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/a8/a0/e71e14c46f03718402f2b653400bfd8669fad5d621b1a475b0bf509b15a3/snakemake-5.23.0.tar.gz"
  sha256 "d8bbde85fa8d93bd6312cae5d39247b316ead0589022aa7b48760374b1994b79"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git"

  livecheck do
    url :stable
  end

  bottle do
    cellar :any_skip_relocation
    sha256 "8965eef441d01e5000bad7b2bd433344cfa7e22f71a6cd7635d807623b1d145b" => :catalina
    sha256 "527efc3118c0260c1ef6226990cfda0db31251687756f126428d43b3e79aa8f1" => :mojave
    sha256 "f69c12a6cefbcc02f6c1adf2e4516e46f5b6bd313515053563d615b241b10c57" => :high_sierra
  end

  depends_on "cbc"
  depends_on "python@3.8"

  resource "amply" do
    url "https://files.pythonhosted.org/packages/7f/11/33cb09557ac838d9488779b79e05a2a3c1f3ce9747cd242ba68332736778/amply-0.1.2.tar.gz"
    sha256 "6e5d53af62772790ba82a989a3de72b8ce5c1cd809613c06f7cb061f7ec34dc8"
  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/c4/d4/c2b5232ecfc0783c697a81c13efc53a4fe285d4e2c00e0d8aed90495fade/attrs-20.1.0.tar.gz"
    sha256 "0ef97238856430dcf9228e07f316aefc17e8939fc8507e18c6501b761ef1a42a"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/40/a7/ded59fa294b85ca206082306bba75469a38ea1c7d44ea7e1d64f5443d67a/certifi-2020.6.20.tar.gz"
    sha256 "5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3"
  end

  resource "chardet" do
    url "https://files.pythonhosted.org/packages/fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d/chardet-3.0.4.tar.gz"
    sha256 "84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae"
  end

  resource "ConfigArgParse" do
    url "https://files.pythonhosted.org/packages/bb/79/3045743bb26ca2e44a1d317c37395462bfed82dbbd38e69a3280b63696ce/ConfigArgParse-1.2.3.tar.gz"
    sha256 "edd17be986d5c1ba2e307150b8e5f5107aba125f3574dddd02c85d5cdcfd37dc"
  end

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

  resource "decorator" do
    url "https://files.pythonhosted.org/packages/da/93/84fa12f2dc341f8cf5f022ee09e109961055749df2d0c75c5f98746cfe6c/decorator-4.4.2.tar.gz"
    sha256 "e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7"
  end

  resource "docutils" do
    url "https://files.pythonhosted.org/packages/2f/e0/3d435b34abd2d62e8206171892f174b180cd37b09d57b924ca5c2ef2219d/docutils-0.16.tar.gz"
    sha256 "c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc"
  end

  resource "gitdb" do
    url "https://files.pythonhosted.org/packages/d1/05/eaf2ac564344030d8b3ce870b116d7bb559020163e80d9aa4a3d75f3e820/gitdb-4.0.5.tar.gz"
    sha256 "c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9"
  end

  resource "GitPython" do
    url "https://files.pythonhosted.org/packages/53/ea/fc34cddaa30bfc5e283f13e754fb3e2648ccd9f7019eaa3518fb5350ae51/GitPython-3.1.7.tar.gz"
    sha256 "2db287d71a284e22e5c2846042d0602465c7434d910406990d5b74df4afb0858"
  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/28/64/8bdde111be57a2a3d54376db29b5f25ab9c68ffd3d6554989db24d5c1b7a/jupyter_core-4.6.3.tar.gz"
    sha256 "394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e"
  end

  resource "nbformat" do
    url "https://files.pythonhosted.org/packages/95/8e/8ffd07ed059a6277fe2f72d1fa411b49a8e512ad62f2ed20b9c2438192dd/nbformat-5.0.7.tar.gz"
    sha256 "54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340"
  end

  resource "psutil" do
    url "https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz"
    sha256 "90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb"
  end

  resource "PuLP" do
    url "https://files.pythonhosted.org/packages/84/9b/5bbd50471fa9749e6f1ee9c88ea276b5357b358820a92e340a1160bb851d/PuLP-2.3.tar.gz"
    sha256 "9d8ecf532868cc31fa9ff59ee5d5b2049600c5c902c18c794a2bad677c1f92e5"
  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/9f/0d/cbca4d0bbc5671822a59f270e4ce3f2195f8a899c97d0d5abb81b191efb5/pyrsistent-0.16.0.tar.gz"
    sha256 "28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3"
  end

  resource "PyYAML" do
    url "https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz"
    sha256 "b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d"
  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/da/67/672b422d9daf07365259958912ba533a0ecab839d4084c487a5fe9a5405f/requests-2.24.0.tar.gz"
    sha256 "b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b"
  end

  resource "six" do
    url "https://files.pythonhosted.org/packages/6b/34/415834bfdafca3c5f451532e8a8d9ba89a21c9743a0c59fbd0205c7f9426/six-1.15.0.tar.gz"
    sha256 "30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259"
  end

  resource "smmap" do
    url "https://files.pythonhosted.org/packages/75/fb/2f594e5364f9c986b2c89eb662fc6067292cb3df2b88ae31c939b9138bb9/smmap-3.0.4.tar.gz"
    sha256 "9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24"
  end

  resource "toposort" do
    url "https://files.pythonhosted.org/packages/e5/d8/9bc1598ddf74410beba243ffeaee8d0b3ca7e9ac5cefe77367da497433e1/toposort-1.5.tar.gz"
    sha256 "dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd"
  end

  resource "traitlets" do
    url "https://files.pythonhosted.org/packages/75/b0/43deb021bc943f18f07cbe3dac1d681626a48997b7ffa1e7fb14ef922b21/traitlets-4.3.3.tar.gz"
    sha256 "d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/81/f4/87467aeb3afc4a6056e1fe86626d259ab97e1213b1dfec14c7cb5f538bf0/urllib3-1.25.10.tar.gz"
    sha256 "91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a"
  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