python312Packages.pyannote-audio: 3.1.1 -> 3.1.2; python312Packages.gpytorch: 1.13 -> 1.14; python312Packages.botorch: 0.12.0 -> 0.13.0: python312Packages.optuna: 4.1.0 -> 4.2.0

pkgs/development/python-modules/ax-platform/default.nix

@@ -13,17 +13,19 @@
   pyfakefs,
   pyre-extensions,
   pytestCheckHook,
+  pythonAtLeast,
   pythonOlder,
   setuptools-scm,
   setuptools,
   sqlalchemy,
+  tabulate,
   typeguard,
   yappi,
 }:
 
 buildPythonPackage rec {
   pname = "ax-platform";
-  version = "0.4.3";
+  version = "0.5.0";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
@@ -32,7 +34,7 @@ buildPythonPackage rec {
     owner = "facebook";
     repo = "ax";
     tag = version;
-    hash = "sha256-jmBjrtxqg4Iu3Qr0HRqjVfwURXzbJaGm+DBFNHYk/vA=";
+    hash = "sha256-CMKdnPvzQ9tvU9/01mRaWi/Beuyo19CtaXNJCoiwLOw=";
   };
 
   env.ALLOW_BOTORCH_LATEST = "1";
@@ -62,16 +64,13 @@ buildPythonPackage rec {
     mercurial
     pyfakefs
     pytestCheckHook
+    tabulate
     yappi
-  ] ++ lib.flatten (builtins.attrValues optional-dependencies);
+  ] ++ lib.flatten (lib.attrValues optional-dependencies);
 
   disabledTestPaths = [
     "ax/benchmark"
     "ax/runners/tests/test_torchx.py"
-    # requires pyre_extensions
-    "ax/telemetry/tests"
-    "ax/core/tests/test_utils.py"
-    "ax/early_stopping/tests/test_strategies.py"
     # broken with sqlalchemy 2
     "ax/core/tests/test_experiment.py"
     "ax/service/tests/test_ax_client.py"
@@ -80,16 +79,30 @@ buildPythonPackage rec {
     "ax/storage"
   ];
 
-  disabledTests = [
-    # exact comparison of floating points
-    "test_optimize_l0_homotopy"
-    # AssertionError: 5 != 2
-    "test_get_standard_plots_moo"
-    # AssertionError: Expected 'warning' to be called once. Called 3 times
-    "test_validate_kwarg_typing"
-    # uses torch.equal
-    "test_convert_observations"
-  ];
+  disabledTests =
+    [
+      # exact comparison of floating points
+      "test_optimize_l0_homotopy"
+      # AssertionError: 5 != 2
+      "test_get_standard_plots_moo"
+      # AssertionError: Expected 'warning' to be called once. Called 3 times
+      "test_validate_kwarg_typing"
+      # uses torch.equal
+      "test_convert_observations"
+      # broken with sqlalchemy 2
+      "test_sql_storage"
+    ]
+    ++ lib.optionals (pythonAtLeast "3.13") [
+      #  Both `metric_aggregation` and `criterion` must be `ReductionCriterion`
+      "test_SingleDiagnosticBestModelSelector_max_mean"
+      "test_SingleDiagnosticBestModelSelector_min_mean"
+      "test_SingleDiagnosticBestModelSelector_min_min"
+      "test_SingleDiagnosticBestModelSelector_model_cv_kwargs"
+      "test_init"
+      "test_gen"
+      # "use MIN or MAX" does not match "Both `metric_aggregation` and `criterion` must be `ReductionCriterion`
+      "test_user_input_error"
+    ];
 
   pythonImportsCheck = [ "ax" ];
 

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

@@ -6,24 +6,26 @@
   gpytorch,
   linear-operator,
   multipledispatch,
+  pyre-extensions,
   pyro-ppl,
   setuptools,
   setuptools-scm,
   torch,
   scipy,
   pytestCheckHook,
+  pythonAtLeast,
 }:
 
 buildPythonPackage rec {
   pname = "botorch";
-  version = "0.12.0";
+  version = "0.13.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pytorch";
     repo = "botorch";
     tag = "v${version}";
-    hash = "sha256-CKlerCUadObpPq4jQAiFDBOZMHZ4QccAKQz30OFe64E=";
+    hash = "sha256-Hik0HPHFoN1+uIeVxG7UPKc1ADBoTTBkL2+LhHDrr+s=";
   };
 
   build-system = [
@@ -35,16 +37,12 @@ buildPythonPackage rec {
     gpytorch
     linear-operator
     multipledispatch
+    pyre-extensions
     pyro-ppl
     scipy
     torch
   ];
 
-  pythonRelaxDeps = [
-    "gpytorch"
-    "linear-operator"
-  ];
-
   nativeCheckInputs = [ pytestCheckHook ];
 
   pytestFlagsArray = [
@@ -55,10 +53,18 @@ buildPythonPackage rec {
 
   disabledTests =
     [ "test_all_cases_covered" ]
+    ++ lib.optionals (pythonAtLeast "3.13") [
+      # RuntimeError: Boolean value of Tensor with more than one value is ambiguous
+      "test_optimize_acqf_mixed_binary_only"
+    ]
     ++ lib.optionals (stdenv.buildPlatform.system == "x86_64-linux") [
       # stuck tests on hydra
       "test_moo_predictive_entropy_search"
     ]
+    ++ lib.optionals (stdenv.hostPlatform.isDarwin) [
+      # RuntimeError: required keyword attribute 'value' has the wrong type
+      "test_posterior_in_trace_mode"
+    ]
     ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
       # Numerical error slightly above threshold
       # AssertionError: Tensor-likes are not close!

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

@@ -15,14 +15,14 @@
 
 buildPythonPackage rec {
   pname = "gpytorch";
-  version = "1.13";
+  version = "1.14";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "cornellius-gp";
     repo = pname;
     tag = "v${version}";
-    hash = "sha256-jdEJdUFIyM7TTKUHY8epjyZCGolH8nrr7FCyfw+x56s=";
+    hash = "sha256-whZjqAs3nyjKMzAGi+OnyBtboq0UuV8m11A4IzkWtec=";
   };
 
   build-system = [

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

@@ -6,43 +6,34 @@
   pythonOlder,
   alembic,
   boto3,
-  botorch,
-  catboost,
-  cma,
   cmaes,
   colorlog,
-  distributed,
   fakeredis,
+  fvcore,
   google-cloud-storage,
-  lightgbm,
+  grpcio,
+  kaleido,
   matplotlib,
-  mlflow,
   moto,
   numpy,
   packaging,
   pandas,
   plotly,
+  protobuf,
   pytest-xdist,
-  pytorch-lightning,
   pyyaml,
   redis,
   scikit-learn,
   scipy,
   setuptools,
-  shap,
   sqlalchemy,
-  tensorflow,
   torch,
-  torchaudio,
-  torchvision,
   tqdm,
-  wandb,
-  xgboost,
 }:
 
 buildPythonPackage rec {
   pname = "optuna";
-  version = "4.1.0";
+  version = "4.2.0";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -51,7 +42,7 @@ buildPythonPackage rec {
     owner = "optuna";
     repo = "optuna";
     tag = "v${version}";
-    hash = "sha256-wIgYExxJEWFxEadBuCsxEIcW2/J6EVybW1jp83gIMjY=";
+    hash = "sha256-NNlwrVrGg2WvkC42nmW7K/mRktE3B97GaL8GaSOKF1Y=";
   };
 
   build-system = [
@@ -69,60 +60,46 @@ buildPythonPackage rec {
   ];
 
   optional-dependencies = {
-    integration = [
-      botorch
-      catboost
-      cma
-      distributed
-      lightgbm
-      mlflow
-      pandas
-      # pytorch-ignite
-      pytorch-lightning
-      scikit-learn
-      shap
-      tensorflow
-      torch
-      torchaudio
-      torchvision
-      wandb
-      xgboost
-    ];
     optional = [
       boto3
-      botorch
       cmaes
+      fvcore
       google-cloud-storage
+      grpcio
       matplotlib
       pandas
       plotly
+      protobuf
       redis
       scikit-learn
+      scipy
     ];
   };
 
   preCheck = ''
     export PATH=$out/bin:$PATH
+
+    # grpc tests are racy
+    sed -i '/"grpc",/d' optuna/testing/storages.py
   '';
 
   nativeCheckInputs =
     [
       fakeredis
+      kaleido
       moto
       pytest-xdist
       pytestCheckHook
-      scipy
+      torch
     ]
     ++ fakeredis.optional-dependencies.lua
     ++ optional-dependencies.optional;
 
-  pytestFlagsArray = [ "-m 'not integration'" ];
-
-  disabledTestPaths = [
-    # require unpackaged kaleido and building it is a bit difficult
-    "tests/visualization_tests"
-    # ImportError: cannot import name 'mock_s3' from 'moto'
-    "tests/artifacts_tests/test_boto3.py"
+  disabledTests = [
+    # ValueError: Transform failed with error code 525: error creating static canvas/context for image server
+    "test_get_pareto_front_plot"
+    # too narrow time limit
+    "test_get_timeline_plot_with_killed_running_trials"
   ];
 
   pythonImportsCheck = [ "optuna" ];

pkgs/development/python-modules/pyannote-audio/default.nix

@@ -31,7 +31,7 @@
 
 buildPythonPackage rec {
   pname = "pyannote-audio";
-  version = "3.3.1";
+  version = "3.3.2";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
@@ -40,7 +40,7 @@ buildPythonPackage rec {
     owner = "pyannote";
     repo = "pyannote-audio";
     tag = version;
-    hash = "sha256-85whRoc3JoDSE4DqivY/3hfvLHcvgsubR/DLCPtLEP0=";
+    hash = "sha256-Qx7NDXkT3eQr9PZXlYuoJD01dzsVCvfq6HNPnyLzyAQ=";
     fetchSubmodules = true;
   };
 

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

@@ -1,19 +1,22 @@
 {
   lib,
+  stdenv,
   buildPythonPackage,
-  cython,
   fetchFromGitHub,
   numba,
   numpy,
+  optuna,
+  pytest-cov-stub,
   pytestCheckHook,
   pythonOlder,
+  setuptools,
   scipy,
 }:
 
 buildPythonPackage rec {
   pname = "resampy";
   version = "0.4.3";
-  format = "setuptools";
+  pyproject = true;
 
   disabled = pythonOlder "3.7";
 
@@ -24,21 +27,26 @@ buildPythonPackage rec {
     hash = "sha256-LOWpOPAEK+ga7c3bR15QvnHmON6ARS1Qee/7U/VMlTY=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [ setuptools ];
+
+  dependencies = [
     numpy
-    cython
     numba
   ];
 
+  optional-dependencies.design = [ optuna ];
+
   nativeCheckInputs = [
+    pytest-cov-stub
     pytestCheckHook
     scipy
-  ];
+  ] ++ optional-dependencies.design;
 
-  postPatch = ''
-    substituteInPlace setup.cfg \
-      --replace " --cov-report term-missing --cov resampy --cov-report=xml" ""
-  '';
+  disabledTests = lib.optionals (stdenv.hostPlatform.system == "aarch64-linux") [
+    # crashing the interpreter
+    "test_quality_sine_parallel"
+    "test_resample_nu_quality_sine_parallel"
+  ];
 
   pythonImportsCheck = [ "resampy" ];