Merge pull request #312985 from GaetanLepage/keras

python311Packages.keras: 3.2.1 -> 3.3.3

pkgs/development/python-modules/keras/default.nix

@@ -1,55 +1,64 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
-  pytest,
-  pytest-cov,
-  pytest-xdist,
-  six,
-  numpy,
-  scipy,
-  pyyaml,
+  pythonOlder,
+  fetchFromGitHub,
+  setuptools,
+  absl-py,
+  dm-tree,
   h5py,
+  markdown-it-py,
+  ml-dtypes,
+  namex,
+  numpy,
   optree,
-  keras-applications,
-  keras-preprocessing,
+  rich,
+  tensorflow,
 }:
 
 buildPythonPackage rec {
   pname = "keras";
-  version = "3.2.1";
-  format = "wheel";
+  version = "3.3.3";
+  pyproject = true;
 
-  src = fetchPypi {
-    inherit format pname version;
-    hash = "sha256-C+HomwQeaXvlYthCLsuVjuVIGs/AiZEyAJJsVh0ligM=";
-    python = "py3";
-    dist = "py3";
+  disabled = pythonOlder "3.9";
+
+  src = fetchFromGitHub {
+    owner = "keras-team";
+    repo = "keras";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-hhY28Ocv4zacZiwFflJtufKpeKfH1MD1PZJ+NTJfpH0=";
   };
 
-  nativeCheckInputs = [
-    pytest
-    pytest-cov
-    pytest-xdist
+  build-system = [
+    setuptools
   ];
 
-  propagatedBuildInputs = [
-    six
-    pyyaml
-    numpy
-    scipy
+  dependencies = [
+    absl-py
+    dm-tree
     h5py
-    keras-applications
-    keras-preprocessing
+    markdown-it-py
+    ml-dtypes
+    namex
+    numpy
+    optree
+    rich
+    tensorflow
+  ];
+
+  pythonImportsCheck = [
+    "keras"
+    "keras._tf_keras"
   ];
 
   # Couldn't get tests working
   doCheck = false;
 
-  meta = with lib; {
-    description = "Deep Learning library for Theano and TensorFlow";
+  meta = {
+    description = "Multi-backend implementation of the Keras API, with support for TensorFlow, JAX, and PyTorch";
     homepage = "https://keras.io";
-    license = licenses.mit;
-    maintainers = with maintainers; [ NikolaMandic ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ NikolaMandic ];
   };
 }

pkgs/development/python-modules/mhcflurry/default.nix

@@ -16,18 +16,18 @@
 
 buildPythonPackage rec {
   pname = "mhcflurry";
-  version = "2.1.0";
-  format = "setuptools";
+  version = "2.1.1";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "openvax";
-    repo = pname;
+    repo = "mhcflurry";
     rev = "refs/tags/v${version}";
-    hash = "sha256-VyPHcNlZYgNJZb2UBFX55x+nE0GnHixkcsiTNjDCju0=";
+    hash = "sha256-absIKvcFo6I1Uu0t+l8OLOU/AQ4kD295P4+KVwMAWMc=";
   };
 
   # keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
-  propagatedBuildInputs = [
+  dependencies = [
     appdirs
     keras
     mhcgnomes
@@ -82,10 +82,13 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "mhcflurry" ];
 
-  meta = with lib; {
+  meta = {
     description = "Peptide-MHC I binding affinity prediction";
     homepage = "https://github.com/openvax/mhcflurry";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ samuela ];
+    changelog = "https://github.com/openvax/mhcflurry/releases/tag/v${version}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ samuela ];
+    # ModuleNotFoundError: No module named 'keras.api._v2' as tensorflow is too outdated
+    broken = true;
   };
 }

pkgs/development/python-modules/namex/default.nix

@@ -0,0 +1,36 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  setuptools,
+  wheel,
+}:
+
+buildPythonPackage rec {
+  pname = "namex";
+  version = "0.0.8";
+  pyproject = true;
+
+  # Not using fetchFromGitHub because the repo does not have any tag/release.
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-MqUPbFZcC7EKp2KYyVlQer3A6FDv4IXcOPNED8s6qQs=";
+  };
+
+  build-system = [
+    setuptools
+    wheel
+  ];
+
+  pythonImportsCheck = [ "namex" ];
+
+  # This packages has no tests.
+  doCheck = false;
+
+  meta = {
+    description = "A simple utility to separate the implementation of your Python package and its public API surface";
+    homepage = "https://github.com/fchollet/namex";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}

pkgs/development/python-modules/trfl/default.nix

@@ -72,5 +72,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/deepmind/trfl";
     license = licenses.asl20;
     maintainers = with maintainers; [ onny ];
+    # ModuleNotFoundError: No module named 'keras.api._v2' as tensorflow is too outdated
+    broken = true;
   };
 }

pkgs/development/python-modules/wandb/default.nix

@@ -297,6 +297,13 @@ buildPythonPackage rec {
     [
       # Timing sensitive
       "test_login_timeout"
+
+      # Tensorflow 2.13 is too old for the current version of keras
+      # ModuleNotFoundError: No module named 'keras.api._v2'
+      "test_saved_model_keras"
+      "test_sklearn_saved_model"
+      "test_pytorch_saved_model"
+      "test_tensorflow_keras_saved_model"
     ]
     ++ lib.optionals stdenv.isDarwin [
       # Disable test that fails on darwin due to issue with python3Packages.psutil:

pkgs/top-level/python-packages.nix

@@ -8610,6 +8610,8 @@ self: super: with self; {
 
   names = callPackage ../development/python-modules/names { };
 
+  namex = callPackage ../development/python-modules/namex { };
+
   name-that-hash = callPackage ../development/python-modules/name-that-hash { };
 
   nameko = callPackage ../development/python-modules/nameko { };