Commit c6435a9d authored by Emily's avatar Emily
Browse files

{irods,irods-icommands}: 4.3.3 -> 5.0.1

parent 8831c775

pkgs/by-name/ir/irods-icommands/package.nix

0 → 100644
+48 −0
Original line number Diff line number Diff line 
{

  lib,

  llvmPackages,

  fetchFromGitHub,

  cmake,

  ninja,

  help2man,

  irods,

}:



llvmPackages.stdenv.mkDerivation (finalAttrs: {

  pname = "irods-icommands";

  inherit (irods) version;



  src = fetchFromGitHub {

    owner = "irods";

    repo = "irods_client_icommands";

    tag = finalAttrs.version;

    hash = "sha256-lo1eCI/CSzl7BJWdPo7KKVHfznkPN6GwsiQThUGuQdw=";

  };



  nativeBuildInputs = [

    cmake

    ninja

    help2man

  ];



  buildInputs = [ irods ];



  cmakeFlags = irods.commonCmakeFlags ++ [

    (lib.cmakeFeature "ICOMMANDS_INSTALL_DIRECTORY" "${placeholder "out"}/bin")

    (lib.cmakeBool "ICOMMANDS_INSTALL_SYMLINKS" false)

  ];



  meta = {

    inherit (irods.meta)

      homepage

      license

      maintainers

      platforms

      ;

    description = irods.meta.description + " CLI clients";

    longDescription = irods.meta.longDescription + ''



      This package provides the CLI clients, called 'icommands'.

    '';

  };

})

pkgs/tools/filesystems/irods/common.nix→pkgs/by-name/ir/irods/package.nix

+115 −0
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  bzip2,

  zlib,

  autoconf,

  automake,

  llvmPackages,

  fetchFromGitHub,

  cmake,

  help2man,

  texinfo,

  libtool,

  cppzmq,

  ninja,

  bison,

  flex,

  libarchive,

  avro-cpp,

  boost,

  zeromq,

  openssl,

  pam,

  libiodbc,

  libkrb5,

  gcc,

  libcxx,

  which,

  catch2,

  nanodbc,

  fmt,

  nlohmann_json,

  unixODBC,

  jsoncons,

  curl,

  spdlog_rods,

  bison,

  flex,

  systemdLibs,

  openssl,

  boost183,

  nlohmann_json,

  nanodbc,

  fmt_9,

  spdlog,

}:



# Common attributes of irods packages

llvmPackages.stdenv.mkDerivation (finalAttrs: {

  pname = "irods";

  version = "5.0.1";



  src = fetchFromGitHub {

    owner = "irods";

    repo = "irods";

    tag = finalAttrs.version;

    hash = "sha256-/mcuqukgDoMc89FL/TfOhHWglsfdLmQbAnQYT8vTFsY=";

  };



{

  nativeBuildInputs = [

    autoconf

    automake

    cmake

    help2man

    texinfo

    which

    gcc

    ninja

    bison

    flex

  ];



  buildInputs = [

    bzip2

    zlib

    libtool

    cppzmq

    libarchive

    avro-cpp

    zeromq

    openssl

    pam

    libiodbc

    libkrb5

    boost

    libcxx

    catch2

    nanodbc

    fmt

    nlohmann_json

    spdlog_rods

    unixODBC

    jsoncons

    curl

    systemdLibs

  ];



  cmakeFlags = [

    "-DIRODS_EXTERNALS_FULLPATH_CLANG=${stdenv.cc}"

    "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME=${stdenv.cc}"

    "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE=${libarchive.lib}"

    "-DIRODS_EXTERNALS_FULLPATH_AVRO=${avro-cpp}"

    "-DIRODS_EXTERNALS_FULLPATH_BOOST=${boost}"

    "-DIRODS_EXTERNALS_FULLPATH_ZMQ=${zeromq}"

    "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ=${cppzmq}"

    "-DIRODS_EXTERNALS_FULLPATH_CATCH2=${catch2}"

    "-DIRODS_EXTERNALS_FULLPATH_NANODBC=${nanodbc}"

    "-DIRODS_EXTERNALS_FULLPATH_FMT=${fmt}"

    "-DIRODS_EXTERNALS_FULLPATH_JSON=${nlohmann_json}"

    "-DIRODS_EXTERNALS_FULLPATH_SPDLOG=${spdlog_rods}"

    "-DIRODS_LINUX_DISTRIBUTION_NAME=nix"

    "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1.0"

    "-DCPACK_GENERATOR=TGZ"

    "-DCMAKE_CXX_FLAGS=-I${lib.getDev libcxx}/include/c++/v1"

    "-DPAM_LIBRARY=${pam}/lib/libpam.so"

    "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}"

    "-DIRODS_HOME_DIRECTORY=${placeholder "out"}"

    "-DCMAKE_INSTALL_SBINDIR=${placeholder "out"}/sbin"

  propagatedBuildInputs = [

    openssl

    # Can potentially be unpinned after:

    # <https://github.com/irods/irods/issues/7248>

    boost183

    nlohmann_json

    nanodbc

    # Tracking issue for `fmt_11`:

    # <https://github.com/irods/irods/issues/8454>

    fmt_9

    (spdlog.override {

      fmt = fmt_9;

    })

  ];



  cmakeFlags = finalAttrs.passthru.commonCmakeFlags ++ [

    # Tracking issues for moving these to `find_package`:

    # * <https://github.com/irods/irods/issues/6249>

    # * <https://github.com/irods/irods/issues/6253>

    (lib.cmakeFeature "IRODS_EXTERNALS_FULLPATH_BOOST" "${boost183}")

    (lib.cmakeFeature "IRODS_EXTERNALS_FULLPATH_NANODBC" "${nanodbc}")

    (lib.cmakeFeature "IRODS_EXTERNALS_FULLPATH_JSONCONS" "${jsoncons}")

  ];



  postPatch = ''

    patchShebangs ./packaging ./scripts

    patchShebangs ./test

    substituteInPlace plugins/database/CMakeLists.txt --replace-fail \

      'COMMAND cpp -E -P -D''${plugin} "''${CMAKE_CURRENT_BINARY_DIR}/src/icatSysTables.sql.pp" ' \

      'COMMAND cpp -E -P -D''${plugin} "''${CMAKE_CURRENT_BINARY_DIR}/src/icatSysTables.sql.pp" -o '

    substituteInPlace server/auth/CMakeLists.txt --replace-fail SETUID ""

  '';



  meta = with lib; {

  passthru = {

    commonCmakeFlags = [

      # We already use Clang in the `stdenv`.

      (lib.cmakeBool "IRODS_BUILD_WITH_CLANG" false)

      # Upstream builds with LLVM 16 and doesn’t handle newer warnings.

      (lib.cmakeBool "IRODS_BUILD_WITH_WERROR" false)

      (lib.cmakeFeature "IRODS_HOME_DIRECTORY" "${placeholder "out"}")

      (lib.cmakeFeature "IRODS_LINUX_DISTRIBUTION_NAME" "NixOS")

      (lib.cmakeFeature "IRODS_LINUX_DISTRIBUTION_VERSION" lib.trivial.release)

      (lib.cmakeFeature "IRODS_LINUX_DISTRIBUTION_VERSION_MAJOR" lib.trivial.release)

      (lib.cmakeFeature "CPACK_GENERATOR" "TGZ")

    ];

  };



  meta = {

    description = "Integrated Rule-Oriented Data System (iRODS)";

    longDescription = ''

      The Integrated Rule-Oriented Data System (iRODS) is open source data management
@@ -105,10 +104,12 @@ 
      As data volumes grow and data services become more complex, iRODS is increasingly

      important in data management. The development infrastructure supports exhaustive

      testing on supported platforms; plug-in support for microservices, storage resources,

      drivers, and databases; and extensive documentation, training and support services.'';

      drivers, and databases; and extensive documentation, training and support services.

    '';

    homepage = "https://irods.org";

    license = lib.licenses.bsd3;

    maintainers = [ lib.maintainers.bzizou ];

    platforms = lib.platforms.linux;

    mainProgram = "irodsServer";

  };

}
 
})

pkgs/tools/filesystems/irods/default.nix

deleted100644 → 0
+0 −169
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  fetchFromGitHub,

  bzip2,

  zlib,

  autoconf,

  automake,

  cmake,

  help2man,

  texinfo,

  libtool,

  cppzmq,

  libarchive,

  avro-cpp_llvm,

  boost,

  zeromq,

  openssl,

  pam,

  libiodbc,

  libkrb5,

  gcc,

  libcxx,

  which,

  catch2,

  nanodbc_llvm,

  fmt,

  nlohmann_json,

  spdlog_llvm,

  curl,

  bison,

  flex,

}:



let

  spdlog_rods = spdlog_llvm.overrideAttrs (attrs: {

    inherit stdenv;

    version = "1.10.0";

    src = attrs.src.override {

      rev = "v1.10.0";

      hash = "sha256-c6s27lQCXKx6S1FhZ/LiKh14GnXMhZtD1doltU4Avws=";

    };

    postPatch = ''

      substituteInPlace cmake/spdlog.pc.in \

        --replace-fail '$'{exec_prefix}/@CMAKE_INSTALL_LIBDIR@ @CMAKE_INSTALL_FULL_LIBDIR@

    '';

  });

in

let

  avro-cpp = avro-cpp_llvm;

  nanodbc = nanodbc_llvm;



  common = import ./common.nix {

    inherit

      lib

      stdenv

      bzip2

      zlib

      autoconf

      automake

      cmake

      help2man

      texinfo

      libtool

      cppzmq

      libarchive

      zeromq

      openssl

      pam

      libiodbc

      libkrb5

      gcc

      libcxx

      boost

      avro-cpp

      which

      catch2

      nanodbc

      fmt

      nlohmann_json

      curl

      spdlog_rods

      bison

      flex

      ;

  };

in

rec {



  # irods: libs and server package

  irods = stdenv.mkDerivation (

    finalAttrs:

    common

    // {

      version = "4.3.3";

      pname = "irods";



      src = fetchFromGitHub {

        owner = "irods";

        repo = "irods";

        rev = finalAttrs.version;

        hash = "sha256-SmN2FzeoA2/gjiDfGs2oifOVj0mK2WdQCgiSdIlENfk=";

        fetchSubmodules = true;

      };



      # fix build with recent llvm versions

      env.NIX_CFLAGS_COMPILE = "-Wno-deprecated-register -Wno-deprecated-declarations";



      cmakeFlags = common.cmakeFlags or [ ] ++ [

        "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath,${placeholder "out"}/lib -D_GLIBCXX_USE_CXX11_ABI=0"

        "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath,${placeholder "out"}/lib"

        "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,${placeholder "out"}/lib"

      ];



      postPatch = common.postPatch + ''

        patchShebangs ./test

        substituteInPlace plugins/database/CMakeLists.txt --replace-fail "COMMAND cpp" "COMMAND ${gcc.cc}/bin/cpp"

        for file in unit_tests/cmake/test_config/*.cmake

        do

          substituteInPlace $file --replace-quiet "CATCH2}/include" "CATCH2}/include/catch2"

        done



        substituteInPlace server/auth/CMakeLists.txt --replace-fail SETUID ""

      '';



      meta = common.meta // {

        longDescription = common.meta.longDescription + "This package provides the servers and libraries.";

        mainProgram = "irodsServer";

      };

    }

  );



  # icommands (CLI) package, depends on the irods package

  irods-icommands = stdenv.mkDerivation (

    finalAttrs:

    common

    // {

      version = "4.3.3";

      pname = "irods-icommands";



      src = fetchFromGitHub {

        owner = "irods";

        repo = "irods_client_icommands";

        rev = finalAttrs.version;

        hash = "sha256-cc0V6BztJk3njobWt27VeJNmQUXyH6aBJkvYIDFEzWY=";

      };



      buildInputs = common.buildInputs ++ [ irods ];



      postPatch = common.postPatch + ''

        patchShebangs ./bin

      '';



      cmakeFlags = common.cmakeFlags ++ [

        "-DCMAKE_INSTALL_PREFIX=${stdenv.out}"

        "-DIRODS_DIR=${irods}/lib/irods/cmake"

        "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"

        "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"

        "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,${irods}/lib"

      ];



      meta = common.meta // {

        description = common.meta.description + " CLI clients";

        longDescription =

          common.meta.longDescription + "This package provides the CLI clients, called 'icommands'.";

      };

    }

  );

}

pkgs/top-level/all-packages.nix

+0 −14
Original line number Diff line number Diff line
@@ -3224,20 +3224,6 @@ with pkgs; 


  icepeak = haskell.lib.compose.justStaticExecutables haskellPackages.icepeak;



  inherit

    (callPackages ../tools/filesystems/irods rec {

      stdenv = llvmPackages_13.libcxxStdenv;

      libcxx = llvmPackages_13.libcxx;

      boost = boost178.override { inherit stdenv; };

      fmt = fmt_9.override { inherit stdenv; };

      nanodbc_llvm = nanodbc.override { inherit stdenv; };

      avro-cpp_llvm = avro-cpp.override { inherit stdenv boost; };

      spdlog_llvm = spdlog.override { inherit stdenv fmt; };

    })

    irods

    irods-icommands

    ;



  ihaskell = callPackage ../development/tools/haskell/ihaskell/wrapper.nix {

    inherit (haskellPackages) ghcWithPackages;