libsbml 5.20.2 (new formula)

[Waschina]

libsbml is a library for handling text files in Systems Biology Markup Language (SBML).

A brief explanation for the additional configuration flags (-DENABLE_FBC=ON -DENABLE_GROUPS=ON):

These enable two optional extensions for the libsbml library, namely "fbc" and "groups". Both are relevant for the research community that uses linear programming to predict metabolic processes in living cells (i.e., flux balance analysis). apt and dnf linux builds also include these two extensions.

• Have you followed the guidelines for contributing?
• Have you checked that there aren't other open pull requests for the same formula update/change?
• Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
• Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

---

This is my first formula. Any feedback is welcome.

[Waschina]

Thank you for approving the CI workflows.

2024-04-25T01:11:02.0384350Z /opt/homebrew/share/cmake/Modules/FindZLIB.cmake -> /opt/homebrew/Cellar/cmake/3.29.2/share/cmake/Modules/FindZLIB.cmake

There seems to be a conflict with the cmake module FindZLIB. cmake itself provides a module under this name, and libSBML comes with its own module using the same name.

Does anyone know how to handle such a conflict in a formula?

[YoshitakaMo]

Thank you for submitting a new formula!
Please test this:

  depends_on "check" => :build
  depends_on "cmake" => :build
  depends_on "pkg-config" => :build
  depends_on "swig" => :build

  uses_from_macos "bzip2"
  uses_from_macos "libxml2"
  uses_from_macos "zlib"

  def install
    # avoid an error "invalid conversion from ‘const xmlError*’"
    ENV.append_to_cflags "-fpermissive" if OS.linux?
    args = %w[
      -DWITH_SWIG=OFF
      -DWITH_ZLIB=OFF
      -DWITH_BZIP2=OFF
      -DENABLE_COMP=ON
      -DENABLE_FBC=ON
      -DENABLE_GROUPS=ON
      -DENABLE_L3V2EXTENDEDMATH=ON
      -DENABLE_LAYOUT=ON
      -DENABLE_MULTI=ON
      -DENABLE_QUAL=ON
      -DENABLE_RENDER=ON
    ]
    args << "-DLIBSBML_DEPENDENCY_DIR=#{HOMEBREW_PREFIX}"
    system "cmake", "-S", ".", "-B", "build", *args, *std_cmake_args
    system "cmake", "--build", "build"
    system "cmake", "--install", "build"
  end

• -DWITH_BZIP2=OFF and -DWITH_ZLIB=OFF are required to solve the conflict.
• -DLIBSBML_DEPENDENCY_DIR=#{HOMEBREW_PREFIX} is required to use Homebrew's libxml2 (for Linux).
• CFLAGS="-fpermissive" was required to compile on Linux.
• If a formula dependency is required on all platforms but can be handled by a component that ships with macOS, specify it with uses_from_macos. On Linux it acts like depends_on, while on macOS it’s ignored unless the host system is older than the optional since: parameter.
• Other arguments were copied from Bioconda's recipes

[Waschina]

Thank you, @YoshitakaMo, for the suggestion and for explaining the changes.

I made only minor modifications to your suggested formula:

• re-included bzip2 since this dependency seems to be without conflict
• removed uses_from_macos "zlib" since zlib is disabled as a dependency of libsbml with the -DWITH_ZLIB=OFF flag
• removed swig as build dependency since it is turned off with -DWITH_SWIG=OFF.

[YoshitakaMo]

I guess args << "-DLIBSBML_DEPENDENCY_DIR=#{HOMEBREW_PREFIX}" is required to pass the CI.

[Waschina]

Sorry, that I missed that line. It's now committed

[YoshitakaMo]

Merged! Thank you for your PR!

[Waschina]

Awesome! Thank you for being so helpful @YoshitakaMo