packages/1c/52/f44d55940bd1c07818c3d45a04a3fe98bb1fb6f7ed3cf2c82b7e6c8467f3/amply-0.1.4.tar.gz"
    sha256 "cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38"
  end

  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/ed/d6/3ebca4ca65157c12bd08a63e20ac0bdc21ac7f3694040711f9fd073c0ffb/attrs-21.2.0.tar.gz"
    sha256 "ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/06/a9/cd1fd8ee13f73a4d4f491ee219deeeae20afefa914dfb4c130cfc9dc397a/certifi-2020.12.5.tar.gz"
    sha256 "1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c"
  end

  resource "chardet" do
    url "https://files.pythonhosted.org/packages/ee/2d/9cdc2b527e127b4c9db64b86647d567985940ac3698eeabc7ffaccb4ea61/chardet-4.0.0.tar.gz"
    sha256 "0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa"
  end

  resource "ConfigArgParse" do
    url "https://files.pythonhosted.org/packages/fa/c2/986a0692857b25d6c7998060b21d40068bfb08a510dcf1bf4b0d161745b6/ConfigArgParse-1.4.1.tar.gz"
    sha256 "6df537158f28c5ef2e8a8146781833abbc6cb7fca81b1b55d18808ce3439235e"
  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/4c/17/559b4d020f4b46e0287a2eddf2d8ebf76318fd3bd495f1625414b052fdc9/docutils-0.17.1.tar.gz"
    sha256 "686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"
  end

  resource "filelock" do
    url "https://files.pythonhosted.org/packages/14/ec/6ee2168387ce0154632f856d5cc5592328e9cf93127c5c9aeca92c8c16cb/filelock-3.0.12.tar.gz"
    sha256 "18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59"
  end

  resource "gitdb" do
    url "https://files.pythonhosted.org/packages/34/fe/9265459642ab6e29afe734479f94385870e8702e7f892270ed6e52dd15bf/gitdb-4.0.7.tar.gz"
    sha256 "96bf5c08b157a666fec41129e6d327235284cca4c81e92109260f353ba138005"
  end

  resource "GitPython" do
    url "https://files.pythonhosted.org/packages/59/d1/e89344ca079f92546558bb5cedb26b4f7ad4afe5319586f49b722c4d99b0/GitPython-3.1.17.tar.gz"
    sha256 "ee24bdc93dce357630764db659edaf6b8d664d4ff5447ccfeedd2dc5c253f41e"
  end

  resource "idna" do
    url "https://files.pythonhosted.org/packages/ea/b7/e0e3c1c467636186c39925827be42f16fee389dc404ac29e930e9136be70/idna-2.10.tar.gz"
    sha256 "b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6"
  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/69/11/a69e2a3c01b324a77d3a7c0570faa372e8448b666300c4117a516f8b1212/jsonschema-3.2.0.tar.gz"
    sha256 "c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a"
  end

  resource "jupyter-core" do
    url "https://files.pythonhosted.org/packages/24/9a/0ca76ccc95eeb3ee376c671e81bda2c61d148c7627443004d1ba0d085b80/jupyter_core-4.7.1.tar.gz"
    sha256 "79025cb3225efcd36847d0840f3fc672c0abd7afd0de83ba8a1d3837619122b4"
  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/e1/b0/7276de53321c12981717490516b7e612364f2cb372ee8901bd4a66a000d7/psutil-5.8.0.tar.gz"
    sha256 "0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6"
  end

  resource "PuLP" do
    url "https://files.pythonhosted.org/packages/4d/44/10b21fb51c4b394f8876cbd7831bd1f152c5cec81d70f099250dd30f3704/PuLP-2.4.tar.gz"
    sha256 "b2aff10989b3692e3a59301a0cb0acddeb25dcea378f8804c86007075eae55b5"
  end

  resource "pyparsing" do
    url "https://files.pythonhosted.org/packages/c1/47/dfc9c342c9842bbe0036c7f763d2d6686bcf5eb1808ba3e170afdb282210/pyparsing-2.4.7.tar.gz"
    sha256 "c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1"
  end

  resource "pyrsistent" do
    url "https://files.pythonhosted.org/packages/4d/70/fd441df751ba8b620e03fd2d2d9ca902103119616f0f6cc42e6405035062/pyrsistent-0.17.3.tar.gz"
    sha256 "2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/a0/a4/d63f2d7597e1a4b55aa3b4d6c5b029991d3b824b5bd331af8d4ab1ed687d/PyYAML-5.4.1.tar.gz"
    sha256 "607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e"
  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/6b/47/c14abc08432ab22dc18b9892252efaf005ab44066de871e72a38d6af464b/requests-2.25.1.tar.gz"
    sha256 "27973dd4a904a4f13b263a19c866c13b92a39ed1c964655f025f3f8d3d75b804"
  end

  resource "six" do
    url "https://files.pythonhosted.org/packages/71/39/171f1c67cd00715f190ba0b100d606d440a28c93c7714febeca8b79af85e/six-1.16.0.tar.gz"
    sha256 "1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"
  end

  resource "smart-open" do
    url "https://files.pythonhosted.org/packages/da/2c/af1fc367c4d9f07693873e71c3bff770d2adecd193735fc11b45508090fa/smart_open-5.0.0.tar.gz"
    sha256 "02e5e02207d955a1f9fd924c37900ac272536bd24393ae731b6945d4f766015f"
  end

  resource "smmap" do
    url "https://files.pythonhosted.org/packages/dd/d4/2b4f196171674109f0fbb3951b8beab06cd0453c1b247ec0c4556d06648d/smmap-4.0.0.tar.gz"
    sha256 "7e65386bd122d45405ddf795637b7f7d2b532e7e401d46bbe3fb49b9986d5182"
  end

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

  resource "toposort" do
    url "https://files.pythonhosted.org/packages/b5/15/a657e32bddf72f69691aa0223df918b5f372eeee709cf8da9be134eac020/toposort-1.6.tar.gz"
    sha256 "a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac"
  end

  resource "traitlets" do
    url "https://files.pythonhosted.org/packages/b8/24/e6dfe45ecfc4c2b0d6774565e631dc1b9e50de2c3536625d377963d56cae/traitlets-5.0.5.tar.gz"
    sha256 "178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/cb/cf/871177f1fc795c6c10787bc0e1f27bb6cf7b81dbde399fd35860472cecbc/urllib3-1.26.4.tar.gz"
    sha256 "e7b021f7241115872f92f43c6508082facffbd1c048e3c6e2bb9c2a157e28937"
  end

  resource "wrapt" do
    url "https://files.pythonhosted.org/packages/82/f7/e43cefbe88c5fd371f4cf0cf5eb3feccd07515af9fd6cf7dbf1d1793a797/wrapt-1.12.1.tar.gz"
    sha256 "b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"
  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