From 5eacb43e8f0e17b474c947d89f59eeb772310f8f Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Thu, 12 Sep 2024 11:37:55 +0200
Subject: [PATCH 01/36] jrl-cmakemodules: update to 0-unstable-2024-09-17

---
 pkgs/by-name/jr/jrl-cmakemodules/package.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/jr/jrl-cmakemodules/package.nix b/pkgs/by-name/jr/jrl-cmakemodules/package.nix
index 8dc01688de66..8ad3f29eac2e 100644
--- a/pkgs/by-name/jr/jrl-cmakemodules/package.nix
+++ b/pkgs/by-name/jr/jrl-cmakemodules/package.nix
@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation {
   pname = "jrl-cmakemodules";
-  version = "0-unstable-2024-08-05";
+  version = "0-unstable-2024-09-17";
 
   src = fetchFromGitHub {
     owner = "jrl-umi3218";
     repo = "jrl-cmakemodules";
-    rev = "88d3cb561d1f9faa3c6281da7b2b8d6aa76b04d5";
-    hash = "sha256-3Su/tGtV39/tto1Hs5sgGgjpFWkBCvI2SZKqBIIDAjA=";
+    rev = "31e46019beda968ba9e516ad645a951c64256eed";
+    hash = "sha256-pe21tE0ngUYGhEuGSI71TMdwyqTmZhc53hPKHngkTGQ=";
   };
 
   nativeBuildInputs = [ cmake ];

From 720ee922ce08d2eb84fa3f24b9db3092f4e28aea Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:41:55 +0200
Subject: [PATCH 02/36] jrl-cmakemodules: set platforms

---
 pkgs/by-name/jr/jrl-cmakemodules/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/jr/jrl-cmakemodules/package.nix b/pkgs/by-name/jr/jrl-cmakemodules/package.nix
index 8ad3f29eac2e..22c9bafe6425 100644
--- a/pkgs/by-name/jr/jrl-cmakemodules/package.nix
+++ b/pkgs/by-name/jr/jrl-cmakemodules/package.nix
@@ -23,5 +23,6 @@ stdenv.mkDerivation {
     homepage = "https://github.com/jrl-umi3218/jrl-cmakemodules";
     license = lib.licenses.lgpl3Plus;
     maintainers = [ lib.maintainers.nim65s ];
+    platforms = lib.platforms.all;
   };
 }

From 3cb8663422a3517782c0b2d574e778ae5177dd24 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 27 Aug 2024 11:32:56 +0200
Subject: [PATCH 03/36] proxsuite: 0.6.6 -> 0.6.7

Diff: https://github.com/simple-robotics/proxsuite/compare/v0.6.6...v0.6.7
---
 pkgs/by-name/pr/proxsuite/package.nix | 39 ++++++---------------------
 1 file changed, 8 insertions(+), 31 deletions(-)

diff --git a/pkgs/by-name/pr/proxsuite/package.nix b/pkgs/by-name/pr/proxsuite/package.nix
index dcaf8bc6f7f2..eb3b28d5520c 100644
--- a/pkgs/by-name/pr/proxsuite/package.nix
+++ b/pkgs/by-name/pr/proxsuite/package.nix
@@ -3,7 +3,7 @@
   stdenv,
   fetchFromGitHub,
   fetchpatch,
-  cereal,
+  cereal_1_3_2,
   cmake,
   doxygen,
   eigen,
@@ -15,47 +15,24 @@
 }:
 stdenv.mkDerivation (finalAttrs: {
   pname = "proxsuite";
-  version = "0.6.6";
+  version = "0.6.7";
 
   src = fetchFromGitHub {
     owner = "simple-robotics";
     repo = "proxsuite";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-3kzFYADk3sCMU827KowilPlmOqgv69DJ3mOb7623Qdg=";
+    hash = "sha256-iKc55WDHArmmIM//Wir6FHrNV84HnEDcBUlwnsbtMME=";
   };
 
   patches = [
-    # Allow use of system jrl-cmakemodules
-    # This was merged upstream, and can be removed on next release
+    # Fix use of system cereal
+    # This was merged upstream and can be removed on next release
     (fetchpatch {
-      url = "https://github.com/Simple-Robotics/proxsuite/pull/334/commits/2bcadd4993a9940c545136faa71bf1e97a972735.patch";
-      hash = "sha256-BPtwogSwSXcEd5FM4eTTCq6LpGWvQ1SOCFmv/GVhl18=";
-    })
-    # Allow use of system cereal
-    # This was merged upstream, and can be removed on next release
-    (fetchpatch {
-      url = "https://github.com/Simple-Robotics/proxsuite/pull/334/commits/878337c6284c9fd73b19f1f80d5fa802def8cdc6.patch";
-      hash = "sha256-+HWYHLGtygjlvjM+FSD9WFDIwO+qPLlzci+7q42bo0I=";
-    })
-    # Allow use of system pybind11
-    # upstream will move to nanobind for next release, so this can be dismissed
-    (fetchpatch {
-      url = "https://github.com/Simple-Robotics/proxsuite/pull/337/commits/bbed9bdfb214da7c6c6909582971bd8b877f87c2.patch";
-      hash = "sha256-pYikPZinjmk7gsagiaIcQspmGFYwlhdiKdZPnqo7pcQ=";
+      url = "https://github.com/Simple-Robotics/proxsuite/pull/352/commits/8305864f13ca7dff7210f89004a56652b71f8891.patch";
+      hash = "sha256-XMS/zHFVrEp1P6aDlGrLbrcmuKq42+GdZRH9ObewNCY=";
     })
   ];
 
-  postPatch = ''
-    # discard failing tests for now
-    substituteInPlace test/CMakeLists.txt \
-      --replace-fail "proxsuite_test(dense_maros_meszaros src/dense_maros_meszaros.cpp)" "" \
-      --replace-fail "proxsuite_test(sparse_maros_meszaros src/sparse_maros_meszaros.cpp)" ""
-
-    # fix CMake syntax
-    substituteInPlace bindings/python/CMakeLists.txt \
-      --replace-fail "SYSTEM PRIVATE" "PRIVATE"
-  '';
-
   outputs = [
     "doc"
     "out"
@@ -78,7 +55,7 @@ stdenv.mkDerivation (finalAttrs: {
     doxygen
   ];
   propagatedBuildInputs = [
-    cereal
+    cereal_1_3_2
     eigen
     jrl-cmakemodules
     simde

From d33c80812d8aacfa4c68c0e2e7648ba5bd78305b Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:44:33 +0200
Subject: [PATCH 04/36] proxsuite: fix doc

---
 pkgs/by-name/pr/proxsuite/package.nix | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pkgs/by-name/pr/proxsuite/package.nix b/pkgs/by-name/pr/proxsuite/package.nix
index eb3b28d5520c..248be6e3e1fa 100644
--- a/pkgs/by-name/pr/proxsuite/package.nix
+++ b/pkgs/by-name/pr/proxsuite/package.nix
@@ -7,6 +7,8 @@
   cmake,
   doxygen,
   eigen,
+  fontconfig,
+  graphviz,
   jrl-cmakemodules,
   simde,
   matio,
@@ -53,6 +55,7 @@ stdenv.mkDerivation (finalAttrs: {
   nativeBuildInputs = [
     cmake
     doxygen
+    graphviz
   ];
   propagatedBuildInputs = [
     cereal_1_3_2
@@ -67,6 +70,12 @@ stdenv.mkDerivation (finalAttrs: {
       python3Packages.scipy
     ];
 
+  # Fontconfig error: Cannot load default config file: No such file: (null)
+  env.FONTCONFIG_FILE = "${fontconfig.out}/etc/fonts/fonts.conf";
+
+  # Fontconfig error: No writable cache directories
+  preBuild = "export XDG_CACHE_HOME=$(mktemp -d)";
+
   doCheck = true;
 
   meta = {

From f49ed4e558818197ab3576ed91d24d28d053e311 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:44:43 +0200
Subject: [PATCH 05/36] proxsuite: python import check

---
 pkgs/by-name/pr/proxsuite/package.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/pr/proxsuite/package.nix b/pkgs/by-name/pr/proxsuite/package.nix
index 248be6e3e1fa..2727d13022f5 100644
--- a/pkgs/by-name/pr/proxsuite/package.nix
+++ b/pkgs/by-name/pr/proxsuite/package.nix
@@ -56,7 +56,7 @@ stdenv.mkDerivation (finalAttrs: {
     cmake
     doxygen
     graphviz
-  ];
+  ] ++ lib.optional pythonSupport python3Packages.pythonImportsCheckHook;
   propagatedBuildInputs = [
     cereal_1_3_2
     eigen
@@ -77,6 +77,7 @@ stdenv.mkDerivation (finalAttrs: {
   preBuild = "export XDG_CACHE_HOME=$(mktemp -d)";
 
   doCheck = true;
+  pythonImportsCheck = [ "proxsuite" ];
 
   meta = {
     description = "The Advanced Proximal Optimization Toolbox";

From f56b1eff0a48175c0d374ee64fd16f710abfa383 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:44:53 +0200
Subject: [PATCH 06/36] proxsuite: set platforms

---
 pkgs/by-name/pr/proxsuite/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/pr/proxsuite/package.nix b/pkgs/by-name/pr/proxsuite/package.nix
index 2727d13022f5..6aba0e20c76e 100644
--- a/pkgs/by-name/pr/proxsuite/package.nix
+++ b/pkgs/by-name/pr/proxsuite/package.nix
@@ -84,5 +84,6 @@ stdenv.mkDerivation (finalAttrs: {
     homepage = "https://github.com/Simple-Robotics/proxsuite";
     license = lib.licenses.bsd2;
     maintainers = with lib.maintainers; [ nim65s ];
+    platforms = lib.platforms.unix;
   };
 })

From 547fc589b92be01ac001fcff5587dc1cec6f66f8 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:49:24 +0200
Subject: [PATCH 07/36] hpp-fcl: use pythonImportsCheckHook

---
 pkgs/by-name/hp/hpp-fcl/package.nix | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/pkgs/by-name/hp/hpp-fcl/package.nix b/pkgs/by-name/hp/hpp-fcl/package.nix
index 78ce6456c301..17812ffbea8d 100644
--- a/pkgs/by-name/hp/hpp-fcl/package.nix
+++ b/pkgs/by-name/hp/hpp-fcl/package.nix
@@ -31,7 +31,10 @@ stdenv.mkDerivation (finalAttrs: {
   nativeBuildInputs = [
     cmake
     doxygen
-  ] ++ lib.optionals pythonSupport [ python3Packages.numpy ];
+  ] ++ lib.optionals pythonSupport [
+    python3Packages.numpy
+    python3Packages.pythonImportsCheckHook
+  ];
 
   propagatedBuildInputs =
     [
@@ -56,11 +59,7 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   doCheck = true;
-  # pythonImportsCheck, but in stdenv.mkDerivation
-  postInstall = lib.optionalString pythonSupport ''
-    PYTHONPATH=$out/${python3Packages.python.sitePackages}:$PYTHONPATH
-    python -c "import hppfcl"
-  '';
+  pythonImportsCheck = [ "hppfcl" ];
 
   outputs = [
     "dev"

From 5edda6c9d0e137b725ede3f241c24dd2f2c83c24 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:49:36 +0200
Subject: [PATCH 08/36] hpp-fcl: set platforms

---
 pkgs/by-name/hp/hpp-fcl/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/hp/hpp-fcl/package.nix b/pkgs/by-name/hp/hpp-fcl/package.nix
index 17812ffbea8d..1c20411b1184 100644
--- a/pkgs/by-name/hp/hpp-fcl/package.nix
+++ b/pkgs/by-name/hp/hpp-fcl/package.nix
@@ -76,5 +76,6 @@ stdenv.mkDerivation (finalAttrs: {
     homepage = "https://github.com/humanoid-path-planner/hpp-fcl";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ nim65s ];
+    platforms = lib.platforms.unix;
   };
 })

From 92f4e6f3c344e60c244f1dbe4c638c27c2519627 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 10:19:22 +0200
Subject: [PATCH 09/36] hpp-fcl: format

---
 pkgs/by-name/hp/hpp-fcl/package.nix | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/pkgs/by-name/hp/hpp-fcl/package.nix b/pkgs/by-name/hp/hpp-fcl/package.nix
index 1c20411b1184..80e715425034 100644
--- a/pkgs/by-name/hp/hpp-fcl/package.nix
+++ b/pkgs/by-name/hp/hpp-fcl/package.nix
@@ -28,13 +28,15 @@ stdenv.mkDerivation (finalAttrs: {
 
   strictDeps = true;
 
-  nativeBuildInputs = [
-    cmake
-    doxygen
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.numpy
-    python3Packages.pythonImportsCheckHook
-  ];
+  nativeBuildInputs =
+    [
+      cmake
+      doxygen
+    ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.numpy
+      python3Packages.pythonImportsCheckHook
+    ];
 
   propagatedBuildInputs =
     [

From 696bd353a6f6aa5b4accd95bc8a04852bf5fe6e1 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Mon, 16 Sep 2024 08:56:16 +0200
Subject: [PATCH 10/36] pinocchio: set MPLCONFIGDIR in check

fix:

> Matplotlib created a temporary cache directory at
> /private/tmp/nix-build-pinocchio-3.2.0.drv-0/matplotlib-cgeg512t
> because the default path (/homeless-shelter/.matplotlib) is not a
> writable directory; it is highly recommended to set the MPLCONFIGDIR
> environment variable to a writable directory, in particular to speed
> up the import of Matplotlib and to better support multiprocessing.
---
 pkgs/development/libraries/pinocchio/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/development/libraries/pinocchio/default.nix b/pkgs/development/libraries/pinocchio/default.nix
index e03ac9ee854d..33fb913ca9e9 100644
--- a/pkgs/development/libraries/pinocchio/default.nix
+++ b/pkgs/development/libraries/pinocchio/default.nix
@@ -41,6 +41,9 @@ stdenv.mkDerivation (finalAttrs: {
 
     # allow package:// uri use in examples
     export ROS_PACKAGE_PATH=${example-robot-data}/share
+
+    # silence matplotlib warning
+    export MPLCONFIGDIR=$(mktemp -d)
   '';
 
   # CMAKE_BUILD_TYPE defaults to Release in this package,

From 4b7ee3013e569488a9b587b9dde7f437e301fcd3 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Mon, 16 Sep 2024 09:03:31 +0200
Subject: [PATCH 11/36] pinocchio: use pythonImportsCheckHook

---
 pkgs/development/libraries/pinocchio/default.nix | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/libraries/pinocchio/default.nix b/pkgs/development/libraries/pinocchio/default.nix
index 33fb913ca9e9..238ae8d46337 100644
--- a/pkgs/development/libraries/pinocchio/default.nix
+++ b/pkgs/development/libraries/pinocchio/default.nix
@@ -59,6 +59,7 @@ stdenv.mkDerivation (finalAttrs: {
     cmake
   ] ++ lib.optionals pythonSupport [
     python3Packages.python
+    python3Packages.pythonImportsCheckHook
   ];
 
   propagatedBuildInputs = [
@@ -91,12 +92,7 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   doCheck = true;
-
-  # pythonImportsCheck, but in stdenv.mkDerivation
-  postInstall = lib.optionalString pythonSupport ''
-    PYTHONPATH=$out/${python3Packages.python.sitePackages}:$PYTHONPATH
-    python -c "import pinocchio"
-  '';
+  pythonImportsCheck = [ "pinocchio" ];
 
   meta = {
     description = "Fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives";

From 49518d287b1f3221e6481e88192258f0a93cb690 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:52:06 +0200
Subject: [PATCH 12/36] pinocchio: move to pkgs/by-name

---
 .../pinocchio/default.nix => by-name/pi/pinocchio/package.nix}  | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{development/libraries/pinocchio/default.nix => by-name/pi/pinocchio/package.nix} (100%)

diff --git a/pkgs/development/libraries/pinocchio/default.nix b/pkgs/by-name/pi/pinocchio/package.nix
similarity index 100%
rename from pkgs/development/libraries/pinocchio/default.nix
rename to pkgs/by-name/pi/pinocchio/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 03e316163bcd..02e5add33ed2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -22977,8 +22977,6 @@ with pkgs;
 
   pingvin-share =  callPackage ../servers/pingvin-share { };
 
-  pinocchio = callPackage ../development/libraries/pinocchio { };
-
   pipelight = callPackage ../tools/misc/pipelight {
     stdenv = stdenv_32bit;
     wine-staging = pkgsi686Linux.wine-staging;

From f048cdeba0b5112a95656e87979b168a8384d5c6 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:52:22 +0200
Subject: [PATCH 13/36] pinocchio: format

---
 pkgs/by-name/pi/pinocchio/package.nix | 87 ++++++++++++++-------------
 1 file changed, 45 insertions(+), 42 deletions(-)

diff --git a/pkgs/by-name/pi/pinocchio/package.nix b/pkgs/by-name/pi/pinocchio/package.nix
index 238ae8d46337..ff1b5cf9572f 100644
--- a/pkgs/by-name/pi/pinocchio/package.nix
+++ b/pkgs/by-name/pi/pinocchio/package.nix
@@ -1,19 +1,20 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, casadi
-, cmake
-, boost
-, eigen
-, example-robot-data
-, casadiSupport ? true
-, collisionSupport ? true
-, console-bridge
-, jrl-cmakemodules
-, hpp-fcl
-, urdfdom
-, pythonSupport ? false
-, python3Packages
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  casadi,
+  cmake,
+  boost,
+  eigen,
+  example-robot-data,
+  casadiSupport ? true,
+  collisionSupport ? true,
+  console-bridge,
+  jrl-cmakemodules,
+  hpp-fcl,
+  urdfdom,
+  pythonSupport ? false,
+  python3Packages,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -55,32 +56,31 @@ stdenv.mkDerivation (finalAttrs: {
 
   strictDeps = true;
 
-  nativeBuildInputs = [
-    cmake
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.python
-    python3Packages.pythonImportsCheckHook
-  ];
+  nativeBuildInputs =
+    [ cmake ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.python
+      python3Packages.pythonImportsCheckHook
+    ];
 
-  propagatedBuildInputs = [
-    console-bridge
-    jrl-cmakemodules
-    urdfdom
-  ] ++ lib.optionals (!pythonSupport) [
-    boost
-    eigen
-  ] ++ lib.optionals (!pythonSupport && collisionSupport) [
-    hpp-fcl
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.boost
-    python3Packages.eigenpy
-  ] ++ lib.optionals (pythonSupport && collisionSupport) [
-    python3Packages.hpp-fcl
-  ] ++ lib.optionals (!pythonSupport && casadiSupport) [
-    casadi
-  ] ++ lib.optionals (pythonSupport && casadiSupport) [
-    python3Packages.casadi
-  ];
+  propagatedBuildInputs =
+    [
+      console-bridge
+      jrl-cmakemodules
+      urdfdom
+    ]
+    ++ lib.optionals (!pythonSupport) [
+      boost
+      eigen
+    ]
+    ++ lib.optionals (!pythonSupport && collisionSupport) [ hpp-fcl ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.boost
+      python3Packages.eigenpy
+    ]
+    ++ lib.optionals (pythonSupport && collisionSupport) [ python3Packages.hpp-fcl ]
+    ++ lib.optionals (!pythonSupport && casadiSupport) [ casadi ]
+    ++ lib.optionals (pythonSupport && casadiSupport) [ python3Packages.casadi ];
 
   checkInputs = lib.optionals (pythonSupport && casadiSupport) [ python3Packages.matplotlib ];
 
@@ -98,7 +98,10 @@ stdenv.mkDerivation (finalAttrs: {
     description = "Fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives";
     homepage = "https://github.com/stack-of-tasks/pinocchio";
     license = lib.licenses.bsd2;
-    maintainers = with lib.maintainers; [ nim65s wegank ];
+    maintainers = with lib.maintainers; [
+      nim65s
+      wegank
+    ];
     platforms = lib.platforms.unix;
   };
 })

From da033dc206c64ba954d740f7f982db5028a19cfa Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 12:20:46 +0200
Subject: [PATCH 14/36] pinocchio: build documentation

---
 pkgs/by-name/pi/pinocchio/package.nix | 32 ++++++++++++++++++---------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/pkgs/by-name/pi/pinocchio/package.nix b/pkgs/by-name/pi/pinocchio/package.nix
index ff1b5cf9572f..e754078a3805 100644
--- a/pkgs/by-name/pi/pinocchio/package.nix
+++ b/pkgs/by-name/pi/pinocchio/package.nix
@@ -1,20 +1,22 @@
 {
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  casadi,
-  cmake,
   boost,
-  eigen,
-  example-robot-data,
+  casadi,
   casadiSupport ? true,
+  cmake,
   collisionSupport ? true,
   console-bridge,
-  jrl-cmakemodules,
+  doxygen,
+  eigen,
+  example-robot-data,
+  fetchFromGitHub,
   hpp-fcl,
-  urdfdom,
+  jrl-cmakemodules,
+  lib,
+  pkg-config,
   pythonSupport ? false,
   python3Packages,
+  stdenv,
+  urdfdom,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -28,6 +30,11 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-8V+n1TwFojXKOVkGG8k9aXVadt2NBFlZKba93L+NRNU=";
   };
 
+  outputs = [
+    "out"
+    "doc"
+  ];
+
   # test failure, ref https://github.com/stack-of-tasks/pinocchio/issues/2277
   prePatch = lib.optionalString (stdenv.isLinux && stdenv.isAarch64) ''
     substituteInPlace unittest/algorithm/utils/CMakeLists.txt \
@@ -57,7 +64,11 @@ stdenv.mkDerivation (finalAttrs: {
   strictDeps = true;
 
   nativeBuildInputs =
-    [ cmake ]
+    [
+      cmake
+      doxygen
+      pkg-config
+    ]
     ++ lib.optionals pythonSupport [
       python3Packages.python
       python3Packages.pythonImportsCheckHook
@@ -89,6 +100,7 @@ stdenv.mkDerivation (finalAttrs: {
     (lib.cmakeBool "BUILD_WITH_LIBPYTHON" pythonSupport)
     (lib.cmakeBool "BUILD_WITH_CASADI_SUPPORT" casadiSupport)
     (lib.cmakeBool "BUILD_WITH_COLLISION_SUPPORT" collisionSupport)
+    (lib.cmakeBool "INSTALL_DOCUMENTATION" true)
   ];
 
   doCheck = true;

From 1e402edf61e73d7c77ef57b316a101e76bdb850e Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Mon, 1 Jul 2024 14:20:50 +0200
Subject: [PATCH 15/36] example-robot-data: propagate pinocchio

---
 pkgs/development/libraries/example-robot-data/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/example-robot-data/default.nix b/pkgs/development/libraries/example-robot-data/default.nix
index d4211be982ef..39ccda1b6309 100644
--- a/pkgs/development/libraries/example-robot-data/default.nix
+++ b/pkgs/development/libraries/example-robot-data/default.nix
@@ -37,7 +37,7 @@ stdenv.mkDerivation (finalAttrs: {
     python3Packages.python
   ];
 
-  buildInputs = lib.optionals pythonSupport [
+  propagatedBuildInputs = lib.optionals pythonSupport [
     python3Packages.pinocchio
   ];
 

From b94714421b4bcc18f7d2449c8f56f54e75ae2527 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 16:15:13 +0200
Subject: [PATCH 16/36] example-robot-data: use pythonImportsCheckHook

---
 pkgs/development/libraries/example-robot-data/default.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/development/libraries/example-robot-data/default.nix b/pkgs/development/libraries/example-robot-data/default.nix
index 39ccda1b6309..a67c16cf0a4e 100644
--- a/pkgs/development/libraries/example-robot-data/default.nix
+++ b/pkgs/development/libraries/example-robot-data/default.nix
@@ -35,6 +35,7 @@ stdenv.mkDerivation (finalAttrs: {
     cmake
   ] ++ lib.optionals pythonSupport [
     python3Packages.python
+    python3Packages.pythonImportsCheckHook
   ];
 
   propagatedBuildInputs = lib.optionals pythonSupport [

From 85e430220204641cf2f7da5f635a3d0936b991b5 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 16:15:44 +0200
Subject: [PATCH 17/36] example-robot-data: clean cmakeFlags

---
 pkgs/development/libraries/example-robot-data/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/libraries/example-robot-data/default.nix b/pkgs/development/libraries/example-robot-data/default.nix
index a67c16cf0a4e..551d7b72479d 100644
--- a/pkgs/development/libraries/example-robot-data/default.nix
+++ b/pkgs/development/libraries/example-robot-data/default.nix
@@ -42,8 +42,8 @@ stdenv.mkDerivation (finalAttrs: {
     python3Packages.pinocchio
   ];
 
-  cmakeFlags = lib.optionals (!pythonSupport) [
-    "-DBUILD_PYTHON_INTERFACE=OFF"
+  cmakeFlags =  [
+    (lib.cmakeBool "BUILD_PYTHON_INTERFACE" pythonSupport)
   ];
 
   doCheck = true;

From 1fd7006d7b5eaa6c28f9d748fb73bf6117571503 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 16:16:39 +0200
Subject: [PATCH 18/36] example-robot-data: move to pkgs/by-name

---
 .../default.nix => by-name/ex/example-robot-data/package.nix}   | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{development/libraries/example-robot-data/default.nix => by-name/ex/example-robot-data/package.nix} (100%)

diff --git a/pkgs/development/libraries/example-robot-data/default.nix b/pkgs/by-name/ex/example-robot-data/package.nix
similarity index 100%
rename from pkgs/development/libraries/example-robot-data/default.nix
rename to pkgs/by-name/ex/example-robot-data/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 02e5add33ed2..ab75913571da 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19832,8 +19832,6 @@ with pkgs;
 
   libesmtp = callPackage ../development/libraries/libesmtp { };
 
-  example-robot-data = callPackage ../development/libraries/example-robot-data { };
-
   exiv2 = callPackage ../development/libraries/exiv2 { };
 
   expat = callPackage ../development/libraries/expat { };

From 9d0031ed340620c104b2d1f8a3069a110804b535 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 16:16:53 +0200
Subject: [PATCH 19/36] example-robot-data: format

---
 .../by-name/ex/example-robot-data/package.nix | 44 +++++++++----------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/pkgs/by-name/ex/example-robot-data/package.nix b/pkgs/by-name/ex/example-robot-data/package.nix
index 551d7b72479d..a63fafed7fd4 100644
--- a/pkgs/by-name/ex/example-robot-data/package.nix
+++ b/pkgs/by-name/ex/example-robot-data/package.nix
@@ -1,10 +1,11 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, fetchpatch
-, cmake
-, pythonSupport ? false
-, python3Packages
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  cmake,
+  pythonSupport ? false,
+  python3Packages,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -31,35 +32,32 @@ stdenv.mkDerivation (finalAttrs: {
     })
   ];
 
-  nativeBuildInputs = [
-    cmake
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.python
-    python3Packages.pythonImportsCheckHook
-  ];
+  nativeBuildInputs =
+    [ cmake ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.python
+      python3Packages.pythonImportsCheckHook
+    ];
 
-  propagatedBuildInputs = lib.optionals pythonSupport [
-    python3Packages.pinocchio
-  ];
+  propagatedBuildInputs = lib.optionals pythonSupport [ python3Packages.pinocchio ];
 
-  cmakeFlags =  [
-    (lib.cmakeBool "BUILD_PYTHON_INTERFACE" pythonSupport)
-  ];
+  cmakeFlags = [ (lib.cmakeBool "BUILD_PYTHON_INTERFACE" pythonSupport) ];
 
   doCheck = true;
   # The package expect to find an `example-robot-data/robots` folder somewhere
   # either in install prefix or in the sources
   # where it can find the meshes for unit tests
   preCheck = "ln -s source ../../${finalAttrs.pname}";
-  pythonImportsCheck = [
-    "example_robot_data"
-  ];
+  pythonImportsCheck = [ "example_robot_data" ];
 
   meta = with lib; {
     description = "Set of robot URDFs for benchmarking and developed examples";
     homepage = "https://github.com/Gepetto/example-robot-data";
     license = licenses.bsd3;
-    maintainers = with maintainers; [ nim65s wegank ];
+    maintainers = with maintainers; [
+      nim65s
+      wegank
+    ];
     platforms = platforms.unix;
   };
 })

From e84ff8070a8e9860c7d2d1ac4a6679d6cba975fc Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 12:17:20 +0200
Subject: [PATCH 20/36] example-robot-data: build documentation

---
 .../by-name/ex/example-robot-data/package.nix | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/pkgs/by-name/ex/example-robot-data/package.nix b/pkgs/by-name/ex/example-robot-data/package.nix
index a63fafed7fd4..63331bbf5a84 100644
--- a/pkgs/by-name/ex/example-robot-data/package.nix
+++ b/pkgs/by-name/ex/example-robot-data/package.nix
@@ -1,11 +1,13 @@
 {
-  lib,
-  stdenv,
+  cmake,
+  doxygen,
   fetchFromGitHub,
   fetchpatch,
-  cmake,
+  lib,
+  pkg-config,
   pythonSupport ? false,
   python3Packages,
+  stdenv,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -20,6 +22,11 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-Heq+c8SSYNO8ksTv5FphRBRStlTakm9T66jlPXon5tI=";
   };
 
+  outputs = [
+    "out"
+    "doc"
+  ];
+
   strictDeps = true;
 
   patches = [
@@ -33,7 +40,11 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   nativeBuildInputs =
-    [ cmake ]
+    [
+      cmake
+      doxygen
+      pkg-config
+    ]
     ++ lib.optionals pythonSupport [
       python3Packages.python
       python3Packages.pythonImportsCheckHook

From 5c9dd453f88acc4b731ac653d67873a83cd28f32 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:53:08 +0200
Subject: [PATCH 21/36] crocoddyl: use pythonImportsCheckHook

---
 pkgs/development/libraries/crocoddyl/default.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/development/libraries/crocoddyl/default.nix b/pkgs/development/libraries/crocoddyl/default.nix
index 046a6a014d1a..ac6efdc90c89 100644
--- a/pkgs/development/libraries/crocoddyl/default.nix
+++ b/pkgs/development/libraries/crocoddyl/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation (finalAttrs: {
     cmake
   ] ++ lib.optionals pythonSupport [
     python3Packages.python
+    python3Packages.pythonImportsCheckHook
   ];
 
   propagatedBuildInputs = lib.optionals (!pythonSupport) [

From 17d7e76bbdd31d6cc2be1d9705b8d8dcfee3de41 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:54:22 +0200
Subject: [PATCH 22/36] crocoddyl: move to pkgs/by-name

---
 .../crocoddyl/default.nix => by-name/cr/crocoddyl/package.nix}  | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{development/libraries/crocoddyl/default.nix => by-name/cr/crocoddyl/package.nix} (100%)

diff --git a/pkgs/development/libraries/crocoddyl/default.nix b/pkgs/by-name/cr/crocoddyl/package.nix
similarity index 100%
rename from pkgs/development/libraries/crocoddyl/default.nix
rename to pkgs/by-name/cr/crocoddyl/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ab75913571da..9ae026075589 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19663,8 +19663,6 @@ with pkgs;
 
   croaring = callPackage ../development/libraries/croaring { };
 
-  crocoddyl = callPackage ../development/libraries/crocoddyl { };
-
   crossguid = callPackage ../development/libraries/crossguid { };
 
   cryptopp = callPackage ../development/libraries/crypto++ { };

From f13a44ac822377063ed16e3f51088241ec12793b Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:54:31 +0200
Subject: [PATCH 23/36] crocoddyl: format

---
 pkgs/by-name/cr/crocoddyl/package.nix | 58 ++++++++++++++-------------
 1 file changed, 30 insertions(+), 28 deletions(-)

diff --git a/pkgs/by-name/cr/crocoddyl/package.nix b/pkgs/by-name/cr/crocoddyl/package.nix
index ac6efdc90c89..dba1442ac0ae 100644
--- a/pkgs/by-name/cr/crocoddyl/package.nix
+++ b/pkgs/by-name/cr/crocoddyl/package.nix
@@ -1,11 +1,12 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, cmake
-, example-robot-data
-, pinocchio
-, pythonSupport ? false
-, python3Packages
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  example-robot-data,
+  pinocchio,
+  pythonSupport ? false,
+  python3Packages,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -21,20 +22,22 @@ stdenv.mkDerivation (finalAttrs: {
 
   strictDeps = true;
 
-  nativeBuildInputs = [
-    cmake
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.python
-    python3Packages.pythonImportsCheckHook
-  ];
+  nativeBuildInputs =
+    [ cmake ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.python
+      python3Packages.pythonImportsCheckHook
+    ];
 
-  propagatedBuildInputs = lib.optionals (!pythonSupport) [
-    example-robot-data
-    pinocchio
-  ] ++ lib.optionals pythonSupport [
-    python3Packages.example-robot-data
-    python3Packages.pinocchio
-  ];
+  propagatedBuildInputs =
+    lib.optionals (!pythonSupport) [
+      example-robot-data
+      pinocchio
+    ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.example-robot-data
+      python3Packages.pinocchio
+    ];
 
   cmakeFlags = lib.optionals (!pythonSupport) [
     "-DBUILD_EXAMPLES=OFF"
@@ -49,18 +52,17 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   doCheck = true;
-  pythonImportsCheck = [
-    "crocoddyl"
-  ];
-  checkInputs = lib.optionals pythonSupport [
-    python3Packages.scipy
-  ];
+  pythonImportsCheck = [ "crocoddyl" ];
+  checkInputs = lib.optionals pythonSupport [ python3Packages.scipy ];
 
   meta = with lib; {
     description = "Crocoddyl optimal control library";
     homepage = "https://github.com/loco-3d/crocoddyl";
     license = licenses.bsd3;
-    maintainers = with maintainers; [ nim65s wegank ];
+    maintainers = with maintainers; [
+      nim65s
+      wegank
+    ];
     platforms = platforms.unix;
   };
 })

From a8dfcd8732924e10ff3c79a2ade4d9953fdaeced Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 11:52:04 +0200
Subject: [PATCH 24/36] crocoddyl: build documentation

---
 pkgs/by-name/cr/crocoddyl/package.nix | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/pkgs/by-name/cr/crocoddyl/package.nix b/pkgs/by-name/cr/crocoddyl/package.nix
index dba1442ac0ae..28f59d44d3e4 100644
--- a/pkgs/by-name/cr/crocoddyl/package.nix
+++ b/pkgs/by-name/cr/crocoddyl/package.nix
@@ -1,12 +1,14 @@
 {
-  lib,
-  stdenv,
-  fetchFromGitHub,
   cmake,
+  doxygen,
   example-robot-data,
+  fetchFromGitHub,
+  lib,
   pinocchio,
+  pkg-config,
   pythonSupport ? false,
   python3Packages,
+  stdenv,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -20,10 +22,19 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-SVV9sleDXLm2QJmNgL25XLHC3y5bfKab4GSlE8jbT8w=";
   };
 
+  outputs = [
+    "out"
+    "doc"
+  ];
+
   strictDeps = true;
 
   nativeBuildInputs =
-    [ cmake ]
+    [
+      cmake
+      doxygen
+      pkg-config
+    ]
     ++ lib.optionals pythonSupport [
       python3Packages.python
       python3Packages.pythonImportsCheckHook
@@ -39,9 +50,10 @@ stdenv.mkDerivation (finalAttrs: {
       python3Packages.pinocchio
     ];
 
-  cmakeFlags = lib.optionals (!pythonSupport) [
-    "-DBUILD_EXAMPLES=OFF"
-    "-DBUILD_PYTHON_INTERFACE=OFF"
+  cmakeFlags = [
+    (lib.cmakeBool "INSTALL_DOCUMENTATION" true)
+    (lib.cmakeBool "BUILD_EXAMPLES" pythonSupport)
+    (lib.cmakeBool "BUILD_PYTHON_INTERFACE" pythonSupport)
   ];
 
   prePatch = ''

From f25bd60c8acd77ce2942ec3cc3262a9cb3ca59c0 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 11:52:42 +0200
Subject: [PATCH 25/36] crocoddyl: update substituteInPlace use

---
 pkgs/by-name/cr/crocoddyl/package.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/by-name/cr/crocoddyl/package.nix b/pkgs/by-name/cr/crocoddyl/package.nix
index 28f59d44d3e4..3dd3058460ff 100644
--- a/pkgs/by-name/cr/crocoddyl/package.nix
+++ b/pkgs/by-name/cr/crocoddyl/package.nix
@@ -60,7 +60,7 @@ stdenv.mkDerivation (finalAttrs: {
     substituteInPlace \
       examples/CMakeLists.txt \
       examples/log/check_logfiles.sh \
-      --replace /bin/bash ${stdenv.shell}
+      --replace-fail /bin/bash ${stdenv.shell}
   '';
 
   doCheck = true;

From a2e568bb557fed13aec0de8f815a3c95bb50b6e9 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 12:08:41 +0200
Subject: [PATCH 26/36] crocoddyl: add optional dependencies

---
 pkgs/by-name/cr/crocoddyl/package.nix | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/cr/crocoddyl/package.nix b/pkgs/by-name/cr/crocoddyl/package.nix
index 3dd3058460ff..a1a283727743 100644
--- a/pkgs/by-name/cr/crocoddyl/package.nix
+++ b/pkgs/by-name/cr/crocoddyl/package.nix
@@ -1,8 +1,11 @@
 {
+  blas,
   cmake,
   doxygen,
   example-robot-data,
   fetchFromGitHub,
+  ipopt,
+  lapack,
   lib,
   pinocchio,
   pkg-config,
@@ -41,13 +44,19 @@ stdenv.mkDerivation (finalAttrs: {
     ];
 
   propagatedBuildInputs =
-    lib.optionals (!pythonSupport) [
+    [
+      blas
+      ipopt
+      lapack
+    ]
+    ++ lib.optionals (!pythonSupport) [
       example-robot-data
       pinocchio
     ]
     ++ lib.optionals pythonSupport [
       python3Packages.example-robot-data
       python3Packages.pinocchio
+      python3Packages.scipy
     ];
 
   cmakeFlags = [

From 641aa81f638b75ab44b2220441c39c5084f22707 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 15:56:10 +0200
Subject: [PATCH 27/36] eiquadprog: set platforms

---
 pkgs/by-name/ei/eiquadprog/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/ei/eiquadprog/package.nix b/pkgs/by-name/ei/eiquadprog/package.nix
index 9380e7f9d2bf..40696872fce9 100644
--- a/pkgs/by-name/ei/eiquadprog/package.nix
+++ b/pkgs/by-name/ei/eiquadprog/package.nix
@@ -34,5 +34,6 @@ stdenv.mkDerivation (finalAttrs: {
     changelog = "https://github.com/stack-of-tasks/eiquadprog/blob/v${finalAttrs.version}/CHANGELOG.md";
     license = lib.licenses.gpl3Only;
     maintainers = with lib.maintainers; [ nim65s ];
+    platforms = lib.platforms.unix;
   };
 })

From 784a937962b8488ca51aaecaa6232d0efa5fe0a2 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 12:14:59 +0200
Subject: [PATCH 28/36] eiquadprog: build documentation

---
 pkgs/by-name/ei/eiquadprog/package.nix | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pkgs/by-name/ei/eiquadprog/package.nix b/pkgs/by-name/ei/eiquadprog/package.nix
index 40696872fce9..70242a2aa9a0 100644
--- a/pkgs/by-name/ei/eiquadprog/package.nix
+++ b/pkgs/by-name/ei/eiquadprog/package.nix
@@ -1,10 +1,12 @@
 {
   boost,
   cmake,
+  doxygen,
   eigen,
   fetchFromGitHub,
   jrl-cmakemodules,
   lib,
+  pkg-config,
   stdenv,
 }:
 
@@ -19,8 +21,15 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-VqRx06sCCZrnB+NWm6Z9OMKzjKQIydGgKQU6fMY7phk=";
   };
 
+  outputs = [
+    "out"
+    "doc"
+  ];
+
   nativeBuildInputs = [
     cmake
+    doxygen
+    pkg-config
     jrl-cmakemodules
   ];
   propagatedBuildInputs = [ eigen ];

From 26f9c195cc10d412e01fb97afdf9f56e07057dd3 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 23:28:08 +0200
Subject: [PATCH 29/36] tsid: set platforms

---
 pkgs/by-name/ts/tsid/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/ts/tsid/package.nix b/pkgs/by-name/ts/tsid/package.nix
index 054857f8b222..80a5e1346bf2 100644
--- a/pkgs/by-name/ts/tsid/package.nix
+++ b/pkgs/by-name/ts/tsid/package.nix
@@ -62,5 +62,6 @@ stdenv.mkDerivation (finalAttrs: {
     homepage = "https://github.com/stack-of-tasks/tsid";
     license = lib.licenses.bsd2;
     maintainers = with lib.maintainers; [ nim65s ];
+    platforms = lib.platforms.unix;
   };
 })

From ad86b6f652c493cf8a7715b8eccdd5512d52c0b1 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 23:28:46 +0200
Subject: [PATCH 30/36] tsid: use pythonImportsCheckHook

---
 pkgs/by-name/ts/tsid/package.nix | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/pkgs/by-name/ts/tsid/package.nix b/pkgs/by-name/ts/tsid/package.nix
index 80a5e1346bf2..d1413f072d2e 100644
--- a/pkgs/by-name/ts/tsid/package.nix
+++ b/pkgs/by-name/ts/tsid/package.nix
@@ -36,11 +36,16 @@ stdenv.mkDerivation (finalAttrs: {
     "out"
   ];
 
-  nativeBuildInputs = [
-    doxygen
-    cmake
-    pkg-config
-  ] ++ lib.optional pythonSupport python3Packages.python;
+  nativeBuildInputs =
+    [
+      doxygen
+      cmake
+      pkg-config
+    ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.python
+      python3Packages.pythonImportsCheckHook
+    ];
 
   propagatedBuildInputs =
     [
@@ -51,11 +56,7 @@ stdenv.mkDerivation (finalAttrs: {
     ++ lib.optional (!pythonSupport) pinocchio ++ lib.optional pythonSupport python3Packages.pinocchio;
 
   doCheck = true;
-  # pythonImportsCheck, but in stdenv.mkDerivation
-  postInstall = lib.optionalString pythonSupport ''
-    PYTHONPATH=$out/${python3Packages.python.sitePackages}:$PYTHONPATH
-    python -c "import tsid"
-  '';
+  pythonImportsCheck = [ "tsid" ];
 
   meta = {
     description = "Efficient Task Space Inverse Dynamics (TSID) based on Pinocchio";

From c2a7f3309661ddc008553e891360c65e0c283200 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Wed, 18 Sep 2024 23:29:14 +0200
Subject: [PATCH 31/36] tsid: outputs out first

---
 pkgs/by-name/ts/tsid/package.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/by-name/ts/tsid/package.nix b/pkgs/by-name/ts/tsid/package.nix
index d1413f072d2e..0bd4b08b6025 100644
--- a/pkgs/by-name/ts/tsid/package.nix
+++ b/pkgs/by-name/ts/tsid/package.nix
@@ -32,8 +32,8 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   outputs = [
-    "doc"
     "out"
+    "doc"
   ];
 
   nativeBuildInputs =

From 22e19d0b933f6ca61b9f2221e96d7a5a66f17090 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Thu, 12 Sep 2024 11:32:04 +0200
Subject: [PATCH 32/36] aligator: init at v0.7.0

---
 pkgs/by-name/al/aligator/package.nix | 97 ++++++++++++++++++++++++++++
 pkgs/top-level/python-packages.nix   |  5 ++
 2 files changed, 102 insertions(+)
 create mode 100644 pkgs/by-name/al/aligator/package.nix

diff --git a/pkgs/by-name/al/aligator/package.nix b/pkgs/by-name/al/aligator/package.nix
new file mode 100644
index 000000000000..8b0eb712ce2e
--- /dev/null
+++ b/pkgs/by-name/al/aligator/package.nix
@@ -0,0 +1,97 @@
+{
+  cmake,
+  crocoddyl,
+  doxygen,
+  fetchFromGitHub,
+  fmt,
+  fontconfig,
+  gbenchmark,
+  graphviz,
+  lib,
+  llvmPackages, # llvm/Support/Host.h required by casadi 3.6.5 and not available in llvm 18
+  pinocchio,
+  pkg-config,
+  proxsuite-nlp,
+  python3Packages,
+  pythonSupport ? false,
+  stdenv,
+  suitesparse,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "aligator";
+  version = "0.7.0";
+
+  src = fetchFromGitHub {
+    owner = "Simple-Robotics";
+    repo = "aligator";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-397WWL3hb5Q/mic54s5LUuz54bh7vwG53WIq5ljDe7g=";
+  };
+
+  outputs = [
+    "doc"
+    "out"
+  ];
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    doxygen
+    cmake
+    graphviz
+    pkg-config
+  ] ++ lib.optional pythonSupport python3Packages.pythonImportsCheckHook;
+  buildInputs = [ fmt ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp;
+  propagatedBuildInputs =
+    [ suitesparse ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.crocoddyl
+      python3Packages.matplotlib
+      python3Packages.pinocchio
+      python3Packages.proxsuite-nlp
+    ]
+    ++ lib.optionals (!pythonSupport) [
+      crocoddyl
+      pinocchio
+      proxsuite-nlp
+    ];
+  checkInputs =
+    [ gbenchmark ]
+    ++ lib.optionals pythonSupport [
+      python3Packages.matplotlib
+      python3Packages.pytest
+    ];
+
+  cmakeFlags =
+    [
+      (lib.cmakeBool "BUILD_PYTHON_INTERFACE" pythonSupport)
+      (lib.cmakeBool "BUILD_WITH_PINOCCHIO_SUPPORT" true)
+      (lib.cmakeBool "BUILD_CROCODDYL_COMPAT" true)
+      (lib.cmakeBool "BUILD_WITH_OPENMP_SUPPORT" true)
+      (lib.cmakeBool "BUILD_WITH_CHOLMOD_SUPPORT" true)
+      (lib.cmakeBool "GENERATE_PYTHON_STUBS" false) # this need git at configure time
+    ]
+    ++ lib.optionals (stdenv.hostPlatform.isDarwin && pythonSupport) [
+      # ignore one failing test for now
+      (lib.cmakeFeature "CMAKE_CTEST_ARGUMENTS" "--exclude-regex;aligator-test-py-integrators")
+    ];
+
+  # Fontconfig error: Cannot load default config file: No such file: (null)
+  env.FONTCONFIG_FILE = "${fontconfig.out}/etc/fonts/fonts.conf";
+
+  # Fontconfig error: No writable cache directories
+  preBuild = "export XDG_CACHE_HOME=$(mktemp -d)";
+
+  doCheck = true;
+  pythonImportsCheck = [ "aligator" ];
+
+  meta = {
+    description = "Versatile and efficient framework for constrained trajectory optimization";
+    homepage = "https://github.com/Simple-Robotics/aligator";
+    changelog = "https://github.com/Simple-Robotics/aligator/blob/v${finalAttrs.version}/CHANGELOG.md";
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ nim65s ];
+    platforms = lib.platforms.unix;
+  };
+})
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 6e673f7f6a83..e4468a54ad4f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -521,6 +521,11 @@ self: super: with self; {
 
   algebraic-data-types = callPackage ../development/python-modules/algebraic-data-types { };
 
+  aligator = toPythonModule (pkgs.aligator.override {
+    python3Packages = self;
+    pythonSupport = true;
+  });
+
   alive-progress = callPackage ../development/python-modules/alive-progress { };
 
   aliyun-python-sdk-cdn = callPackage ../development/python-modules/aliyun-python-sdk-cdn { };

From d69eafbf4856045ba6fea3bf6c1989aa06813fea Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 17 Sep 2024 11:56:42 +0200
Subject: [PATCH 33/36] proxsuite-nlp: 0.7.1 -> 0.8.0

Diff: https://github.com/Simple-Robotics/proxsuite-nlp/compare/v0.7.1...v0.8.0

Changelog: https://github.com/Simple-Robotics/proxsuite-nlp/blob/v0.8.0/CHANGELOG.md
---
 pkgs/by-name/pr/proxsuite-nlp/package.nix | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/pkgs/by-name/pr/proxsuite-nlp/package.nix b/pkgs/by-name/pr/proxsuite-nlp/package.nix
index 234cc93febc7..211d9a634063 100644
--- a/pkgs/by-name/pr/proxsuite-nlp/package.nix
+++ b/pkgs/by-name/pr/proxsuite-nlp/package.nix
@@ -19,13 +19,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "proxsuite-nlp";
-  version = "0.7.1";
+  version = "0.8.0";
 
   src = fetchFromGitHub {
     owner = "Simple-Robotics";
     repo = "proxsuite-nlp";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-aMTEjAu1ltjorx5vhz7klB0cGgdm+7STAPhi+NA6mnI=";
+    hash = "sha256-Dy8+pPTv/B6vVdpGndVOV16WSLiENJfaIrn1+FYwcI0=";
   };
 
   outputs = [
@@ -37,14 +37,8 @@ stdenv.mkDerivation (finalAttrs: {
     # Fix use of system jrl-cmakemodules
     # This patch was merged upstream and can be removed on next release
     (fetchpatch {
-      url = "https://github.com/Simple-Robotics/proxsuite-nlp/pull/106/commits/c653ab67860fdf7b53b1a919f0b8a7746eba016b.patch";
-      hash = "sha256-Kw2obJGOWms/Lr4cVkLFpaLTickCq5WQyDVbwi8Bd58=";
-    })
-    # Fix use of system EigenRand
-    # This patch was merged upstream and can be removed on next release
-    (fetchpatch {
-      url = "https://github.com/Simple-Robotics/proxsuite-nlp/pull/106/commits/25370417755f003708b5b2b81e253797e8d96928.patch";
-      hash = "sha256-PKijVmttt5JakF3X/GiVWptncxHJUbs/aikgwgB5NME=";
+      url = "https://github.com/Simple-Robotics/proxsuite-nlp/pull/109/commits/9bf741ce6010052a773071472891f42adc6cbbea.patch";
+      hash = "sha256-sluMVrTw7EXLFa0dqkoZTkpGjKe7zODqIqbJxCdfSwY=";
     })
   ];
 

From 4908d90b1a8c7a4f4a5400fe3e8b67c009f46b24 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Thu, 19 Sep 2024 01:14:04 +0200
Subject: [PATCH 34/36] proxsuite-nlp: outputs out first

---
 pkgs/by-name/pr/proxsuite-nlp/package.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/by-name/pr/proxsuite-nlp/package.nix b/pkgs/by-name/pr/proxsuite-nlp/package.nix
index 211d9a634063..194ff2fe967d 100644
--- a/pkgs/by-name/pr/proxsuite-nlp/package.nix
+++ b/pkgs/by-name/pr/proxsuite-nlp/package.nix
@@ -29,8 +29,8 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   outputs = [
-    "doc"
     "out"
+    "doc"
   ];
 
   patches = [

From 08c9dcf9621a1f85ef29d8ac12d4c08040d2840d Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Thu, 19 Sep 2024 01:15:50 +0200
Subject: [PATCH 35/36] aligator: 0.7.0 -> 0.8.0

Diff: https://github.com/Simple-Robotics/aligator/compare/v0.7.0...v0.8.0

Changelog: https://github.com/Simple-Robotics/aligator/blob/v0.8.0/CHANGELOG.md
---
 pkgs/by-name/al/aligator/package.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/by-name/al/aligator/package.nix b/pkgs/by-name/al/aligator/package.nix
index 8b0eb712ce2e..53346434be78 100644
--- a/pkgs/by-name/al/aligator/package.nix
+++ b/pkgs/by-name/al/aligator/package.nix
@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "aligator";
-  version = "0.7.0";
+  version = "0.8.0";
 
   src = fetchFromGitHub {
     owner = "Simple-Robotics";
     repo = "aligator";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-397WWL3hb5Q/mic54s5LUuz54bh7vwG53WIq5ljDe7g=";
+    hash = "sha256-o4QjxTaZUa17hZsCv4hCI2cedaHoojBtLe8SVUkl0bo=";
   };
 
   outputs = [

From 5108a107b244c127ea2d1097a8322ff06aebaab5 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Thu, 19 Sep 2024 15:11:45 +0200
Subject: [PATCH 36/36] python3Packages.eigenpy: 3.9.0 -> 3.9.1

Diff: https://github.com/stack-of-tasks/eigenpy/compare/refs/tags/v3.9.0...v3.9.1

Changelog: https://github.com/stack-of-tasks/eigenpy/releases/tag/v3.9.1
---
 pkgs/development/python-modules/eigenpy/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/eigenpy/default.nix b/pkgs/development/python-modules/eigenpy/default.nix
index 41066ba788a6..e45b5424a4b0 100644
--- a/pkgs/development/python-modules/eigenpy/default.nix
+++ b/pkgs/development/python-modules/eigenpy/default.nix
@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "eigenpy";
-  version = "3.9.0";
+  version = "3.9.1";
   pyproject = false; # Built with cmake
 
   src = fetchFromGitHub {
     owner = "stack-of-tasks";
     repo = "eigenpy";
     rev = "refs/tags/v${version}";
-    hash = "sha256-fJLX3ZhcgevXcXkR00fzDh9LtfMwaHsJWQgUexmuKLc=";
+    hash = "sha256-nRslQMnVaVN7S20RuJDp+e9p+oMhsR03EjHYpvkuBYk=";
   };
 
   outputs = [