homes/common.nix

@@ -1,7 +1,24 @@
 { config, lib, pkgs, pkgs-unstable, ... }:
 let
   conda_init = shell: ''
-    eval "$(${pkgs.micromamba}/bin/micromamba shell hook --shell ${shell})"
+    # >>> conda initialize >>>
+    # !! Contents within this block are managed by 'conda init' !!
+    __conda_setup="$(${config.xdg.dataHome}/miniconda3/bin/conda shell.${shell} 'hook' 2> /dev/null)"
+    if [ $? -eq 0 ]; then
+        eval "$__conda_setup"
+    else
+        if [ -f "${config.xdg.dataHome}/miniconda3/etc/profile.d/conda.sh" ]; then
+            . "${config.xdg.dataHome}/miniconda3/etc/profile.d/conda.sh"
+        else
+            export PATH="${config.xdg.dataHome}/miniconda3/bin:$PATH"
+        fi
+    fi
+    unset __conda_setup
+
+    if [ -f "${config.xdg.dataHome}/miniconda3/etc/profile.d/mamba.sh" ]; then
+      . "${config.xdg.dataHome}/miniconda3/etc/profile.d/mamba.sh"
+    fi
+    # <<< conda initialize <<<
 
   '';
   nd_bash_function = ''
@@ -16,7 +33,6 @@ in {
     file = { ".p10k.zsh".source = ./../dotfiles/p10k.zsh; };
     packages = with pkgs; [
       act
-      btop
       cowsay
       earthly
       ffmpeg
@@ -31,9 +47,7 @@ in {
       jq
       julia-bin
       lynx
-      micromamba
       most
-      nextflow
       nil
       nixd
       nixfmt-classic
@@ -47,11 +61,10 @@ in {
     ];
     sessionVariables = {
       PAGER = "most";
-      MAMBA_ROOT_PREFIX = "${config.xdg.dataHome}/micromamba";
       NXF_HOME = "${config.xdg.dataHome}/nextflow";
       NXF_CACHE = "${config.xdg.cacheHome}/nextflow";
-      NXF_CONDA_CACHEDIR = "${config.xdg.cacheHome}/nextflow/conda";
+      NXF_CONDA_CACHEDIR = "$NXF_CACHE/conda";
-      NXF_SINGULARITY_CACHEDIR = "${config.xdg.cacheHome}/nextflow/singularity";
+      NXF_SINGULARITY_CACHEDIR = "$NXF_CACHE/singularity";
       JULIA_DEPOT_PATH = "${config.xdg.dataHome}/julia:";
       JULIA_PKG_USE_CLI_GIT = "true";
     };

homes/harmony.nix

@@ -58,28 +58,4 @@
       pinentryPackage = pkgs.pinentry-qt;
     };
   };
-  xdg = {
-    configFile = {
-      "nextflow.config".text = ''
-        params {
-            config_profile_description = 'harmony Asahi Linux local profile'
-            config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
-            config_profile_url         = null
-
-            max_memory = 12.GB
-            max_cpus   = 12
-            max_time   = 7.d
-        }
-
-        apptainer {
-            enabled    = true
-            autoMounts = true
-        }
-
-        process {
-            executor = 'local'
-        }
-      '';
-    };
-  };
 }

programs/zed.nix

@@ -20,7 +20,7 @@
     assistant = {
       default_model = {
         provider = "zed.dev";
-        model = "claude-3-7-sonnet-latest";
+        model = "claude-3-5-sonnet-latest";
       };
       version = "2";
     };