<commit_before>class Rdkit < Formula
  desc "Open-source chemoinformatics library"
  homepage "https://rdkit.org/"
  url "https://github.com/rdkit/rdkit/archive/Release_2022_03_5.tar.gz"
  sha256 "38e6fb9f063b6132310f17e654f2c4350876f9164b0a17b49fe3df7d0555a744"
  license "BSD-3-Clause"
  revision 2
  head "https://github.com/rdkit/rdkit.git", branch: "master"

  livecheck do
    url :stable
    regex(/^Release[._-](\d+(?:[._]\d+)+)$/i)
    strategy :git do |tags|
      tags.map { |tag| tag[regex, 1]&.gsub("_", ".") }.compact
    end
  end

  bottle do
    sha256 cellar: :any,                 arm64_monterey: "78475e78e4bf5bcbe98afe7dea77f0b93a44de5d1bdeeec028c08e3d7d302b72"
    sha256 cellar: :any,                 arm64_big_sur:  "540f8d9291e17cd4c44b4d56bbac714e525812ac03dfd9cbbf01d73928a71088"
    sha256 cellar: :any,                 monterey:       "1034abba3684d3b859717449e23e2bad586a7e9d076432d38f39cda3bba7bc09"
    sha256 cellar: :any,                 big_sur:        "2f807f48039e21653b76a6b1374684ea30d1cf7df5fbb6d0f00eeaf18c4c3794"
    sha256 cellar: :any,                 catalina:       "15d1d7ee27e43e5a24118bf8de8e67c217d708e00fceecb727198cb851b62877"
    sha256 cellar: :any_skip_relocation, x86_64_linux:   "4285f2fdbb4613eba4dc8ea89887c5e25ead13fad79cf9e77242be8381db0f75"
  end

  depends_on "cmake" => :build
  depends_on "swig" => :build
  depends_on "boost"
  depends_on "boost-python3"
  depends_on "eigen"
  depends_on "freetype"
  depends_on "numpy"
  depends_on "postgresql@14"
  depends_on "py3cairo"
  depends_on "python@3.10"

  def python
    deps.map(&:to_formula)
        .find { |f| f.name.match?(/^python@\d\.\d+$/) }
  end

  def postgresql
    Formula["postgresql@14"]
  end

  def install
    ENV.cxx11
    ENV.libcxx
    ENV.append "CFLAGS", "-Wno-parentheses -Wno-logical-op-parentheses -Wno-format"
    ENV.append "CXXFLAGS", "-Wno-parentheses -Wno-logical-op-parentheses -Wno-format"

    # Get Python location
    python_executable = python.opt_bin/"python3"
    py3ver = Language::Python.major_minor_version python_executable
    py3prefix = if OS.mac?
      python.opt_frameworks/"Python.framework/Versions"/py3ver
    else
      python.opt_prefix
    end
    py3include = py3prefix/"include/python#{py3ver}"
    site_packages = Language::Python.site_packages(python_executable)
    numpy_include = Formula["numpy"].opt_prefix/site_packages/"numpy/core/include"

    pg_config = postgresql.opt_bin/"pg_config"
    postgresql_lib = Utils.safe_popen_read(pg_config, "--pkglibdir").chomp
    postgresql_include = Utils.safe_popen_read(pg_config, "--includedir-server").chomp

    # set -DMAEPARSER and COORDGEN_FORCE_BUILD=ON to avoid conflicts with some formulae i.e. open-babel
    args = %W[
      -DCMAKE_INSTALL_RPATH=#{lib}
      -DRDK_INSTALL_INTREE=OFF
      -DRDK_BUILD_SWIG_WRAPPERS=OFF
      -DRDK_BUILD_AVALON_SUPPORT=ON
      -DRDK_BUILD_PGSQL=ON
      -DRDK_PGSQL_STATIC=ON
      -DMAEPARSER_FORCE_BUILD=ON
      -DCOORDGEN_FORCE_BUILD=ON
      -DRDK_BUILD_INCHI_SUPPORT=ON
      -DRDK_BUILD_CPP_TESTS=OFF
      -DRDK_INSTALL_STATIC_LIBS=OFF
      -DRDK_BUILD_CAIRO_SUPPORT=ON
      -DRDK_BUILD_YAEHMOP_SUPPORT=ON
      -DRDK_BUILD_FREESASA_SUPPORT=ON
      -DBoost_NO_BOOST_CMAKE=ON
      -DPYTHON_INCLUDE_DIR=#{py3include}
      -DPYTHON_EXECUTABLE=#{python_executable}
      -DPYTHON_NUMPY_INCLUDE_PATH=#{numpy_include}
      -DPostgreSQL_LIBRARY=#{postgresql_lib}
      -DPostgreSQL_INCLUDE_DIR=#{postgresql_include}
    ]

    system "cmake", "-S", ".", "-B", "build", *args, *std_cmake_args
    system "cmake", "--build", "build"
    system "cmake", "--install", "build"

    (prefix/site_packages/"homebrew-rdkit.pth").write libexec/site_packages
  end

  def caveats
    <<~EOS
      You may need to add RDBASE to your environment variables.
      For Bash, put something like this in your $HOME/.bashrc:
        export RDBASE=#{opt_share}/RDKit
    EOS
  end

  test do
    system python.opt_bin/"python3", "-c", "import rdkit"
    (testpath/"test.py").write <<~EOS
      from rdkit import Chem ; print(Chem.MolToSmiles(Chem.MolFromSmiles('C1=CC=CN=C1')))
    EOS
    assert_match "c1ccncc1", shell_output("#{python.opt_bin}/python3 test.py 2>&1")
  end<commit_msg>rdkit: fix `python3` references. (#110535)<commit_after>class Rdkit < Formula
  desc "Open-source chemoinformatics library"
  homepage "https://rdkit.org/"
  url "https://github.com/rdkit/rdkit/archive/Release_2022_03_5.tar.gz"
  sha256 "38e6fb9f063b6132310f17e654f2c4350876f9164b0a17b49fe3df7d0555a744"
  license "BSD-3-Clause"
  revision 2
  head "https://github.com/rdkit/rdkit.git", branch: "master"

  livecheck do
    url :stable
    regex(/^Release[._-](\d+(?:[._]\d+)+)$/i)
    strategy :git do |tags|
      tags.map { |tag| tag[regex, 1]&.gsub("_", ".") }.compact
    end
  end

  bottle do
    sha256 cellar: :any,                 arm64_monterey: "78475e78e4bf5bcbe98afe7dea77f0b93a44de5d1bdeeec028c08e3d7d302b72"
    sha256 cellar: :any,                 arm64_big_sur:  "540f8d9291e17cd4c44b4d56bbac714e525812ac03dfd9cbbf01d73928a71088"
    sha256 cellar: :any,                 monterey:       "1034abba3684d3b859717449e23e2bad586a7e9d076432d38f39cda3bba7bc09"
    sha256 cellar: :any,                 big_sur:        "2f807f48039e21653b76a6b1374684ea30d1cf7df5fbb6d0f00eeaf18c4c3794"
    sha256 cellar: :any,                 catalina:       "15d1d7ee27e43e5a24118bf8de8e67c217d708e00fceecb727198cb851b62877"
    sha256 cellar: :any_skip_relocation, x86_64_linux:   "4285f2fdbb4613eba4dc8ea89887c5e25ead13fad79cf9e77242be8381db0f75"
  end

  depends_on "cmake" => :build
  depends_on "swig" => :build
  depends_on "boost"
  depends_on "boost-python3"
  depends_on "eigen"
  depends_on "freetype"
  depends_on "numpy"
  depends_on "postgresql@14"
  depends_on "py3cairo"
  depends_on "python@3.10"

  def python
    deps.map(&:to_formula)
        .find { |f| f.name.match?(/^python@\d\.\d+$/) }
  end

  # Get Python location
  def python_executable
    python.opt_libexec/"bin/python"
  end

  def postgresql
    Formula["postgresql@14"]
  end

  def install
    ENV.cxx11
    ENV.libcxx
    ENV.append "CFLAGS", "-Wno-parentheses -Wno-logical-op-parentheses -Wno-format"
    ENV.append "CXXFLAGS", "-Wno-parentheses -Wno-logical-op-parentheses -Wno-format"

    py3ver = Language::Python.major_minor_version python_executable
    py3prefix = if OS.mac?
      python.opt_frameworks/"Python.framework/Versions"/py3ver
    else
      python.opt_prefix
    end
    py3include = py3prefix/"include/python#{py3ver}"
    site_packages = Language::Python.site_packages(python_executable)
    numpy_include = Formula["numpy"].opt_prefix/site_packages/"numpy/core/include"

    pg_config = postgresql.opt_bin/"pg_config"
    postgresql_lib = Utils.safe_popen_read(pg_config, "--pkglibdir").chomp
    postgresql_include = Utils.safe_popen_read(pg_config, "--includedir-server").chomp

    # set -DMAEPARSER and COORDGEN_FORCE_BUILD=ON to avoid conflicts with some formulae i.e. open-babel
    args = %W[
      -DCMAKE_INSTALL_RPATH=#{lib}
      -DRDK_INSTALL_INTREE=OFF
      -DRDK_BUILD_SWIG_WRAPPERS=OFF
      -DRDK_BUILD_AVALON_SUPPORT=ON
      -DRDK_BUILD_PGSQL=ON
      -DRDK_PGSQL_STATIC=ON
      -DMAEPARSER_FORCE_BUILD=ON
      -DCOORDGEN_FORCE_BUILD=ON
      -DRDK_BUILD_INCHI_SUPPORT=ON
      -DRDK_BUILD_CPP_TESTS=OFF
      -DRDK_INSTALL_STATIC_LIBS=OFF
      -DRDK_BUILD_CAIRO_SUPPORT=ON
      -DRDK_BUILD_YAEHMOP_SUPPORT=ON
      -DRDK_BUILD_FREESASA_SUPPORT=ON
      -DBoost_NO_BOOST_CMAKE=ON
      -DPYTHON_INCLUDE_DIR=#{py3include}
      -DPYTHON_EXECUTABLE=#{python_executable}
      -DPYTHON_NUMPY_INCLUDE_PATH=#{numpy_include}
      -DPostgreSQL_LIBRARY=#{postgresql_lib}
      -DPostgreSQL_INCLUDE_DIR=#{postgresql_include}
    ]

    system "cmake", "-S", ".", "-B", "build", *args, *std_cmake_args
    system "cmake", "--build", "build"
    system "cmake", "--install", "build"

    (prefix/site_packages/"homebrew-rdkit.pth").write libexec/site_packages
  end

  def caveats
    <<~EOS
      You may need to add RDBASE to your environment variables.
      For Bash, put something like this in your $HOME/.bashrc:
        export RDBASE=#{opt_share}/RDKit
    EOS
  end

  test do
    system python_executable, "-c", "import rdkit"
    (testpath/"test.py").write <<~EOS
      from rdkit import Chem ; print(Chem.MolToSmiles(Chem.MolFromSmiles('C1=CC=CN=C1')))
    EOS
    assert_match "c1ccncc1", shell_output("#{python_executable} test.py 2>&1")
  end
{'fraction_non_alphanumeric': 0.11145038167938931, 'fraction_numerical': 0.08032883147386964, 'mean_word_length': 3.5858912224017234, 'pattern_counts': {'":': 0, '<': 13, '<?xml version=': 0, '>': 9, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5583217', 'n_tokens_mistral': 3826, 'n_tokens_neox': 3386, 'n_words': 495}