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/77/2a/c1c339b29ad216ee966e7e687bb4a087bf63284d11c435a6db0727a785f0/snakemake-7.14.0.tar.gz"
  sha256 "fe22082e4f322ffafb9018d896670ae4088e984117db670de9003a199f491447"
  license "MIT"
  head "https://github.com/snakemake/snakemake.git", branch: "main"

  bottle do
    rebuild 1
    sha256 cellar: :any_skip_relocation, arm64_monterey: "11f1921944cf7600c7a24570fe6be9f5b6958e6439a7a9d129b292a497d00072"
    sha256 cellar: :any_skip_relocation, arm64_big_sur:  "1bf0110c22a67a7f7b68e724fc83e6fde12edd0e24ae606aa6c7fb37ddc2bf50"
    sha256 cellar: :any_skip_relocation, monterey:       "078ac171998b15d55b123af4938a3feb23ce970085d7b637f70885522bbf5e37"
    sha256 cellar: :any_skip_relocation, big_sur:        "9221427f034129c29b93f12542e9773da8eb9da6892b00df1893361e09e38f7d"
    sha256 cellar: :any_skip_relocation, catalina:       "a6742f918d525f9bca39a2927ba95041f0edc409708e41d5ce1265d093cbd051"
    sha256 cellar: :any_skip_relocation, x86_64_linux:   "f17f4434811502f2266b9dc2114b0a21e8eb0dde00dfc925572bd8207e7994ee"
  end

  depends_on "cbc"
  depends_on "jsonschema"
  depends_on "libpython-tabulate"
  depends_on "python@3.10"
  depends_on "pyyaml"

  resource "appdirs" do
    url "https://files.pythonhosted.org/packages/d7/d8/05696357e0311f5b5c316d7b95f46c669dd9c15aaeecbb48c7d0aeb88c40/appdirs-1.4.4.tar.gz"
    sha256 "7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"
  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/a1/34/44964211e5410b051e4b8d2869c470ae8a68ae274953b1c7de6d98bbcf94/charset-normalizer-2.1.1.tar.gz"
    sha256 "5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845"
  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 "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 "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/dc/9c/607fcf509f0019188fa7e0c3f6e1870abadb119bf6d7d673fba2105a5ef2/smart_open-6.1.0.tar.gz"
    sha256 "c8fd9e9f90f0e285f1346481b0ae0fb57bd04b1138826c5e826ee98b2029d7f3"
  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 "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/b2/56/d87d6d3c4121c0bcec116919350ca05dc3afd2eeb7dc88d07e8083f8ea94/urllib3-1.26.12.tar.gz"
    sha256 "3fa96cf423e6987997fc326ae8df396db2a8b7c667747d47ddd8ecba91f4a74e"
  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

    # we depend on jsonschema, but that's a separate formula, so install a `.pth` file to link them
    site_packages = Language::Python.site_packages("python3.10")
    jsonschema = Formula["jsonschema"].opt_libexec
    (libexec/site_packages/"homebrew-jsonschema.pth").write jsonschema/site_packages
  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