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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 (#380409)

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This commit is contained in:
Martin Weinelt
2025-02-10 23:21:00 +01:00
committed by GitHub
parent 051837d800 f09da94afd
commit 79808f49d7
7 changed files with 113 additions and 86 deletions
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pkgs/development/python-modules/ax-platform/default.nix
+30 -17
View File
@@ -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
+13 -7
View File
@@ -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${version}";
hash = "sha256-CKlerCUadObpPq4jQAiFDBOZMHZ4QccAKQz30OFe64E=";
hash = "sha256-Hik0HPHFoN1+uIeVxG7UPKc1ADBoTTBkL2+LhHDrr+s=";
};
build-system = [
@@ -35,16 +37,12 @@ buildPythonPackage rec {
gpytorch
linear-operator
multipledispatch
pyre-extensions
pyro-ppl
scipy
torch
];
pythonRelaxDeps = [
"gpytorch"
"linear-operator"
];
nativeCheckInputs = [ pytestCheckHook ];
pytestFlagsArray = [
@@ -55,10 +53,18 @@ buildPythonPackage rec {
disabledTests =
[ "test_all_cases_covered" ]
++ lib.optionals (pythonAtLeast "3.13") [
# RuntimeError: Boolean value of Tensor with more than one value is ambiguous
"test_optimize_acqf_mixed_binary_only"
]
++ lib.optionals (stdenv.buildPlatform.system == "x86_64-linux") [
# stuck tests on hydra
"test_moo_predictive_entropy_search"
]
++ lib.optionals (stdenv.hostPlatform.isDarwin) [
# RuntimeError: required keyword attribute 'value' has the wrong type
"test_posterior_in_trace_mode"
]
++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
# Numerical error slightly above threshold
# AssertionError: Tensor-likes are not close!
pkgs/development/python-modules/gpytorch/default.nix
+2 -2
View File
@@ -15,14 +15,14 @@
buildPythonPackage rec {
pname = "gpytorch";
version = "1.13";
version = "1.14";
pyproject = true;
src = fetchFromGitHub {
owner = "cornellius-gp";
repo = pname;
tag = "v${version}";
hash = "sha256-jdEJdUFIyM7TTKUHY8epjyZCGolH8nrr7FCyfw+x56s=";
hash = "sha256-whZjqAs3nyjKMzAGi+OnyBtboq0UuV8m11A4IzkWtec=";
};
build-system = [
pkgs/development/python-modules/optuna/default.nix
+20 -43
View File
@@ -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
+2 -2
View File
@@ -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
+17 -9
View File
@@ -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" ];
pkgs/development/python-modules/synergy/default.nix
+29 -6
View File
@@ -1,31 +1,36 @@
{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
pytestCheckHook,
pythonOlder,
setuptools,
numpy,
scipy,
matplotlib,
plotly,
pandas,
hypothesis,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "synergy";
version = "1.0.0";
format = "setuptools";
pyproject = true;
disabled = pythonOlder "3.5";
# Pypi does not contain unit tests
src = fetchFromGitHub {
owner = "djwooten";
repo = "synergy";
tag = "v${version}";
sha256 = "sha256-df5CBEcRx55/rSMc6ygMVrHbbEcnU1ISJheO+WoBSCI=";
hash = "sha256-df5CBEcRx55/rSMc6ygMVrHbbEcnU1ISJheO+WoBSCI=";
};
propagatedBuildInputs = [
build-system = [ setuptools ];
dependencies = [
numpy
scipy
matplotlib
@@ -33,7 +38,25 @@ buildPythonPackage rec {
pandas
];
nativeCheckInputs = [ pytestCheckHook ];
nativeCheckInputs = [
hypothesis
pytestCheckHook
];
disabledTests =
[
# flaky: hypothesis.errors.FailedHealthCheck
"test_asymptotic_limits"
"test_inverse"
# AssertionError: synthetic_BRAID_reference_1.csv
# E3=0 not in (0.10639582639915163, 1.6900177333904622)
"test_BRAID_fit_bootstrap"
]
++ lib.optionals stdenv.hostPlatform.isDarwin [
# AssertionError: np.False_ is not true
"test_fit_loewe_antagonism"
];
pythonImportsCheck = [ "synergy" ];
meta = with lib; {