Add nix flake for fixed dev env

Author: patrickCNMartin

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/306332649.svg)](https://zenodo.org/badge/latestdoi/306332649)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15733817.svg)](https://doi.org/10.5281/zenodo.15733817)
 
-![R-CMD-check](https://github.com/WonLab-CS/Vesalius/actions/workflows/R-CMD-check.yml/badge.svg?branch=main)
+![R-CMD-check](https://github.com/WonLab-CS/Vesalius/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)
 
 # Vesalius
 

flake.nix

@@ -0,0 +1,78 @@
+{
+  description = "Vesalius Development Shell";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.05";
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+
+        rpkgs = builtins.attrValues {
+          inherit (pkgs.rPackages)
+              deldir
+              sp
+              tvR
+              Matrix
+              RColorBrewer
+              future
+              future_apply
+              imagerExtra
+              Signac
+              ggpubr
+              lmtest
+              infix
+              Seurat
+              SeuratObject
+              imager
+              DESeq2
+              RANN
+              dplyr
+              edgeR
+              ggplot2
+              igraph
+              pwr
+              purrr
+              patchwork
+              ggnewscale
+              kohonen
+              Rcpp
+              RcppEigen
+              TreeDist
+              devtools
+              tidyr;
+        };
+
+        
+        
+        system_packages = builtins.attrValues {
+          inherit (pkgs)
+            glibcLocales
+            nix
+            R
+            pandoc
+            which;
+        };
+      in
+      {
+        devShells.default = pkgs.mkShell {
+        LOCALE_ARCHIVE = if pkgs.stdenv.hostPlatform.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
+        LANG = "en_US.UTF-8";
+        LC_ALL = "en_US.UTF-8";
+        LC_TIME = "en_US.UTF-8";
+        LC_MONETARY = "en_US.UTF-8";
+        LC_PAPER = "en_US.UTF-8";
+        LC_MEASUREMENT = "en_US.UTF-8";
+
+        buildInputs = rpkgs ++ system_packages;
+        shellHook = ''
+            echo "Vesalius Shell activated"
+
+           '';
+        };
+      }
+    );
+}