Merge branch 'master' of https://github.com/ISCAM4/ISCAM

Author: VisruthSK

.Rbuildignore

@@ -12,4 +12,6 @@
 ^air\.toml$
 ^flake\.lock$
 ^flake\.nix$
-^dev$
+^dev$
+^\.direnv$
+^\.envrc$

.gitignore

@@ -2,7 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
-
-.direnv/*
-result
-result-*
+.direnv/

README.md

@@ -29,12 +29,6 @@ You can load the workspace by running
 load(url("http://www.rossmanchance.com/iscam4/ISCAM.RData"))
 ```
 
-or 
-
-```r
-load(url("https://iscam4.github.io/ISCAM/ISCAM.RData"))
-```
-
 <!-- 
 TODO:
 - Create vignette

flake.lock

@@ -1,51 +1,232 @@
 {
-  description = "Minimal reproducible R dev environment (no workspace save, no history)";
+  description = "Opiniated Flake for Developing R Software--for ISCAM";
 
   inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable"; # Unstable to get the latest version of R + packages. Pretty safe.
     flake-utils.url = "github:numtide/flake-utils";
+    nix-vscode-extensions = {
+      url = "github:nix-community/nix-vscode-extensions";
+      inputs.nixpkgs.follows = "nixpkgs";
+      inputs.flake-utils.follows = "flake-utils";
+    };
   };
 
   outputs =
     {
       self,
       nixpkgs,
       flake-utils,
+      nix-vscode-extensions,
     }:
-    flake-utils.lib.eachDefaultSystem (
+    flake-utils.lib.eachSystem [ "x86_64-linux" ] (
       system:
       let
-        pkgs = import nixpkgs { inherit system; };
-        Rnosave = pkgs.writeShellScriptBin "R" (
-          let
-            r = pkgs.rWrapper.override {
-              packages = with pkgs.rPackages; [
-                devtools
-                roxygen2
-                testthat
-                usethis
-                pkgdown
-                languageserver
-              ];
+        pkgs = import nixpkgs {
+          inherit system;
+          config.allowUnfree = true;
+          overlays = [ nix-vscode-extensions.overlays.default ];
+        };
+
+        # List the packages you wish to have installed instead of installing packages interactively
+        # Useful links:
+        # https://search.nixos.org/packages?channel=unstable&from=0&size=50&sort=relevance&type=packages&query=rPackages.
+        # https://nixos.wiki/wiki/R#Install_an_R-package_from_GitHub
+        rPkgs = with pkgs.rPackages; [
+          # ! NOTE: ADD YOUR R PACKAGES HERE
+          devtools
+          roxygen2
+          testthat
+          usethis
+          pkgdown
+          languageserver
+          lintr
+          withr
+        ];
+
+        rWithPkgs = pkgs.rWrapper.override {
+          packages = rPkgs;
+        };
+
+        # Minimal open-vsx extensions
+        # Note that positron-bin will probably lag behind stable release, so extensions which target the latest version of code-oss may not work.
+        # e.g. on 20250817, vscode-pull-request-github-116.1 reports that it "is not compatible with Code 1.102.0. Extension requires: ^1.103.0."
+        # https://nix-community.github.io/nix4vscode/
+        extensions = with pkgs.open-vsx; [
+          # Default Positron extensions
+          github.vscode-pull-request-github
+          posit.air-vscode
+          quarto.quarto
+
+          # ! NOTE: ADD YOUR OPEN-VSX EXTENSIONS HERE
+          eamodio.gitlens
+          usernamehw.errorlens
+          edwinhuish.better-comments-next
+          tomoki1207.pdf
+          tombi-toml.tombi
+          oderwat.indent-rainbow
+          robole.marky-stats
+
+          # Catppuccin theme extensions
+          catppuccin.catppuccin-vsc
+          catppuccin.catppuccin-vsc-icons
+        ];
+
+        # Declerative Positron settings.json
+        # Clear settings by running: $ rm ~/.config/Positron/User/settings.json
+        settingsJson = pkgs.writeText "settings.json" (
+          builtins.toJSON {
+            "workbench.keybindings.rstudioKeybindings" = true;
+            "workbench.colorTheme" = "Catppuccin Mocha";
+            "workbench.iconTheme" = "catppuccin-mocha";
+            "workbench.list.smoothScrolling" = true;
+
+            "catppuccin.accentColor" = "pink";
+
+            "catppuccin.colorOverrides" = {
+              "mocha" = {
+                "base" = "#000000";
+                "mantle" = "#010101";
+                "crust" = "#020202";
+              };
             };
-          in
-          ''
-            exec ${r}/bin/R --no-save --no-restore-data --no-restore-history "$@"
-          ''
+
+            "catppuccin.customUIColors" = {
+              "mocha" = {
+                "statusBar.foreground" = "accent";
+              };
+            };
+
+            "git.autofetch" = true;
+            "git.confirmSync" = false;
+
+            "editor.formatOnSave" = true;
+            "editor.fontFamily" = "JetBrainsMono Nerd Font";
+            "editor.fontLigatures" = true;
+            "editor.semanticHighlighting.enabled" = true;
+            "editor.pasteAs.preferences" = [
+              "typst.link"
+              "markdown.link"
+            ];
+
+            "terminal.integrated.fontFamily" = "IosevkaTerm Nerd Font";
+
+            "positron.plots.darkFilter" = "off";
+
+            "[r]" = {
+              "editor.formatOnSave" = true;
+              "editor.defaultFormatter" = "Posit.air-vscode";
+            };
+            "[quarto]" = {
+              "editor.formatOnSave" = true;
+              "editor.defaultFormatter" = "quarto.quarto";
+            };
+          }
         );
+
+        # Symlink farm of extensions (read-only source)
+        extensionsRO = pkgs.buildEnv {
+          name = "positron-extensions";
+          paths = extensions;
+          pathsToLink = [ "/share/vscode/extensions" ];
+        };
+
+        # FHS environment for Positron
+        positronFHS = pkgs.buildFHSEnv {
+          name = "positron-fhs";
+          targetPkgs =
+            pkgs: with pkgs; [
+              # Core Positron and R
+              positron-bin
+              R
+              air-formatter
+
+              # Patched fonts
+              nerd-fonts.iosevka-term
+              nerd-fonts.jetbrains-mono
+
+              # Basic system libraries for dynamic linking
+              glibc
+              gcc-unwrapped.lib
+              stdenv.cc.cc.lib
+              zlib
+              git
+              gcc
+              gfortran
+              pkg-config
+            ];
+
+          runScript = pkgs.writeScript "positron-run" ''
+            #!/bin/bash
+            set -euo pipefail
+
+            EXT_BASE="''${XDG_CACHE_HOME:-$HOME/.cache}"
+            EXT_DST="$EXT_BASE/positron/extensions"
+            SRC="${extensionsRO}/share/vscode/extensions"
+
+            CONFIG_BASE="''${XDG_CONFIG_HOME:-$HOME/.config}"
+            APP_ID="Positron"
+            SETTINGS_DIR="$CONFIG_BASE/$APP_ID/User"
+            SETTINGS_FILE="$SETTINGS_DIR/settings.json"
+
+            mkdir -p "$EXT_DST" "$SETTINGS_DIR"
+
+            # rm ~/.config/Positron/User/settings.json
+            # Copy settings.json if it doesn't exist
+            [ ! -f "$SETTINGS_FILE" ] && cp "${settingsJson}" "$SETTINGS_FILE"
+
+            # Sync extensions (copy if not exists)
+            for s in "$SRC"/*; do
+              [ -d "$s" ] || continue
+              bn="$(basename "$s")"
+              [ -d "$EXT_DST/$bn" ] || cp -r "$s" "$EXT_DST/$bn"
+            done
+
+            # Set up environment
+            export R_HOME='${pkgs.R}/lib/R'
+            export R_LIBS_USER='${rWithPkgs}/lib/R/library'
+            export PATH="${pkgs.R}/bin:${rWithPkgs}/bin:${pkgs.air-formatter}/bin:$PATH"
+
+            # Run Positron
+            exec positron --extensions-dir "$EXT_DST" "$@"
+          '';
+        };
+
+        positronWrapper = pkgs.writeShellScriptBin "positron-with-extensions" ''
+          exec ${positronFHS}/bin/positron-fhs "$@"
+        '';
+
+        rstudioWrapper = pkgs.writeShellScriptBin "rstudio-with-r" ''
+          export R_HOME='${pkgs.R}/lib/R'
+          export R_LIBS_USER='${rWithPkgs}/lib/R/library'
+          export PATH="${pkgs.R}/bin:${rWithPkgs}/bin:${pkgs.air-formatter}/bin:$PATH"
+          exec ${pkgs.rstudio}/bin/rstudio "$@"
+        '';
       in
       {
+        packages.positron = positronWrapper;
+        packages.rstudio = rstudioWrapper;
+
+        apps.positron = {
+          type = "app";
+          program = "${positronWrapper}/bin/positron-with-extensions";
+          meta = {
+            description = "Positron IDE with R environment and extensions";
+            platforms = [ "x86_64-linux" ];
+          };
+        };
+
+        apps.rstudio = {
+          type = "app";
+          program = "${rstudioWrapper}/bin/rstudio-with-r";
+          meta = {
+            description = "RStudio IDE with R environment";
+            platforms = [ "x86_64-linux" ];
+          };
+        };
+
         devShells.default = pkgs.mkShell {
-          packages = [
-            Rnosave
-            pkgs.gcc
-            pkgs.gfortran
-            pkgs.pkg-config
-          ];
           shellHook = ''
-            export R_LIBS_USER="$PWD/.Rlibs"
-            mkdir -p "$R_LIBS_USER"
-            export R_HISTFILE=/dev/null
+            echo "Use: nix run .#positron or nix run .#rstudio"
           '';
         };
       }