diff --git a/pkgs/development/python-modules/equinox/default.nix b/pkgs/development/python-modules/equinox/default.nix
index 834e6f5d732b..0b99125f4fc1 100644
--- a/pkgs/development/python-modules/equinox/default.nix
+++ b/pkgs/development/python-modules/equinox/default.nix
@@ -22,14 +22,14 @@
 
 buildPythonPackage rec {
   pname = "equinox";
-  version = "0.11.12";
+  version = "0.12.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "patrick-kidger";
     repo = "equinox";
     tag = "v${version}";
-    hash = "sha256-hor2qw+aTL7yhV53E/y5DUwyDEYJA8RPRS39xxa8xcw=";
+    hash = "sha256-mw2fk+527b6Rx6FGe6QJf3ZbxZ3rjYFXKleX2g6AryU=";
   };
 
   # Relax speed constraints on tests that can fail on busy builders
@@ -56,14 +56,6 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  pytestFlagsArray = [
-    # Since jax 0.5.3:
-    # DeprecationWarning: shape requires ndarray or scalar arguments, got <class 'jax._src.api.ShapeDtypeStruct'> at position 0. In a future JAX release this will be an error.
-    # https://github.com/patrick-kidger/equinox/issues/979
-    "-W"
-    "ignore::DeprecationWarning"
-  ];
-
   disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [
     # SystemError: nanobind::detail::nb_func_error_except(): exception could not be translated!
     "test_filter"
diff --git a/pkgs/development/python-modules/lineax/default.nix b/pkgs/development/python-modules/lineax/default.nix
index 8f6a41af46d8..3f31208364de 100644
--- a/pkgs/development/python-modules/lineax/default.nix
+++ b/pkgs/development/python-modules/lineax/default.nix
@@ -16,32 +16,20 @@
   beartype,
   pytest,
   python,
-
-  fetchpatch,
 }:
 
 buildPythonPackage rec {
   pname = "lineax";
-  version = "0.0.7";
+  version = "0.0.8";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "patrick-kidger";
     repo = "lineax";
     tag = "v${version}";
-    hash = "sha256-HcFI55Ww/y7ZaUkawj7xWSb7VDTBec3u0ulWL8kTm2c=";
+    hash = "sha256-VMTDCExgxfCcd/3UZAglfAxAFaSjzFJJuvSWJAx2tJs=";
   };
 
-  patches = [
-    (fetchpatch {
-      # Reported upstream: https://github.com/patrick-kidger/lineax/issues/118
-      # Fixed by https://github.com/patrick-kidger/lineax/pull/119
-      name = "fix-vmap-tests";
-      url = "https://github.com/patrick-kidger/lineax/pull/119/commits/d21552ac4c504d7b139ad8e4f15d5f102b54d705.patch";
-      hash = "sha256-pBejiqIVNjXi7dXuDBQdAy892wro1WxzwbI7v07N86c=";
-    })
-  ];
-
   build-system = [ hatchling ];
 
   dependencies = [
diff --git a/pkgs/development/python-modules/stable-baselines3/default.nix b/pkgs/development/python-modules/stable-baselines3/default.nix
index a5f5e6a1e5c6..37ea041b1c79 100644
--- a/pkgs/development/python-modules/stable-baselines3/default.nix
+++ b/pkgs/development/python-modules/stable-baselines3/default.nix
@@ -65,6 +65,9 @@ buildPythonPackage rec {
   ];
 
   disabledTests = [
+    # Flaky: Can fail if it takes too long, which happens when the system is under heavy load
+    "test_fps_logger"
+
     # Tests that attempt to access the filesystem
     "test_make_atari_env"
     "test_vec_env_monitor_kwargs"