Merge pull request #39 from mc-rtc/topic/cython

Add cython bindings

Author: arntanguy

README.md

@@ -10,7 +10,7 @@ Current status:
       Allows to build mc-rtc and configure its runtime dependencies (`robots`, `controllers`, `observers`, `plugins`)
 - [x] Run `MCFrankaControl` with real Panda robots
 - [x] `mc-rtc-magnum` support (with older `glfw/imgui/implot` as submodules, as done in `mc-rtc-superbuild`)
-- [ ] Robots - all most commonly used robots are supported:
+- [x] Robots - all most commonly used robots are supported:
   - [x] JVRC1
   - [x] HRP-2Kai
   - [x] HRP-4
@@ -24,9 +24,9 @@ Current status:
     - [ ] UR10
 - [ ] Controllers
   - [x] Rolkneematics `panda-prosthesis` (through downstream flake in `panda-prosthesis` repository)
-  - [ ] WIP: Hugo's polytopeController
+  - [x] Hugo's polytopeController
 - [ ] `mc-mujoco`: building and running but some HiDPI scaling issues on Wayland with glfw 3.4
-- [ ] magnum packaging (external): in progress
+- [x] magnum packaging
   - [x] magnum
     - [x] SDL2Application: works
     - [x] GlfwApplication:

module.nix

@@ -14,7 +14,7 @@ let
   rawOverlays = [
     {
       name = "mc-rtc-pkgs";
-      value = import ./overlay.nix { inherit with-ros; };
+      value = import ./overlay.nix { inherit lib with-ros; };
     }
   ]
   ++ (lib.optional enablePrivateOverlay {
@@ -69,9 +69,11 @@ in
           // {
             # Main dependencies
             inherit (pkgs)
+              eigen3-to-python
               spacevecalg
               rbdyn
               sch-core
+              sch-core-python
               tasks
               tasks-qld
               tvm

overlay.nix

@@ -6,6 +6,7 @@
     Use this to access and override existing packages, or to call functions from the underlying package set.
 */
 {
+  lib,
   with-ros ? false,
   ...
 }:
@@ -45,11 +46,13 @@
       '';
     });
 
+    eigen3-to-python = prev.callPackage ./pkgs/eigen3-to-python { };
     spacevecalg = prev.callPackage ./pkgs/spacevecalg { };
     rbdyn = prev.callPackage ./pkgs/rbdyn { };
     eigen-qld = prev.callPackage ./pkgs/eigen-qld { };
     eigen-quadprog = prev.callPackage ./pkgs/eigen-quadprog { };
     sch-core = prev.callPackage ./pkgs/sch-core { };
+    sch-core-python = prev.callPackage ./pkgs/sch-core-python { };
     #sch-visualization = prev.callPackage ./pkgs/sch-visualization {};
     sch-visualization = prev.callPackage ./pkgs/sch-visualization { };
     tasks-qld = prev.callPackage ./pkgs/tasks { };
@@ -221,7 +224,7 @@
     # This is not per-say recomended, but it can drastically reduce build time for these components, and also allow for seamless LSP integration in your editor.
     #
     # TODO: investigate use of ccacheStdenv
-    # mc-rtc-superbuild = prev.callPackage ./pkgs/mc-rtc/mc-rtc-superbuild-symlinkjoin.nix.nix {
+    # mc-rtc-superbuild = prev.callPackage ./pkgs/mc-rtc/mc-rtc-superbuild-symlinkjoin.nix.nix
 
     # minimal superbuild environment (jvrc1, mc_rtc_ticker)
     mc-rtc-superbuild-minimal = prev.callPackage ./pkgs/mc-rtc/mc-rtc-superbuild-standalone.nix {
@@ -265,5 +268,18 @@
     };
 
     sphinx-cmake = prev.callPackage ./pkgs/sphinx-cmake.nix { };
+
+    pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [
+      (
+        python-final: _python-prev:
+        {
+          # custom overrides would go here see gepetto/nix for examples
+        }
+        // lib.filesystem.packagesFromDirectoryRecursive {
+          inherit (python-final) callPackage;
+          directory = ./py-pkgs;
+        }
+      )
+    ];
   }
 )

pkgs/eigen3-to-python/default.nix

@@ -0,0 +1,80 @@
+{
+  stdenv,
+  lib,
+  cmake,
+  pkg-config,
+  eigen,
+  fetchFromGitHub,
+  python3Packages,
+}:
+
+stdenv.mkDerivation {
+  pname = "eigen3-to-python";
+  version = "1.0.7";
+
+  # pr 35
+  src = fetchFromGitHub {
+    owner = "Kooolkimooov";
+    repo = "Eigen3ToPython";
+    rev = "a1dfb35c204b2732d0b60d4d2bb6edb4c6941f59";
+    hash = "sha256-zNaMmaexyDBD2frMkO4z+Qj/AKtIxt6sRdwYcwoNJh8=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    python3Packages.cython
+    python3Packages.python
+    python3Packages.distutils
+    python3Packages.pytest
+    python3Packages.pip
+  ];
+
+  propagatedBuildInputs = [
+    eigen
+    python3Packages.numpy
+  ];
+
+  cmakeFlags = [
+    "-DPIP_INSTALL_PREFIX=$out/lib/python3"
+    "-DCMAKE_BUILD_TYPE=Release"
+    "-DCYTHON_USE_CACHE=OFF"
+  ];
+
+  # Force pip to ignore the EXTERNALLY-MANAGED restriction in the sandbox
+  PIP_BREAK_SYSTEM_PACKAGES = 1;
+  # Force pip to use the Nix-provided python packages instead of checking PyPI
+  PIP_NO_BUILD_ISOLATION = 1;
+
+  # Force Cython/Python to use the build directory for caching instead of /homeless-shelter
+  preBuild = ''
+    export HOME=$TMPDIR
+  '';
+
+  doCheck = true;
+
+  # Override the default CMake install step
+  installPhase = ''
+    runHook preInstall
+
+    # 1. Define the destination directory inside the Nix store output
+    # Using python.sitePackages handles the "lib/python3.13/site-packages" string automatically
+    local targetDir="$out/${python3Packages.python.sitePackages}/eigen"
+    mkdir -p "$targetDir"
+
+    ls -lR
+
+    # 2. Copy your built files from the build tree to the target store path
+    # (Adjust 'build/python/Release/eigen/' path if your build folder structure differs slightly)
+    cp -r python/Release/eigen/* "$targetDir"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Provide Eigen3 to numpy conversion";
+    homepage = "https://github.com/jrl-umi3218/Eigen3ToPython";
+    license = licenses.bsd2;
+    platforms = platforms.all;
+  };
+}

pkgs/mc-rtc/mc-rtc-common.nix

@@ -4,11 +4,12 @@
 
 let
   version = "2.14.1";
+  # TODO: PR 538
   src = fetchFromGitHub {
-    owner = "jrl-umi3218";
+    owner = "Kooolkimooov";
     repo = "mc_rtc";
-    rev = "d1bb28f9bfab85a04ce1ff103289676cfa5bf4fc";
-    hash = "sha256-a8Wh5Xhvs+vM7k0uEJzSDCSUOK58AJSRSJx3XyboHO0=";
+    rev = "2846f365824531f162635323d0c32796842e02a8";
+    hash = "sha256-zTxxZOZCwlMGrRGG8B9kRLJcCvXLvYSigej8yDpihwg=";
   };
 in
 {

pkgs/mc-rtc/mc-rtc.nix

@@ -15,6 +15,7 @@
   libtool,
   geos,
   spdlog,
+  fmt,
   ndcurves,
   mc-rtc-data,
   state-observation,
@@ -23,9 +24,8 @@
   rapidjson,
   boost,
   mesh-sampling,
-  python313Packages,
+  python3Packages,
   qt5,
-  eigen-fmt,
   doxygen,
   bundler, # Ruby for bundle dependencies
   with-ros ? false,
@@ -61,6 +61,10 @@ in
     pkg-config
     jrl-cmakemodules
     qt5.wrapQtAppsHook
+    python3Packages.distutils
+    python3Packages.pytest
+    python3Packages.cython
+    python3Packages.python
   ]
   ++ [
     # for documentation
@@ -83,13 +87,16 @@ in
     rapidjson
     boost
     mesh-sampling
-    eigen-fmt
-  ]
-  ++ [
-    python313Packages.gitpython
-    python313Packages.pyqt5
-    python313Packages.matplotlib
+    fmt
+    python3Packages.tasks
   ]
+  ++
+    # for python utils (mc_rtc_new_fsm_controller, mc_log_ui, etc)
+    [
+      python3Packages.gitpython
+      python3Packages.pyqt5
+      python3Packages.matplotlib
+    ]
   ++ lib.optional (with-ros && rclcpp != null) rclcpp
   ++ lib.optional (with-ros && nav-msgs != null) nav-msgs
   ++ lib.optional (with-ros && sensor-msgs != null) sensor-msgs
@@ -106,7 +113,6 @@ in
   cmakeFlags = [
     "-DBUILD_MC_RTC_PYTHON_UTILS=ON"
     "-DBUILD_TESTING=OFF"
-    "-DPYTHON_BINDING=OFF"
     "-DINSTALL_DOCUMENTATION=ON"
   ];
 

pkgs/rbdyn/default.nix

@@ -7,6 +7,7 @@
   tinyxml-2,
   boost,
   fetchurl,
+  python3Packages,
 }:
 
 stdenv.mkDerivation rec {
@@ -18,20 +19,26 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-IFqX4z8r2JTwgNnPB35/vZKwgWoPO78ebnUvPdNOnjY=";
   };
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [
+    cmake
+    python3Packages.cython
+    python3Packages.python
+    python3Packages.distutils
+    python3Packages.pytest
+  ];
+
   propagatedBuildInputs = [
     spacevecalg
     yaml-cpp
     tinyxml-2
     boost
+    python3Packages.spacevecalg
   ]; # Add other dependencies here
 
-  postPatch = ''
-    # Remove the include from the main CMakeLists.txt
-    sed -i '/include(cmake\/cython\/cython.cmake)/d' CMakeLists.txt
-
-    # Add the include to the top of the python binding CMakeLists.txt
-    sed -i '1i include(cmake/cython/cython.cmake)' binding/python/CMakeLists.txt
+  # XXX: Without this fixupPhase fails due to RPATHS references to /build/
+  preFixup = ''
+    patchelf --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" $out/${python3Packages.python.sitePackages}/rbdyn/rbdyn.so
+    patchelf --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" $out/${python3Packages.python.sitePackages}/rbdyn/parsers/parsers.so
   '';
 
   doCheck = true;

pkgs/sch-core-python/default.nix

@@ -0,0 +1,65 @@
+{
+  lib,
+  stdenv,
+  cmake,
+  sch-core,
+  spacevecalg,
+  python3Packages,
+  fetchFromGitHub,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "sch-core-python";
+  version = "1.0.5";
+
+  src = fetchFromGitHub {
+    owner = "jrl-umi3218";
+    repo = "sch-core-python";
+    rev = "9b4a7d8189de30dc49edc7ccb0e1283e85686e62";
+    hash = "sha256-Ml0fATe61R7tJ5m20Y7hjDwCa/WwIIG3f+qwV1zSz8k=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    python3Packages.cython
+    python3Packages.python
+    python3Packages.distutils
+    python3Packages.pytest
+  ];
+  propagatedBuildInputs = [
+    sch-core
+    spacevecalg
+    python3Packages.spacevecalg
+  ];
+
+  cmakeFlags = [
+    "-DINSTALL_DOCUMENTATION=OFF"
+  ];
+
+  # Override the default CMake install step
+  installPhase = ''
+    runHook preInstall
+
+    # 1. Define the destination directory inside the Nix store output
+    # Using python.sitePackages handles the "lib/python3.13/site-packages" string automatically
+    local targetDir="$out/${python3Packages.python.sitePackages}/sch"
+    mkdir -p "$targetDir"
+
+    ls -lR
+
+    # 2. Copy your built files from the build tree to the target store path
+    # (Adjust 'build/python/Release/eigen/' path if your build folder structure differs slightly)
+    cp -r python/Release/sch/* "$targetDir"
+
+    runHook postInstall
+  '';
+
+  doCheck = false;
+
+  meta = with lib; {
+    description = "sch-core: python bindings for sch-core - effective proximity queries";
+    homepage = "https://github.com/jrl-umi3218/sch-core-python";
+    license = licenses.bsd2;
+    platforms = platforms.all;
+  };
+}