From 51d7d3592d94002a7337483a997782aaa6c4b149 Mon Sep 17 00:00:00 2001
From: Samuel Ainsworth <skainsworth@gmail.com>
Date: Mon, 24 Oct 2022 11:04:20 -0700
Subject: [PATCH 1/3] python3Packages.dm-tree: unstable-2021-12-20 -> 0.1.7

---
 pkgs/development/python-modules/dm-tree/default.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/dm-tree/default.nix b/pkgs/development/python-modules/dm-tree/default.nix
index 04feb7de93f3..1b9437096648 100644
--- a/pkgs/development/python-modules/dm-tree/default.nix
+++ b/pkgs/development/python-modules/dm-tree/default.nix
@@ -13,14 +13,13 @@
 
 buildPythonPackage rec {
   pname = "dm-tree";
-  # As of 2021-12-29, the latest stable version still builds with Bazel.
-  version = "unstable-2021-12-20";
+  version = "0.1.7";
 
   src = fetchFromGitHub {
     owner = "deepmind";
     repo = "tree";
-    rev = "b452e5c2743e7489b4ba7f16ecd51c516d7cd8e3";
-    sha256 = "1r187xwpvnnj98lyasngcv3lbxz0ziihpl5dbnjbfbjr0kh6z0j9";
+    rev = version;
+    hash = "sha256-rg6dcGcbTGfK3h4WAyhwCjgM3o64Jj2SImxNsZXJHHM=";
   };
 
   patches = [

From 547d127691be2d834bc10e979faf6c1d2cc15edd Mon Sep 17 00:00:00 2001
From: Samuel Ainsworth <skainsworth@gmail.com>
Date: Mon, 24 Oct 2022 11:04:42 -0700
Subject: [PATCH 2/3] python3Packages.chex: 0.1.4 -> 0.1.5

---
 pkgs/development/python-modules/chex/default.nix | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/chex/default.nix b/pkgs/development/python-modules/chex/default.nix
index 79eeb9319973..cad84146c483 100644
--- a/pkgs/development/python-modules/chex/default.nix
+++ b/pkgs/development/python-modules/chex/default.nix
@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "chex";
-  version = "0.1.4";
+  version = "0.1.5";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "deepmind";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-FiZElESyOVu1VJxUDNiN6HVADiaubDrGdQHYp2CN8f4=";
+    hash = "sha256-FYB0IhokM74HBY2wOJYE6xJrHxHHWhDSAZpWFs6HFu0=";
   };
 
   propagatedBuildInputs = [
@@ -39,6 +39,11 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
+  disabledTests = [
+    # See https://github.com/deepmind/chex/issues/204.
+    "test_uninspected_checks"
+  ];
+
   meta = with lib; {
     description = "Chex is a library of utilities for helping to write reliable JAX code.";
     homepage = "https://github.com/deepmind/chex";

From 9714106447e4dca5f6b2f7655742732db49c398a Mon Sep 17 00:00:00 2001
From: Samuel Ainsworth <skainsworth@gmail.com>
Date: Mon, 24 Oct 2022 11:19:04 -0700
Subject: [PATCH 3/3] python3Packages.flax: 0.6.0 -> 0.6.1

---
 .../python-modules/flax/default.nix           | 30 +++++++++++--------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/python-modules/flax/default.nix b/pkgs/development/python-modules/flax/default.nix
index ebdb3ac898ad..d9171d14e41d 100644
--- a/pkgs/development/python-modules/flax/default.nix
+++ b/pkgs/development/python-modules/flax/default.nix
@@ -17,25 +17,15 @@
 
 buildPythonPackage rec {
   pname = "flax";
-  version = "0.6.0";
+  version = "0.6.1";
 
   src = fetchFromGitHub {
     owner = "google";
     repo = pname;
     rev = "refs/tags/v${version}";
-    sha256 = "sha256-egTYYFZxhE/Kk7jXRi1HmjCjyFia2LoRigH042isDu0=";
+    sha256 = "sha256-fZiODo+izOwGjCCTvi11GvUG/VQL1DV9bNXKjvIIw4A=";
   };
 
-  patches = [
-    # Bump rich dependency, should be fixed in releases after 0.6.0
-    # https://github.com/google/flax/pull/2407
-    (fetchpatch {
-      url = "https://github.com/google/flax/commit/72189153f9779022b97858ae747c23fbaf571e3d.patch";
-      sha256 = "sha256-hKOn/M7qpBM6R1RIJpnXpRoZgIHqkwQZApN4L0fBzIE=";
-      name = "bump_rich_dependency.patch";
-    })
-  ];
-
   buildInputs = [ jaxlib ];
 
   propagatedBuildInputs = [
@@ -76,6 +66,22 @@ buildPythonPackage rec {
     "examples/*"
   ];
 
+  disabledTests = [
+    # See https://github.com/google/flax/issues/2554.
+    "test_async_save_checkpoints"
+    "test_jax_array0"
+    "test_jax_array1"
+    "test_keep0"
+    "test_keep1"
+    "test_optimized_lstm_cell_matches_regular"
+    "test_overwrite_checkpoints"
+    "test_save_restore_checkpoints_target_empty"
+    "test_save_restore_checkpoints_target_none"
+    "test_save_restore_checkpoints_target_singular"
+    "test_save_restore_checkpoints_w_float_steps"
+    "test_save_restore_checkpoints"
+  ];
+
   meta = with lib; {
     description = "Neural network library for JAX";
     homepage = "https://github.com/google/flax";