From 5dda9ad9576fdad4f51cecf23837ffc96cd5c364 Mon Sep 17 00:00:00 2001
From: Antoine Fauroux <antoine.fauroux@uhn.ca>
Date: Tue, 9 Jun 2026 16:23:01 -0400
Subject: [PATCH] kcnhub: packages: python: nestml

---
 flake.nix                           |  5 +-
 machines/kcnhub/packages/python.nix |  4 ++
 overlays/packages.nix               | 12 +++++
 overlays/python-packages.nix        | 84 +++++++++++++++++++++++++++++
 4 files changed, 103 insertions(+), 2 deletions(-)
 create mode 100644 overlays/packages.nix

diff --git a/flake.nix b/flake.nix
index 73a5229..5bdabb0 100644
--- a/flake.nix
+++ b/flake.nix
@@ -43,6 +43,7 @@
       };
     };
     python-overlay = import ./overlays/python.nix attrs;
+    package-overlays = import ./overlays/packages.nix attrs;
     applyOverlays = overlays: ({...}:{ nixpkgs.overlays = overlays; });
     flakes = {...}: {nix.settings.experimental-features = [ "nix-command" "flakes" ];};
   in {
@@ -51,7 +52,7 @@
       specialArgs = attrs;
       modules = [ 
          flakes
-         (applyOverlays [ unfree-overlay unstable-overlay python-overlay ])
+         (applyOverlays [ unfree-overlay unstable-overlay python-overlay package-overlays ])
          vscode-server.nixosModules.default
          ./machines/kcnhub/configuration.nix
          sops-nix.nixosModules.sops
@@ -59,7 +60,7 @@
     };
 
     overlays = {
-      default = applyOverlays [ unfree-overlay unstable-overlay python-overlay ];
+      default = applyOverlays [ unfree-overlay unstable-overlay python-overlay package-overlays ];
       unstable = unstable-overlay;
     };
   };
diff --git a/machines/kcnhub/packages/python.nix b/machines/kcnhub/packages/python.nix
index c8a67f5..9f52ad1 100644
--- a/machines/kcnhub/packages/python.nix
+++ b/machines/kcnhub/packages/python.nix
@@ -9,6 +9,9 @@
   };
   config = {
     environment.systemPackages = with pkgs; [
+      # For nestml
+      cmake
+      gnumake
       ((pkgs.python3.withPackages config.pythonPackages).override (args: { ignoreCollisions = true; }))
     ];
     pythonPackages = (p: with p; [
@@ -40,6 +43,7 @@
       (nest.override {
         withMpi = false;
       })
+      nestml
       brian2
       # SpiNNaker simulator
       spynnaker
diff --git a/overlays/packages.nix b/overlays/packages.nix
new file mode 100644
index 0000000..40430b3
--- /dev/null
+++ b/overlays/packages.nix
@@ -0,0 +1,12 @@
+inputs: final: prev: {
+  nest = prev.nest.overrideAttrs (old: {
+    postPatch = old.postPatch + ''
+      sed -e 's#-L$prefix/#-L#g' -i bin/nest-config.in
+    '';
+  });
+  nest-mpi = prev.nest-mpi.overrideAttrs (old: {
+    postPatch = old.postPatch + ''
+      sed -e 's#-L$prefix/#-L#g' -i bin/nest-config.in
+    '';
+  });
+}
diff --git a/overlays/python-packages.nix b/overlays/python-packages.nix
index 9c01133..c6cc8d1 100644
--- a/overlays/python-packages.nix
+++ b/overlays/python-packages.nix
@@ -1,4 +1,88 @@
 final: final-py: prev-py: {
+  nestml = let
+    pname = "nestml";
+    # Newer versions require newer antlr4
+    version = "7.0.2";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+
+    src = final.fetchFromGitHub {
+      owner = "nest";
+      repo = pname;
+      rev = "v${version}";
+      hash = "sha256-BQzwIh2Gdq+rLwIwe7dyltDfEzpaIWGlXF0AfZGBUDw=";
+    };
+
+    doCheck = false;
+    dontUseCmakeConfigure = true;
+    
+    propagatedBuildInputs = with final-py; [
+      numpy
+      scipy
+      sympy
+      antlr4-python3-runtime
+      #setuptools
+      jinja2
+      astropy
+      semver
+      odetoolbox
+    ];
+  };
+  
+  odetoolbox = let
+    pname = "ode-toolbox";
+    version = "2.5.8";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+
+    src = final.fetchFromGitHub {
+      owner = "nest";
+      repo = pname;
+      rev = "v${version}";
+      hash = "sha256-do/R9tNXVdeoqQO5ofetP7jdq9VUq4UotO6LH3LL6jI=";
+    };
+
+    buildInputs = with final-py; [
+      pytest
+      pytest-runner
+    ];    
+
+    doCheck = false;
+    
+    propagatedBuildInputs = with final-py; [
+      matplotlib
+      graphviz
+      sympy
+      scipy
+      numpy
+      cython
+    ];
+  };
+
+  pytest-runner = let
+    pname = "pytest-runner";
+    version = "6.0.0";
+  in final-py.buildPythonPackage {
+    inherit pname version;
+    pyproject = true;
+
+    src = final.fetchFromGitHub {
+      owner = "pytest-dev";
+      repo = pname;
+      rev = "v${version}";
+      leaveDotGit = true;
+      hash = "sha256-cfUqEu3vN2i8jKZcTxId8Q/T/ld25qBeXY63g0eJnPs=";
+    };
+
+    nativeBuildInputs = [
+      final.git
+    ];
+    
+    propagatedBuildInputs = with final-py; [
+      setuptools-scm
+    ];
+  };  
+
   mne-python = prev-py.mne-python.overridePythonAttrs (old: {
     pyproject = true;
     format = null;