Merge pull request #26 from dwinkler1/copilot/refactor-package-modules-structure

Refactor R packages into modular structure with alphabetic subdirectories

.github/workflows/check.yml

@@ -4,7 +4,9 @@ on:
   push:
     paths:
       - 'flake.lock'
+      - 'flake.nix'
       - 'versions/*.json'
+      - 'packages/**/*.nix'
       - '.github/workflows/*.yml'
       - 'test/*.R'
 concurrency:

flake.nix

@@ -40,81 +40,7 @@
       extraRPackageDeps = {
         julia-fwildclusterboot = prev.julia-bin.withPackages ["WildBootTests" "StableRNGs"];
       };
-      extraRPackages = let
-        fetchfromGitHubJSONFile = path: prev.fetchFromGitHub (builtins.fromJSON (builtins.readFile path));
-      in {
-        ## F
-        fwildclusterboot =
-          (prev.rPackages.buildRPackage {
-            name = "fwildclusterboot";
-            src = fetchfromGitHubJSONFile ./versions/fwildclusterboot.json;
-            propagatedBuildInputs = builtins.attrValues {
-              inherit
-                (prev.rPackages)
-                collapse
-                dqrng
-                dreamerr
-                Formula
-                generics
-                gtools
-                JuliaConnectoR
-                Matrix
-                Rcpp
-                rlang
-                RcppArmadillo
-                RcppEigen
-               ;
-              inherit (final.extraRPackages) summclust;
-            };
-          }).overrideAttrs (old: {
-            passthru = (old.passthru or {}) // {juliaPackages = ["WildBootTests" "StableRNGs"];};
-          });
-
-        ## H
-        httpgd = prev.rPackages.buildRPackage {
-          name = "httpgd";
-          src = fetchfromGitHubJSONFile ./versions/httpgd.json;
-          propagatedBuildInputs = builtins.attrValues {
-            inherit
-              (prev.rPackages)
-              unigd
-              cpp11
-              AsioHeaders
-              ;
-          };
-        };
-
-        ## M
-        musicMetadata = prev.rPackages.buildRPackage {
-          name = "musicMetadata";
-          src = fetchfromGitHubJSONFile ./versions/musicMetadata.json;
-        };
-
-        ## S
-        summclust = prev.rPackages.buildRPackage {
-          name = "summclust";
-
-          src = fetchfromGitHubJSONFile ./versions/summclust.json;
-
-          propagatedBuildInputs = builtins.attrValues {
-            inherit
-              (prev.rPackages)
-            dreamerr
-            MASS
-            collapse
-            generics
-            cli
-            rlang
-            ;
-          };
-        };
-
-        synthdid = prev.rPackages.buildRPackage {
-          name = "synthdid";
-          src = fetchfromGitHubJSONFile ./versions/synthdid.json;
-          propagatedBuildInputs = [prev.rPackages.mvtnorm];
-        };
-      };
+      extraRPackages = import ./packages {inherit final prev;};
     };
   in {
     # Helper to install R with system dependencies if required

packages/default.nix

@@ -0,0 +1,34 @@
+{
+  final,
+  prev,
+}:
+let
+  # Shared helper function to fetch from GitHub using JSON version files
+  fetchfromGitHubJSONFile = path: prev.fetchFromGitHub (builtins.fromJSON (builtins.readFile path));
+  
+  # Reference to the versions directory at the repo root
+  versionsDir = ../versions;
+  
+  # Common arguments passed to package modules that don't need 'final'
+  baseArgs = {
+    inherit prev fetchfromGitHubJSONFile versionsDir;
+  };
+  
+  # Arguments for packages that need access to 'final' (for cross-package dependencies)
+  argsWithFinal = baseArgs // {
+    inherit final;
+  };
+in {
+  ## F
+  fwildclusterboot = import ./f/fwildclusterboot.nix argsWithFinal;
+  
+  ## H
+  httpgd = import ./h/httpgd.nix baseArgs;
+  
+  ## M
+  musicMetadata = import ./m/musicMetadata.nix baseArgs;
+  
+  ## S
+  summclust = import ./s/summclust.nix baseArgs;
+  synthdid = import ./s/synthdid.nix baseArgs;
+}

packages/f/fwildclusterboot.nix

@@ -0,0 +1,30 @@
+{
+  final,
+  prev,
+  fetchfromGitHubJSONFile,
+  versionsDir,
+}:
+(prev.rPackages.buildRPackage {
+  name = "fwildclusterboot";
+  src = fetchfromGitHubJSONFile "${versionsDir}/fwildclusterboot.json";
+  propagatedBuildInputs = builtins.attrValues {
+    inherit
+      (prev.rPackages)
+      collapse
+      dqrng
+      dreamerr
+      Formula
+      generics
+      gtools
+      JuliaConnectoR
+      Matrix
+      Rcpp
+      rlang
+      RcppArmadillo
+      RcppEigen
+      ;
+    inherit (final.extraRPackages) summclust;
+  };
+}).overrideAttrs (old: {
+  passthru = (old.passthru or {}) // {juliaPackages = ["WildBootTests" "StableRNGs"];};
+})

packages/h/httpgd.nix

@@ -0,0 +1,17 @@
+{
+  prev,
+  fetchfromGitHubJSONFile,
+  versionsDir,
+}:
+prev.rPackages.buildRPackage {
+  name = "httpgd";
+  src = fetchfromGitHubJSONFile "${versionsDir}/httpgd.json";
+  propagatedBuildInputs = builtins.attrValues {
+    inherit
+      (prev.rPackages)
+      unigd
+      cpp11
+      AsioHeaders
+      ;
+  };
+}

packages/m/musicMetadata.nix

@@ -0,0 +1,9 @@
+{
+  prev,
+  fetchfromGitHubJSONFile,
+  versionsDir,
+}:
+prev.rPackages.buildRPackage {
+  name = "musicMetadata";
+  src = fetchfromGitHubJSONFile "${versionsDir}/musicMetadata.json";
+}

packages/s/summclust.nix

@@ -0,0 +1,20 @@
+{
+  prev,
+  fetchfromGitHubJSONFile,
+  versionsDir,
+}:
+prev.rPackages.buildRPackage {
+  name = "summclust";
+  src = fetchfromGitHubJSONFile "${versionsDir}/summclust.json";
+  propagatedBuildInputs = builtins.attrValues {
+    inherit
+      (prev.rPackages)
+      dreamerr
+      MASS
+      collapse
+      generics
+      cli
+      rlang
+      ;
+  };
+}

packages/s/synthdid.nix

@@ -0,0 +1,10 @@
+{
+  prev,
+  fetchfromGitHubJSONFile,
+  versionsDir,
+}:
+prev.rPackages.buildRPackage {
+  name = "synthdid";
+  src = fetchfromGitHubJSONFile "${versionsDir}/synthdid.json";
+  propagatedBuildInputs = [prev.rPackages.mvtnorm];
+}