refactor: use juliaWithPackage

.github/workflows/ci.yml

@@ -67,13 +67,6 @@ jobs:
       run: |
         nix build -L .#jupyterlab-kernel-${{ matrix.kernel }}
 
-    # TODO remove once we have a better solution. For more info see
-    # https://github.com/tweag/jupyterWith/pull/280
-    - name: Install IJulia
-      if: contains(matrix.kernel, 'julia')
-      run: |
-        result/bin/julia examples/$( echo "${{ matrix.kernel }}" | sed -e "s|example-||" | sed -e "s|-|/|g" )/installDeps.jl
-
     - name: Test notebook for ${{ matrix.kernel }} kernel
       run: |
         echo 'If Julia fails, see if IJulia was updated recently.'

.gitignore

@@ -4,7 +4,7 @@ result*
 /.pre-commit-config.yaml
 
 .ipynb_checkpoints/
-*.ipynb
+/*.ipynb
 
 # generated folder of jupyter distribution
 /jupyterlab/

examples/julia/minimal/default.nix

@@ -1,5 +1,8 @@
 {pkgs, ...}: {
   kernel.julia.minimal-example = {
     enable = true;
+    extraJuliaPackages = [
+      "Plots"
+    ];
   };
 }

examples/python/native/default.nix

@@ -1,5 +1,5 @@
 {pkgs, ...}: {
-  kernel.python.science-example = {
+  kernel.python.native-example = {
     enable = true;
     env = pkgs.python3.withPackages (ps:
       with ps; [

examples/python/native/test.ipynb

@@ -0,0 +1,69 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d13cad64-62c0-4b87-b8ef-0242658baa0f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import scipy as sp\n",
+    "import matplotlib as mpl"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16f8a525-ab66-407d-b978-78af1ee27a4d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x = np.arange(5)\n",
+    "print(x)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97728667-fbc5-4e71-a3b7-52f174309b92",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "y_new = sp.interpolate.interp1d(x, x ** 2)(x[:-1] + 0.5)\n",
+    "print(y_new)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d03e077a-add4-472f-afba-0c1f17e0159a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(mpl.colormaps['viridis'].resampled(8)(0.56))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Example Python Kernel",
+   "language": "python",
+   "name": "example-python-science"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

examples/python/native/test.py

@@ -3,7 +3,7 @@
 
 current_dir = os.path.dirname(os.path.abspath(__file__))
 
-@testbook(f'{current_dir}/test.ipynb', execute=True, kernel_name="python-science-example")
+@testbook(f'{current_dir}/test.ipynb', execute=True, kernel_name="python-native-example")
 def test_nb(tb):
     np_result = tb.cell_output_text(1)
     assert np_result == "[0 1 2 3 4]"

examples/python/science/test.ipynb

@@ -8,8 +8,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import scipy as sp\n",
-    "import matplotlib as mpl"
+    "import scipy as sp"
    ]
   },
   {

flake.nix

@@ -10,6 +10,7 @@
 
   inputs.nixpkgs.url = "github:nixos/nixpkgs/2de8efefb6ce7f5e4e75bdf57376a96555986841";
   inputs.nixpkgs-stable.url = "github:nixos/nixpkgs/nixos-23.05";
+  inputs.nixpkgs-julia.url = "github:NixOS/nixpkgs/?ref=refs/pull/225513/head";
   inputs.flake-compat.url = "github:edolstra/flake-compat";
   inputs.flake-compat.flake = false;
   inputs.flake-utils.url = "github:numtide/flake-utils";
@@ -49,7 +50,8 @@
     pre-commit-hooks,
     poetry2nix,
     rust-overlay,
-  }: let
+    ...
+  } @ inputs: let
     inherit (nixpkgs) lib;
 
     SYSTEMS = [

modules/kernels/julia/default.nix

@@ -20,28 +20,25 @@
       self,
       system,
       # custom arguments
-      pkgs ? self.inputs.nixpkgs.legacyPackages.${system},
+      pkgs,
       name ? "julia",
       displayName ? "Julia",
       requiredRuntimePackages ? [],
       runtimePackages ? [],
       julia ? pkgs.julia,
-      julia_depot_path ? "~/.julia",
-      activateDir ? "",
-      ijuliaRev ? "6TIq1",
+      ijuliaRev ? "Vo51o",
+      extraJuliaPackages ? [],
+      override ? {},
     }: let
       inherit (pkgs) writeText;
       inherit (pkgs.lib) optionalString;
 
-      startupFile = writeText "startup.jl" ''
-        import Pkg
-        Pkg.activate("${activateDir}")
-        Pkg.instantiate()
-      '';
-
       allRuntimePackages = requiredRuntimePackages ++ runtimePackages;
 
-      env = julia;
+      env = (self.inputs.nixpkgs-julia.legacyPackages.${system}.julia_19.withPackages.override override) ([
+          "IJulia"
+        ]
+        ++ extraJuliaPackages);
 
       wrappedEnv =
         pkgs.runCommand "wrapper-${env.name}"
@@ -52,7 +49,7 @@
             filename=$(basename $i)
             ln -s ${env}/bin/$filename $out/bin/$filename
             wrapProgram $out/bin/$filename \
-              --set PATH "${pkgs.lib.makeSearchPath "bin" allRuntimePackages}" ${optionalString (activateDir != "") ''--add-flags "-L ${startupFile}"''}
+              --set PATH "${pkgs.lib.makeSearchPath "bin" allRuntimePackages}"
           done
         '';
     in {
@@ -63,7 +60,7 @@
         "-i"
         "--startup-file=yes"
         "--color=yes"
-        "${julia_depot_path}/packages/IJulia/${ijuliaRev}/src/kernel.jl"
+        "${env.projectAndDepot}/depot/packages/IJulia/${ijuliaRev}/src/kernel.jl"
         "{connection_file}"
       ];
       codemirrorMode = "julia";
@@ -72,37 +69,32 @@
   in {
     options =
       {
-        julia_depot_path = lib.mkOption {
+        ijuliaRev = lib.mkOption {
           type = types.str;
-          default = "~/.julia";
-          example = "~/.julia";
+          default = "Vo51o";
           description = lib.mdDoc ''
-            Julia path
+            IJulia revision
           '';
         };
-
-        activateDir = lib.mkOption {
-          type = types.str;
-          default = "";
-          example = "";
+        julia = lib.mkOption {
+          type = types.package;
+          default = config.nixpkgs.julia;
           description = lib.mdDoc ''
-            Julia activate directory
+            Julia Version
           '';
         };
-
-        ijuliaRev = lib.mkOption {
-          type = types.str;
-          default = "6TIq1";
-          example = "6TIq1";
+        extraJuliaPackages = lib.mkOption {
+          type = types.listOf types.str;
+          default = [];
           description = lib.mdDoc ''
-            iJulia revision
+            Extra Julia packages to install
           '';
         };
-        julia = lib.mkOption {
-          type = types.package;
-          default = config.nixpkgs.julia;
+        override = lib.mkOption {
+          type = types.attrs;
+          default = {};
           description = lib.mdDoc ''
-            Julia Version
+            Override JuliaWithPackages
           '';
         };
       }
@@ -112,7 +104,7 @@
       build = mkKernel (kernelFunc config.kernelArgs);
       kernelArgs =
         {
-          inherit (config) julia_depot_path activateDir ijuliaRev julia;
+          inherit (config) override extraJuliaPackages ijuliaRev julia;
         }
         // kernelModule.kernelArgs;
     };

modules/kernels/scala/default.nix

@@ -36,7 +36,7 @@
 
       almondSh = let
         baseName = "almond";
-        version = "0.13.1";
+        version = "0.14.0-RC7";
         scalaVersion = scala.version;
         deps = stdenv.mkDerivation {
           name = "${baseName}-deps-${version}";
@@ -50,7 +50,7 @@
 
           outputHashMode = "recursive";
           outputHashAlgo = "sha256";
-          outputHash = "iPWMAvEW83aETWrxt9CmBAYMNouWsHHDoEa+Qy9inyE=";
+          outputHash = "sha256-JIYAuhV3+PQBceGEIgn5DkHTG80cKNV11FeJTefRHi8=";
         };
       in
         stdenv.mkDerivation {