Source-level packaging using a Nix flake

Enables running a defined version of KGD from the Nix store, which required
a recent version of Rcpp with this bugfix:
RcppCore/Rcpp#1346

For example usage see gbs_prism eri-dev branch.

Author: Simon Guest

.envrc

@@ -0,0 +1 @@
+use flake

.gitignore

@@ -1 +1,2 @@
 *.$$$
+/.direnv/

flake.lock

@@ -0,0 +1,111 @@
+{
+  description = "Naive Nix packaging for KGD";
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05";
+
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  # KGD is not a first-class R package, merely a collection of R source files
+  # to be source'd into the caller's environment.
+  #
+  # The Nix package enables these R sources to be used directly from the Nix store.
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem
+      (system:
+        let
+          pkgs = import nixpkgs {
+            inherit system;
+          };
+
+          # we need a recent Rcpp with this fix:
+          # https://github.com/RcppCore/Rcpp/pull/1346
+          recent-Rcpp = pkgs.rPackages.buildRPackage {
+            name = "Rcpp";
+
+            version = "1.0.13.6";
+
+            src = pkgs.fetchFromGitHub {
+              owner = "RcppCore";
+              repo = "Rcpp";
+              rev = "83e640b55aeaeba8a746d0da6152cabe8af41154";
+              hash = "sha256-x0s9BRIAxxZmNFXRYwtpmT5asD4+mhIUTqwYsaPOgi4=";
+            };
+          };
+
+          # TODO: it should be possible to simply override the Rcpp dependency for RcppArmadillo in nixpkgs,
+          # but I didn't work out how to do that
+          RcppArmadillo-with-recent-Rcpp = pkgs.rPackages.buildRPackage {
+            name = "RcppArmadillo";
+
+            version = "0.12.8.1.0";
+
+            src = pkgs.fetchFromGitHub {
+              owner = "RcppCore";
+              repo = "RcppArmadillo";
+              rev = "8abe7be9fc4dd7c1d2b02ed200707232d6fd1f09"; # 0.12.8.1.0
+              hash = "sha256-+Li4ln/4ZyBY+I8S8X4uSmFaG1D3q5UJOJJB5pLRubo=";
+            };
+
+            propagatedBuildInputs = [ recent-Rcpp ];
+          };
+
+
+          KDG-R = pkgs.rWrapper.override
+            {
+              packages = with pkgs.rPackages; [
+                RcppArmadillo-with-recent-Rcpp
+                data_table
+                R_utils
+                plotly
+                heatmaply
+                parallelDist
+                MethComp
+                MASS
+              ];
+            };
+
+          KDG-src = pkgs.stdenv.mkDerivation {
+            pname = "KDG-src";
+            version = "1.2.2";
+
+            src = ./.;
+
+            buildInputs = [ KDG-R ];
+
+            propagatedBuildInputs = [ KDG-R ];
+
+            nativeBuildInputs = [ pkgs.dos2unix ];
+
+            installPhase = ''
+              mkdir $out
+              runHook preInstall
+              cp GBS-Chip-Gmatrix.R GBSPedAssign.R GBS-PopGen.R GBSRun.R GBS-Rcpp-functions.cpp $out
+              chmod 755 $out/GBSRun.R
+              dos2unix $out/*
+              runHook postInstall
+            '';
+
+            postFixup = ''
+              substituteInPlace $out/GBSRun.R --replace '<source directory>' $out
+            '';
+          };
+        in
+        {
+          devShells.default = pkgs.mkShell {
+            buildInputs = [ KDG-R ];
+
+            shellHook = ''
+              mkdir -p "$(pwd)/_libs"
+              export R_LIBS_USER="$(pwd)/_libs"
+            
+              export NIX_CFLAGS_COMPILE=" -isystem ${pkgs.rPackages.RcppArmadillo}/library/RcppArmadillo/include -isystem ${pkgs.rPackages.Rcpp}/library/Rcpp/include -isystem ${pkgs.R}/lib/R/include " 
+            '';
+          };
+
+          packages = {
+            src = KDG-src;
+          };
+        });
+}