KCNHUB: Matlab: Add Support for PAM-auth

flake.nix

@@ -35,6 +35,7 @@
         config.cudaSupport = true;
       };
     };
+    python-overlay = import ./overlays/python.nix;
     applyOverlays = overlays: ({...}:{ nixpkgs.overlays = overlays; });
     flakes = {...}: {nix.settings.experimental-features = [ "nix-command" "flakes" ];};
   in {
@@ -43,7 +44,7 @@
       specialArgs = attrs;
       modules = [ 
          flakes
-         (applyOverlays [ unfree-overlay unstable-overlay ])
+         (applyOverlays [ unfree-overlay unstable-overlay python-overlay ])
          ./machines/kcnhub/configuration.nix
          sops-nix.nixosModules.sops
       ];

machines/kcnhub/packages/containers.nix

@@ -2,8 +2,14 @@
   virtualisation = {
     podman = {
       enable = true;
-      dockerCompat = true;
     };
+    docker.rootless = {
+      enable = true;
+      setSocketVariable = true;
+    };
+    # For compatability, and for some reason this isn't able to be per
+    # container?
+    oci-containers.backend = "docker";
   };
 
   environment.systemPackages = with pkgs; [

machines/kcnhub/packages/matlab.nix

@@ -59,7 +59,9 @@
   # matlab's installers)
   matlab-env = pkgs.buildFHSUserEnv {
     name = "matlab-env";
-    targetPkgs = (ps: nix-matlab.targetPkgs ps);
+    targetPkgs = (ps: (nix-matlab.targetPkgs ps) ++ (with ps; [
+      linux-pam
+    ]));
   };
 
   # Script used to get the most up to date version of the desired MATLAB
@@ -126,7 +128,7 @@
     '';
     runScript = pkgs.writeScript "matlab-run-${f}-script" ''
       export QT_QPA_PLATFORM=xcb
-      ${MATLAB_INSTALL_DIR}/bin/${f} "$@"
+      "$MATLAB_INSTALL_DIR/bin/${f}" "$@"
     '';
   };
 
@@ -144,6 +146,7 @@ in {
   environment.systemPackages =(with pkgs; [
     matlab-update-script
     matlab
+    matlab-env
     matlab-mex
     octaveFull
   ]);

machines/kcnhub/packages/python.nix

@@ -1,12 +1,62 @@
 {config, lib, pkgs, ...}: {
-  environment.systemPackages = with pkgs; [
-    (pkgs.python3.withPackages (p: with p; [
+  options = {
+    pythonPackages = lib.mkOption {
+      type = lib.types.anything;
+      default = p: with p; [];
+      example = p: with p; [ numpy scipy ];
+      description = "List of Python Packages installed";
+    };
+  };
+  config = {
+    environment.systemPackages = with pkgs; [
+      ((pkgs.python3.withPackages config.pythonPackages).override (args: { ignoreCollisions = true; }))
+    ];
+    pythonPackages = (p: with p; [
+      # Common Python Libraries
       numpy
       scipy
+      scikit-learn
       pandas
+      openpyxl
       matplotlib
-      tqdm
+      ipympl
+      matplotlib-inline
       seaborn
-    ]))
-  ];
+
+      # Neural Data Processing Libraries
+      # Temporarily broken?: https://github.com/NixOS/nixpkgs/issues/259812
+      mne-python
+      edfio
+      nibabel
+      # View niftis!
+      ipyniivue
+      neo
+      
+      # Neurosimulators
+      neuronpy
+      # nest with MPI is incompatible with Jupyter:
+      # https://www.nest-simulator.org/pynest-api/_modules/nest.html
+      # see pynestkernel comments about their workaround
+      (nest.override {
+        withMpi = false;
+      })
+      brian2
+
+      # Machine learning toolkits:
+      tensorflow
+      tensorboard
+      keras
+      edward
+      transformers
+      tflearn
+      torch
+      torchvision
+      torchsde
+      torchmetrics
+      torchio
+      torchdiffeq
+      botorch
+      lion-pytorch
+    ]);
+  };
 }

machines/kcnhub/servers/jupyterhub.nix

@@ -133,7 +133,7 @@
     # Configuration options defined ^
     # mem_limit must be higher to allow for MATLAB
     extraConfig = ''
-      c.SystemdSpawner.mem_limit = '8G'
+      c.SystemdSpawner.mem_limit = '32G'
       c.SystemdSpawner.cpu_limit = 2.0
       c.SystemdSpawner.isolate_devices = False
       c.SystemdSpawner.extra_paths = [
@@ -164,7 +164,7 @@
       jupyterhub
       jupyterlab
       # Extensions:
-      jupyter-collaboration
+      # jupyter-collaboration
       jupyter-server-mathjax
       jupyter-console
       jupyterlab-lsp
@@ -175,7 +175,8 @@
     
     kernels = {
       python3 = let
-        env = (pkgs.python3.withPackages (pythonPackages: with pythonPackages; [
+        env = (pkgs.python3.withPackages (pythonPackages: with pythonPackages;
+          (config.pythonPackages pythonPackages) ++ [
           # Necessary for use as a kernel
           ipykernel
           ipdb
@@ -185,52 +186,8 @@
           mediapy
           # Progress bars etc. for in Jupyter/IPython
           halo
-
-          # Common Python Libraries
-          numpy
-          scipy
-          scikit-learn
-          pandas
           # Tables displayed in Jupyter: like Pandas Dataframes
           ipytablewidgets
-          matplotlib
-          ipympl
-          matplotlib-inline
-          seaborn
-
-          # Neural Data Processing Libraries
-          # Temporarily broken?: https://github.com/NixOS/nixpkgs/issues/259812
-          # mne-python
-          nibabel
-          # View niftis!
-          ipyniivue
-          neo
-          
-          # Neurosimulators
-          neuronpy
-          # nest with MPI is incompatible with Jupyter:
-          # https://www.nest-simulator.org/pynest-api/_modules/nest.html
-          # see pynestkernel comments about their workaround
-          (nest.override {
-            withMpi = false;
-          })
-          brian2
-
-          # Machine learning toolkits:
-          tensorflow
-          tensorboard
-          keras
-          edward
-          transformers
-          tflearn
-          torch
-          torchvision
-          torchsde
-          torchmetrics
-          torchio
-          torchdiffeq
-          botorch
-          lion-pytorch
         ])).override (args: { ignoreCollisions = true; });
         # Odd collision between tensorboard of torch & tensorflow
         # need to resolve later

machines/kcnhub/servers/overleaf.nix

@@ -9,6 +9,7 @@ in {
       # "Normal" User: for Podman Usage
       isNormalUser = true;
       home = stateDir;
+      linger = true;
     };
     groups.overleaf = {};
   };

machines/kcnhub/users.nix

@@ -11,6 +11,12 @@
     ./users/ngilab.nix
     ./users/milad.nix
     ./users/nooshin.nix
+    ./users/zoe.nix
+    ./users/yupeng.nix
+    ./users/reza.nix
+    ./users/michael.nix
+    ./users/ryan.nix
+    ./users/josh.nix
 
     # Groups
     ./users/groups/admin.nix

machines/kcnhub/users/groups/nfrf.nix

@@ -3,6 +3,8 @@
     members = [
       "spandan"
       "frances"
+      "nooshin"
+      "josh"
     ];
   };
 }

machines/kcnhub/users/josh.nix

@@ -0,0 +1,11 @@
+{ pkgs, ... }: {
+  users.users.josh = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 117;
+    packages = with pkgs; [
+
+    ];
+  };
+}

machines/kcnhub/users/michael.nix

@@ -0,0 +1,12 @@
+{ pkgs, ... }: {
+  users.users.michael = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 114;
+    initialHashedPassword = "$y$j9T$i8NenYjqKmfJvKvmx2UmY0$5lqRmnrq2PDjELQj4F7xr/MS2Dd0iEOXDWp9kJwXYZ7";
+    packages = with pkgs; [
+
+    ];
+  };
+}

machines/kcnhub/users/reza.nix

@@ -0,0 +1,12 @@
+{ pkgs, ... }: {
+  users.users.reza = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 115;
+    initialHashedPassword = "$y$j9T$i8NenYjqKmfJvKvmx2UmY0$5lqRmnrq2PDjELQj4F7xr/MS2Dd0iEOXDWp9kJwXYZ7";
+    packages = with pkgs; [
+
+    ];
+  };
+}

machines/kcnhub/users/ryan.nix

@@ -0,0 +1,12 @@
+{ pkgs, ... }: {
+  users.users.ryan = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 116;
+    initialHashedPassword = "$y$j9T$i8NenYjqKmfJvKvmx2UmY0$5lqRmnrq2PDjELQj4F7xr/MS2Dd0iEOXDWp9kJwXYZ7";
+    packages = with pkgs; [
+
+    ];
+  };
+}

machines/kcnhub/users/yupeng.nix

@@ -0,0 +1,12 @@
+{ pkgs, ... }: {
+  users.users.yupeng = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 113;
+    initialHashedPassword = "$y$j9T$i8NenYjqKmfJvKvmx2UmY0$5lqRmnrq2PDjELQj4F7xr/MS2Dd0iEOXDWp9kJwXYZ7";
+    packages = with pkgs; [
+
+    ];
+  };
+}

machines/kcnhub/users/zoe.nix

@@ -0,0 +1,12 @@
+{ pkgs, ... }: {
+  users.users.zoe = {
+    isNormalUser = true;
+    extraGroups = [ ];
+    homeSize = "50g";
+    homeProjectId = 112;
+    initialHashedPassword = "$y$j9T$i8NenYjqKmfJvKvmx2UmY0$5lqRmnrq2PDjELQj4F7xr/MS2Dd0iEOXDWp9kJwXYZ7";
+    packages = with pkgs; [
+
+    ];
+  };
+}

overlays/python-packages.nix

@@ -0,0 +1,33 @@
+final: final-py: prev-py: {
+  mne-python = prev-py.mne-python.overridePythonAttrs (old: {
+    pyproject = true;
+    format = null;
+    propagatedBuildInputs = old.propagatedBuildInputs ++ [
+      final-py.setuptools-scm
+    ];
+  });
+
+  edfio = let
+    version = "0.4.1";
+    pname = "edfio";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+    format = "pyproject";
+    
+    src = final.fetchFromGitHub {
+      owner = "the-siesta-group";
+      repo = pname;
+      rev = "v${version}";
+      hash = "sha256-+yb3Q/JximkVS6SOTFnjMYghbOi+UBbqW2Bs29eSonA=";
+    };
+
+    nativeBuildInputs = with final-py; [
+      poetry-core
+      poetry-dynamic-versioning
+    ];
+    
+    propagatedBuildInputs = with final-py; [
+      numpy
+    ];
+  };
+}

overlays/python.nix

@@ -0,0 +1,5 @@
+final: prev: {
+  pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [(
+    (import ./python-packages.nix final)
+  )];
+}