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/82/85/3b22beea9683a1c5b5eb6cabf38567b6690c48232964e06dcf56e51373f4/snakemake-7.12.0.tar.gz"
  sha256 "ecf447ca60db29e83cd6e692ec628ff2913ac6e9f05402a07bbd33d4ee3f8ef6"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git", branch: "main"

  bottle do
    sha256 cellar: :any_skip_relocation, arm64_monterey: "edbbb7eb2f752354011ba68429aaa336621fbc1a90a10c3a7f22b98299d0d012"
    sha256 cellar: :any_skip_relocation, arm64_big_sur:  "220a5d6d1cef3aa081673f385a88fc20e34fd922ea24f06ac93b37fe2cf60680"
    sha256 cellar: :any_skip_relocation, monterey:       "72e690a785975d87bd376cd689e9bedf9b1b2f836f95f83f548e2120dff8f83c"
    sha256 cellar: :any_skip_relocation, big_sur:        "0fb18cf10eb56937ef49643ad777aa8cc8eaebb39d35534db5e08e78cb8edf3f"
    sha256 cellar: :any_skip_relocation, catalina:       "b601e14f27b339d95622d58ded427da141ae3f8ea57cb23206b6a57aec56a55b"
    sha256 cellar: :any_skip_relocation, x86_64_linux:   "a9ccb311144148b967fe5949c2281514eab7c380d82734128a46d136ae51b42c"
  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/1a/cb/c4ffeb41e7137b23755a45e1bfec9cbb76ecf51874c6f1d113984ecaa32c/attrs-22.1.0.tar.gz"
    sha256 "29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"
  end

  resource "certifi" do
    url "https://files.pythonhosted.org/packages/cc/85/319a8a684e8ac6d87a1193090e06b6bbb302717496380e225ee10487c888/certifi-2022.6.15.tar.gz"
    sha256 "84c85a9078b11105f04f3036a9482ae10e4621616db313fe045dd24743a0820d"
  end

  resource "charset-normalizer" do
    url "https://files.pythonhosted.org/packages/93/1d/d9392056df6670ae2a29fcb04cfa5cee9f6fbde7311a1bb511d4115e9b7a/charset-normalizer-2.1.0.tar.gz"
    sha256 "575e708016ff3a5e3681541cb9d79312c416835686d054a23accb873b254f413"
  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 "decorator" do
    url "https://files.pythonhosted.org/packages/66/0c/8d907af351aa16b42caae42f9d6aa37b900c67308052d10fdce809f8d952/decorator-5.1.1.tar.gz"
    sha256 "637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"
  end

  resource "docutils" do
    url "https://files.pythonhosted.org/packages/6b/5c/330ea8d383eb2ce973df34d1239b3b21e91cd8c865d21ff82902d952f91f/docutils-0.19.tar.gz"
    sha256 "33995a6753c30b7f577febfc2c50411fec6aac7f7ffeb7c4cfe5991072dcf9e6"
  end

  resource "dpath" do
    url "https://files.pythonhosted.org/packages/a0/cf/cf35f8b7f212be18634970a5b2d7a50adc715e649a0a8fedb06c909603d8/dpath-2.0.6.tar.gz"
    sha256 "5a1ddae52233fbc8ef81b15fb85073a81126bb43698d3f3a1b6aaf561a46cdc0"
  end

  resource "fastjsonschema" do
    url "https://files.pythonhosted.org/packages/2f/ca/b8cd48dde1f4f1811c7ffd49253af87c1cb6523d2aaa5402a83d9fecc197/fastjsonschema-2.16.1.tar.gz"
    sha256 "d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334"
  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/d6/39/5b91b6c40570dc1c753359de7492404ba8fe7d71af40b618a780c7ad1fc7/GitPython-3.1.27.tar.gz"
    sha256 "1c885ce809e8ba2d88a29befeb385fcea06338d3640712b59ca623c220bb5704"
  end

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

  resource "Jinja2" do
    url "https://files.pythonhosted.org/packages/7a/ff/75c28576a1d900e87eb6335b063fab47a8ef3c8b4d88524c4bf78f670cce/Jinja2-3.1.2.tar.gz"
    sha256 "31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"
  end

  resource "jsonschema" do
    url "https://files.pythonhosted.org/packages/9d/c7/213df24d4dcf2eb115e2843205c6073c192976684388d6912cf674db2b8a/jsonschema-4.8.0.tar.gz"
    sha256 "c1d410e379b210ba903bee6adf3fce6d5204cea4c2b622d63f914d2dbfef0993"
  end

  resource "jupyter-core" do
    url "https://files.pythonhosted.org/packages/e4/e0/13fc7f8b72f39d87c1c32918a99475911b7b2f28c1a9f2734a5ab5cc35ef/jupyter_core-4.11.1.tar.gz"
    sha256 "2e5f244d44894c4154d06aeae3419dd7f1b0ef4494dc5584929b398c61cfd314"
  end

  resource "MarkupSafe" do
    url "https://files.pythonhosted.org/packages/1d/97/2288fe498044284f39ab8950703e88abbac2abbdf65524d576157af70556/MarkupSafe-2.1.1.tar.gz"
    sha256 "7f91197cc9e48f989d12e4e6fbc46495c446636dfc81b9ccf50bb0ec74b91d4b"
  end

  resource "nbformat" do
    url "https://files.pythonhosted.org/packages/2c/ed/ce3e63f5e757442cbb01ac45683fb0338d48f7e824606957d933bc831a58/nbformat-5.4.0.tar.gz"
    sha256 "44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501"
  end

  resource "plac" do
    url "https://files.pythonhosted.org/packages/45/39/db67ba7731ab4461c1d365aac1df695712bb6b9629e56540789a36d5c3aa/plac-1.3.5.tar.gz"
    sha256 "38bdd864d0450fb748193aa817b9c458a8f5319fbf97b2261151cfc0a5812090"
  end

  resource "psutil" do
    url "https://files.pythonhosted.org/packages/d6/de/0999ea2562b96d7165812606b18f7169307b60cd378bc29cf3673322c7e9/psutil-5.9.1.tar.gz"
    sha256 "57f1819b5d9e95cdfb0c881a8a5b7d542ed0b7c522d575706a80bedc848c8954"
  end

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

  resource "py" do
    url "https://files.pythonhosted.org/packages/98/ff/fec109ceb715d2a6b4c4a85a61af3b40c723a961e8828319fbcb15b868dc/py-1.11.0.tar.gz"
    sha256 "51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"
  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/a5/61/a867851fd5ab77277495a8709ddda0861b28163c4613b011bc00228cc724/requests-2.28.1.tar.gz"
    sha256 "7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983"
  end

  resource "retry" do
    url "https://files.pythonhosted.org/packages/9d/72/75d0b85443fbc8d9f38d08d2b1b67cc184ce35280e4a3813cda2f445f3a4/retry-0.9.2.tar.gz"
    sha256 "f8bfa8b99b69c4506d6f5bd3b0aabf77f98cdb17f3c9fc3f5ca820033336fba4"
  end

  resource "smart-open" do
    url "https://files.pythonhosted.org/packages/e5/fd/8f944b4520298f3256d77adaa5994ca969985062e3c83d7f9e6217abc910/smart_open-6.0.0.tar.gz"
    sha256 "d60106b96f0bcaedf5f1cd46ff5524a1c3d02d5653425618bb0fa66e158d22b0"
  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/7a/53/afac341569b3fd558bf2b5428e925e2eb8753ad9627c1f9188104c6e0c4a/tabulate-0.8.10.tar.gz"
    sha256 "6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519"
  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/b2/ed/3c842dbe5a8f0f1ebf3f5b74fc1a46601ed2dfe0a2d256c8488d387b14dd/traitlets-5.3.0.tar.gz"
    sha256 "0bb9f1f9f017aa8ec187d8b1b2a7a6626a2a1d877116baba52a129bfa124f8e2"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/6d/d5/e8258b334c9eb8eb78e31be92ea0d5da83ddd9385dc967dd92737604d239/urllib3-1.26.11.tar.gz"
    sha256 "ea6e8fb210b19d950fab93b60c9009226c63a28808bc8386e05301e25883ac0a"
  end

  resource "wrapt" do
    url "https://files.pythonhosted.org/packages/11/eb/e06e77394d6cf09977d92bff310cb0392930c08a338f99af6066a5a98f92/wrapt-1.14.1.tar.gz"
    sha256 "380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"
  end

  resource "yte" do
    url "https://files.pythonhosted.org/packages/bd/ec/85b6f67edccf6789bd5feeabe8906f5626e9328c9b340008ac0378668c59/yte-1.5.1.tar.gz"
    sha256 "6d0b315b78af83276d78f5f67c107c84238f772a76d74f4fc77905b46f3731f5"
  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