From 7a690fd410546df1e11bb2da9e57e242b4e788b5 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sat, 27 Sep 2025 21:12:14 +0000
Subject: [PATCH 1/3] python3Packages.keras: unmark as broken

---
 pkgs/development/python-modules/keras/default.nix | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pkgs/development/python-modules/keras/default.nix b/pkgs/development/python-modules/keras/default.nix
index a1aa7438c423..93f8a3a14784 100644
--- a/pkgs/development/python-modules/keras/default.nix
+++ b/pkgs/development/python-modules/keras/default.nix
@@ -214,7 +214,5 @@ buildPythonPackage rec {
     changelog = "https://github.com/keras-team/keras/releases/tag/v${version}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ GaetanLepage ];
-    # Not yet released for tensorflow >= 2.20.0
-    broken = lib.versionAtLeast tensorflow.version "2.20";
   };
 }

From 62c60b6ed92b6573cb87a138e57e6c749657735d Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sat, 27 Sep 2025 22:26:31 +0000
Subject: [PATCH 2/3] python3Packages.mhcflurry: fix for python 3.13

---
 pkgs/development/python-modules/mhcflurry/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/mhcflurry/default.nix b/pkgs/development/python-modules/mhcflurry/default.nix
index 611b67645165..88b99c0da802 100644
--- a/pkgs/development/python-modules/mhcflurry/default.nix
+++ b/pkgs/development/python-modules/mhcflurry/default.nix
@@ -31,6 +31,14 @@ buildPythonPackage rec {
     hash = "sha256-TNb3oKZvgBuXoSwsTuEJjFKEVZyHynazuPInj7wVKs8=";
   };
 
+  # pipes has been removed in python 3.13
+  postPatch = ''
+    substituteInPlace mhcflurry/downloads.py \
+      --replace-fail \
+        "from pipes import quote" \
+        "from shlex import quote"
+  '';
+
   # keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
   dependencies = [
     appdirs

From dfb46856cc1d56533d19fdd653b0435ba2979a7a Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sat, 27 Sep 2025 22:30:03 +0000
Subject: [PATCH 3/3] python3Packages.brax: skip failing tests

---
 pkgs/development/python-modules/brax/default.nix | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/brax/default.nix b/pkgs/development/python-modules/brax/default.nix
index 11b4ac0dc9c6..3af04fe0b318 100644
--- a/pkgs/development/python-modules/brax/default.nix
+++ b/pkgs/development/python-modules/brax/default.nix
@@ -82,7 +82,14 @@ buildPythonPackage rec {
     transforms3d
   ];
 
-  disabledTests = lib.optionals stdenv.hostPlatform.isAarch64 [
+  disabledTests = [
+    # AttributeError: 'functools.partial' object has no attribute 'value'
+    "testModelEncoding0"
+    "testModelEncoding1"
+    "testTrain"
+    "testTrainDomainRandomize"
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isAarch64 [
     # Flaky:
     # AssertionError: Array(-0.00135638, dtype=float32) != 0.0 within 0.001 delta (Array(0.00135638, dtype=float32) difference)
     "test_pendulum_period2"