default.nix 17.5 KB
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{ # host package set (unused except for fetching nixpkgs)
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  hostPkgs         ? import <nixpkgs> {}
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  # versioned nixpkgs
, pkgs             ? import (hostPkgs.nix-update-source.fetch ./pkgs.json).src {}
, bleeding         ? import (hostPkgs.nix-update-source.fetch ./bleeding.json).src {}
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, # fetcher alias for the remaining arguments
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  fetched          ? s: (pkgs.nix-update-source.fetch s).src
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, #source overrides: core nrm components
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  aml-src          ? fetched aml/pin.json
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, numabench-src    ? fetched numabench/pin.json
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, excit-src        ? fetched excit/pin.json
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, libnrm-src       ? fetched libnrm/pin.json
, nrm-src          ? fetched nrm/pin.json
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, nrm-schema-src   ? fetched nrm-schema/pin.json
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, containers-src   ? fetched containers/pin.json
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, #source overrides: applications
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  amg-src          ? fetched amg/pin.json
, qmcpack-src      ? fetched qmcpack/pin.json
, openmc-src       ? fetched openmc/pin.json
, stream-src       ? fetched stream/pin.json
, lammps-src       ? fetched lammps/pin.json
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, candle-src       ? fetched candle/pin.json
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  #source overrides: tooling
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, repoquality-src  ? builtins.fetchGit {inherit (fetched repoquality/pin.json) url rev;}
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, dhrun-src        ? builtins.fetchGit {inherit (pkgs.stdenv.lib.importJSON dhrun/pin.json) url rev;}
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, powerplots-src   ? builtins.fetchGit {inherit (fetched powerplots/pin.json) url rev;}
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, argonix-src      ? builtins.fetchGit {inherit (fetched argonix/pin.json) url rev;}
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, experiments-src  ? fetched experiments/pin.json
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, #used for hardware experiments.
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  sudoPath         ? null
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, #whether to graft apps on libnrm.
  graftLibnrm      ? false
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, #name for the generic test builder
  genericTestName  ? "run"
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}:
let
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  panhandle-src = fetched panhandle/pin.json;
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  callPackage = pkgs.lib.callPackageWith (pkgs // argopkgs);
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  addBI = drv: bi: drv.overrideAttrs
    (old:{buildInputs=old.buildInputs ++ [ bi ];});

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  argopkgs = rec {
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    singularity = bleeding.singularity;
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    # library of nix expressions
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    argolib       = import ../lib/utils.nix;
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    # Argo components (source overridabel via argument)
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    aml           = callPackage ./aml        {
      src=aml-src;
      hwloc=hwloc2;
      inherit excit;
      inherit numabench;
    };
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    numabench     = callPackage ./numabench  {src=numabench-src; hwloc = hwloc2;};
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    excit         = callPackage ./excit      {src=excit-src;};
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pypack  
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    nrm           = (callPackage ./nrm       { src=nrm-src;}).overrideAttrs (o:{
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      installPhase=o.installPhase+''
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        mkdir -p $out/share
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        cp -r nrm/schemas $out/lib/python2.7/site-packages/nrm/
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        cp -r examples $out/share
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      '';
    });
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    nrm-dist      = pkgs.stdenv.mkDerivation {
      name = "nrm-dist";
      src = nrm-src;
      buildInputs =
      [
        pkgs.curl
        pkgs.bash
        pkgs.coreutils
        (pkgs.python.withPackages (ps: [
          ps.sphinx_rtd_theme
          ps.sphinx
          ps.breathe
          ps.recommonmark
        ]))
      ];
      buildPhase = ''
        python ./setup.py build_sphinx --build-dir doc
        python ./setup.py sdist
      '';
      installPhase = ''
        mkdir -p $out
        cp dist/* $out/
      '';
    };

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    containers    = callPackage ./containers {src=containers-src;};
    libnrm        = callPackage ./libnrm     {src=libnrm-src;};
    libnrm-pinned = callPackage ./libnrm     {src=fetched libnrm/pin.json;};
    libnrm-pmpi   = libnrm.overrideAttrs (oldAttrs: rec {
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      configureFlags = "--enable-pmpi";
      buildInputs = oldAttrs.buildInputs ++ [ pkgs.mpich2 ];
    });
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    #jsonschema3 = pkgs.pythonPackages.jsonschema.overrideAttrs(o:{
      #src=pkgs.fetchurl{
        #url="https://files.pythonhosted.org/packages/1f/7f/a020327823b9c405ee6f85ab3053ff171e10801b19cfe55c78bb0b3810e7/jsonschema-3.0.1.tar.gz";
        #sha256 = "03g20i1xfg4qdlk4475pl4pp7y0h37g1fbgs5qhy678q9xb822hc";
      #};
    #});

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    #nrm-pytest    = nrm.overrideAttrs (old:{buildInputs = old.buildInputs++[nrm]; doCheck=true;checkPhase="py.test --deselect=test/test_messaging.py";});
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    aml-check = aml.overrideAttrs (old:{
      doCheck = true;
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      checkPhase = "make check";
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    });

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    mkl =  callPackage ./mkl {compiler_path = "/opt/intel/compilers_and_libraries/linux";};
    icc = callPackage ./icc {compiler_path = "/opt/intel/compilers_and_libraries/linux";};

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    aml-check-knl = aml-check.overrideAttrs (old:{
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      makeFlags = [ "-j64" "V=1"];
      configureFlags = [ "--enable-benchmarks" ];
      buildInputs = old.buildInputs ++ [pkgs.man-db icc mkl];
      CC="${icc}/bin/icc";
      preConfigure =  ''
        export CFLAGS="-mkl -xhost"
        export CC="${icc}/bin/icc"
        find . -name '*.o'
        find . -name '*.o' -delete
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      '';
    });

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    aml-dist      = aml.overrideAttrs (old:{
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      nativeBuildInputs = old.nativeBuildInputs ++
      [
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        pkgs.doxygen
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        pkgs.curl
        pkgs.bash
        pkgs.coreutils
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        (pkgs.python.withPackages (ps: [
          ps.sphinx_rtd_theme
          ps.sphinx
          ps.breathe
          ps.recommonmark
        ]))
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      ];
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      buildPhase = "make dist";
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      installPhase = ''
        mkdir -p $out
        cp *.tar.gz $out/
      '';
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    });
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    numabench-check = numabench.overrideAttrs(old: {
      buildPhase = "make check";
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      installPhase =''
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        mkdir -p $out/tests
        cp ./tests/*.log $out/tests
        cp ./tests/*.trs $out/tests
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        cp -r ./tests/tmp $out/tests
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        '';
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    });
    excit-check = excit.overrideAttrs(old: {
      buildPhase = "make check";
    });

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    # applications with replaceDependency for libnrm.
    repLibnrm = path: src: extra:
    let
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      drv = callPackage path ({
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        nrmSupport = true;
        src = src;
        libnrm = libnrm-pinned;
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      }//extra);
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      rebuilt = drv.override {libnrm = libnrm;};
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      grafted = pkgs.replaceDependency {
        drv = drv;
        oldDependency = libnrm-pinned;
        newDependency = libnrm;
      };
    in if graftLibnrm then grafted else rebuilt;
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    amg          = repLibnrm ./amg     amg-src     {};
    qmcpack      = repLibnrm ./qmcpack qmcpack-src {};
    openmc       = repLibnrm ./openmc  openmc-src  {};
    lammps       = repLibnrm ./lammps  lammps-src  {};
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    stream       = repLibnrm ./stream  stream-src  {iterationCount="2000";};
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    callCandlePackage = candlePkgs.lib.callPackageWith (candlePkgs);
    candleOverlay = self: super: rec { clblas = callCandlePackage ./clblas {
      inherit (pkgs.darwin.apple_sdk.frameworks) Accelerate CoreGraphics CoreVideo OpenCL;
      };
    };
    candlePkgs = import pkgs.path {
      overlays = [ candleOverlay ] ;
    };
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    candle       = callCandlePackage ./candle {src = candle-src; nrm = nrm;};
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    # data (static, non source overridable via arguments)
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    openmc-data = fetched openmc/data.json;
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    # tools
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    checkpatch = callPackage ./checkpatch {src=pkgs.linux_testing.src;};
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    zymake = callPackage ./zymake {
      inherit (pkgs.ocamlPackages) findlib ocamlbuild topkg batteries;
    };
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    haskellPackages = pkgs.haskellPackages.override {
      overrides = self: super: with pkgs.haskell.lib;
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      rec {
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        panpipe        = doJailbreak super.panpipe;
        #panhandle      = doJailbreak super.panhandle;
        spdx           = doJailbreak super.spdx;
        monad-mock     = doJailbreak super.monad-mock;
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        generic-pretty = doJailbreak super.generic-pretty;
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        jsonschema-gen = doJailbreak super.jsonschema-gen;
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        aeson-t = doJailbreak super.aeson-t;
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        #minor cabal and version fix
        panhandle    = (self.callCabal2nix "panhandle" (builtins.fetchGit {
                      inherit (panhandle-src) url rev; })) {};
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        inline-r = dontCheck super.inline-r;
        argonix     = (self.callCabal2nix "argonix"     argonix-src     ) {};
        repoquality = (self.callCabal2nix "repoquality" repoquality-src ) {};
        powerplots  = (self.callCabal2nix "powerplots"  powerplots-src  ) {};

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        generic-aeson   = doJailbreak super.generic-aeson;
        nrm-schema  = (self.callCabal2nix "nrm-schema"  nrm-schema-src ) {};
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        zmcat = self.callPackage ./zmcat {};
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      };
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    };
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    bleedingHaskellPackages = bleeding.haskellPackages.override {
      overrides = self: super: with bleeding.haskell.lib;
      rec {
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        panpipe        = doJailbreak super.panpipe;
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        panhandle      = (self.callCabal2nix "panhandle" (builtins.fetchGit {
                        inherit (panhandle-src) url rev; })) {};
        multistate      = doJailbreak super.multistate;
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        #hspec       = doJailbreak super.hspec;
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        dhrun       = (self.callCabal2nix "dhrun"       dhrun-src ) {};
      };
    };

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    # re-export from hpkgs and add non-haskell build rule specialization
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    inherit (haskellPackages) repoquality;
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    #inherit (bleedingHaskellPackages) dhall dhall-lsp-server dhall-json;
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    nrm-schema = haskellPackages.nrm-schema.overrideAttrs (old:{
      buildInputs = old.buildInputs ++ [
        (pkgs.python.withPackages (ps: [
          ps.warlock
          ps.jsonschema
        ]))
      ];
    });
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    dhrun = bleedingHaskellPackages.dhrun.overrideAttrs (old:{
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        installPhase = old.installPhase + ''
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          mkdir -p $out/share/
          cp -r resources $out/share/
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        '';
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      });

    argonix = haskellPackages.argonix.overrideAttrs (old:{
        installPhase = old.installPhase + ''
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          mkdir -p $out/share/
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          $out/bin/argonix --bash-completion-script argonix > $out/share/argonix.sh
        '';
      });
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    powerplots =
    let
      pkl = with pkgs.rPackages; [ docopt pracma tidyr readr magrittr formatR
          purrr wrapr knitr cowplot plotly lubridate dplyr ggplot2 fpp2
          prospectr gridExtra zoo xtable ggthemes data_table
        ];
      myR = (pkgs.rWrapper.override{ packages = [pkl];});
    in
    haskellPackages.powerplots.overrideDerivation (drv: rec {
      buildInputs = (drv.buildInputs or []) ++ [
        pkgs.makeWrapper
        myR
      ];

      installPhase = drv.installPhase + ''
        wrapProgram "$out/bin/powerplots" \
          --set R_LIBS_SITE `Rscript -e "Sys.getenv(\"R_LIBS_SITE\")"`
      '';

    });

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    # fix for nrm
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pypack  
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    pyzmq = pkgs.pythonPackages.pyzmq.override { zeromq3 = pkgs.zeromq; };
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    hwloc2 = pkgs.hwloc.overrideAttrs (old:{
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      name="hwloc-2";
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      src = pkgs.fetchurl {
        url = "https://download.open-mpi.org/release/hwloc/v2.0/hwloc-2.0.3.tar.gz";
        sha256 = "0707ml34ylrr8zwwhddp64q6q57248m9646f27jadcx5m93g5pk4";
      };
    });

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    # ci/experimental environments
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    test = pkgs.stdenv.mkDerivation rec {
      name = "testEnv";
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      buildInputs = [
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        # tooling may run mpiexec or hwloc:
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        pkgs.mpich2
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        hwloc2
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        # these are needed for some reason:
        pkgs.coreutils
        pkgs.utillinux
        pkgs.git
        # argo tools
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        dhrun
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        # argo components
        containers
        nrm
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        libnrm
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      ];
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      #required to be able to build the drv.
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      installPhase = "mkdir $out";
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      unpackPhase = "true";
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      __noChroot = true;
      shellHook =''
        echo ""
        echo "ENTERING ENVIRONMENT: Sources of impurity for this build are: /tmp/ /etc/argo/ /var/run/ /var/lock/".
        echo "ENTERING ENVIRONMENT: Moreover, sandboxing is disabled, in particular because of:"
        echo "ENTERING ENVIRONMENT: /tmp/nrm-* sockets, /etc/argo, /var/run/, /var/lock/ which all need read access. "
        echo "ENTERING ENVIRONMENT: until these components are patched to allow for alternative paths, no sandbox use is possible."
        echo ""
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      '';
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      #argotk uses this environment variable.
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      #OPENMC_PWD = "${argotk}/share/openmc";
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    };
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    analysis = pkgs.stdenv.mkDerivation rec {
      name = "analysis";
      src = experiments-src;

      #required to be able to build the drv.
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      installPhase = ''
        mkdir -p $out
      '';
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      unpackPhase = "true";

      buildInputs = [
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        pkgs.pandoc
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        (pkgs.rWrapper.override{ packages = with pkgs.rPackages; [
          pkgs.rlwrap
          pkgs.pandoc
          docopt
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          pracma
          tidyr
          readr
          magrittr
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          formatR
          purrr
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          wrapr
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          knitr
          cowplot
          plotly
          lubridate
          dplyr
          ggplot2
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          fpp2
          prospectr
          gridExtra
          zoo
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          xtable
          ggthemes
          data_table
        ];})
      ];
    };

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    hanalysis = analysis.overrideAttrs (old:{
      buildInputs = old.buildInputs ++ [
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        (haskellPackages.ghcWithPackages(p:[
          p.protolude
          p.optparse-applicative
          (p.inline-r.overrideAttrs(old:{doCheck=false;}))
        ]))
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      ];
    });

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    f = { mkDerivation, base, protolude, data-default
    , optparse-applicative, typed-process, inline-r
    , R, stdenv }:
    mkDerivation {
      pname = "hsr";
      version = "1.0.0";
      src = "";
      isLibrary = true;
      isExecutable = false;
      libraryHaskellDepends = [
        base
        protolude
        inline-r
        typed-process
        optparse-applicative
        data-default
      ];
      librarySystemDepends = [
        pkgs.pandoc
        R
        pkgs.rPackages.docopt
        pkgs.rPackages.pracma
        pkgs.rPackages.tidyr
        pkgs.rPackages.readr
        pkgs.rPackages.magrittr
        pkgs.rPackages.formatR
        pkgs.rPackages.purrr
        pkgs.rPackages.wrapr
        pkgs.rPackages.knitr
        pkgs.rPackages.cowplot
        pkgs.rPackages.plotly
        pkgs.rPackages.lubridate
        pkgs.rPackages.dplyr
        pkgs.rPackages.ggplot2
        pkgs.rPackages.fpp2
        pkgs.rPackages.prospectr
        pkgs.rPackages.gridExtra
        pkgs.rPackages.zoo
        pkgs.rPackages.xtable
        pkgs.rPackages.ggthemes
        pkgs.rPackages.data_table
      ];
      license = stdenv.lib.licenses.bsd3;
    };
    hanal = argolib.getHackEnv (pkgs//argopkgs)
      haskellPackages (haskellPackages.callPackage f {});

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    report = analysis.overrideAttrs (old:{
      buildPhase = ''
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        echo "analysis/zymakefolder.R ${powerexpe}"
        analysis/zymakefolder.R ${powerexpe}
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      '';
      installPhase = ''
        mkdir -p $out
        cp -r index* $out
      '';
    });
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    dhrunTestConfigLayer = pkgs.stdenv.mkDerivation rec {
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      name = "dhrunSpecs";
      src = ../dhrun ;
      installPhase = ''
        mkdir -p $out
        cp -r $src/* $out
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        substituteInPlace $out/test_assets/simple-H2O.xml --replace \
          H2O.HF.wfs.xml $out/test_assets/H2O.HF.wfs.xml
        substituteInPlace $out/test_assets/simple-H2O.xml --replace \
          O.BFD.xml $out/test_assets/O.BFD.xml
        substituteInPlace $out/test_assets/simple-H2O.xml --replace \
          H.BFD.xml $out/test_assets/H.BFD.xml
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        '';
      unpackPhase = "true";
    };

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    doDhrun = dhallcall: test.overrideAttrs (old:{
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      buildPhase = ''
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        dhrun run <<< 'let all = ${dhrunTestConfigLayer}/all-tests.dh
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                      "${dhrunTestConfigLayer}/" "${nrm}/share/examples/" True in all.${dhallcall}'
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      '';
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      installPhase = ''
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        mkdir -p $out
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        cp _output/* $out/
      '';
    });

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    testGeneric     =  doDhrun genericTestName;
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    testBrokenMessage = (doDhrun "run-singularity").overrideAttrs (o:{
      buildInputs = o.buildInputs ++ [haskellPackages.zmcat];
    });
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    testSingularity = (doDhrun "run-singularity").overrideAttrs (o:{
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      buildPhase = "PATH=$PATH:/tmp/argonix/ " + o.buildPhase;
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      __noChroot = true; # the test needs OS singularity installation so we disable sanboxing here.
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    });
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    testSTREAM      = addBI (doDhrun "stream") stream;
    testAMG         = addBI (doDhrun "amg") amg;
    testOpenMC      = (addBI (doDhrun "openmc") openmc).overrideAttrs
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      (old:{ OPENMC_CROSS_SECTIONS = "${openmc-data}/cross_sections.xml"; });
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    testLAMMPS      = addBI (doDhrun "lammps") lammps;
    testQMCPack     = addBI (doDhrun "qmcpack") qmcpack ;
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    testAll         = (doDhrun "hello").overrideAttrs
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    (old:{
      buildInputs = old.buildInputs ++ [
        lammps
        qmcpack
        openmc
        stream
        amg
        openmc-data
      ];
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      OPENMC_CROSS_SECTIONS = "${openmc-data}/cross_sections.xml";
      });
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    powerexpe = testAll.overrideAttrs (old:{
      name = "power-experiments";
      buildInputs = old.buildInputs ++ [
        #debug tools
        pkgs.which
        #experiment tools
        zymake
      ];
      buildPhase = "zymake ${experiments-src}/experiments/zymakefile";
      installPhase = ''
        mkdir -p $out
        cp -r o/* $out
      '';
    });
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    bld = bleeding;
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    deployment = pkgs.mkShell rec {
      buildInputs = [pkgs.nixops pkgs.nix];
    };
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    dhallVersion = "1.23.0";
    dhall =
      pkgs.stdenv.mkDerivation rec {
        name = "dhall-${version}";
        version = dhallVersion;
        src = pkgs.fetchurl {
            url = "https://github.com/dhall-lang/dhall-haskell/releases/download/${dhallVersion}/dhall-${version}-x86_64-linux.tar.bz2";
            sha256 = "1fy41fy0n2yc7f2dr3bx44977380rh8dx25zjgvrp4yygrf3nlgp";
        };

        installPhase = ''
          mkdir -p $out/bin
          cp dhall $out/bin/
        '';
      };
    dhall-lsp-server  =
      pkgs.stdenv.mkDerivation rec {
        name = "dhall-lsp-server-${version}";
        version = "0.1.0.1";
        src = pkgs.fetchurl {
            url = "https://github.com/dhall-lang/dhall-haskell/releases/download/${dhallVersion}/dhall-lsp-server-${version}-x86_64-linux.tar.bz2";
            sha256 = "1mckdw03kqssspbfkpa413wmfnv68mx99im4n2s10w4gw2if3983";
        };

    installPhase = ''
      mkdir -p $out/bin
      cp dhall-lsp-server  $out/bin/
    '';
  };

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  };
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# re-exporting a full nixpkgs-like package set
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in pkgs // argopkgs