flake.nix

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

machines/kcnhub/packages/containers.nix

@@ -2,14 +2,8 @@
   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

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

machines/kcnhub/packages/python.nix

@@ -1,62 +1,12 @@
 {config, lib, pkgs, ...}: {
-  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
+  environment.systemPackages = with pkgs; [
+    (pkgs.python3.withPackages (p: with p; [
       numpy
       scipy
-      scikit-learn
       pandas
-      openpyxl
       matplotlib
-      ipympl
-      matplotlib-inline
+      tqdm
       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 = '32G'
+      c.SystemdSpawner.mem_limit = '8G'
       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
@@ -175,8 +175,7 @@
     
     kernels = {
       python3 = let
-        env = (pkgs.python3.withPackages (pythonPackages: with pythonPackages;
-          (config.pythonPackages pythonPackages) ++ [
+        env = (pkgs.python3.withPackages (pythonPackages: with pythonPackages; [
           # Necessary for use as a kernel
           ipykernel
           ipdb
@@ -186,8 +185,52 @@
           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

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

machines/kcnhub/users.nix

@@ -11,12 +11,6 @@
     ./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

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

machines/kcnhub/users/josh.nix

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

machines/kcnhub/users/michael.nix

@@ -1,12 +0,0 @@
-{ 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

@@ -1,12 +0,0 @@
-{ 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

@@ -1,12 +0,0 @@
-{ 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

@@ -1,12 +0,0 @@
-{ 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

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

overlays/python-packages.nix

@@ -1,33 +0,0 @@
-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

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