Modernize for GHC 9: DevTools, formatting, CI, and compatibility fixes

- Add Nix flake with DevTools (direnv, treefmt, lefthook)
- Format codebase using treefmt (Ormolu)
- Add GitHub Actions CI workflow with submodule support
- Update all submodules to modernized versions
- Fix random-fu API migration (IORef PureMT -> AtomicGenM PureMT)
- Drop random-source dependency (incompatible with GHC 9)
- Add AllowAmbiguousTypes for GHC 9 type family changes
- Add missing dependencies (random, linear-vect) to cabal file
- Update stack.yaml resolver to lts-22.11

Author: lostbean

.claude/settings.local.json

@@ -0,0 +1,8 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(stack build:*)",
+      "Bash(stack exec:*)"
+    ]
+  }
+}

.envrc

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

.github/workflows/ci.yml

@@ -0,0 +1,21 @@
+name: CI
+on:
+  push:
+    branches: [ master, main ]
+  pull_request:
+    branches: [ master, main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: cachix/install-nix-action@v25
+      with:
+        nix_path: nixpkgs=channel:nixos-unstable
+    - name: Check formatting
+      run: nix fmt -- --check
+    - name: Build
+      run: nix develop --command stack build --system-ghc

.gitignore

@@ -0,0 +1,3 @@
+.direnv
+.stack-work
+dist-newstyle/

VirMat.cabal

@@ -1,89 +1,80 @@
-Name:                VirMat
-Version:             0.4.1
-License:             GPL-3
-License-file:        LICENSE
-Author:              Edgar Gomes de Araujo
-Maintainer:          Edgar Gomes de Araujo <talktoedgar@gmail.com>
-Homepage:
-Stability:           Experimental
-Synopsis:            3D Microstructure Generator
-Description:
-    Creates virtual microstructure in 3 dimesions.
-Cabal-version:       >= 1.8
-Build-type:          Simple
-Category:            Data, Math
+name:          VirMat
+version:       0.4.1
+license:       GPL-3
+license-file:  LICENSE
+author:        Edgar Gomes de Araujo
+maintainer:    Edgar Gomes de Araujo <talktoedgar@gmail.com>
+homepage:
+stability:     Experimental
+synopsis:      3D Microstructure Generator
+description:   Creates virtual microstructure in 3 dimesions.
+cabal-version: >=1.8
+build-type:    Simple
+category:      Data, Math
 
-Flag generator
-    Description:        Build the exectable using command line.
-    Default:            True
+flag generator
+  description: Build the exectable using command line.
+  default:     True
 
-Executable virmatgen
-    hs-source-dirs:     src
-    main-is:            Main.hs
-    ghc-options:        -Wall
-                        -O3
-                        -threaded
-                        -rtsopts
-                        -auto-all
-                        -caf-all
+executable virmatgen
+  hs-source-dirs: src
+  main-is:        Main.hs
+  ghc-options:    -Wall -O3 -threaded -rtsopts -auto-all -caf-all
+  build-depends:
+      base                    >=4    && <5
+    , containers              >=0.5
+    , DeUni                   >=0.3
+    , hammer                  >=0.3
+    , linear-vect             >=0.2
+    , mersenne-random-pure64  >=0.2
+    , mtl                     >=2.1
+    , optparse-applicative    >=0.7
+    , random                  >=1.2
+    , random-fu               >=0.2
+    , sledge                  >=0.3
+    , SubZero                 >=0.1
+    , transformers            >=0.3
+    , unordered-containers    >=0.2
+    , vector                  >=0.10
+    , VirMat
 
-    Build-Depends:      VirMat
-                      , base                   == 4.*
-                      , hammer                 >= 0.3
-                      , sledge                 >= 0.3
-                      , DeUni                  >= 0.3
-                      , containers             >= 0.5
-                      , unordered-containers   >= 0.2
-                      , vector                 >= 0.10
-                      , SubZero                >= 0.1
-                      , mersenne-random-pure64 >= 0.2
-                      , random-source          >= 0.3
-                      , random-fu              >= 0.2
-                      , transformers           >= 0.3
-                      , mtl                    >= 2.1
-                      , optparse-applicative   >= 0.7
-    if flag(generator)
-      Buildable:        True
-    else
-      Buildable:        False
+  if flag(generator)
+    buildable: True
 
-library
-    ghc-options: -Wall
-                 -fwarn-tabs
-                 -funbox-strict-fields
-                 -O2
-    hs-source-dirs:     src
-    Build-Depends:      base                   == 4.*
-                      , hammer                 >= 0.3
-                      , sledge                 >= 0.3
-                      , DeUni                  >= 0.3
-                      , containers             >= 0.5
-                      , unordered-containers   >= 0.2
-                      , vector                 >= 0.10
-                      , SubZero                >= 0.1
-                      , mersenne-random-pure64 >= 0.2
-                      , random-source          >= 0.3
-                      , random-fu              >= 0.2
-                      , transformers           >= 0.3
-                      , mtl                    >= 2.1
-                      , linear-vect            >= 0.2
-
-    Exposed-modules:    VirMat.Run2D
-                        VirMat.Run3D
-                        VirMat.Types
-
-                        VirMat.Core.Packer
-                        VirMat.Core.Sampling
-                        VirMat.Core.VoronoiMicro
-                        VirMat.Core.FlexMicro
+  else
+    buildable: False
 
-                        VirMat.Distributions.GrainSize.GrainDistributionGenerator
-                        VirMat.Distributions.GrainSize.GrainQuery
-                        VirMat.Distributions.Texture.ODFSampling
-
-                        VirMat.IO.Export.ANG.RasterEngine
-                        VirMat.IO.Export.Types
-
-                        VirMat.IO.Import.Types
+library
+  ghc-options:     -Wall -fwarn-tabs -funbox-strict-fields -O2
+  hs-source-dirs:  src
+  build-depends:
+      base                    >=4    && <5
+    , containers              >=0.5
+    , DeUni                   >=0.3
+    , hammer                  >=0.3
+    , linear-vect             >=0.2
+    , mersenne-random-pure64  >=0.2
+    , mtl                     >=2.1
+    , random                  >=1.2
+    , random-fu               >=0.2
+    , sledge                  >=0.3
+    , SubZero                 >=0.1
+    , transformers            >=0.3
+    , unordered-containers    >=0.2
+    , vector                  >=0.10
 
-                        VirMat.PhaseTrans
+  exposed-modules:
+    VirMat.Core.FlexMicro
+    VirMat.Core.Packer
+    VirMat.Core.Sampling
+    VirMat.Core.VoronoiMicro
+    VirMat.Distributions.GrainSize.GrainDistributionGenerator
+    VirMat.Distributions.GrainSize.GrainQuery
+    VirMat.Distributions.Texture.ODFSampling
+    VirMat.IO.Export.ANG.RasterEngine
+    VirMat.IO.Export.Types
+    VirMat.IO.Import.Types
+    VirMat.PhaseTrans
+    VirMat.Run2D
+    VirMat.Run3D
+    VirMat.Types

flake.lock

@@ -0,0 +1,49 @@
+{
+  description = "VirMat - 3D Microstructure Generator";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    flake-utils.url = "github:numtide/flake-utils";
+    treefmt-nix = {
+      url = "github:numtide/treefmt-nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  outputs = { self, nixpkgs, flake-utils, treefmt-nix }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+
+        treefmtWrapper = treefmt-nix.lib.evalModule pkgs ./treefmt.nix;
+
+        haskellStack = pkgs.haskellPackages.ghc;
+
+        hls = pkgs.haskell-language-server;
+
+      in
+      {
+        formatter = treefmtWrapper.config.build.wrapper;
+
+        devShells.default = pkgs.mkShell {
+          buildInputs = [
+            haskellStack
+            pkgs.stack
+            pkgs.cabal-install
+            hls
+            pkgs.pkg-config
+            pkgs.zlib
+            pkgs.clang
+            treefmtWrapper.config.build.wrapper
+            pkgs.nixpkgs-fmt
+            pkgs.lefthook
+          ];
+
+          shellHook = ''
+            echo "VirMat Dev Environment Loaded"
+            echo "GHC version: $(ghc --version)"
+          '';
+        };
+      }
+    );
+}

flake.nix

@@ -0,0 +1,5 @@
+pre-commit:
+  commands:
+    format:
+      glob: "*"
+      run: nix fmt {staged_files} && git add {staged_files}