adds jupyter shell environment.

pkgs/default.nix

@@ -30,26 +30,26 @@
 }:
 let
   callPackage = pkgs.lib.callPackageWith (pkgs // argopkgs);
+
   argopkgs = rec {
     # library of nix expressions
     argolib     = import ../lib/utils.nix;
     # Argo components (source overridabel via argument)
-    aml        = callPackage ./aml        {src = aml-src;};
-    nrm        = callPackage ./nrm        {src = nrm-src;};
-    containers = callPackage ./containers {src = containers-src;};
-    libnrm     = callPackage ./libnrm     {src = libnrm-src;};
+    aml        = callPackage ./aml        {src=aml-src;};
+    nrm        = callPackage ./nrm        {src=nrm-src;};
+    containers = callPackage ./containers {src=containers-src;};
+    libnrm     = callPackage ./libnrm     {src=libnrm-src;};
     libnrm-pmpi = libnrm.overrideAttrs (oldAttrs: rec {
       configureFlags = "--enable-pmpi";
       buildInputs = oldAttrs.buildInputs ++ [ pkgs.mpich2 ];
     });
 
     # applications (source overridable via argument)
-
-    amg     = callPackage ./amg     { nrmSupport=true; src = amg-src; };
-    qmcpack = callPackage ./qmcpack { nrmSupport=true; src = qmcpack-src; };
-    openmc  = callPackage ./openmc  { nrmSupport=true; src = openmc-src; };
-    stream  = callPackage ./stream  { nrmSupport=true; src = stream-src; };
-    lammps  = callPackage ./lammps  { nrmSupport=true; src = lammps-src; };
+    amg     = callPackage ./amg     {nrmSupport=true;src=amg-src;};
+    qmcpack = callPackage ./qmcpack {nrmSupport=true;src=qmcpack-src;};
+    openmc  = callPackage ./openmc  {nrmSupport=true;src=openmc-src;};
+    stream  = callPackage ./stream  {nrmSupport=true;src=stream-src;};
+    lammps  = callPackage ./lammps  {nrmSupport=true;src=lammps-src;};
 
     # data (static, non source overridable via arguments)
     openmc-data = fetched openmc/data.json;
@@ -108,32 +108,32 @@ let
     #zmcat = pkgs-stable.haskellPackages.callPackage ./tools/zmcat {};
 
     # ci/experimental environments
+    testBuildInputs =  [
+      # argotk runs mpiexec:
+      pkgs.mpich2
+      # argotk uses hwloc to choose CPU counts:
+      pkgs.hwloc
+      # these are needed for some reason:
+      pkgs.coreutils
+      pkgs.utillinux
+      pkgs.git
+      # argo tools
+      argotk
+      # argo components
+      containers
+      nrm
+    ];
+
     test = pkgs.stdenv.mkDerivation rec {
       name = "testEnv";
 
+      buildInputs = testBuildInputs ++ [ stream ];
+
       #required to be able to build the drv.
       installPhase = "mkdir $out";
       unpackPhase = "true";
 
       __noChroot = true;
-
-      buildInputs =  [
-        # argotk runs mpiexec:
-        pkgs.mpich2
-        # argotk uses hwloc to choose CPU counts:
-        pkgs.hwloc
-        # these are needed for some reason:
-        pkgs.coreutils
-        pkgs.utillinux
-        pkgs.git
-        # argo tools
-        argotk
-        # argo components
-        containers
-        nrm
-        # sample application for testing progress reports:
-        (stream.override {libnrm = libnrm; iterationCount = "20";})
-      ];
       shellHook =''
         echo ""
         echo "ENTERING ENVIRONMENT: Sources of impurity for this build are: /tmp/ /etc/argo/ /var/run/ /var/lock/".
@@ -143,17 +143,23 @@ let
         source ${argotk}/share/argotk.sh # bash completion
         echo ""
       '';
-      # for argotk to find its versioned data
+      #argotk uses this environment variable.
       ARGOTK_SHARE = "${argotk}/share";
-      #SUDO = builtins.toPath sudoPath;
     };
 
     expe = test.overrideAttrs (old:{
-      buildInputs = old.buildInputs ++ [
+      buildInputs = testBuildInputs ++ [
+        #debug tools
+        pkgs.which
+
+        #experiment tools
+        zymake
+
+        #applications
+        (stream.override {iterationCount = "20000";})
         amg
         lammps
         qmcpack
-        (stream.override {iterationCount = "2000000";})
         openmc
         openmc-data
       ];
@@ -161,6 +167,30 @@ let
       OPENMC_PWD = "${argotk}/share/openmc";
     });
 
+    jupyter =
+      let
+        jupyter = import (fetched jupyter/pin.json) {};
+      in
+       (jupyter.jupyterlabWith {
+          kernels = [
+            (jupyter.kernels.juniperWith {
+              name = "analysis";
+              packages = p: with p; [ ggplot2
+                  pkgs.which
+                  docopt
+                  knitr
+                  cowplot
+                  lubridate
+                  dplyr
+                  ggplot2
+                  xtable
+                  ggthemes
+                  data_table
+              ];
+            })
+          ];
+         }).env;
+
     doArgotk = command: test.overrideAttrs (old:{
       buildPhase = "argotk "+command;
       installPhase = ''

pkgs/jupyter/pin.json

+{
+  "fetch": {
+    "args": {
+      "fetchSubmodules": false,
+      "rev": "3bbe91d6d0bd4526cc70b6ebcfa0871432dff329",
+      "sha256": "04nx4rpvc96l1impv1j75acdpji3p77iszkkgkp7pi8xfrq6hrwg",
+      "url": "https://github.com/tweag/jupyterWith.git"
+    },
+    "fn": "fetchgit"
+  },
+  "rev": "refs/heads/master",
+  "type": "fetchgit",
+  "url": "https://github.com/tweag/jupyterWith.git"
+}
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