Working template

templates/n/flake.lock

@@ -6,7 +6,6 @@
         "nixpkgs": [
           "nixpkgs"
         ],
-        "nixpkgs-unstable": "nixpkgs-unstable",
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
         "plugins-cmp-r": "plugins-cmp-r",
         "plugins-r": "plugins-r",
@@ -15,11 +14,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1756305715,
+        "lastModified": 1756379633,
-        "narHash": "sha256-GuNro+bHHMde1X2uoaDS0UwJa1aaVTDvG4KmQOmCAWE=",
+        "narHash": "sha256-REv+GIfWkyCIHfcPzotqpaSHha0LPZ300KsJL+9kP40=",
         "owner": "dwinkler1",
         "repo": "nixCatsConfig",
-        "rev": "e0f5193d7299c36724d17728511260e0d453f0dc",
+        "rev": "e39a1272ef82cd467fb0c29d0b8a0ccdca672f67",
         "type": "github"
       },
       "original": {
@@ -45,27 +44,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1756159630,
+        "lastModified": 1756288264,
-        "narHash": "sha256-ohMvsjtSVdT/bruXf5ClBh8ZYXRmD4krmjKrXhEvwMg=",
+        "narHash": "sha256-Om8adB1lfkU7D33VpR+/haZ2gI5r3Q+ZbIPzE5sYnwE=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "84c256e42600cb0fdf25763b48d28df2f25a0c8b",
+        "rev": "ddd1826f294a0ee5fdc198ab72c8306a0ea73aa9",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nixos",
-        "ref": "nixpkgs-unstable",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
-    "nixpkgs-unstable": {
-      "locked": {
-        "lastModified": 1756159630,
-        "narHash": "sha256-ohMvsjtSVdT/bruXf5ClBh8ZYXRmD4krmjKrXhEvwMg=",
-        "owner": "nixos",
-        "repo": "nixpkgs",
-        "rev": "84c256e42600cb0fdf25763b48d28df2f25a0c8b",
         "type": "github"
       },
       "original": {

templates/n/flake.nix

@@ -3,10 +3,12 @@
   inputs = {
     rixpkgs.url = "https://github.com/rstats-on-nix/nixpkgs/archive/2025-08-11.tar.gz";
     nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable";
-    nixCats.url = "github:dwinkler1/nixCatsConfig";
+    nixCats = {
-    nixCats.inputs.nixpkgs.follows = "nixpkgs";
+      url = "github:dwinkler1/nixCatsConfig";
-    nixCats.inputs.rixpkgs.follows = "rixpkgs";
+      inputs.nixpkgs.follows = "nixpkgs";
-    ## All git packages managed per project
+      inputs.rixpkgs.follows = "rixpkgs";
+    };
+    ## Git Plugins
     "plugins-r" = {
       url = "github:R-nvim/R.nvim";
       flake = false;
@@ -26,38 +28,35 @@
     nixCats,
     ...
   } @ inputs: let
-    forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all;
+    #######################
+    ### PROJECT CONFIG ####
+    #######################
+    ## Set options below:
+    config = rec {
+      ## Set project name
       defaultPackageName = "p";
-    projectConfig = forSystems (
+      ## Enable languages
-      system: let
+      enabledLanguages = {
-        inherit (nixCats) utils;
+        julia = false;
-        inherit defaultPackageName;
+        python = false;
-        prevPackage = nixCats.packages.${system}.default;
+        r = false;
-        finalPackage = prevPackage.override (prev: {
+      };
-          name = defaultPackageName;
+      ## Enable packages
-          dependencyOverlays =
+      enabledPackages = {
-            prev.dependencyOverlays
+        ## Plugins loaded via flake input
-            ++ [
+        ### Always enable when R is enabled
-              (utils.standardPluginOverlay inputs)
+        ### You can use your own R installation and just enable the plugin
-              ## Pull in local rix copy
+        gitPlugins = enabledLanguages.r;
-              (final: prev: {
+      };
-                rpkgs = inputs.rixpkgs.legacyPackages.${prev.system};
+    };
-              })
+    # R packages
-              ## Define project level R packages
+    rixOverlay = final: prev: {rpkgs = inputs.rixpkgs.legacyPackages.${prev.system};};
-              (
+    rOverlay = final: prev: let
-                final: prev: let
+      reqPkgs = with final.rpkgs.rPackages; [
-                  reqPkgs = with prev.rpkgs.rPackages; [
-                    Hmisc
-                    Rcpp
-                    arm
         broom
-                    car
         data_table
-                    devtools
         janitor
-                    konfound
         languageserver
-                    quarto
         reprex
         styler
         tidyverse
@@ -74,25 +73,176 @@
         })
       ];
     in {
-                  quarto = prev.rpkgs.quarto.override {extraRPackages = reqPkgs;};
+      quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;};
-                  rWrapper = prev.rpkgs.rWrapper.override {packages = reqPkgs;};
+      rWrapper = final.rpkgs.rWrapper.override {packages = reqPkgs;};
-                }
+    };
+
+    # Python packages
+    pythonOverlay = final: prev: {
+      python = prev.python3.withPackages (pyPackages:
+        with pyPackages; [
+          requests
+        ]);
+    };
+
+    ###################################
+    ## ⬆️ BASIC CONFIG ABOVE HERE ⬆️ ##
+    ###################################
+
+    projectScriptsOverlay = final: prev: let
+      initPython = ''
+        #!/usr/bin/env bash
+        set -euo pipefail
+        if [[ ! -f "pyproject.toml" ]]; then
+          echo "🐍 Initializing UV project..."
+          uv init
+          echo "📦 Adding ipython and marimo..."
+          uv add ipython
+          uv add marimo
+          echo "--------------------------------------------------------------------------"
+          echo "✅ Python project initialized!"
+          echo "--------------------------------------------------------------------------"
+        else
+          echo "--------------------------------------------------------------------------"
+          echo "🔄 Existing Python project detected."
+          echo "Run '${config.defaultPackageName}-updateDeps' to update dependencies."
+          echo "--------------------------------------------------------------------------"
+        fi
+      '';
+
+      mkDirsScript = ''
+        #!/usr/bin/env bash
+        set -euo pipefail
+
+        PROJECT_NAME="''${1:-${config.defaultPackageName}}"
+
+        echo "🚀 Setting up project: $PROJECT_NAME"
+
+        # Create directory structure
+        directories=(
+          "data/raw"
+          "data/processed"
+          "data/interim"
+          "docs"
+          "figures"
+          "tables"
+          "src/analysis"
+          "src/data_prep"
+          "src/explore"
+          "src/utils"
         )
 
-              ## Define project level Python Packages
+        for dir in "''${directories[@]}"; do
-              ## Only use if uv should not be used
+          mkdir -p "$dir"
-              (
+          echo "✓ Created $dir/"
-                final: prev: let
+        done
-                  reqPkgs = pyPackages:
+
-                    with pyPackages; [
+        # Create essential files
-                      numpy
+        if [[ ! -f "README.md" ]]; then
-                      polars
+          cat > README.md << 'EOF'
-                      requests
+        # $PROJECT_NAME
-                    ];
+
+        ## Project Structure
+        - `data/`: Data files (gitignored)
+        - `docs/`: Documentation
+        - `figures/`: Output figures
+        - `tables/`: Output tables
+        - `src/`: Source code
+
+        ## Usage
+        - Julia environment: `$PROJECT_NAME-jl`
+        - Python environment: `$PROJECT_NAME-m` (Marimo)
+        - R environment: `$PROJECT_NAME-r`
+        - Neovide: `$PROJECT_NAME-g`
+        - Neovim: `$PROJECT_NAME`
+        - Update: `$PROJECT_NAME-updateDeps`
+        EOF
+        fi
+
+        # Create .gitignore
+        if [[ ! -f ".gitignore" ]]; then
+          cat > .gitignore << 'EOF'
+        # Data files
+        data/
+        *.csv
+        *.docx
+        *.xlsx
+        *.parquet
+
+        # R specific
+        .Rproj.user/
+        .Rhistory
+        .RData
+        .Ruserdata
+        *.Rproj
+        .Rlibs/
+
+        # Python specific
+        __pycache__/
+        *.pyc
+        .pytest_cache/
+        .venv/
+
+        # Jupyter
+        .ipynb_checkpoints/
+
+        # IDE
+        .vscode/
+        .idea/
+
+        # OS
+        .DS_Store
+        Thumbs.db
+        EOF
+        fi
+
+        echo "✅ Project setup completed successfully!"
+      '';
+
+      updateDepsScript = ''
+        #!/usr/bin/env bash
+        set -euo pipefail
+
+        echo "🔄 Updating project dependencies..."
+
+        if [[ -f "flake.lock" ]]; then
+          nix flake update
+          echo "✅ Flake inputs updated"
+        fi
+
+        if [[ -f "pyproject.toml" ]]; then
+          uv sync --upgrade
+          echo "✅ Python dependencies updated"
+        fi
+
+        if [[ -f "Project.toml" ]]; then
+          ${config.defaultPackageName}-jl -e "using Pkg; Pkg.update()"
+          echo "✅ Julia dependencies updated"
+        fi
+
+        echo "🎉 All dependencies updated!"
+      '';
     in {
-                  python = prev.python3.withPackages reqPkgs;
+      initPython = prev.writeShellScriptBin "initPython" initPython;
-                }
+      mkDirs = prev.writeShellScriptBin "mkDirs" mkDirsScript;
-              )
+      updateDeps = prev.writeShellScriptBin "updateDeps" updateDepsScript;
+    };
+    forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all;
+    projectConfig = forSystems (
+      system: let
+        inherit (nixCats) utils;
+        inherit (config) defaultPackageName;
+        prevPackage = nixCats.packages.${system}.default;
+        finalPackage = prevPackage.override (prev: {
+          name = config.defaultPackageName;
+          dependencyOverlays =
+            prev.dependencyOverlays
+            ++ [
+              (utils.standardPluginOverlay inputs)
+              rixOverlay
+              rOverlay
+              pythonOverlay
+              projectScriptsOverlay
             ];
           categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
             {
@@ -198,7 +348,7 @@
           packageDefinitions =
             prev.packageDefinitions
             // {
-              "${defaultPackageName}" = utils.mergeCatDefs prev.packageDefinitions.n (
+              p = utils.mergeCatDefs prev.packageDefinitions.n (
                 {
                   pkgs,
                   name,
@@ -221,74 +371,64 @@
                         };
                       };
                       m = let
-                        preHookInit = ''
+                        marimoInit = ''
-                          # Check if pyproject.toml exists
+                          set -euo pipefail
-                          if [ ! -f "pyproject.toml" ]; then
+                          echo "🔄 Syncing existing project..."
-                              echo "pyproject.toml not found. Initializing new UV project..."
-
-                              # Initialize UV project
-                              uv init
-
-                              # Check if uv init was successful
-                              if [ $? -eq 0 ]; then
-                                  echo "UV project initialized successfully."
-
-                                  # Add marimo dependency
-                                  echo "Adding marimo dependency..."
-                                  uv add marimo
-
-                                  if [ $? -eq 0 ]; then
-                                      echo "Marimo added successfully!"
-                                  else
-                                      echo "Error: Failed to add marimo dependency."
-                                      exit 1
-                                  fi
-                              else
-                                  echo "Error: Failed to initialize UV project."
-                                  exit 1
-                              fi
-                          else
-                              echo "pyproject.toml already exists. Syncing...."
                           uv sync
-                          fi
                         '';
                       in {
-                        enable = true;
+                        enable = config.enabledLanguages.python;
                         path = {
                           value = "${pkgs.uv}/bin/uv";
                           args = [
                             "--run"
-                            "${preHookInit}"
+                            "${marimoInit}"
                             "--add-flags"
-                            "run marimo edit"
+                            "run marimo edit \"$@\""
                           ];
                         };
                       };
                       jl = {
-                        enable = false;
+                        enable = config.enabledLanguages.julia;
                         path = {
                           value = "${pkgs.julia-bin}/bin/julia";
-                          args = ["--add-flags" "--project=@."];
+                          args = ["--add-flags" "--project=."];
                         };
                       };
                       r = {
-                        enable = true;
+                        enable = config.enabledLanguages.r;
                         path = {
                           value = "${pkgs.rWrapper}/bin/R";
                           args = ["--add-flags" "--no-save --no-restore"];
                         };
                       };
+                      initPython = {
+                        enable = config.enabledLanguages.python;
+                        path.value = "${pkgs.initPython}/bin/initPython";
+                      };
+                      mkDirs = {
+                        enable = true;
+                        path = {
+                          value = "${pkgs.mkDirs}/bin/mkDirs";
+                        };
+                      };
+                      updateDeps = {
+                        enable = true;
+                        path = {
+                          value = "${pkgs.updateDeps}/bin/updateDeps";
+                        };
+                      };
                       node.enable = true;
                       perl.enable = true;
                       ruby.enable = true;
                     };
                   };
                   categories = {
-                    julia = false;
+                    julia = config.enabledLanguages.julia;
-                    python = false;
+                    python = config.enabledLanguages.python;
-                    r = true;
+                    r = config.enabledLanguages.r;
                     project = true;
-                    gitPlugins = true;
+                    gitPlugins = config.enabledPackages.gitPlugins;
                   };
                 }
               );
@@ -302,11 +442,33 @@
     devShells = forSystems (system: let
       pkgs = import nixpkgs {inherit system;};
     in {
-      default = pkgs.mkShell {
+      default = let
-        name = defaultPackageName;
+        shellCmds = pkgs.lib.concatLines (pkgs.lib.filter (cmd: cmd != "") [
+          (pkgs.lib.optionalString config.enabledLanguages.r "  - ${config.defaultPackageName}-r: Launch R console")
+          (pkgs.lib.optionalString config.enabledLanguages.julia "  - ${config.defaultPackageName}-jl: Launch Julia REPL")
+          (pkgs.lib.optionalString config.enabledLanguages.python "  - ${config.defaultPackageName}-m: Launch Marimo notebook")
+          "See options in flake.nix"
+        ]);
+      in
+        pkgs.mkShell {
+          name = config.defaultPackageName;
           packages = [projectConfig.${system}.default];
           inputsFrom = [];
           shellHook = ''
+            echo ""
+            ${pkgs.lib.optionalString config.enabledLanguages.python "${config.defaultPackageName}-initPython"}
+            echo "=========================================================================="
+            echo "🎯  ${config.defaultPackageName} Development Environment"
+            echo "---"
+            echo "📝  Run '${config.defaultPackageName}-mkDirs' to set up project structure"
+            echo "🔄  Run '${config.defaultPackageName}-updateDeps' to update all dependencies"
+            echo "---"
+            echo "🚀  Available commands:"
+            echo "  - ${config.defaultPackageName}: Launch Neovim"
+            echo "  - ${config.defaultPackageName}-g: Launch Neovide"
+            echo "${shellCmds}"
+            echo "=========================================================================="
+            echo ""
           '';
         };
     });