diff --git a/pkgs/development/python-modules/ax-platform/default.nix b/pkgs/development/python-modules/ax-platform/default.nix index 513e6ec00184..80b8990474e6 100644 --- a/pkgs/development/python-modules/ax-platform/default.nix +++ b/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" ]; diff --git a/pkgs/development/python-modules/botorch/default.nix b/pkgs/development/python-modules/botorch/default.nix index 65db0322ba9d..a36e88faa5d0 100644 --- a/pkgs/development/python-modules/botorch/default.nix +++ b/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${version}"; - hash = "sha256-CKlerCUadObpPq4jQAiFDBOZMHZ4QccAKQz30OFe64E="; + hash = "sha256-Hik0HPHFoN1+uIeVxG7UPKc1ADBoTTBkL2+LhHDrr+s="; }; build-system = [ @@ -35,16 +37,12 @@ buildPythonPackage rec { gpytorch linear-operator multipledispatch + pyre-extensions pyro-ppl scipy torch ]; - pythonRelaxDeps = [ - "gpytorch" - "linear-operator" - ]; - nativeCheckInputs = [ pytestCheckHook ]; pytestFlagsArray = [ @@ -55,10 +53,18 @@ buildPythonPackage rec { disabledTests = [ "test_all_cases_covered" ] + ++ lib.optionals (pythonAtLeast "3.13") [ + # RuntimeError: Boolean value of Tensor with more than one value is ambiguous + "test_optimize_acqf_mixed_binary_only" + ] ++ lib.optionals (stdenv.buildPlatform.system == "x86_64-linux") [ # stuck tests on hydra "test_moo_predictive_entropy_search" ] + ++ lib.optionals (stdenv.hostPlatform.isDarwin) [ + # RuntimeError: required keyword attribute 'value' has the wrong type + "test_posterior_in_trace_mode" + ] ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [ # Numerical error slightly above threshold # AssertionError: Tensor-likes are not close! diff --git a/pkgs/development/python-modules/gpytorch/default.nix b/pkgs/development/python-modules/gpytorch/default.nix index fd81ffcf897b..275dda93c06a 100644 --- a/pkgs/development/python-modules/gpytorch/default.nix +++ b/pkgs/development/python-modules/gpytorch/default.nix @@ -15,14 +15,14 @@ buildPythonPackage rec { pname = "gpytorch"; - version = "1.13"; + version = "1.14"; pyproject = true; src = fetchFromGitHub { owner = "cornellius-gp"; repo = pname; tag = "v${version}"; - hash = "sha256-jdEJdUFIyM7TTKUHY8epjyZCGolH8nrr7FCyfw+x56s="; + hash = "sha256-whZjqAs3nyjKMzAGi+OnyBtboq0UuV8m11A4IzkWtec="; }; build-system = [ diff --git a/pkgs/development/python-modules/optuna/default.nix b/pkgs/development/python-modules/optuna/default.nix index 0c9b03f4a0e9..aff26527574f 100644 --- a/pkgs/development/python-modules/optuna/default.nix +++ b/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" ]; diff --git a/pkgs/development/python-modules/pyannote-audio/default.nix b/pkgs/development/python-modules/pyannote-audio/default.nix index 80998ea1f1d7..9e239ec88fdc 100644 --- a/pkgs/development/python-modules/pyannote-audio/default.nix +++ b/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; }; diff --git a/pkgs/development/python-modules/resampy/default.nix b/pkgs/development/python-modules/resampy/default.nix index 7a4c3cf0dacd..f6ac5014be4a 100644 --- a/pkgs/development/python-modules/resampy/default.nix +++ b/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" ]; diff --git a/pkgs/development/python-modules/synergy/default.nix b/pkgs/development/python-modules/synergy/default.nix index 8d958862b675..2a60f4b23e5c 100644 --- a/pkgs/development/python-modules/synergy/default.nix +++ b/pkgs/development/python-modules/synergy/default.nix @@ -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; {