From 0443b97a68875f31992091a1e8607b2a6e100535 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Sat, 26 Apr 2025 21:42:59 +0100
Subject: [PATCH 01/38] Created a nix development to try

---
 .envrc         |  1 +
 CMakeLists.txt |  4 ++--
 flake.lock     | 25 +++++++++++++++++++++++++
 flake.nix      | 45 +++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 73 insertions(+), 2 deletions(-)
 create mode 100644 .envrc
 create mode 100644 flake.lock
 create mode 100644 flake.nix

diff --git a/.envrc b/.envrc
new file mode 100644
index 000000000..3550a30f2
--- /dev/null
+++ b/.envrc
@@ -0,0 +1 @@
+use flake
diff --git a/CMakeLists.txt b/CMakeLists.txt
index d8f491c16..6d3223b46 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,7 +4,7 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
   cmake_policy(SET CMP0167 NEW) #  Use the new boost configuration
 endif()
 
-set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
+#set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
 
 project(DynamO) #Project name
 enable_testing() #Enable build of test executables and 'make test' command
@@ -96,7 +96,7 @@ endif()
 ######### Dependencies
 ######################################################################
 
-set(Boost_USE_STATIC_LIBS ON)
+#set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(Boost 1.70.0 REQUIRED system filesystem program_options unit_test_framework)
diff --git a/flake.lock b/flake.lock
new file mode 100644
index 000000000..1d0fc8626
--- /dev/null
+++ b/flake.lock
@@ -0,0 +1,25 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1739736696,
+        "narHash": "sha256-zON2GNBkzsIyALlOCFiEBcIjI4w38GYOb+P+R4S8Jsw=",
+        "rev": "d74a2335ac9c133d6bbec9fc98d91a77f1604c1f",
+        "revCount": 754461,
+        "type": "tarball",
+        "url": "https://api.flakehub.com/f/pinned/NixOS/nixpkgs/0.1.754461%2Brev-d74a2335ac9c133d6bbec9fc98d91a77f1604c1f/01951426-5a87-7b75-8413-1a0d9ec5ff04/source.tar.gz"
+      },
+      "original": {
+        "type": "tarball",
+        "url": "https://flakehub.com/f/NixOS/nixpkgs/0.1.%2A.tar.gz"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/flake.nix b/flake.nix
new file mode 100644
index 000000000..6908895d6
--- /dev/null
+++ b/flake.nix
@@ -0,0 +1,45 @@
+{
+  description = "A Nix-flake-based C/C++ development environment";
+
+  inputs.nixpkgs.url = "https://flakehub.com/f/NixOS/nixpkgs/0.1.*.tar.gz";
+
+  outputs = { self, nixpkgs }:
+    let
+      supportedSystems = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
+      forEachSupportedSystem = f: nixpkgs.lib.genAttrs supportedSystems (system: f {
+        pkgs = import nixpkgs { inherit system; };
+      });
+      extraOutputsToInstall = [ "dev" ];
+    in
+    {
+      devShells = forEachSupportedSystem ({ pkgs }: {
+        default = pkgs.mkShell.override
+          {
+            # Override stdenv in order to change compiler:
+            #stdenv = pkgs.clangStdenv;
+          }
+          {
+            packages = with pkgs; [
+              clang
+              clang-tools
+              cmake
+              ninja
+              doxygen
+              vcpkg
+              vcpkg-tool
+              boost.dev
+              eigen
+              bzip2.dev
+              python3
+              gtkmm3.dev
+              ffmpeg.dev
+              freeglut
+              glew
+              cairomm
+              pkg-config
+            ] ++ (if system == "aarch64-darwin" then [ ] else [ gdb ]);
+          };
+      });
+    };
+}
+

From cec7b5a0e3552cb524c140d03d9fbea4a6472304 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 28 Apr 2025 22:21:12 +0100
Subject: [PATCH 02/38] Enabled VScode build on nix for now

---
 CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6d3223b46..de7f0a9f2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,7 +4,8 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
   cmake_policy(SET CMP0167 NEW) #  Use the new boost configuration
 endif()
 
-#set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
+set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
+set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
 
 project(DynamO) #Project name
 enable_testing() #Enable build of test executables and 'make test' command

From e692969ccb91d301fb0e0d57acf4d612deb7aa1a Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 29 Apr 2025 05:56:37 +0100
Subject: [PATCH 03/38] A fix for MSVC

---
 CMakeLists.txt | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index de7f0a9f2..1b933c98d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,7 +4,12 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
   cmake_policy(SET CMP0167 NEW) #  Use the new boost configuration
 endif()
 
-set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
+
+if(NOT MSVC)
+  # To make this compile on NixOS, we need to use the static linked MSVC
+  # But this is not available on windows
+  set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
+endif()
 set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
 
 project(DynamO) #Project name

From 902d325a6e6c7cab51da371bfbbdf8f0dceda7ef Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 29 Apr 2025 06:18:40 +0100
Subject: [PATCH 04/38] Another fix for MSVC

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1b933c98d..5ab6e7f51 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -102,7 +102,7 @@ endif()
 ######### Dependencies
 ######################################################################
 
-#set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(Boost 1.70.0 REQUIRED system filesystem program_options unit_test_framework)

From 2aa1feca7217dff13d95263a3b56c158d76cd41c Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 12 May 2025 11:54:04 +0100
Subject: [PATCH 05/38] Removed vcpkg as we move to nix

---
 .gitmodules    |  3 ---
 CMakeLists.txt | 13 +++++++------
 derivation.nix | 37 +++++++++++++++++++++++++++++++++++++
 extern/vcpkg   |  1 -
 shell.nix      | 42 ++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 86 insertions(+), 10 deletions(-)
 create mode 100644 derivation.nix
 delete mode 160000 extern/vcpkg
 create mode 100644 shell.nix

diff --git a/.gitmodules b/.gitmodules
index 499547f6f..1d2c96bf4 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +1,3 @@
 [submodule "extern/stator"]
 	path = extern/stator
 	url = https://github.com/toastedcrumpets/stator.git
-[submodule "vcpkg"]
-	path = extern/vcpkg
-	url = https://github.com/microsoft/vcpkg.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5ab6e7f51..e89210568 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,12 +5,13 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
 endif()
 
 
-if(NOT MSVC)
-  # To make this compile on NixOS, we need to use the static linked MSVC
-  # But this is not available on windows
-  set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
-endif()
-set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
+# Disabled VCPKG as we move to nix
+#if(NOT MSVC)
+#  # To make this compile on NixOS, we need to use the static linked MSVC
+#  # But this is not available on windows
+#  set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
+#endif()
+#set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
 
 project(DynamO) #Project name
 enable_testing() #Enable build of test executables and 'make test' command
diff --git a/derivation.nix b/derivation.nix
new file mode 100644
index 000000000..158769589
--- /dev/null
+++ b/derivation.nix
@@ -0,0 +1,37 @@
+{
+  pkgs ? import <nixpkgs> {}
+}:
+pkgs.stdenv.mkDerivation rec {
+  pname = "dynamomd";
+  version = "1.6.0";
+  src = pkgs.fetchgit {
+    url = "https://github.com/dynamomd/dynamo";
+    rev = "refs/heads/nix";
+    sha256 = "sha256-p8+OoNBW7VABgIWXme6iLWEkiPe7v9yZqPveN4A+hKY=";
+  };
+
+  buildInputs = [
+    pkgs.cmake
+    pkgs.git
+    pkgs.ninja
+    pkgs.gcc
+    pkgs.pkg-config
+    pkgs.bzip2.dev
+    ((pks: pks.python3.withPackages (ps: with ps; [
+      numpy
+    ])) pkgs)
+  ];
+
+  configurePhase = ''
+    cmake .
+  '';
+
+  buildPhase = ''
+    cmake --build .
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mv chord $out/bin
+  '';
+}
diff --git a/extern/vcpkg b/extern/vcpkg
deleted file mode 160000
index b02e341c9..000000000
--- a/extern/vcpkg
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b02e341c927f16d991edbd915d8ea43eac52096c
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 000000000..d4336d1af
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1,42 @@
+{ pkgs ? import <nixpkgs> {
+  config.allowUnfree = true;
+} }:
+let
+  envname = "platformio-fhs";
+in
+(pkgs.buildFHSUserEnv {
+  name = envname;
+  targetPkgs = pkgs: (with pkgs; [
+    bashInteractive # Needed to fix shell in vscode
+    git
+    ((pks: pks.python3.withPackages (ps: with ps; [
+      numpy
+    ])) pkgs)
+
+    # Basic build dependencies
+    cmake
+    
+    # VSCode with all the extensions I use
+    (vscode-with-extensions.override {
+      vscodeExtensions = with pkgs.vscode-extensions; [
+      tuttieee.emacs-mcx
+	    ms-vscode.cpptools
+	    ms-vscode.cpptools-extension-pack
+	    xaver.clang-format
+	    ms-vscode.cmake-tools
+	    #brobeson.ctest-lab
+	    batisteo.vscode-django
+	    grapecity.gc-excelviewer
+	    github.vscode-github-actions
+	    github.copilot
+	    ms-vscode.live-server
+	    #elagil.pre-commit-helper
+	    ms-python.python
+	    ms-python.debugpy
+      ms-vscode-remote.remote-ssh
+      dbaeumer.vscode-eslint
+      tomoki1207.pdf
+      ];
+    })
+  ]);
+}).env

From 31324ef5949270f8763bd21f8aa982a9f6ee5886 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 12 May 2025 21:41:57 +0100
Subject: [PATCH 06/38] Trying to build the derivation

---
 CMakeLists.txt                |  2 +-
 derivation.nix => default.nix | 35 ++++++++++++++++++++++++++---------
 2 files changed, 27 insertions(+), 10 deletions(-)
 rename derivation.nix => default.nix (56%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e89210568..fe38beacd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -103,7 +103,7 @@ endif()
 ######### Dependencies
 ######################################################################
 
-set(Boost_USE_STATIC_LIBS ON)
+# set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(Boost 1.70.0 REQUIRED system filesystem program_options unit_test_framework)
diff --git a/derivation.nix b/default.nix
similarity index 56%
rename from derivation.nix
rename to default.nix
index 158769589..ae8581ac4 100644
--- a/derivation.nix
+++ b/default.nix
@@ -10,16 +10,34 @@ pkgs.stdenv.mkDerivation rec {
     sha256 = "sha256-p8+OoNBW7VABgIWXme6iLWEkiPe7v9yZqPveN4A+hKY=";
   };
 
-  buildInputs = [
-    pkgs.cmake
-    pkgs.git
-    pkgs.ninja
-    pkgs.gcc
-    pkgs.pkg-config
-    pkgs.bzip2.dev
+  buildInputs = with pkgs; [
+    # Basic build dependencies
+    cmake
+    git
+    ninja
+    gcc
+    pkg-config
+    bzip2.dev
+    boost.dev
+    clang-tools
+    eigen
     ((pks: pks.python3.withPackages (ps: with ps; [
       numpy
+      #alive-progress
+      uncertainties
+      pandas
+      scipy
+      freud
+      networkx
     ])) pkgs)
+
+    # Visualiser
+    gtkmm3.dev
+    ffmpeg.dev
+    freeglut
+    glew
+    cairomm
+    libpng
   ];
 
   configurePhase = ''
@@ -31,7 +49,6 @@ pkgs.stdenv.mkDerivation rec {
   '';
 
   installPhase = ''
-    mkdir -p $out/bin
-    mv chord $out/bin
+    cmake --install .
   '';
 }

From 212f40aee1b5b1c1803f41bdc6cf3980750fbb30 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 12 May 2025 22:17:52 +0100
Subject: [PATCH 07/38] Package works but dynavis does not

---
 default.nix | 37 +++++++++++++++++++------------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/default.nix b/default.nix
index ae8581ac4..d876bdd4c 100644
--- a/default.nix
+++ b/default.nix
@@ -3,18 +3,19 @@
 }:
 pkgs.stdenv.mkDerivation rec {
   pname = "dynamomd";
-  version = "1.6.0";
-  src = pkgs.fetchgit {
-    url = "https://github.com/dynamomd/dynamo";
-    rev = "refs/heads/nix";
-    sha256 = "sha256-p8+OoNBW7VABgIWXme6iLWEkiPe7v9yZqPveN4A+hKY=";
-  };
+  version = "1.7.0";
+  #src = pkgs.fetchgit {
+  #  url = "https://github.com/dynamomd/dynamo";
+  #  rev =  "f1fd582cd9ed09b52b7c99cdbf00cd1cebb3958c"; # "refs/heads/nix";
+  #  sha256 = "sha256-S3D15QD4NTVSM6PR7xqRQj7yvpq2MQj4WmHzspDKzTI=";
+  #};
 
+  src = ./.;
+  
   buildInputs = with pkgs; [
     # Basic build dependencies
     cmake
     git
-    ninja
     gcc
     pkg-config
     bzip2.dev
@@ -40,15 +41,15 @@ pkgs.stdenv.mkDerivation rec {
     libpng
   ];
 
-  configurePhase = ''
-    cmake .
-  '';
-
-  buildPhase = ''
-    cmake --build .
-  '';
-
-  installPhase = ''
-    cmake --install .
-  '';
+  #configurePhase = ''
+  #  cmake .
+  #'';
+  #
+  #buildPhase = ''
+  #  cmake --build . -j32
+  #'';
+  #
+  #installPhase = ''
+  #  cmake --install .
+  #'';
 }

From 51d6371aa4a82a53d88058080c15f317e67ad321 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 12:34:01 +0100
Subject: [PATCH 08/38] Got a build and install working, not sure about python
 packaging yet

---
 default.nix    | 57 ++------------------------------------------------
 derivation.nix | 46 ++++++++++++++++++++++++++++++++++++++++
 flake.nix      | 45 ---------------------------------------
 pyproject.toml |  2 +-
 shell.nix      | 42 -------------------------------------
 5 files changed, 49 insertions(+), 143 deletions(-)
 create mode 100644 derivation.nix
 delete mode 100644 flake.nix
 delete mode 100644 shell.nix

diff --git a/default.nix b/default.nix
index d876bdd4c..469c3f9b1 100644
--- a/default.nix
+++ b/default.nix
@@ -1,55 +1,2 @@
-{
-  pkgs ? import <nixpkgs> {}
-}:
-pkgs.stdenv.mkDerivation rec {
-  pname = "dynamomd";
-  version = "1.7.0";
-  #src = pkgs.fetchgit {
-  #  url = "https://github.com/dynamomd/dynamo";
-  #  rev =  "f1fd582cd9ed09b52b7c99cdbf00cd1cebb3958c"; # "refs/heads/nix";
-  #  sha256 = "sha256-S3D15QD4NTVSM6PR7xqRQj7yvpq2MQj4WmHzspDKzTI=";
-  #};
-
-  src = ./.;
-  
-  buildInputs = with pkgs; [
-    # Basic build dependencies
-    cmake
-    git
-    gcc
-    pkg-config
-    bzip2.dev
-    boost.dev
-    clang-tools
-    eigen
-    ((pks: pks.python3.withPackages (ps: with ps; [
-      numpy
-      #alive-progress
-      uncertainties
-      pandas
-      scipy
-      freud
-      networkx
-    ])) pkgs)
-
-    # Visualiser
-    gtkmm3.dev
-    ffmpeg.dev
-    freeglut
-    glew
-    cairomm
-    libpng
-  ];
-
-  #configurePhase = ''
-  #  cmake .
-  #'';
-  #
-  #buildPhase = ''
-  #  cmake --build . -j32
-  #'';
-  #
-  #installPhase = ''
-  #  cmake --install .
-  #'';
-}
+{ pkgs ? import <nixpkgs> {} }:
+pkgs.callPackage ./derivation.nix {}
diff --git a/derivation.nix b/derivation.nix
new file mode 100644
index 000000000..6b6a59118
--- /dev/null
+++ b/derivation.nix
@@ -0,0 +1,46 @@
+# see https://unix.stackexchange.com/questions/717168/how-to-package-my-software-in-nix-or-write-my-own-package-derivation-for-nixpkgs
+{ pkgs, python3 }:
+python3.pkgs.buildPythonPackage rec {
+  name = "dynamomd";
+  src = ./.;
+  pyproject = true;
+
+  dontUseCmakeConfigure = true;
+  
+  propagatedBuildInputs = with python3.pkgs; [
+      scikit-build-core
+      numpy
+      alive-progress
+      uncertainties
+      pandas
+      scipy
+      freud
+      networkx
+      pytest
+  ];
+
+  nativeBuildInputs = with pkgs; [
+    cmake
+    ninja
+    git
+    gcc
+    pkg-config
+    clang-tools
+    wrapGAppsHook3
+  ]  ++ propagatedBuildInputs;
+  
+  buildInputs = with pkgs; [
+    # Basic build dependencies
+    bzip2.dev
+    boost.dev
+    eigen
+    
+    # Visualiser
+    gtkmm3.dev
+    ffmpeg.dev
+    freeglut
+    glew
+    cairomm.dev
+    libpng
+  ];
+}
diff --git a/flake.nix b/flake.nix
deleted file mode 100644
index 6908895d6..000000000
--- a/flake.nix
+++ /dev/null
@@ -1,45 +0,0 @@
-{
-  description = "A Nix-flake-based C/C++ development environment";
-
-  inputs.nixpkgs.url = "https://flakehub.com/f/NixOS/nixpkgs/0.1.*.tar.gz";
-
-  outputs = { self, nixpkgs }:
-    let
-      supportedSystems = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
-      forEachSupportedSystem = f: nixpkgs.lib.genAttrs supportedSystems (system: f {
-        pkgs = import nixpkgs { inherit system; };
-      });
-      extraOutputsToInstall = [ "dev" ];
-    in
-    {
-      devShells = forEachSupportedSystem ({ pkgs }: {
-        default = pkgs.mkShell.override
-          {
-            # Override stdenv in order to change compiler:
-            #stdenv = pkgs.clangStdenv;
-          }
-          {
-            packages = with pkgs; [
-              clang
-              clang-tools
-              cmake
-              ninja
-              doxygen
-              vcpkg
-              vcpkg-tool
-              boost.dev
-              eigen
-              bzip2.dev
-              python3
-              gtkmm3.dev
-              ffmpeg.dev
-              freeglut
-              glew
-              cairomm
-              pkg-config
-            ] ++ (if system == "aarch64-darwin" then [ ] else [ gdb ]);
-          };
-      });
-    };
-}
-
diff --git a/pyproject.toml b/pyproject.toml
index df39c0331..52c7e8ed8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
 ]
-dependencies = ["alive-progress", "pandas", "scipy", "uncertainties", "freud", "networkx"]
+dependencies = ["alive-progress", "pandas", "scipy", "uncertainties", "networkx"]
 
 [tool.scikit-build]
 cmake.build-type = "Release"
diff --git a/shell.nix b/shell.nix
deleted file mode 100644
index d4336d1af..000000000
--- a/shell.nix
+++ /dev/null
@@ -1,42 +0,0 @@
-{ pkgs ? import <nixpkgs> {
-  config.allowUnfree = true;
-} }:
-let
-  envname = "platformio-fhs";
-in
-(pkgs.buildFHSUserEnv {
-  name = envname;
-  targetPkgs = pkgs: (with pkgs; [
-    bashInteractive # Needed to fix shell in vscode
-    git
-    ((pks: pks.python3.withPackages (ps: with ps; [
-      numpy
-    ])) pkgs)
-
-    # Basic build dependencies
-    cmake
-    
-    # VSCode with all the extensions I use
-    (vscode-with-extensions.override {
-      vscodeExtensions = with pkgs.vscode-extensions; [
-      tuttieee.emacs-mcx
-	    ms-vscode.cpptools
-	    ms-vscode.cpptools-extension-pack
-	    xaver.clang-format
-	    ms-vscode.cmake-tools
-	    #brobeson.ctest-lab
-	    batisteo.vscode-django
-	    grapecity.gc-excelviewer
-	    github.vscode-github-actions
-	    github.copilot
-	    ms-vscode.live-server
-	    #elagil.pre-commit-helper
-	    ms-python.python
-	    ms-python.debugpy
-      ms-vscode-remote.remote-ssh
-      dbaeumer.vscode-eslint
-      tomoki1207.pdf
-      ];
-    })
-  ]);
-}).env

From 5e63f1aac9b144e4a9639fdb8690a22c002d4cc6 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 13:11:34 +0100
Subject: [PATCH 09/38] Fix python package name

---
 derivation.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/derivation.nix b/derivation.nix
index 6b6a59118..2788724ae 100644
--- a/derivation.nix
+++ b/derivation.nix
@@ -1,7 +1,7 @@
 # see https://unix.stackexchange.com/questions/717168/how-to-package-my-software-in-nix-or-write-my-own-package-derivation-for-nixpkgs
 { pkgs, python3 }:
 python3.pkgs.buildPythonPackage rec {
-  name = "dynamomd";
+  name = "pydynamo";
   src = ./.;
   pyproject = true;
 

From 5367ecc01a043a0038564e849d14efca98f83c32 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 13:32:21 +0100
Subject: [PATCH 10/38] Testing a new CI workflow using nix

---
 .github/workflows/ci.yaml | 109 +++++++++++++-------------------------
 derivation.nix            |   3 ++
 2 files changed, 40 insertions(+), 72 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9db15845c..70b41bd76 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -6,93 +6,58 @@ on:
   - push
   - pull_request
 jobs:
-  build-project:
+  nix-build:
     name: ${{ matrix.os }}-${{ github.workflow }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, ubuntu-24.04, macos-15, windows-2022]
-    env:
-      # Indicates the location of the vcpkg as a Git submodule of the project repository.
-      # Not using "VCPKG_ROOT" because a variable with the same name is defined in the VS's
-      # Developer Command Prompt environment in VS 2022 17.6, which would override this one
-      # if it had the same name.
-      _VCPKG_: ${{ github.workspace }}/vcpkg
-      # Tells vcpkg where binary packages are stored.
-      VCPKG_DEFAULT_BINARY_CACHE: ${{ github.workspace }}/vcpkg/bincache
-      # Let's use GitHub Action cache as storage for the vcpkg Binary Caching feature.
-      VCPKG_BINARY_SOURCES: "clear;x-gha,readwrite"
+        os: [ubuntu-22.04, ubuntu-24.04, macos-15] #windows-2022
     steps:
-      - uses: actions/github-script@v7
-        with:
-          script: |
-            core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
-            core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
       - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - name: "Create directory '${{ env.VCPKG_DEFAULT_BINARY_CACHE }}'"
-        run: mkdir -p $VCPKG_DEFAULT_BINARY_CACHE
-        shell: bash
-
-      # Setup the build machine with the most recent versions of CMake and Ninja. Both are cached if not already: on subsequent runs both will be quickly restored from GitHub cache service.
-      - uses: lukka/get-cmake@latest
-
-      # Restore vcpkg from the GitHub Action cache service. Note that packages are restored by vcpkg's binary caching
-      # when it is being run afterwards by CMake.
-      - name: Restore vcpkg
-        uses: actions/cache@v4
+      - name: Install Nix
+        uses: cachix/install-nix-action@v31
         with:
-          # The first path is the location of vcpkg: it contains the vcpkg executable and data files, as long as the
-          # built package archives (aka binary cache) which are located by VCPKG_DEFAULT_BINARY_CACHE env var.
-          # The other paths starting with '!' are exclusions: they contain termporary files generated during the build of the installed packages.
-          path: |
-            ${{ env._VCPKG_ }}
-            !${{ env._VCPKG_ }}/buildtrees
-            !${{ env._VCPKG_ }}/packages
-            !${{ env._VCPKG_ }}/downloads
-            !${{ env._VCPKG_ }}/installed
-          # The key is composed in a way that it gets properly invalidated whenever a different version of vcpkg is being used.
-          key: |
-            ${{ hashFiles( '.git/modules/vcpkg/HEAD' )}}
-
-      # On Windows runners, let's ensure to have the Developer Command Prompt environment setup correctly.
-      # As used here the Developer Command Prompt created is targeting x64 and using the default the Windows SDK.
-      - uses: ilammy/msvc-dev-cmd@v1
-
-      # Run CMake to generate Ninja project files.
-      - name: Configure the build system
-        run: |
-          cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release
+          nix_path: nixpkgs=channel:nixos-stable
+          extra_nix_config: |
+            experimental-features = nix-command flakes
+            allow-import-from-derivation = true
+            sandbox = false
+
+      - name: Build the nix package
+        run: nix-build
+        
+  hand-build:
+    name: ${{ matrix.os }}-${{ github.workflow }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04, ubuntu-24.04, macos-15] #windows-2022
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Install Nix
+        uses: cachix/install-nix-action@v31
+        with:
+          nix_path: nixpkgs=channel:nixos-stable
+          extra_nix_config: |
+            experimental-features = nix-command flakes
+            allow-import-from-derivation = true
+            sandbox = false
+      
+      - name: Configure the project
+        run: nix-shell --run "cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release"
 
       - name: Check code formatting
         if: runner.os == 'Linux'
-        run: |
-          cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release
-
-      # Build (Release configuration only) the whole project with Ninja (which is spawn by CMake).
-      - name: Build (Release configuration)
-        run: |
-          cmake --build ${{github.workspace}}/build -j4 --config Release
+        run: nix-shell --run "cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release"
 
       # Test the whole project with CTest
       - name: Test (Release configuration)
         working-directory: ${{github.workspace}}/build
-        run: |
-          ctest -j 4 --output-on-failure -C Release
-
-      - name: Package the project (python packages include more)
-        run: |
-          cmake --build ${{github.workspace}}/build -j4 -t package --config Release
-
-      - name: Upload packages as artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: dynamo-${{ matrix.os }}
-          path: |
-            ${{ github.workspace }}/build/*.deb
-            ${{ github.workspace }}/build/*.sh
-            ${{ github.workspace }}/build/*.tar.gz
-            ${{ github.workspace }}/build/*.exe
+        run: nix-shell --run "ctest -j 4 --output-on-failure -C Release"
\ No newline at end of file
diff --git a/derivation.nix b/derivation.nix
index 2788724ae..e6a6a7f6c 100644
--- a/derivation.nix
+++ b/derivation.nix
@@ -1,4 +1,7 @@
 # see https://unix.stackexchange.com/questions/717168/how-to-package-my-software-in-nix-or-write-my-own-package-derivation-for-nixpkgs
+# To install `nix-env -u -f default.nix`
+# To develop `nix-shell` (will build the shell with dependencies)
+# To test build `nix-build`
 { pkgs, python3 }:
 python3.pkgs.buildPythonPackage rec {
   name = "pydynamo";

From bb1395468639f182283d5e1a68dfc01f4c093912 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 13:44:25 +0100
Subject: [PATCH 11/38] Fixed nix channel

---
 .github/workflows/ci.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 70b41bd76..b68c8e3bd 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -21,7 +21,7 @@ jobs:
       - name: Install Nix
         uses: cachix/install-nix-action@v31
         with:
-          nix_path: nixpkgs=channel:nixos-stable
+          nix_path: nixpkgs=channel:nixos-24.11
           extra_nix_config: |
             experimental-features = nix-command flakes
             allow-import-from-derivation = true
@@ -44,7 +44,7 @@ jobs:
       - name: Install Nix
         uses: cachix/install-nix-action@v31
         with:
-          nix_path: nixpkgs=channel:nixos-stable
+          nix_path: nixpkgs=channel:nixos-24.11
           extra_nix_config: |
             experimental-features = nix-command flakes
             allow-import-from-derivation = true

From aff4c0d4dbdd698d9fb3937e364b9550de460be7 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 13:48:37 +0100
Subject: [PATCH 12/38] Made CI recursively checkout submodules

---
 .github/workflows/ci.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index b68c8e3bd..07a15bcd6 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: true
+          submodules: recursive
 
       - name: Install Nix
         uses: cachix/install-nix-action@v31
@@ -40,7 +40,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: true
+          submodules: recursive
       - name: Install Nix
         uses: cachix/install-nix-action@v31
         with:

From efd84d8b697c2fd170c6d1c7e29bcf50f8600d80 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 14:58:38 +0100
Subject: [PATCH 13/38] More fixes for nix CI

---
 .github/workflows/ci.yaml            | 12 ++++++------
 .github/workflows/python_wheels.yaml |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 07a15bcd6..e1c1e00b5 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -38,9 +38,6 @@ jobs:
       matrix:
         os: [ubuntu-22.04, ubuntu-24.04, macos-15] #windows-2022
     steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
       - name: Install Nix
         uses: cachix/install-nix-action@v31
         with:
@@ -49,15 +46,18 @@ jobs:
             experimental-features = nix-command flakes
             allow-import-from-derivation = true
             sandbox = false
-      
+
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive 
+
       - name: Configure the project
         run: nix-shell --run "cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release"
 
       - name: Check code formatting
-        if: runner.os == 'Linux'
         run: nix-shell --run "cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release"
 
       # Test the whole project with CTest
       - name: Test (Release configuration)
         working-directory: ${{github.workspace}}/build
-        run: nix-shell --run "ctest -j 4 --output-on-failure -C Release"
\ No newline at end of file
+        run: nix-shell --run ${{github.workspace}} "ctest -j 4 --output-on-failure -C Release"
\ No newline at end of file
diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 9dd96f492..06d86d5bd 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -20,7 +20,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: true
+          submodules: recursive
 
       - uses: actions/setup-python@v5
         with:

From 887ef6720707699067309ee6567cfbd563b2c063 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 15:07:03 +0100
Subject: [PATCH 14/38] Another attempt to fix CI for nix

---
 .github/workflows/ci.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index e1c1e00b5..2dfcdde89 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -52,12 +52,12 @@ jobs:
           submodules: recursive 
 
       - name: Configure the project
-        run: nix-shell --run "cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release"
+        run: nix-shell ${{github.workspace}} --run "cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release"
 
       - name: Check code formatting
-        run: nix-shell --run "cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release"
+        run: nix-shell ${{github.workspace}} --run "cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release"
 
       # Test the whole project with CTest
       - name: Test (Release configuration)
         working-directory: ${{github.workspace}}/build
-        run: nix-shell --run ${{github.workspace}} "ctest -j 4 --output-on-failure -C Release"
\ No newline at end of file
+        run: nix-shell ${{github.workspace}} --run  "ctest -j 4 --output-on-failure -C Release"
\ No newline at end of file

From 29ba81635bb044ed9ca39b3b0708fa1b496f4109 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 15:12:52 +0100
Subject: [PATCH 15/38] Add missing build step to nix CI

---
 .github/workflows/ci.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2dfcdde89..eb15061f1 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -54,6 +54,9 @@ jobs:
       - name: Configure the project
         run: nix-shell ${{github.workspace}} --run "cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release"
 
+      - name: Build the project
+        run: nix-shell ${{github.workspace}} --run "cmake --build ${{github.workspace}}/build -j4 --config Release"
+
       - name: Check code formatting
         run: nix-shell ${{github.workspace}} --run "cmake --build ${{github.workspace}}/build -j4 -t check-src-format --config Release"
 

From c0c203df97bd379a30616aea46e38c15d016f4af Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 15:36:18 +0100
Subject: [PATCH 16/38] Added libGL dependency

---
 derivation.nix |  1 +
 flake.lock     | 25 -------------------------
 2 files changed, 1 insertion(+), 25 deletions(-)
 delete mode 100644 flake.lock

diff --git a/derivation.nix b/derivation.nix
index e6a6a7f6c..0f5870721 100644
--- a/derivation.nix
+++ b/derivation.nix
@@ -39,6 +39,7 @@ python3.pkgs.buildPythonPackage rec {
     eigen
     
     # Visualiser
+    libGL.dev
     gtkmm3.dev
     ffmpeg.dev
     freeglut
diff --git a/flake.lock b/flake.lock
deleted file mode 100644
index 1d0fc8626..000000000
--- a/flake.lock
+++ /dev/null
@@ -1,25 +0,0 @@
-{
-  "nodes": {
-    "nixpkgs": {
-      "locked": {
-        "lastModified": 1739736696,
-        "narHash": "sha256-zON2GNBkzsIyALlOCFiEBcIjI4w38GYOb+P+R4S8Jsw=",
-        "rev": "d74a2335ac9c133d6bbec9fc98d91a77f1604c1f",
-        "revCount": 754461,
-        "type": "tarball",
-        "url": "https://api.flakehub.com/f/pinned/NixOS/nixpkgs/0.1.754461%2Brev-d74a2335ac9c133d6bbec9fc98d91a77f1604c1f/01951426-5a87-7b75-8413-1a0d9ec5ff04/source.tar.gz"
-      },
-      "original": {
-        "type": "tarball",
-        "url": "https://flakehub.com/f/NixOS/nixpkgs/0.1.%2A.tar.gz"
-      }
-    },
-    "root": {
-      "inputs": {
-        "nixpkgs": "nixpkgs"
-      }
-    }
-  },
-  "root": "root",
-  "version": 7
-}

From 6cf114419a2f15a0a880b607be11abd631daf940 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 15:57:13 +0100
Subject: [PATCH 17/38] Removing macos builds for now too.

---
 .github/workflows/ci.yaml        | 4 ++--
 src/magnet/magnet/GL/context.hpp | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index eb15061f1..719d4fde9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, ubuntu-24.04, macos-15] #windows-2022
+        os: [ubuntu-22.04, ubuntu-24.04] #windows-2022, macos-15
     steps:
       - uses: actions/checkout@v4
         with:
@@ -36,7 +36,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, ubuntu-24.04, macos-15] #windows-2022
+        os: [ubuntu-22.04, ubuntu-24.04] #windows-2022, macos-15
     steps:
       - name: Install Nix
         uses: cachix/install-nix-action@v31
diff --git a/src/magnet/magnet/GL/context.hpp b/src/magnet/magnet/GL/context.hpp
index 12b12d826..615fe6516 100644
--- a/src/magnet/magnet/GL/context.hpp
+++ b/src/magnet/magnet/GL/context.hpp
@@ -24,6 +24,9 @@
 #ifdef _WIN32
 #include <windows.h>
 typedef HGLRC ContextKey;
+#elif
+#include <OpenGL/CGLCurrent.h>
+typedef  ContextKey;
 #else
 #include <GL/glx.h>
 typedef GLXContext ContextKey;
@@ -74,6 +77,8 @@ class Context {
   inline static ContextKey getCurrentContextKey() {
 #ifdef _WIN32
     ContextKey key = wglGetCurrentContext();
+#elif __APPLE__
+    ContextKey key = CGLGetCurrentContext(); 
 #else
     ContextKey key = glXGetCurrentContext();
 #endif

From 20151c20e492f8af243c8d0a4d40d4bd9586adeb Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 16:00:32 +0100
Subject: [PATCH 18/38] Fix for GL

---
 src/magnet/magnet/GL/context.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/magnet/magnet/GL/context.hpp b/src/magnet/magnet/GL/context.hpp
index 615fe6516..abd372266 100644
--- a/src/magnet/magnet/GL/context.hpp
+++ b/src/magnet/magnet/GL/context.hpp
@@ -24,7 +24,7 @@
 #ifdef _WIN32
 #include <windows.h>
 typedef HGLRC ContextKey;
-#elif
+#elif __APPLE__
 #include <OpenGL/CGLCurrent.h>
 typedef  ContextKey;
 #else

From 00986738cefd31b154fc751c882c8a95bcc45f6e Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 16:10:27 +0100
Subject: [PATCH 19/38] Added build dependencies to CIBW

---
 .github/workflows/python_wheels.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 06d86d5bd..a101a13f6 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -32,8 +32,11 @@ jobs:
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_ARCHS_LINUX: auto64 # Seems 32 bit vcpkg dependencies are missing, so force 64 bit on linux
-          CIBW_SKIP: "*-musllinux_* pp*" # Skip musllinux builds for now as they fail, and skip pypy builds as they'll be disabled in cibuildwheel 3 anyway
+          #CIBW_ARCHS_LINUX: auto64 # Seems 32 bit vcpkg dependencies are missing, so force 64 bit on linux
+          #CIBW_SKIP: "*-musllinux_* pp*" # Skip musllinux builds for now as they fail, and skip pypy builds as they'll be disabled in cibuildwheel 3 anyway
+          CIBW_BEFORE_ALL_LINUX : sudo apt-get update && sudo apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev 
+            
+
 
       - uses: actions/upload-artifact@v4
         with:

From 47e697cb0acbd2846c2af31de12dbe704a1e2450 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 16:20:28 +0100
Subject: [PATCH 20/38] Another attempt to build wheels

---
 .github/workflows/python_wheels.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index a101a13f6..2decbd949 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -33,11 +33,9 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
           #CIBW_ARCHS_LINUX: auto64 # Seems 32 bit vcpkg dependencies are missing, so force 64 bit on linux
-          #CIBW_SKIP: "*-musllinux_* pp*" # Skip musllinux builds for now as they fail, and skip pypy builds as they'll be disabled in cibuildwheel 3 anyway
-          CIBW_BEFORE_ALL_LINUX : sudo apt-get update && sudo apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev 
+          CIBW_SKIP: "pp*" # Skip pypy builds as they'll be disabled in cibuildwheel 3 anyway (Might need to disable *-musllinux_* too)
+          CIBW_BEFORE_ALL_LINUX : yum install -y boost-devel bzip2-devel eigen3-devel ||  apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev 
             
-
-
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}

From 1b660efa54d820dc449d8a1d004d2b26d9c67dd0 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 16:53:44 +0100
Subject: [PATCH 21/38] Bumped cibuildwheel, but no solution for out of date
 boost yet

---
 .github/workflows/python_wheels.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 2decbd949..e9468388e 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -27,7 +27,7 @@ jobs:
           python-version: 3.11
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.23.2
+        run: python -m pip install cibuildwheel==2.23.3
 
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse

From c4bd263e6a7a8be4abd8325e1f50abb3be9b45e6 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Tue, 13 May 2025 22:15:55 +0100
Subject: [PATCH 22/38] Trying to use vcpkg on cibuildwheels

---
 pyproject.toml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 52c7e8ed8..8d995af4e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,12 @@ minimum-version = "build-system.requires"
 #testpaths = ["tests"]
 #
 #
-#[tool.cibuildwheel]
+
+[tool.cibuildwheel]
+# Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
+before-all = "(yum install -y boost-devel bzip2-devel eigen3-devel zip unzip || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+# Skip the pypy builds (they're deprecated anyhoo)
+skip = "pp*"
 #build-frontend = "build[uv]"
 #test-command = "pytest {project}/tests"
 #test-extras = ["test"]

From 353063cda548b227a339c0c0a89d9915254bde71 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Fri, 16 May 2025 15:00:22 +0100
Subject: [PATCH 23/38] Fixed cibuildwheels to use vcpkg

---
 .github/workflows/python_wheels.yaml |  9 +++------
 CMakeLists.txt                       | 12 +++++-------
 pyproject.toml                       |  2 ++
 3 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index e9468388e..3ed55c990 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -11,9 +11,9 @@ jobs:
       matrix:
         os: [
             ubuntu-latest,
-            #ubuntu-24.04-arm,
+            ubuntu-24.04-arm,
             windows-latest,
-            #macos-13,
+            macos-13,
             macos-latest,
           ]
 
@@ -31,12 +31,9 @@ jobs:
 
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
-        env:
-          #CIBW_ARCHS_LINUX: auto64 # Seems 32 bit vcpkg dependencies are missing, so force 64 bit on linux
-          CIBW_SKIP: "pp*" # Skip pypy builds as they'll be disabled in cibuildwheel 3 anyway (Might need to disable *-musllinux_* too)
-          CIBW_BEFORE_ALL_LINUX : yum install -y boost-devel bzip2-devel eigen3-devel ||  apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev 
             
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
+f
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fe38beacd..70eb0f130 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,14 +4,12 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
   cmake_policy(SET CMP0167 NEW) #  Use the new boost configuration
 endif()
 
-
 # Disabled VCPKG as we move to nix
-#if(NOT MSVC)
-#  # To make this compile on NixOS, we need to use the static linked MSVC
-#  # But this is not available on windows
-#  set(VCPKG_BOOTSTRAP_OPTIONS "-musl")
-#endif()
-#set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/extern/vcpkg/scripts/buildsystems/vcpkg.cmake)
+if(DEFINED ENV{VCPKG_ROOT})
+  message(STATUS "VCPKG_ROOT is set to $ENV{VCPKG_ROOT}")
+  set(VCPKG_ROOT $ENV{VCPKG_ROOT})
+  set(CMAKE_TOOLCHAIN_FILE ${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake)
+endif()
 
 project(DynamO) #Project name
 enable_testing() #Enable build of test executables and 'make test' command
diff --git a/pyproject.toml b/pyproject.toml
index 8d995af4e..a5b9be446 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,6 +51,8 @@ minimum-version = "build-system.requires"
 [tool.cibuildwheel]
 # Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
 before-all = "(yum install -y boost-devel bzip2-devel eigen3-devel zip unzip || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+# We enable dynamo VCPKG integration using the environment variable.
+environment = {VCPKG_ROOT="/opt/vcpkg/"}
 # Skip the pypy builds (they're deprecated anyhoo)
 skip = "pp*"
 #build-frontend = "build[uv]"

From 7aebda46be09bfb13034244b18c416599dcd2c76 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Fri, 16 May 2025 15:01:24 +0100
Subject: [PATCH 24/38] Typo fix

---
 .github/workflows/python_wheels.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 3ed55c990..09a650448 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -35,5 +35,4 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl
-f
\ No newline at end of file
+          path: ./wheelhouse/*.whl
\ No newline at end of file

From 28168d18aecedaaa4fe93aa9f828a74f2420d3cf Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Sat, 17 May 2025 07:15:41 +0100
Subject: [PATCH 25/38] Update pyproject.toml

Removed eigen3-devel as it's missing on some wheel systems
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a5b9be446..06c13ad53 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ minimum-version = "build-system.requires"
 
 [tool.cibuildwheel]
 # Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
-before-all = "(yum install -y boost-devel bzip2-devel eigen3-devel zip unzip || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+before-all = "(yum install -y boost-devel bzip2-devel zip unzip || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
 # We enable dynamo VCPKG integration using the environment variable.
 environment = {VCPKG_ROOT="/opt/vcpkg/"}
 # Skip the pypy builds (they're deprecated anyhoo)

From 1fa6cc2cad24a621eaf44ae2f02654ec49468b99 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Sat, 17 May 2025 09:06:50 +0100
Subject: [PATCH 26/38] Update pyproject.toml

Another fix for normal wheels
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 06c13ad53..458c575ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ minimum-version = "build-system.requires"
 
 [tool.cibuildwheel]
 # Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
-before-all = "(yum install -y boost-devel bzip2-devel zip unzip || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+before-all = "(yum install -y boost-devel bzip2-devel zip unzip ninja || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
 # We enable dynamo VCPKG integration using the environment variable.
 environment = {VCPKG_ROOT="/opt/vcpkg/"}
 # Skip the pypy builds (they're deprecated anyhoo)

From daac80d9fadcdd8fb1927ec16a51e063b877e7f6 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Sat, 17 May 2025 15:05:11 +0100
Subject: [PATCH 27/38] Update pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 458c575ca..2da95811d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ minimum-version = "build-system.requires"
 
 [tool.cibuildwheel]
 # Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
-before-all = "(yum install -y boost-devel bzip2-devel zip unzip ninja || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+before-all = "(yum install -y boost-devel bzip2-devel zip unzip ninja-build || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
 # We enable dynamo VCPKG integration using the environment variable.
 environment = {VCPKG_ROOT="/opt/vcpkg/"}
 # Skip the pypy builds (they're deprecated anyhoo)

From 7ae4428a1d97a96d467d1074073991aeb4ab78bb Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Sat, 17 May 2025 18:49:21 +0100
Subject: [PATCH 28/38] Added make instead of ninja

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2da95811d..b14134a19 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ minimum-version = "build-system.requires"
 
 [tool.cibuildwheel]
 # Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
-before-all = "(yum install -y boost-devel bzip2-devel zip unzip ninja-build || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+before-all = "(yum install -y boost-devel bzip2-devel zip unzip make || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
 # We enable dynamo VCPKG integration using the environment variable.
 environment = {VCPKG_ROOT="/opt/vcpkg/"}
 # Skip the pypy builds (they're deprecated anyhoo)

From ae196f5094310cd5178be96ed5e85f9637d71ba4 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 08:47:24 +0100
Subject: [PATCH 29/38] Another patch for musllinux compilation

---
 .gitignore                          |  3 ++-
 CMakeLists.txt                      |  7 +++----
 pyproject.toml                      | 27 +++++++++++++++++----------
 src/dynamo/programs/dynahist_rw.cpp |  2 +-
 4 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/.gitignore b/.gitignore
index 5f6d4b286..9f98cc17f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,5 @@ __pycache__
 
 Testing/Temporary/CTestCostData.txt
 .eggs
-wheelhouse
\ No newline at end of file
+wheelhouse
+vcpkg_installed
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 70eb0f130..2b31294d9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,10 +5,9 @@ if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the wa
 endif()
 
 # Disabled VCPKG as we move to nix
-if(DEFINED ENV{VCPKG_ROOT})
-  message(STATUS "VCPKG_ROOT is set to $ENV{VCPKG_ROOT}")
-  set(VCPKG_ROOT $ENV{VCPKG_ROOT})
-  set(CMAKE_TOOLCHAIN_FILE ${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake)
+if(DEFINED ENV{DYNAMO_VCPKG_ROOT})
+  message(STATUS "DYNAMO_VCPKG_ROOT is set to $ENV{DYNAMO_VCPKG_ROOT}, enabling VCPKG")
+  set(CMAKE_TOOLCHAIN_FILE $ENV{DYNAMO_VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake)
 endif()
 
 project(DynamO) #Project name
diff --git a/pyproject.toml b/pyproject.toml
index b14134a19..b8d382aee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,9 @@
 [build-system]
-requires = ["scikit-build-core>=0.10", "numpy", "pytest"]
+requires = [
+  "scikit-build-core>=0.10", 
+  "numpy", 
+  "pytest",
+]
 build-backend = "scikit_build_core.build"
 
 
@@ -49,12 +53,15 @@ minimum-version = "build-system.requires"
 #
 
 [tool.cibuildwheel]
-# Here we install desired libraries for their build dependencies, then use vcpkg to update to latest files from vcpkg.json
-before-all = "(yum install -y boost-devel bzip2-devel zip unzip make || apt-get install -y libboost-all-dev libbz2-dev libeigen3-dev ninja zip unzip) && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
-# We enable dynamo VCPKG integration using the environment variable.
-environment = {VCPKG_ROOT="/opt/vcpkg/"}
-# Skip the pypy builds (they're deprecated anyhoo)
-skip = "pp*"
-#build-frontend = "build[uv]"
-#test-command = "pytest {project}/tests"
-#test-extras = ["test"]
+# Skip the pypy builds (they're deprecated anyhoo), and the 32bit builds due to issues with build tools
+skip = "pp* *-manylinux_i686" 
+# Setup install of vcpkg, to download c++ dependencies
+before-all = "yum install -y zip unzip make && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
+environment = {DYNAMO_VCPKG_ROOT="/opt/vcpkg/"}
+build-frontend = "build[uv]"
+
+[[tool.cibuildwheel.overrides]]
+# musllinux uses apk instead of yum
+select = "*-musllinux*"
+#install ninja-is-really-ninja, as the ninja package is a link to samurai which is incompatible with vcpkg it seems
+before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
\ No newline at end of file
diff --git a/src/dynamo/programs/dynahist_rw.cpp b/src/dynamo/programs/dynahist_rw.cpp
index 96ed251f4..c5089857f 100644
--- a/src/dynamo/programs/dynahist_rw.cpp
+++ b/src/dynamo/programs/dynahist_rw.cpp
@@ -520,7 +520,7 @@ int main(int argc, char *argv[]) {
             << "under certain conditions. See the licence you obtained with\n"
             << "the code\n";
 
-#if !defined(__APPLE__) && !defined(_WIN32)
+#ifdef __GLIBC__
   // This is so the program crashes out when floating point errors occur
   feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW | FE_UNDERFLOW);
 #endif

From 43c843fd0691be1c55a160a1b5f7f9c3f0f11c3a Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 09:17:28 +0100
Subject: [PATCH 30/38] Got x86_64 builds working

---
 pyproject.toml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b8d382aee..07da6ae32 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,8 +53,9 @@ minimum-version = "build-system.requires"
 #
 
 [tool.cibuildwheel]
-# Skip the pypy builds (they're deprecated anyhoo), and the 32bit builds due to issues with build tools
-skip = "pp* *-manylinux_i686" 
+# Skip the pypy builds (they're deprecated anyhoo)
+# Skip 32bit builds due to issues with build tools
+skip = "pp* *i686" 
 # Setup install of vcpkg, to download c++ dependencies
 before-all = "yum install -y zip unzip make && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
 environment = {DYNAMO_VCPKG_ROOT="/opt/vcpkg/"}
@@ -64,4 +65,10 @@ build-frontend = "build[uv]"
 # musllinux uses apk instead of yum
 select = "*-musllinux*"
 #install ninja-is-really-ninja, as the ninja package is a link to samurai which is incompatible with vcpkg it seems
-before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
\ No newline at end of file
+before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
+
+[[tool.cibuildwheel.overrides]]
+# arm linux is tempermental with vcpkg
+select = "*-aarch64"
+before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
+

From 5de88720260c9f6df969a55fd2fbf77b08abfd49 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 10:04:21 +0100
Subject: [PATCH 31/38] Moved away from vcpkg in the wheels

---
 .github/workflows/python_wheels.yaml |  2 +-
 CMakeLists.txt                       |  7 +++---
 pyproject.toml                       | 33 +++++++++++++++++++---------
 src/magnet/CMakeLists.txt            |  2 +-
 4 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 09a650448..557a5207e 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -12,7 +12,7 @@ jobs:
         os: [
             ubuntu-latest,
             ubuntu-24.04-arm,
-            windows-latest,
+            # windows-latest,
             macos-13,
             macos-latest,
           ]
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2b31294d9..19e095b68 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,8 @@
 cmake_minimum_required(VERSION 3.28)
 
-if(POLICY CMP0167) # Must be before project otherwise VCPKG hooks trigger the warning
-  cmake_policy(SET CMP0167 NEW) #  Use the new boost configuration
+# We want to set this to new, but the python wheels need boost 1.70 minimum before this can happen
+if(POLICY CMP0167) 
+  cmake_policy(SET CMP0167 OLD)
 endif()
 
 # Disabled VCPKG as we move to nix
@@ -103,7 +104,7 @@ endif()
 # set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-find_package(Boost 1.70.0 REQUIRED system filesystem program_options unit_test_framework)
+find_package(Boost 1.66.0 REQUIRED system filesystem program_options unit_test_framework)
 
 add_subdirectory(src/magnet)
 find_package(Eigen3)
diff --git a/pyproject.toml b/pyproject.toml
index 07da6ae32..88df45cdd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,22 +53,35 @@ minimum-version = "build-system.requires"
 #
 
 [tool.cibuildwheel]
-# Skip the pypy builds (they're deprecated anyhoo)
+# Skip the pypy builds (they're deprecated and use an old toolchain)
 # Skip 32bit builds due to issues with build tools
-skip = "pp* *i686" 
-# Setup install of vcpkg, to download c++ dependencies
-before-all = "yum install -y zip unzip make && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install"
-environment = {DYNAMO_VCPKG_ROOT="/opt/vcpkg/"}
+skip = "pp* *i686 *win32"
+# More modern install/build with uv
 build-frontend = "build[uv]"
 
+# For future reference on a windows build
+# To use VCPKG, add the environment variable
+#environment = {DYNAMO_VCPKG_ROOT="/opt/vcpkg/"}
+# And add this to before-all to download vcpkg
+#&& git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -disableMetrics && /opt/vcpkg/vcpkg install
+
+
+[tool.cibuildwheel.linux]
+# We switch to the 2025 default images now
+manylinux-x86_64-image = "manylinux_2_28"
+manylinux-aarch64-image = "manylinux_2_28"
+musllinux-x86_64-image = "musllinux_1_2"
+musllinux-aarch64-image = "musllinux_1_2"
+before-all = "yum install -y zip unzip make boost-devel eigen3-devel bzip2-devel"
+
 [[tool.cibuildwheel.overrides]]
 # musllinux uses apk instead of yum
 select = "*-musllinux*"
 #install ninja-is-really-ninja, as the ninja package is a link to samurai which is incompatible with vcpkg it seems
-before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
+before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
+
+
+[tool.cibuildwheel.macos]
+before-all = "brew install cmake boost bzip2 eigen"
 
-[[tool.cibuildwheel.overrides]]
-# arm linux is tempermental with vcpkg
-select = "*-aarch64"
-before-all = "apk add zip unzip ninja-is-really-ninja && git clone https://github.com/microsoft/vcpkg.git /opt/vcpkg && /opt/vcpkg/bootstrap-vcpkg.sh -musl -disableMetrics && /opt/vcpkg/vcpkg install"
 
diff --git a/src/magnet/CMakeLists.txt b/src/magnet/CMakeLists.txt
index 98cf98fcc..9fecb218d 100644
--- a/src/magnet/CMakeLists.txt
+++ b/src/magnet/CMakeLists.txt
@@ -1,6 +1,6 @@
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DMAGNET_DEBUG")
 
-find_package(Boost 1.70.0 REQUIRED)
+find_package(Boost 1.66.0 REQUIRED)
 
 add_library(magnet INTERFACE)
 target_include_directories(magnet INTERFACE

From a95a6004cdb7d249c5abebbaa93ea41e5630c36b Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 10:12:15 +0100
Subject: [PATCH 32/38] A fix for macos now

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 88df45cdd..1da6d3c7f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,8 @@ minimum-version = "build-system.requires"
 # Skip 32bit builds due to issues with build tools
 skip = "pp* *i686 *win32"
 # More modern install/build with uv
-build-frontend = "build[uv]"
+# Doesn't work on macos github actions! Need to install it using brew?
+#build-frontend = "build[uv]"
 
 # For future reference on a windows build
 # To use VCPKG, add the environment variable
@@ -80,7 +81,6 @@ select = "*-musllinux*"
 #install ninja-is-really-ninja, as the ninja package is a link to samurai which is incompatible with vcpkg it seems
 before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
 
-
 [tool.cibuildwheel.macos]
 before-all = "brew install cmake boost bzip2 eigen"
 

From 70368425fa77b3bc1aed4d83a39ecf9f79810b4e Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 11:27:18 +0100
Subject: [PATCH 33/38] Another patch for macos

---
 .github/workflows/python_wheels.yaml | 11 ++++++++++-
 pyproject.toml                       |  6 +++---
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 557a5207e..453a7e480 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -12,9 +12,9 @@ jobs:
         os: [
             ubuntu-latest,
             ubuntu-24.04-arm,
-            # windows-latest,
             macos-13,
             macos-latest,
+            # windows-latest, # Needs a way to install the build dependencies (or VCPKG)
           ]
 
     steps:
@@ -29,6 +29,15 @@ jobs:
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.23.3
 
+      - name: Install boost on macos
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
+        uses: MarkusJx/install-boost@v2
+        id: install-boost
+        with:
+        # https://github.com/MarkusJx/prebuilt-boost/blob/main/versions-manifest.json
+          boost_version: 1.71.0
+          platform_version: 10.15  #Using this to allow for older macos versions in the wheel
+          
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
             
diff --git a/pyproject.toml b/pyproject.toml
index 1da6d3c7f..33022941b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,6 @@ classifiers = [
   "Development Status :: 4 - Beta",
   "License :: OSI Approved :: GPL License",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.7",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
@@ -55,6 +53,7 @@ minimum-version = "build-system.requires"
 [tool.cibuildwheel]
 # Skip the pypy builds (they're deprecated and use an old toolchain)
 # Skip 32bit builds due to issues with build tools
+# Dropping some older python versions too
 skip = "pp* *i686 *win32"
 # More modern install/build with uv
 # Doesn't work on macos github actions! Need to install it using brew?
@@ -82,6 +81,7 @@ select = "*-musllinux*"
 before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
 
 [tool.cibuildwheel.macos]
-before-all = "brew install cmake boost bzip2 eigen"
+# Dont install boost, need system compiled for older mac versions
+before-all = "brew install cmake eigen"
 
 

From 83d1cb41e03a1439956d657bafed166fe9939c7c Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 11:37:57 +0100
Subject: [PATCH 34/38] Trying to build boost from source on macos to enable
 portable wheels

---
 .github/workflows/python_wheels.yaml | 9 ---------
 pyproject.toml                       | 3 +--
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/.github/workflows/python_wheels.yaml b/.github/workflows/python_wheels.yaml
index 453a7e480..1ac1591ad 100644
--- a/.github/workflows/python_wheels.yaml
+++ b/.github/workflows/python_wheels.yaml
@@ -28,15 +28,6 @@ jobs:
 
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.23.3
-
-      - name: Install boost on macos
-        if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
-        uses: MarkusJx/install-boost@v2
-        id: install-boost
-        with:
-        # https://github.com/MarkusJx/prebuilt-boost/blob/main/versions-manifest.json
-          boost_version: 1.71.0
-          platform_version: 10.15  #Using this to allow for older macos versions in the wheel
           
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
diff --git a/pyproject.toml b/pyproject.toml
index 33022941b..2fc68ba7e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,7 +81,6 @@ select = "*-musllinux*"
 before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
 
 [tool.cibuildwheel.macos]
-# Dont install boost, need system compiled for older mac versions
-before-all = "brew install cmake eigen"
+before-all = "brew install cmake eigen && brew install --build-from-source boost"
 
 

From d27d1f69287d13b5db867f058a5475c38cddfc8b Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 11:58:16 +0100
Subject: [PATCH 35/38] Trying static boost

---
 CMakeLists.txt | 2 +-
 pyproject.toml | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 19e095b68..5dfb86c2a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -101,7 +101,7 @@ endif()
 ######### Dependencies
 ######################################################################
 
-# set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(Boost 1.66.0 REQUIRED system filesystem program_options unit_test_framework)
diff --git a/pyproject.toml b/pyproject.toml
index 2fc68ba7e..776d4ab19 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,6 +81,4 @@ select = "*-musllinux*"
 before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
 
 [tool.cibuildwheel.macos]
-before-all = "brew install cmake eigen && brew install --build-from-source boost"
-
-
+before-all = "brew install cmake eigen boost"
\ No newline at end of file

From 83c081dc7e0d3f3fe374fd857c0a9ed1efd18674 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 12:14:22 +0100
Subject: [PATCH 36/38] Trying boost static

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 776d4ab19..51e3f380a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,13 +72,13 @@ manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 musllinux-x86_64-image = "musllinux_1_2"
 musllinux-aarch64-image = "musllinux_1_2"
-before-all = "yum install -y zip unzip make boost-devel eigen3-devel bzip2-devel"
+before-all = "yum install -y zip unzip make boost-devel boost-static eigen3-devel bzip2-devel"
 
 [[tool.cibuildwheel.overrides]]
 # musllinux uses apk instead of yum
 select = "*-musllinux*"
 #install ninja-is-really-ninja, as the ninja package is a link to samurai which is incompatible with vcpkg it seems
-before-all = "apk add zip unzip ninja-is-really-ninja boost-dev eigen-dev bzip2-dev"
+before-all = "apk add zip unzip ninja-is-really-ninja boost-dev boost-static eigen-dev bzip2-dev"
 
 [tool.cibuildwheel.macos]
 before-all = "brew install cmake eigen boost"
\ No newline at end of file

From 25f72aea61cfdc91aa5198d996df02461c130e7c Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 12:22:40 +0100
Subject: [PATCH 37/38] Setup Prefer boost static, to allow wheel build on all
 platforms supported.

---
 CMakeLists.txt | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5dfb86c2a..eacc8ab17 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -104,7 +104,12 @@ endif()
 set(Boost_USE_STATIC_LIBS ON)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-find_package(Boost 1.66.0 REQUIRED system filesystem program_options unit_test_framework)
+find_package(Boost 1.66.0 COMPONENTS system filesystem program_options unit_test_framework)
+if(NOT Boost_FOUND)
+  message(WARNING "Static Boost not found, trying shared Boost")
+  set(Boost_USE_STATIC_LIBS OFF)
+  find_package(Boost 1.66.0 REQUIRED COMPONENTS system filesystem program_options unit_test_framework)
+endif()
 
 add_subdirectory(src/magnet)
 find_package(Eigen3)

From 7738983d777d9d72b4f15bf1720f0ee5dd92f9b1 Mon Sep 17 00:00:00 2001
From: Marcus Bannerman <m.bannerman@gmail.com>
Date: Mon, 19 May 2025 22:09:59 +0100
Subject: [PATCH 38/38] Update src/magnet/magnet/GL/context.hpp

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 src/magnet/magnet/GL/context.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/magnet/magnet/GL/context.hpp b/src/magnet/magnet/GL/context.hpp
index abd372266..5d4241d0e 100644
--- a/src/magnet/magnet/GL/context.hpp
+++ b/src/magnet/magnet/GL/context.hpp
@@ -26,7 +26,7 @@
 typedef HGLRC ContextKey;
 #elif __APPLE__
 #include <OpenGL/CGLCurrent.h>
-typedef  ContextKey;
+typedef CGLContextObj ContextKey;
 #else
 #include <GL/glx.h>
 typedef GLXContext ContextKey;