clean up and improve docs

modules/nixos/applications/calibre.nix

@@ -14,6 +14,8 @@
       home.packages = with pkgs; [ calibre ];
       # home.sessionVariables = { CALIBRE_USE_DARK_PALETTE = 1; };
     };
+
+    # Forces Calibre to use dark mode
     environment.sessionVariables = { CALIBRE_USE_DARK_PALETTE = "1"; };
   };
 }

modules/nixos/applications/nautilus.nix

@@ -18,12 +18,14 @@
 
     home-manager.users.${config.user} = {
 
+      # Quick button for launching nautilus
       xsession.windowManager.i3.config.keybindings = {
         "${
           config.home-manager.users.${config.user}.xsession.windowManager.i3.config.modifier
         }+n" = "exec --no-startup-id ${pkgs.gnome.nautilus}/bin/nautilus";
       };
 
+      # Generates a QR code and previews it with sushi
       programs.fish.functions = {
         qr = {
           body =
@@ -31,7 +33,7 @@
         };
       };
 
-      # Set default for opening directories
+      # Set Nautilus as default for opening directories
       xdg.mimeApps = {
         associations.added."inode/directory" = [ "org.gnome.Nautilus.desktop" ];
         # associations.removed = {

modules/nixos/system/auto-upgrade.nix

@@ -0,0 +1,47 @@
+{ config, pkgs, lib, ... }: {
+
+  # This setting only applies to NixOS, different on Darwin
+  nix.gc.dates = "03:03"; # Run every morning (but before upgrade)
+
+  # Update the system daily by pointing it at the flake repository
+  system.autoUpgrade = {
+    enable = config.server; # Only auto upgrade servers
+    dates = "03:33";
+    flake = "git+${config.dotfilesRepo}";
+    randomizedDelaySec = "25min";
+    operation = "switch";
+    allowReboot = true;
+    rebootWindow = {
+      lower = "00:01";
+      upper = "06:00";
+    };
+  };
+
+  # Create an email notification service for failed jobs
+  systemd.services."notify-email@" =
+    let address = "system@${config.mail.server}";
+    in {
+      enable = config.mail.enable;
+      environment.SERVICE_ID = "%i";
+      script = ''
+        TEMPFILE=$(mktemp)
+        echo "From: ${address}" > $TEMPFILE
+        echo "To: ${address}" >> $TEMPFILE
+        echo "Subject: Failure in $SERVICE_ID" >> $TEMPFILE
+        echo -e "\nGot an error with $SERVICE_ID\n\n" >> $TEMPFILE
+        set +e
+        systemctl status $SERVICE_ID >> $TEMPFILE
+        set -e
+        ${pkgs.msmtp}/bin/msmtp \
+            --file=${config.homePath}/.config/msmtp/config \
+            --account=system \
+            ${address} < $TEMPFILE
+      '';
+    };
+
+  # Send an email whenever auto upgrade fails
+  systemd.services.nixos-upgrade.onFailure =
+    lib.mkIf config.systemd.services."notify-email@".enable
+    [ "notify-email@%i.service" ];
+
+}

modules/nixos/system/default.nix

@@ -1,6 +1,7 @@
 { config, pkgs, lib, ... }: {
 
-  imports = [ ./doas.nix ./journald.nix ./user.nix ./timezone.nix ];
+  imports =
+    [ ./auto-upgrade.nix ./doas.nix ./journald.nix ./user.nix ./timezone.nix ];
 
   config = lib.mkIf pkgs.stdenv.isLinux {
 
@@ -8,54 +9,6 @@
     system.stateVersion =
       config.home-manager.users.${config.user}.home.stateVersion;
 
-    # This setting only applies to NixOS, different on Darwin
-    nix.gc.dates = "weekly";
-
-    systemd.timers.nix-gc.timerConfig = { WakeSystem = true; };
-    systemd.services.nix-gc.postStop =
-      lib.mkIf (!config.server) "systemctl suspend";
-
-    # Update the system daily
-    system.autoUpgrade = {
-      enable = config.server; # Only auto upgrade servers
-      dates = "03:33";
-      flake = "git+${config.dotfilesRepo}";
-      randomizedDelaySec = "45min";
-      operation = "switch";
-      allowReboot = config.server; # Reboot servers
-      rebootWindow = {
-        lower = "00:01";
-        upper = "06:00";
-      };
-    };
-
-    # Create an email notification service for failed jobs
-    systemd.services."notify-email@" =
-      let address = "system@${config.mail.server}";
-      in {
-        enable = config.mail.enable;
-        environment.SERVICE_ID = "%i";
-        script = ''
-          TEMPFILE=$(mktemp)
-          echo "From: ${address}" > $TEMPFILE
-          echo "To: ${address}" >> $TEMPFILE
-          echo "Subject: Failure in $SERVICE_ID" >> $TEMPFILE
-          echo -e "\nGot an error with $SERVICE_ID\n\n" >> $TEMPFILE
-          set +e
-          systemctl status $SERVICE_ID >> $TEMPFILE
-          set -e
-          ${pkgs.msmtp}/bin/msmtp \
-              --file=${config.homePath}/.config/msmtp/config \
-              --account=system \
-              ${address} < $TEMPFILE
-        '';
-      };
-
-    # Send an email whenever auto upgrade fails
-    systemd.services.nixos-upgrade.onFailure =
-      lib.mkIf config.systemd.services."notify-email@".enable
-      [ "notify-email@%i.service" ];
-
   };
 
 }

modules/nixos/system/doas.nix

@@ -13,11 +13,11 @@
       doas = {
         enable = true;
 
-        # No password required
+        # No password required for trusted users
         wheelNeedsPassword = false;
 
         # Pass environment variables from user to root
-        # Also requires removing password here
+        # Also requires specifying that we are removing password here
         extraRules = [{
           groups = [ "wheel" ];
           noPass = true;
@@ -26,6 +26,7 @@
       };
     };
 
+    # Alias sudo to doas for convenience
     home-manager.users.${config.user}.programs.fish.shellAliases = {
       sudo = "doas";
     };

modules/nixos/system/journald.nix

@@ -1,6 +1,7 @@
 { ... }: {
 
   # How long to keep journalctl entries
+  # This helps to make sure log disk usage doesn't grow too unwieldy
   services.journald.extraConfig = ''
     SystemMaxUse=100M
     MaxFileSec=1month

modules/nixos/system/user.nix

@@ -1,4 +1,4 @@
-{ config, pkgs, lib, ... }: {
+{ config, lib, ... }: {
 
   options = {
 
@@ -11,7 +11,7 @@
 
   };
 
-  config = lib.mkIf (pkgs.stdenv.isLinux) {
+  config = {
 
     # Allows us to declaritively set password
     users.mutableUsers = false;