search

automl / RoBO

RoBO: a Robust Bayesian Optimization framework
BSD 3-Clause "New" or "Revised" License
483 stars 133 forks source link

nosetest fails #76

Open pbalapra opened 7 years ago

pbalapra commented 7 years ago

I followed the install instructions and managed to get it right. Please note that I have to install george and random_forest_run separately. After the install, nosetest fails. Is this due to new versions of george and random forest?

conda list output: #############

blas 1.1 openblas conda-forge george 0.3.0 np113py36_0 conda-forge numpy 1.13.1 py36_blas_openblas_200 [blas_openblas] conda-forge openblas 0.2.19 2 conda-forge pybind11 2.2.1 py36_0 conda-forge scipy 0.19.1 py36_blas_openblas_202 [blas_openblas] conda-forge hpolib2 0.0.1 icc_rt 16.0.3 intel_14 [intel] intel intelpython 2018.0.0 3 intel mkl 2017.0.2 intel_1 [intel] intel openmp 2018.0.0 intel_7 intel openssl 1.0.2k intel_3 [intel] intel pip 9.0.1 py36_intel_0 [intel] intel python 3.6.2 intel_3 [intel] intel setuptools 27.2.0 py36_intel_0 [intel] intel sqlite 3.13.0 intel_15 [intel] intel tcl 8.6.4 intel_17 [intel] intel tk 8.6.4 intel_26 [intel] intel wheel 0.29.0 py36_intel_5 [intel] intel xz 5.2.2 intel_16 [intel] intel zlib 1.2.11 intel_3 [intel] intel libgfortran 3.0.0 1
py 1.4.34 py36_0
pyrfr 0.6.0 pytest 3.2.1 py36_0
sgmcmc 0.0.1

nosetest output:

.EEEEEE.......EEE.E....DIRECT Version 2.0.4 Problem Dimension n : 1 Eps value : 0.1000E-03 Epsilon is constant. Maximum number of f-evaluations (maxf) : 400 Maximum number of iterations (MaxT) : 200 Value of f_global : -0.1000+101 Global percentage wanted : 0.1000E-01 Volume percentage wanted : -0.1000E+01 Measure percentage wanted : -0.1000E+01 Jones original DIRECT algorithm is used. Bounds on variable x 1 : 0.00000 <= xi <= 1.00000

Call-back cb_fcn_in_directuserroutines failed. E..DIRECT Version 2.0.4 Problem Dimension n : 2 Eps value : 0.1000E-03 Epsilon is constant. Maximum number of f-evaluations (maxf) : 400 Maximum number of iterations (MaxT) : 200 Value of f_global : -0.1000+101 Global percentage wanted : 0.1000E-01 Volume percentage wanted : -0.1000E+01 Measure percentage wanted : -0.1000E+01 Jones original DIRECT algorithm is used. Bounds on variable x 1 : 0.00000 <= xi <= 1.00000 Bounds on variable x 2 : 0.00000 <= xi <= 1.00000

Call-back cb_fcn_in_directuserroutines failed. EE.....EEEEEEEEEEEEEE......EE

ERROR: test_compute (test.test_acquisition_functions.test_information_gain.TestInformationGain)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain.py", line 17, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_compute_pmin (test.test_acquisition_functions.test_information_gain.TestInformationGain)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain.py", line 17, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_innovations (test.test_acquisition_functions.test_information_gain.TestInformationGain)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain.py", line 17, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_sampling_representer_points (test.test_acquisition_functions.test_information_gain.TestInformationGain)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain.py", line 17, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_compute (test.test_acquisition_functions.test_information_gain_per_unit_cost.Test)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain_per_unit_cost.py", line 24, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_sampling_representer_points (test.test_acquisition_functions.test_information_gain_per_unit_cost.Test)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_acquisition_functions/test_information_gain_per_unit_cost.py", line 24, in setUp self.model.train(self.X, self.y) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 109, in train self.hypers = self.optimize() File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 200, in optimize p0 = self.gp.kernel.vector File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'vector'

====================================================================== ERROR: test_bayesian_optimization (test.test_fmin.test_fabolas.TestFminInterfaceFabolas)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_fmin/test_fabolas.py", line 32, in test_bayesian_optimization num_iterations=3) File "/home/pbalapra/Projects/projects/RoBO/robo/fmin/fabolas.py", line 106, in fabolas ndim=n_dims+1, dim=d) TypeError: init() got an unexpected keyword argument 'dim'

====================================================================== ERROR: test_bayesian_optimization (test.test_fmin.test_fmin_interface.TestFminInterface)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_fmin/test_fmin_interface.py", line 31, in test_bayesian_optimization num_iterations=3) File "/home/pbalapra/Projects/projects/RoBO/robo/fmin/bayesian_optimization.py", line 133, in bayesian_optimization x_best, f_min = bo.run(num_iterations) File "/home/pbalapra/Projects/projects/RoBO/robo/solver/bayesian_optimization.py", line 167, in run new_x = self.choose_next(self.X, self.y, do_optimize) File "/home/pbalapra/Projects/projects/RoBO/robo/solver/bayesian_optimization.py", line 236, in choose_next self.model.train(X, y, do_optimize=do_optimize) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process_mcmc.py", line 115, in train len(self.kernel.pars) + 1, File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 67, in getattr raise AttributeError(name) AttributeError: pars -------------------- >> begin captured logging << -------------------- robo.solver.bayesian_optimization: INFO: Evaluate: [ 0.4204129] robo.solver.bayesian_optimization: INFO: Configuration achieved a performance of 0.006334 in 0.000011 seconds robo.solver.bayesian_optimization: INFO: Evaluate: [ 0.00399815] robo.solver.bayesian_optimization: INFO: Configuration achieved a performance of 0.246018 in 0.000010 seconds robo.solver.bayesian_optimization: INFO: Start iteration 2 ... robo.solver.bayesian_optimization: INFO: Train model... robo.solver.bayesian_optimization: ERROR: Model could not be trained! --------------------- >> end captured logging << ---------------------

====================================================================== ERROR: test_bohamiann (test.test_fmin.test_fmin_interface.TestFminInterface)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_fmin/test_fmin_interface.py", line 41, in test_bohamiann num_iterations=3) File "/home/pbalapra/Projects/projects/RoBO/robo/fmin/bohamiann.py", line 65, in bohamiann normalize_output=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/bnn.py", line 122, in init raise ValueError("If you want to use Bayesian Neural Networks you " ValueError: If you want to use Bayesian Neural Networks you have to install the following dependencies: Theano (pip install theano) Lasagne (pip install lasagne) sgmcmc (see https://github.com/stokasto/sgmcmc)

====================================================================== ERROR: test_bayesian_optimization (test.test_fmin.test_mtbo.TestFminInterface)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_fmin/test_mtbo.py", line 28, in test_bayesian_optimization num_iterations=3) File "/home/pbalapra/Projects/projects/RoBO/robo/fmin/mtbo.py", line 98, in mtbo ndim=n_dims+1, dim=d) TypeError: init() got an unexpected keyword argument 'dim'

====================================================================== ERROR: test_direct (test.test_maximizer.test_maximizers_one_dim.TestMaximizers1D)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_maximizer/test_maximizers_one_dim.py", line 24, in test_direct x = maximizer.maximize() File "/home/pbalapra/Projects/projects/RoBO/robo/maximizers/direct.py", line 58, in maximize maxf=self.n_func_evals) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/DIRECT/init.py", line 202, in solve cdata ValueError: data type must provide an itemsize

====================================================================== ERROR: test_cmaes (test.test_maximizer.test_maximizers_two_dim.TestMaximizers2D)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_maximizer/test_maximizers_two_dim.py", line 33, in test_cmaes x = maximizer.maximize() File "/home/pbalapra/Projects/projects/RoBO/robo/maximizers/cmaes.py", line 81, in maximize "maxfevals": self.n_func_evals}) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 3822, in fmin es = CMAEvolutionStrategy(x0, sigma_factor * sigma0, opts) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 1377, in init if not self.boundary_handler.has_bounds(): File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/constraints_handler.py", line 113, in has_bounds if bounds in (None, [None, None]): ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

====================================================================== ERROR: test_direct (test.test_maximizer.test_maximizers_two_dim.TestMaximizers2D)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_maximizer/test_maximizers_two_dim.py", line 24, in test_direct x = maximizer.maximize() File "/home/pbalapra/Projects/projects/RoBO/robo/maximizers/direct.py", line 58, in maximize maxf=self.n_func_evals) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/DIRECT/init.py", line 202, in solve cdata ValueError: data type must provide an itemsize

====================================================================== ERROR: test_get_incumbent (test.test_models.test_bnn.TestBayesianNeuralNetwork)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_bnn.py", line 12, in setUp self.model = BayesianNeuralNetwork(normalize_output=True, normalize_input=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/bnn.py", line 122, in init raise ValueError("If you want to use Bayesian Neural Networks you " ValueError: If you want to use Bayesian Neural Networks you have to install the following dependencies: Theano (pip install theano) Lasagne (pip install lasagne) sgmcmc (see https://github.com/stokasto/sgmcmc)

====================================================================== ERROR: test_predict (test.test_models.test_bnn.TestBayesianNeuralNetwork)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_bnn.py", line 12, in setUp self.model = BayesianNeuralNetwork(normalize_output=True, normalize_input=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/bnn.py", line 122, in init raise ValueError("If you want to use Bayesian Neural Networks you " ValueError: If you want to use Bayesian Neural Networks you have to install the following dependencies: Theano (pip install theano) Lasagne (pip install lasagne) sgmcmc (see https://github.com/stokasto/sgmcmc)

====================================================================== ERROR: Failure: ValueError (If you want to use DNGO you have to install the following dependencies: Theano (pip install theano) Lasagne (pip install lasagne))

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/robo/models/dngo.py", line 11, in import lasagne File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/lasagne/init.py", line 19, in from . import layers File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/lasagne/layers/init.py", line 7, in from .pool import * File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/lasagne/layers/pool.py", line 6, in from theano.tensor.signal import downsample ImportError: cannot import name 'downsample'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/imp.py", line 234, in load_module return load_source(name, filename, file) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/imp.py", line 172, in load_source module = _load(spec) File "", line 675, in _load File "", line 655, in _load_unlocked File "", line 678, in exec_module File "", line 205, in _call_with_frames_removed File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_dngo.py", line 4, in from robo.models.dngo import DNGO File "/home/pbalapra/Projects/projects/RoBO/robo/models/dngo.py", line 14, in raise ValueError("If you want to use DNGO you have to install the following dependencies:\n" ValueError: If you want to use DNGO you have to install the following dependencies: Theano (pip install theano) Lasagne (pip install lasagne)

====================================================================== ERROR: test_get_incumbent (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_nll (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_optimize (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_predict (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_predict_variance (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_sample_function (test.test_models.test_gaussian_process.TestGaussianProcess)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process.py", line 23, in setUp self.model.train(self.X, self.y, do_optimize=False) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process.py", line 113, in train self.hypers = self.gp.kernel[:] File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 148, in getitem return self.get_parameter(self._get_name(name_or_index)) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 461, in get_parameter return self._apply_to_parameter("get_parameter", name) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/modeling.py", line 435, in _apply_to_parameter comp = name.split(":") AttributeError: 'slice' object has no attribute 'split'

====================================================================== ERROR: test_get_incumbent (test.test_models.test_gaussian_process_mcmc.TestGaussianProcessMCMC)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process_mcmc.py", line 24, in setUp self.model.train(self.X, self.y, do_optimize=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process_mcmc.py", line 115, in train len(self.kernel.pars) + 1, File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'pars'

====================================================================== ERROR: test_loglikelihood (test.test_models.test_gaussian_process_mcmc.TestGaussianProcessMCMC)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process_mcmc.py", line 24, in setUp self.model.train(self.X, self.y, do_optimize=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process_mcmc.py", line 115, in train len(self.kernel.pars) + 1, File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'pars'

====================================================================== ERROR: test_predict (test.test_models.test_gaussian_process_mcmc.TestGaussianProcessMCMC)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_models/test_gaussian_process_mcmc.py", line 24, in setUp self.model.train(self.X, self.y, do_optimize=True) File "/home/pbalapra/Projects/projects/RoBO/robo/models/base_model.py", line 71, in func_wrapper return func(self, X, y, *args, **kwargs) File "/home/pbalapra/Projects/projects/RoBO/robo/models/gaussian_process_mcmc.py", line 115, in train len(self.kernel.pars) + 1, File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/george/kernels.py", line 66, in getattr return getattr(self.models[None], name) AttributeError: 'BaseMatern52Kernel' object has no attribute 'pars'

====================================================================== ERROR: test_choose_next (test.test_solver.test_bayesian_optimization.TestBayesianOptimization)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_solver/test_bayesian_optimization.py", line 21, in setUp kernel = george.kernels.Matern52Kernel(np.array([1]), dim=1, ndim=1) TypeError: init() got an unexpected keyword argument 'dim'

====================================================================== ERROR: test_run (test.test_solver.test_bayesian_optimization.TestBayesianOptimization)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_solver/test_bayesian_optimization.py", line 21, in setUp kernel = george.kernels.Matern52Kernel(np.array([1]), dim=1, ndim=1) TypeError: init() got an unexpected keyword argument 'dim'

====================================================================== ERROR: test_posterior_mean_optimization (test.test_util.test_posterior_optimization.TestPosteriorOptimization)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_util/test_posterior_optimization.py", line 22, in test_posterior_mean_optimization x = posterior_mean_optimization(self.model, self.lower, self.upper, method="cma", n_restarts=1) File "/home/pbalapra/Projects/projects/RoBO/robo/util/posterior_optimization.py", line 61, in posterior_mean_optimization res = cma.fmin(f, startpoint, 0.6, options={"bounds": [lower, upper]}) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 3822, in fmin es = CMAEvolutionStrategy(x0, sigma_factor * sigma0, opts) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 1377, in init if not self.boundary_handler.has_bounds(): File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/constraints_handler.py", line 113, in has_bounds if bounds in (None, [None, None]): ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

====================================================================== ERROR: test_posterior_mean_plus_std_optimization (test.test_util.test_posterior_optimization.TestPosteriorOptimization)

Traceback (most recent call last): File "/home/pbalapra/Projects/projects/RoBO/test/test_util/test_posterior_optimization.py", line 29, in test_posterior_mean_plus_std_optimization x = posterior_mean_plus_std_optimization(self.model, self.lower, self.upper, method="cma", n_restarts=1) File "/home/pbalapra/Projects/projects/RoBO/robo/util/posterior_optimization.py", line 129, in posterior_mean_plus_std_optimization res = cma.fmin(f, startpoint, 0.6, options={"bounds": [lower, upper]}) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 3822, in fmin es = CMAEvolutionStrategy(x0, sigma_factor * sigma0, opts) File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/evolution_strategy.py", line 1377, in init if not self.boundary_handler.has_bounds(): File "/home/pbalapra/.conda/envs/robo3/lib/python3.6/site-packages/cma/constraints_handler.py", line 113, in has_bounds if bounds in (None, [None, None]): ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Ran 55 tests in 0.445s

FAILED (errors=29)

numairmansur commented 7 years ago

Hi, Can you try to run it on python 3.4 ? we currently have some problems when running on python 3.6 .

mukherjees commented 7 years ago

I am having the same problem (tests are failing) even with Python 3.4.5. Here's my environment (output of conda list):

# packages in environment at //anaconda/envs/py34-robo:
#
_license                  1.1                      py34_1
alabaster                 0.7.9                    py34_0
anaconda                  4.3.1               np111py34_0
anaconda-client           1.6.0                    py34_0
anaconda-navigator        1.5.0                    py34_0
anaconda-project          0.4.1                    py34_0
appnope                   0.1.0                    py34_0
appscript                 1.0.1                    py34_0
argcomplete               1.0.0                    py34_1
astroid                   1.4.9                    py34_0
astropy                   1.3                 np111py34_0
autograd                  1.2                       <pip>
babel                     2.3.4                    py34_0
backports                 1.0                      py34_0
backports_abc             0.5                      py34_0
beautifulsoup4            4.5.3                    py34_0
bitarray                  0.8.1                    py34_0
blaze                     0.10.1                   py34_0
bokeh                     0.12.4                   py34_0
boto                      2.45.0                   py34_0
bottleneck                1.2.0               np111py34_0
cffi                      1.9.1                    py34_0
chardet                   2.3.0                    py34_0
chest                     0.2.3                    py34_0
click                     6.7                      py34_0
cloudpickle               0.2.2                    py34_0
clyent                    1.2.2                    py34_0
cma                       2.3.1                     <pip>
colorama                  0.3.7                    py34_0
configobj                 5.0.6                    py34_0
contextlib2               0.5.4                    py34_0
cryptography              1.7.1                    py34_0
curl                      7.52.1                        0
cycler                    0.10.0                   py34_0
cython                    0.25.2                   py34_0
cytoolz                   0.8.2                    py34_0
dask                      0.13.0                   py34_0
datashape                 0.5.4                    py34_0
decorator                 4.0.11                   py34_0
dill                      0.2.5                    py34_0
DIRECT                    1.0.1                     <pip>
docutils                  0.13.1                   py34_0
emcee                     2.2.1                     <pip>
entrypoints               0.2.2                    py34_0
et_xmlfile                1.0.1                    py34_0
fastcache                 1.0.2                    py34_1
flask                     0.12                     py34_0
flask-cors                3.0.2                    py34_0
freetype                  2.5.5                         2
future                    0.16.0                    <pip>
george                    0.2.1                     <pip>
get_terminal_size         1.0.0                    py34_0
gevent                    1.2.1                    py34_0
greenlet                  0.4.11                   py34_0
h5py                      2.6.0               np111py34_2
hdf5                      1.8.17                        1
heapdict                  1.0.0                    py34_1
hpolib2                   0.0.1                     <pip>
icu                       54.1                          0
idna                      2.2                      py34_0
imagesize                 0.7.1                    py34_0
ipykernel                 4.5.2                    py34_0
ipython                   5.1.0                    py34_1
ipython_genutils          0.1.0                    py34_0
ipywidgets                5.2.2                    py34_1
isort                     4.2.5                    py34_0
itsdangerous              0.24                     py34_0
jbig                      2.1                           0
jdcal                     1.3                      py34_0
jedi                      0.9.0                    py34_1
jinja2                    2.9.4                    py34_0
jpeg                      9b                            0
jsonschema                2.5.1                    py34_0
jupyter                   1.0.0                    py34_3
jupyter_client            4.4.0                    py34_0
jupyter_console           5.0.0                    py34_0
jupyter_core              4.2.1                    py34_0
Lasagne                   0.2.dev1                  <pip>
lazy-object-proxy         1.2.2                    py34_0
libiconv                  1.14                          0
libpng                    1.6.27                        0
libtiff                   4.0.6                         3
libxml2                   2.9.4                         0
libxslt                   1.1.29                        0
llvmlite                  0.15.0                   py34_0
locket                    0.2.0                    py34_1
lxml                      3.7.2                    py34_0
markupsafe                0.23                     py34_2
matplotlib                2.0.0               np111py34_0
mistune                   0.7.3                    py34_1
mkl                       2017.0.1                      0
mkl-service               1.1.2                    py34_3
mpmath                    0.19                     py34_1
multipledispatch          0.4.9                    py34_0
nbconvert                 4.2.0                    py34_0
nbformat                  4.2.0                    py34_0
networkx                  1.11                     py34_0
nltk                      3.2.2                    py34_0
nose                      1.3.7                    py34_1
notebook                  4.3.1                    py34_0
numba                     0.30.1              np111py34_0
numexpr                   2.6.1               np111py34_2
numpy                     1.11.3                   py34_0
numpy                     1.13.3                    <pip>
numpydoc                  0.6.0                    py34_0
odo                       0.5.0                    py34_1
openpyxl                  2.4.1                    py34_0
openssl                   1.0.2k                        1
pandas                    0.19.2              np111py34_1
partd                     0.3.7                    py34_0
path.py                   10.0                     py34_0
pathlib2                  2.2.0                    py34_0
patsy                     0.4.1                    py34_0
pep8                      1.7.0                    py34_0
pexpect                   4.2.1                    py34_0
pickleshare               0.7.4                    py34_0
pillow                    4.0.0                    py34_0
pip                       9.0.1                    py34_1
ply                       3.9                      py34_0
prompt_toolkit            1.0.9                    py34_0
psutil                    5.0.1                    py34_0
ptyprocess                0.5.1                    py34_0
py                        1.4.32                   py34_0
pyasn1                    0.1.9                    py34_0
pycosat                   0.6.1                    py34_1
pycparser                 2.17                     py34_0
pycrypto                  2.6.1                    py34_4
pycurl                    7.43.0                   py34_2
pyflakes                  1.5.0                    py34_0
pygments                  2.1.3                    py34_0
pylint                    1.6.4                    py34_1
pyopenssl                 16.2.0                   py34_0
pyparsing                 2.1.4                    py34_0
pyqt                      5.6.0                    py34_1
pytables                  3.3.0               np111py34_0
pytest                    3.0.5                    py34_0
python                    3.4.5                         0
python-dateutil           2.6.0                    py34_0
python.app                1.2                      py34_4
pytz                      2016.10                  py34_0
pyyaml                    3.12                     py34_0
pyzmq                     16.0.2                   py34_0
qt                        5.6.2                         0
qtawesome                 0.4.3                    py34_0
qtconsole                 4.2.1                    py34_1
qtpy                      1.2.1                    py34_0
readline                  6.2                           2
redis                     3.2.0                         0
redis-py                  2.10.5                   py34_0
requests                  2.12.4                   py34_0
rope                      0.9.4                    py34_1
ruamel_yaml               0.11.14                  py34_1
scandir                   1.4                      py34_0
scikit-image              0.12.3              np111py34_1
scikit-learn              0.18.1              np111py34_1
scipy                     0.18.1              np111py34_1
seaborn                   0.7.1                    py34_0
setuptools                27.2.0                   py34_0
sgmcmc                    0.0.1                     <pip>
simplegeneric             0.8.1                    py34_1
singledispatch            3.4.0.3                  py34_0
sip                       4.18                     py34_0
six                       1.10.0                   py34_0
snowballstemmer           1.2.1                    py34_0
sockjs-tornado            1.0.3                    py34_0
sphinx                    1.5.1                    py34_0
spyder                    3.1.2                    py34_0
sqlalchemy                1.1.5                    py34_0
sqlite                    3.13.0                        0
statsmodels               0.6.1               np111py34_1
sympy                     1.0                      py34_0
terminado                 0.6                      py34_0
Theano                    0.9.0                     <pip>
tk                        8.5.18                        0
toolz                     0.8.2                    py34_0
tornado                   4.4.2                    py34_0
traitlets                 4.3.1                    py34_0
unicodecsv                0.14.1                   py34_0
wcwidth                   0.1.7                    py34_0
werkzeug                  0.11.15                  py34_0
wheel                     0.29.0                   py34_0
widgetsnbextension        1.2.6                    py34_0
wrapt                     1.10.8                   py34_0
xlrd                      1.0.0                    py34_0
xlsxwriter                0.9.6                    py34_0
xlwings                   0.10.2                   py34_0
xlwt                      1.2.0                    py34_0
xz                        5.2.2                         1
yaml                      0.1.6                         0
zlib                      1.2.8                         3
mfeurer commented 6 years ago

It appears that the property vector was removed from george shortly after the fork (https://github.com/dfm/george/commit/a503c3df7decf65a53f4c5c0c419c88c8f398433#diff-833395cfe79e402fa3d01855374655b0L76). I assume using the george version from https://github.com/automl/george helps.