From 3fc5f627496b21c1cc4dac34a676337962fef4bd Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Thu, 19 Sep 2024 08:49:25 +0200
Subject: [PATCH 1/2] python312Packages.treescope: init at 0.1.5

---
 .../python-modules/treescope/default.nix      | 65 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 67 insertions(+)
 create mode 100644 pkgs/development/python-modules/treescope/default.nix

diff --git a/pkgs/development/python-modules/treescope/default.nix b/pkgs/development/python-modules/treescope/default.nix
new file mode 100644
index 000000000000..c27e95cdff38
--- /dev/null
+++ b/pkgs/development/python-modules/treescope/default.nix
@@ -0,0 +1,65 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  flit-core,
+
+  # dependencies
+  numpy,
+
+  # optional-dependencies
+  ipython,
+  jax,
+  palettable,
+
+  # tests
+  absl-py,
+  jaxlib,
+  pytestCheckHook,
+  torch,
+}:
+
+buildPythonPackage rec {
+  pname = "treescope";
+  version = "0.1.5";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "google-deepmind";
+    repo = "treescope";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-+Hm60O9tEXIiE0av1O0BsOdMln4e1s7ijb3WNiQ74jE=";
+  };
+
+  build-system = [ flit-core ];
+
+  dependencies = [ numpy ];
+
+  optional-dependencies = {
+    notebook = [
+      ipython
+      jax
+      palettable
+    ];
+  };
+
+  pythonImportsCheck = [ "treescope" ];
+
+  nativeCheckInputs = [
+    absl-py
+    jax
+    jaxlib
+    pytestCheckHook
+    torch
+  ];
+
+  meta = {
+    description = "An interactive HTML pretty-printer for machine learning research in IPython notebooks";
+    homepage = "https://github.com/google-deepmind/treescope";
+    changelog = "https://github.com/google-deepmind/treescope/releases/tag/v${version}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 2c4b0027a301..e743b3dc785a 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -15773,6 +15773,8 @@ self: super: with self; {
 
   treeo = callPackage ../development/python-modules/treeo { };
 
+  treescope = callPackage ../development/python-modules/treescope { };
+
   treex = callPackage ../development/python-modules/treex { };
 
   treq = callPackage ../development/python-modules/treq { };

From 588d188d954164f9e4e7a82de3dd544f36664cde Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Tue, 27 Aug 2024 20:03:45 +0200
Subject: [PATCH 2/2] python312Packages.flax: 0.8.5 -> 0.9.0

Diff: https://github.com/google/flax/compare/refs/tags/v0.8.5...v0.9.0

Changelog: https://github.com/google/flax/releases/tag/v0.9.0
---
 pkgs/development/python-modules/flax/default.nix | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/python-modules/flax/default.nix b/pkgs/development/python-modules/flax/default.nix
index c176c825943c..098e6cf28e6b 100644
--- a/pkgs/development/python-modules/flax/default.nix
+++ b/pkgs/development/python-modules/flax/default.nix
@@ -1,7 +1,6 @@
 {
   lib,
   buildPythonPackage,
-  pythonOlder,
   fetchFromGitHub,
 
   # build-system
@@ -26,6 +25,7 @@
   pytest-xdist,
   pytestCheckHook,
   tensorflow,
+  treescope,
 
   # optional-dependencies
   matplotlib,
@@ -33,16 +33,14 @@
 
 buildPythonPackage rec {
   pname = "flax";
-  version = "0.8.5";
+  version = "0.9.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.9";
-
   src = fetchFromGitHub {
     owner = "google";
     repo = "flax";
     rev = "refs/tags/v${version}";
-    hash = "sha256-6WOFq0758gtNdrlWqSQBlKmWVIGe5e4PAaGrvHoGjr0=";
+    hash = "sha256-iDWuUJKO7V4QrbVsS4ALgy6fbllOC43o7W4mhjtZ9xc=";
   };
 
   build-system = [
@@ -75,6 +73,7 @@ buildPythonPackage rec {
     pytest-xdist
     pytestCheckHook
     tensorflow
+    treescope
   ];
 
   pytestFlagsArray = [
@@ -95,13 +94,18 @@ buildPythonPackage rec {
     "flax/nnx/examples/*"
     # See https://github.com/google/flax/issues/3232.
     "tests/jax_utils_test.py"
-    # Requires tree
+    # Too old version of tensorflow:
+    # ModuleNotFoundError: No module named 'keras.api._v2'
     "tests/tensorboard_test.py"
   ];
 
   disabledTests = [
     # ValueError: Checkpoint path should be absolute
     "test_overwrite_checkpoints0"
+    # Fixed in more recent versions of jax: https://github.com/google/flax/issues/4211
+    # TODO: Re-enable when jax>0.4.28 will be available in nixpkgs
+    "test_vmap_and_cond_passthrough" # ValueError: vmap has mapped output but out_axes is None
+    "test_vmap_and_cond_passthrough_error" # AssertionError: "at vmap.*'broadcast'.*got axis spec ...
   ];
 
   meta = {