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/dc/44/a08cde4ad3d552892791ca9ea59a5bc9ac0ad6c12fff6d3b1d9bd590d4cf/snakemake-6.12.3.tar.gz"
  sha256 "af86af9a540da3dceb05dad1040f1d3d733e6a695f8b3f8c30f8cf3bc6570a88"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git", branch: "main"

  bottle do
    sha256 cellar: :any_skip_relocation, arm64_big_sur: "1b9fbb0beb8d760964b15dc35158b0d9f88c203f31e5212d5ffd5349f4fc1642"
    sha256 cellar: :any_skip_relocation, monterey:      "62965a4aadef3b22e6279356beee8586bb555cef9279590ecb882697006034d3"
    sha256 cellar: :any_skip_relocation, big_sur:       "4c8905b2a7037c75fe88faccfa8d914e8f73f32ca86c8e96aa70d188fe831c32"
    sha256 cellar: :any_skip_relocation, catalina:      "b65888ad9937f2c95eef454a5f260746dbe246b30e2b609cd2e633d286e2385c"
    sha256 cellar: :any_skip_relocation, x86_64_linux:  "4e1b44b46d22a0083065ccc479bf43c58c22c62b598c5828b43eaf72e161c1f3"
  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/ed/d6/3ebca4ca65157c12bd08a63e20ac0bdc21ac7f3694040711f9fd073c0ffb/attrs-21.2.0.tar.gz"
    sha256 "ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"
  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/68/e4/e014e7360fc6d1ccc507fe0b563b4646d00e0d4f9beec4975026dd15850b/charset-normalizer-2.0.9.tar.gz"
    sha256 "b0b883e8e874edfdece9c28f314e3dd5badf067342e42fb162203335ae61aa2c"
  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/79/3f/aae4a951dc5bd2738901e053c057f4b317bf12199f09351f63a002442117/filelock-3.4.0.tar.gz"
    sha256 "93d512b32a23baf4cac44ffd72ccf70732aeff7b8050fcaf6d3ec406d954baf4"
  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/34/cc/aaa7a0d066ac9e94fbffa5fcf0738f5742dd7095bdde950bd582fca01f5a/GitPython-3.1.24.tar.gz"
    sha256 "df83fdf5e684fef7c6ee2c02fc68a5ceb7e7e759d08b694088d0cacb4eba59e5"
  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/ff/09/fa40d16ddcce69fc79e264c9458ac5ae693586d5f4c552e1e11889bdf971/jsonschema-4.2.1.tar.gz"
    sha256 "390713469ae64b8a58698bb3cbc3859abe6925b565a973f87323ef21b09a27a8"
  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/e1/b0/7276de53321c12981717490516b7e612364f2cb372ee8901bd4a66a000d7/psutil-5.8.0.tar.gz"
    sha256 "0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6"
  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/f4/d7/0fa558c4fb00f15aabc6d42d365fcca7a15fcc1091cd0f5784a14f390b7f/pyrsistent-0.18.0.tar.gz"
    sha256 "773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b"
  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/e7/01/3569e0b535fb2e4a6c384bdbed00c55b9d78b5084e0fb7f4d0bf523d7670/requests-2.26.0.tar.gz"
    sha256 "b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7"
  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/80/be/3ee43b6c5757cabea19e75b8f46eaf05a2f5144107d7db48c7cf3a864f73/urllib3-1.26.7.tar.gz"
    sha256 "4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece"
  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