apbs: init at 3.4.1 (#230644)

* apbs: init at 3.4.1

* Update pkgs/applications/science/chemistry/apbs/default.nix

---------

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

pkgs/applications/science/chemistry/apbs/default.nix

@@ -0,0 +1,101 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, blas
+, superlu
+, suitesparse
+, python3
+, libintl
+, libiconv
+}:
+let
+  # this is a fork version of fetk (http://www.fetk.org/)
+  # which is maintained by apbs team
+  fetk = stdenv.mkDerivation (finalAttrs: {
+    pname = "fetk";
+    version = "1.9.3";
+
+    src = fetchFromGitHub {
+      owner = "Electrostatics";
+      repo = "fetk";
+      rev = "refs/tags/${finalAttrs.version}";
+      hash = "sha256-uFA1JRR05cNcUGaJj9IyGNONB2hU9IOBPzOj/HucNH4=";
+    };
+
+    nativeBuildInputs = [
+      cmake
+    ];
+
+    cmakeFlags = [
+      "-DBLAS_LIBRARIES=${blas}/lib"
+      "-DBLA_STATIC=OFF"
+      "-DBUILD_SUPERLU=OFF"
+    ];
+
+    buildInputs = [
+      blas
+      superlu
+      suitesparse
+    ];
+
+    meta = with lib; {
+      description = "Fork of the Finite Element ToolKit from fetk.org";
+      homepage = "https://github.com/Electrostatics/FETK";
+      changelog = "https://github.com/Electrostatics/FETK/releases/tag/${finalAttrs.version}";
+      license = licenses.lgpl21Plus;
+      maintainers = with maintainers; [ natsukium ];
+      platforms = platforms.unix;
+    };
+  });
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "apbs";
+  version = "3.4.1";
+
+  src = fetchFromGitHub {
+    owner = "Electrostatics";
+    repo = "apbs";
+    rev = "refs/tags/v${finalAttrs.version}";
+    hash = "sha256-2DnHU9hMDl4OJBaTtcRiB+6R7gAeFcuOUy7aI63A3gQ=";
+  };
+
+  postPatch = ''
+    # ImportFETK.cmake downloads source and builds fetk
+    substituteInPlace CMakeLists.txt \
+      --replace "include(ImportFETK)" "" \
+      --replace 'import_fetk(''${FETK_VERSION})' ""
+  '';
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  buildInputs = [
+    fetk
+    suitesparse
+    blas
+    python3
+  ] ++ lib.optionals stdenv.isDarwin [
+    libintl
+    libiconv
+  ];
+
+  cmakeFlags = [
+    "-DPYTHON_VERSION=${python3.version}"
+    "-DAPBS_LIBS=mc;maloc"
+    "-DCMAKE_MODULE_PATH=${fetk}/share/fetk/cmake;"
+    "-DENABLE_TESTS=1"
+  ];
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "Software for biomolecular electrostatics and solvation calculations";
+    homepage = "https://www.poissonboltzmann.org/";
+    changelog = "https://github.com/Electrostatics/apbs/releases/tag/v${finalAttrs.version}";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+})

pkgs/top-level/all-packages.nix

@@ -37396,6 +37396,8 @@ with pkgs;
 
   ### SCIENCE/CHEMISTY
 
+  apbs = callPackage ../applications/science/chemistry/apbs { };
+
   avogadro = callPackage ../applications/science/chemistry/avogadro {
     openbabel = openbabel2;
     eigen = eigen2;