kcnhub: packages: python: nestml

flake.nix

@@ -43,6 +43,7 @@
       };
     };
     python-overlay = import ./overlays/python.nix attrs;
+    package-overlays = import ./overlays/packages.nix attrs;
     applyOverlays = overlays: ({...}:{ nixpkgs.overlays = overlays; });
     flakes = {...}: {nix.settings.experimental-features = [ "nix-command" "flakes" ];};
   in {
@@ -51,7 +52,7 @@
       specialArgs = attrs;
       modules = [ 
          flakes
-         (applyOverlays [ unfree-overlay unstable-overlay python-overlay ])
+         (applyOverlays [ unfree-overlay unstable-overlay python-overlay package-overlays ])
          vscode-server.nixosModules.default
          ./machines/kcnhub/configuration.nix
          sops-nix.nixosModules.sops
@@ -59,7 +60,7 @@
     };
 
     overlays = {
-      default = applyOverlays [ unfree-overlay unstable-overlay python-overlay ];
+      default = applyOverlays [ unfree-overlay unstable-overlay python-overlay package-overlays ];
       unstable = unstable-overlay;
     };
   };

machines/kcnhub/configuration.nix

@@ -18,12 +18,14 @@
       ./users.nix
       # Disable sleep (so SSH remains accessible)
       ./nosleep.nix
+     # <nix-ld/modules/nix-ld.nix>
     ];
 
+
   sops.age.keyFile = "/root/.config/sops/age/keys.txt";
   sops.defaultSopsFile = ./secrets/system.yaml;
 
-  networking.networkmanager.enable = true;
+  # networking.networkmanager.enable = true;
 
   # Support NTFS(3g)
   boot.supportedFilesystems = ["ntfs"];
@@ -44,6 +46,32 @@
   # Enable the X11 forwarding over ssh
   programs.ssh.forwardX11 = true;
   programs.ssh.setXAuthLocation = true;
+  environment.etc."vnc/xstartup-minimal".mode = "0755";
+  environment.etc."vnc/xstartup-plasma".mode = "0755";
+  environment.etc."vnc/xstartup-xfce".mode = "0755";
+
+  # trying to install matlab runtime
+  #systemd.services.vnc-scripts.enable = false;
+  #programs.nix-ld.enable = true;
+  #programs.nix-ld.package = pkgs.nix-ld;
+  #programs.nix-ld.dev.enable = true;
+  programs.nix-ld = {
+  enable = true;
+  package = pkgs.nix-ld;
+  libraries = with pkgs; [
+    glibc
+    gcc.cc.lib
+    zlib
+    pam
+    libuuid
+    libxcrypt
+    openssl
+    xorg.libX11
+    xorg.libXext
+    xorg.libXrender
+    xorg.libXtst
+  ];
+  };
 
   # Enable KDE Plasma
   services.xserver.displayManager.sddm.enable = true;

machines/kcnhub/packages.nix

@@ -8,5 +8,6 @@
     ./packages/containers.nix
     ./packages/deeplabcut.nix
     ./packages/vnc.nix
+    ./packages/virtualization.nix
   ];  
 }

machines/kcnhub/packages/python.nix

@@ -9,6 +9,9 @@
   };
   config = {
     environment.systemPackages = with pkgs; [
+      # For nestml
+      cmake
+      gnumake
       ((pkgs.python3.withPackages config.pythonPackages).override (args: { ignoreCollisions = true; }))
     ];
     pythonPackages = (p: with p; [
@@ -40,6 +43,7 @@
       (nest.override {
         withMpi = false;
       })
+      nestml
       brian2
       # SpiNNaker simulator
       spynnaker

machines/kcnhub/packages/virtualization.nix

@@ -0,0 +1,5 @@
+{ config, pkgs, lib, ... }: {
+  environment.systemPackages = with pkgs; [
+    qemu
+  ];
+}

overlays/packages.nix

@@ -0,0 +1,12 @@
+inputs: final: prev: {
+  nest = prev.nest.overrideAttrs (old: {
+    postPatch = old.postPatch + ''
+      sed -e 's#-L$prefix/#-L#g' -i bin/nest-config.in
+    '';
+  });
+  nest-mpi = prev.nest-mpi.overrideAttrs (old: {
+    postPatch = old.postPatch + ''
+      sed -e 's#-L$prefix/#-L#g' -i bin/nest-config.in
+    '';
+  });
+}

overlays/python-packages.nix

@@ -1,4 +1,88 @@
 final: final-py: prev-py: {
+  nestml = let
+    pname = "nestml";
+    # Newer versions require newer antlr4
+    version = "7.0.2";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+
+    src = final.fetchFromGitHub {
+      owner = "nest";
+      repo = pname;
+      rev = "v${version}";
+      hash = "sha256-BQzwIh2Gdq+rLwIwe7dyltDfEzpaIWGlXF0AfZGBUDw=";
+    };
+
+    doCheck = false;
+    dontUseCmakeConfigure = true;
+    
+    propagatedBuildInputs = with final-py; [
+      numpy
+      scipy
+      sympy
+      antlr4-python3-runtime
+      #setuptools
+      jinja2
+      astropy
+      semver
+      odetoolbox
+    ];
+  };
+  
+  odetoolbox = let
+    pname = "ode-toolbox";
+    version = "2.5.8";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+
+    src = final.fetchFromGitHub {
+      owner = "nest";
+      repo = pname;
+      rev = "v${version}";
+      hash = "sha256-do/R9tNXVdeoqQO5ofetP7jdq9VUq4UotO6LH3LL6jI=";
+    };
+
+    buildInputs = with final-py; [
+      pytest
+      pytest-runner
+    ];    
+
+    doCheck = false;
+    
+    propagatedBuildInputs = with final-py; [
+      matplotlib
+      graphviz
+      sympy
+      scipy
+      numpy
+      cython
+    ];
+  };
+
+  pytest-runner = let
+    pname = "pytest-runner";
+    version = "6.0.0";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+    pyproject = true;
+
+    src = final.fetchFromGitHub {
+      owner = "pytest-dev";
+      repo = pname;
+      rev = "v${version}";
+      leaveDotGit = true;
+      hash = "sha256-cfUqEu3vN2i8jKZcTxId8Q/T/ld25qBeXY63g0eJnPs=";
+    };
+
+    nativeBuildInputs = [
+      final.git
+    ];
+    
+    propagatedBuildInputs = with final-py; [
+      setuptools-scm
+    ];
+  };  
+
   mne-python = prev-py.mne-python.overridePythonAttrs (old: {
     pyproject = true;
     format = null;