class Paml < Formula
  # cite Yang_2007: "https://doi.org/10.1093/molbev/msm088"
  desc "Phylogenetic analysis by maximum likelihood"
  homepage "http://abacus.gene.ucl.ac.uk/software/paml.html"
  url "http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz"
  version "4.9j"
  sha256 "9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d"

  bottle do
    root_url "https://ghcr.io/v2/brewsci/bio"
    sha256 cellar: :any_skip_relocation, catalina:     "f38a4f56221825dfd56ee64855fc3731c97e38347b3aabafee63541c1926240e"
    sha256 cellar: :any_skip_relocation, x86_64_linux: "0bb90b5cac3f74c0d03d26fbde658dcd2edca8ea8847662da0e682c56c028cf5"
  end

  def install
    # Restore permissions, as some are wrong in the tarball archives
    chmod_R "u+rw", "."

    cd "src" do
      system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}"
      bin.install %w[baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00]
    end

    pkgshare.install "dat"
    pkgshare.install Dir["*.ctl"]
    doc.install Dir["doc/*"]
    doc.install "examples"
  end

  def caveats
    <<~EOS
      Documentation and examples:
        #{HOMEBREW_PREFIX}/share/doc/paml
      Dat and ctl files:
        #{HOMEBREW_PREFIX}/share/paml
    EOS
  end

  test do
    cp Dir[doc/"examples/DatingSoftBound/*.*"], testpath
    system "#{bin}/infinitesites"
  end
end