hi all, with my today's efforts I got down to 13 errors and 15 failures out of 284 tests, so it's getting better :) on the same branch the same set of unittests passes without errors or failures with python 2.7, so I assume I did not break anything important.
I attach here the error logs in case someone else feels like having a look. the remaining errors and failures are probably out of my reach, as fixing them requires a much deeper understanding of the very rich data types structure of PyMVPA ;) I am available for a short sprint in case someone is orbiting around northern germany... there are some commits that I think would require a deeper review by some core developer, as I am not 100% sure those changes are really as neutral as the lack of failures in the unittests seems to suggest. I had to disable a test that was hanging in an infinite loop: test_nfold_random_counted_selection_partitioner no idea what the problem there is, really. one point where I can directly ask for a solution is the usage of the variable nproc in BaseSearchlight (mvpa2/measures/searchlight.py): the doc-string seems to imply that setting it to None would use all available cores, but if the pprocess module is not installed this is not true, and an error is spit only in the case nproc > 1 (which is false if nproc is None). so maybe the doc-string could be updated to say something like: nproc : None or int How many processes to use for computation. Requires `pprocess` external module. If None -- all available cores will be used if `pprocess` is available, a single core will be used otherwise. ciao, tiziano
python3 setup.py config --noisy Converting to Python3 via 2to3... running config python3 setup.py build_ext --inplace Converting to Python3 via 2to3... running build_ext running build_src build_src building extension "mvpa2.clfs.libsmlrc.smlrc" sources building extension "mvpa2.clfs.libsvmc._svmc" sources building data_files sources build_src: building npy-pkg config files customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons touch build3-stamp I: Running py3-compatible unittests. None of them should ever fail. T: MVPA_SEED=1251509818 T: Testing for availability of external software packages. WARNING: libsvm verbosity control is not available. * Please note: warnings are printed only once, but underlying problem might occur many times * test_externals (mvpa2.tests.test_externals.TestExternals) ... ok test_externals_correct2nd_invocation (mvpa2.tests.test_externals.TestExternals) ... ok test_externals_no_double_invocation (mvpa2.tests.test_externals.TestExternals) ... ok test_basic (mvpa2.tests.test_dochelpers.DochelpersTests) ... ok test_borrow_doc (mvpa2.tests.test_dochelpers.DochelpersTests) ... ok test_borrow_kwargs (mvpa2.tests.test_dochelpers.DochelpersTests) ... ok test_searchlight_doc (mvpa2.tests.test_dochelpers.DochelpersTests) ... ok test_simple_som (mvpa2.tests.test_som.SOMMapperTests) ... ERROR test_blank_state (mvpa2.tests.test_state.StateTests) ... ok test_deep_copying_state_variable (mvpa2.tests.test_state.StateTests) ... ok Check if we can store/restore set of enabled ca ... ok test_parametrized (mvpa2.tests.test_state.StateTests) ... ERROR test_proper_state (mvpa2.tests.test_state.StateTests) ... ok Simple test if child gets conditional attributes from the parent as well ... ok test_read_only (mvpa2.tests.test_state.StateTests) ... ok To test new ca ... ok test_stored_temporarily (mvpa2.tests.test_state.StateTests) ... ok test_value_in_constructor (mvpa2.tests.test_state.StateTests) ... ok test_blank (mvpa2.tests.test_params.ParamsTests) ... ok test_classifier (mvpa2.tests.test_params.ParamsTests) ... ok test_incorrect_parameter_error (mvpa2.tests.test_params.ParamsTests) ... ok test_mixed (mvpa2.tests.test_params.ParamsTests) ... ok test_simple (mvpa2.tests.test_params.ParamsTests) ... ok test_config (mvpa2.tests.test_config.ConfigTests) ... ok test_asobjarray (mvpa2.tests.test_support.SupportFxTests) ... ok test_break_points (mvpa2.tests.test_support.SupportFxTests) ... ok test_correlation (mvpa2.tests.test_support.SupportFxTests) ... ok test_event (mvpa2.tests.test_support.SupportFxTests) ... ok test_id_hash (mvpa2.tests.test_support.SupportFxTests) ... FAIL test_map_overlap (mvpa2.tests.test_support.SupportFxTests) ... ok test_mof_n_combinations (mvpa2.tests.test_support.SupportFxTests) ... ok Test our ad-hoc SmartVersion ... ERROR test_transform_with_boxcar (mvpa2.tests.test_support.SupportFxTests) ... ok Test conversion of versions from strings ... ok test_xrandom_unique_combinations (mvpa2.tests.test_support.SupportFxTests) ... ok mvpa2.tests.test_support.test_value2idx ... ok mvpa2.tests.test_support.test_limit_filter ... ok Test if works fine with carriage return (cr) symbol ... ok test_debug (mvpa2.tests.test_verbosity.VerboseOutputTest) ... ok test_debug_rgexp (mvpa2.tests.test_verbosity.VerboseOutputTest) ... ok Test error message ... ok Test if it works fine with no newline (LF) symbol ... ok Test once logger ... ok Test if it doesn't output at higher levels ... ok Test if outputs at lower levels and indents ... ok Test indent symbol ... ok Test if chokes on negative level ... ok Test all available reports, real or dummy for just working ... T: Tests from "test_ridge" are skipped due to missing externals: scipy T: Tests from "test_gpr" are skipped due to missing externals: scipy T: Tests from "test_hamster" are skipped due to missing externals: ['cPickle', 'gzip'] T: Warning -- following test files were found but will not be tested: test_gpr.py, test_hamster.py, test_atlases.py, test_ridge.py WARNING: You are using DummyReport - no action will be taken. Please install reportlab to enjoy reporting facility within PyMVPA ok Test if we are not missing basic parts ... ok Test if we are not missing basic parts ... ok Test the group_kwargs decorator ... ok test_tuebingen_meg (mvpa2.tests.test_meg.MEGTests) ... ok test_binary_decorator (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_boosted (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_boosted_state_propagation (mvpa2.tests.test_clf.ClassifiersTests) ... ok Simple test if classifiers can generalize ok on simple data ... ok To check if known/present Classifiers are working properly ... ok Simple test if a learner could cope with custom sa not targets ... ok Test how clf handles degenerate cases ... WARNING: SMLR: detected ties in categories ['L0' 'L1']. Small amount of noise will be injected into result estimates upon prediction to break the ties ok test_dummy (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_feature_selection_classifier (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_feature_selection_classifier_with_regression (mvpa2.tests.test_clf.ClassifiersTests) ... ok Test all classifiers for conformant behavior ... WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: SMLR: detected ties in categories [2]. Small amount of noise will be injected into result estimates upon prediction to break the ties WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: SMLR: detected ties in categories [2]. Small amount of noise will be injected into result estimates upon prediction to break the ties WARNING: SMLR: detected ties in categories [2]. Small amount of noise will be injected into result estimates upon prediction to break the ties WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. WARNING: kNN: input data is in integers. Overflow on arithmetic operations might result in errors. Please convert dataset's samples into floating datatype if any error is reported. ok Test if MappedClassifier could handle a mapper altering number of samples ... ERROR test_mapped_classifier (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_multiclass_classifier (mvpa2.tests.test_clf.ClassifiersTests) ... ok Basic tests of metaclass for using regressions as classifiers ... ok test_retrainables (mvpa2.tests.test_clf.ClassifiersTests) ... ok Test if binary and multiclass can handle single class training/testing ... WARNING: SMLR: detected ties in categories ['L0']. Small amount of noise will be injected into result estimates upon prediction to break the ties ok test_split_classifier (mvpa2.tests.test_clf.ClassifiersTests) ... ok test_split_classifier_extended (mvpa2.tests.test_clf.ClassifiersTests) ... ok Basic testing of the clf summary ... ok test_svms (mvpa2.tests.test_clf.ClassifiersTests) ... ok Basic tests for TreeClassifier ... ERROR test_values (mvpa2.tests.test_clf.ClassifiersTests) ... ok Test If binary regression-based classifiers have proper tag ... ok Simple tests on regressions ... ok Simple tests on regressions being used as classifiers ... ok Test "sensitivities" provided by regressions ... ok test_knn_state (mvpa2.tests.test_knn.KNNTests) ... ok test_multivariate (mvpa2.tests.test_knn.KNNTests) ... ok test_gnb (mvpa2.tests.test_gnb.GNBTests) ... ok test_cper_class (mvpa2.tests.test_svm.SVMTests) ... ok test_multivariate (mvpa2.tests.test_svm.SVMTests) ... ERROR Test if we raise exceptions on incorrect specifications ... ok test_plr (mvpa2.tests.test_plr.PLRTests) ... ok test_plr_state (mvpa2.tests.test_plr.PLRTests) ... ok test_smlr (mvpa2.tests.test_smlr.SMLRTests) ... ok test_smlr_sensitivities (mvpa2.tests.test_smlr.SMLRTests) ... ok test_smlr_state (mvpa2.tests.test_smlr.SMLRTests) ... ok test_more_svd (mvpa2.tests.test_svdmapper.SVDMapperTests) ... ok test_simple_svd (mvpa2.tests.test_svdmapper.SVDMapperTests) ... ok test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... ok test_basic_functioning (mvpa2.tests.test_hyperalignment.HyperAlignmentTests) ... ok test_absolute (mvpa2.tests.test_transformers.TransformerTests) ... ok test_absolute2 (mvpa2.tests.test_transformers.TransformerTests) ... ok Basic testing of DistPValue ... ok test_first_axis_sum_not_zero (mvpa2.tests.test_transformers.TransformerTests) ... ok test_l1_norm (mvpa2.tests.test_transformers.TransformerTests) ... ok test_l2_norm (mvpa2.tests.test_transformers.TransformerTests) ... ok test_over_axis (mvpa2.tests.test_transformers.TransformerTests) ... ok test_rank_order (mvpa2.tests.test_transformers.TransformerTests) ... ok test_1d_multispace_searchlight (mvpa2.tests.test_searchlight.SearchlightTests) ... ok test_chi_square_searchlight (mvpa2.tests.test_searchlight.SearchlightTests) ... ok test_gnbsearchlight_doc (mvpa2.tests.test_searchlight.SearchlightTests) ... ok test_partial_searchlight_with_confusion_matrix (mvpa2.tests.test_searchlight.SearchlightTests) ... ok test_partial_searchlight_with_full_report (mvpa2.tests.test_searchlight.SearchlightTests) ... ok test_regression_with_additional_sa (mvpa2.tests.test_searchlight.SearchlightTests) ... ERROR Tests both generic and GNBSearchlight ... FAIL test_usecase_concordancesl (mvpa2.tests.test_searchlight.SearchlightTests) ... ERROR test_best_detector (mvpa2.tests.test_rfe.RFETests) ... ok test_feature_selection_pipeline (mvpa2.tests.test_rfe.RFETests) ... ok Test feature selector ... ok Test stopping criterion ... ok test_james_problem (mvpa2.tests.test_rfe.RFETests) ... ERROR test_james_problem_multiclass (mvpa2.tests.test_rfe.RFETests) ... ERROR Test multiple stop criteria ... ok Test stopping criterion ... ok Test stopping criterion ... ok test_rfe (mvpa2.tests.test_rfe.RFETests) ... ok test_sensitivity_based_feature_selection (mvpa2.tests.test_rfe.RFETests) ... ok test_ifs (mvpa2.tests.test_ifs.IFSTests) ... ok test_perturbation_sensitivity_analyzer (mvpa2.tests.test_perturbsensana.PerturbationSensitivityAnalyzerTests) ... ok test_docstrings (mvpa2.tests.test_suite.SuiteTest) ... FAIL Test if we are loading fine ... ok Very basic testing -- just to see if it doesn't crash ... ok mvpa2.tests.test_collections.test_basic_collectable ... ok mvpa2.tests.test_collections.test_array_collectable ... ok mvpa2.tests.test_collections.test_collections ... ok mvpa2.tests.test_collections.test_conditional_attr ... ok mvpa2.tests.test_attrmap.test_attrmap ... FAIL mvpa2.tests.test_attrmap.test_attrmap_conflicts ... ok mvpa2.tests.test_attrmap.test_attrmap_repr ... ok mvpa2.tests.test_datasetng.test_from_wizard ... ok mvpa2.tests.test_datasetng.test_ds_array ... ok mvpa2.tests.test_datasetng.test_labelschunks_access ... ok mvpa2.tests.test_datasetng.test_ex_from_masked ... ok mvpa2.tests.test_datasetng.test_shape_conversion ... ok mvpa2.tests.test_datasetng.test_multidim_attrs ... ok mvpa2.tests.test_datasetng.test_samples_shape ... ok mvpa2.tests.test_datasetng.test_basic_datamapping ... ok mvpa2.tests.test_datasetng.test_ds_shallowcopy ... ok mvpa2.tests.test_datasetng.test_ds_deepcopy ... ok mvpa2.tests.test_datasetng.test_mergeds ... ok Additional tests for hstacking of datasets ... ok Test composition of new datasets by addition of existing ones ... ok mvpa2.tests.test_datasetng.test_combined_samplesfeature_selection ... ok mvpa2.tests.test_datasetng.test_labelpermutation_randomsampling ... ok mvpa2.tests.test_datasetng.test_masked_featureselection ... ok mvpa2.tests.test_datasetng.test_origmask_extraction ... ok mvpa2.tests.test_datasetng.test_feature_masking ... ok mvpa2.tests.test_datasetng.test_origid_handling ... ok mvpa2.tests.test_datasetng.test_idhash ... FAIL mvpa2.tests.test_datasetng.test_arrayattributes ... ok mvpa2.tests.test_datasetng.test_repr ... ok mvpa2.tests.test_datasetng.test_str ... ok mvpa2.tests.test_datasetng.test_other_samples_dtypes ... SKIP: External scipy is not present thus tests battery skipped mvpa2.tests.test_datasetng.test_dataset_summary ... ok mvpa2.tests.test_datasetng.test_h5py_io ... SKIP: External h5py is not present thus tests battery skipped mvpa2.tests.test_datasetng.test_hollow_samples ... ok test_aggregation (mvpa2.tests.test_datasetfx.MiscDatasetFxTests) ... ok test_binds (mvpa2.tests.test_datasetfx.MiscDatasetFxTests) ... ok Just basic testing for now ... ok test_invar_features_removal (mvpa2.tests.test_datasetfx.MiscDatasetFxTests) ... ok Test sequence statistics ... ok mvpa2.tests.test_dataset_formats.test_format_lightsvm_basic ... ERROR test_counted_splitting (mvpa2.tests.test_splitter.SplitterTests) ... FAIL test_custom_split (mvpa2.tests.test_splitter.SplitterTests) ... FAIL test_discarded_boundaries (mvpa2.tests.test_splitter.SplitterTests) ... ok test_half_split (mvpa2.tests.test_splitter.SplitterTests) ... FAIL test_label_splitter (mvpa2.tests.test_splitter.SplitterTests) ... ok Test NGroupSplitter alongside with the reversal of the ... FAIL test_nfold_random_counted_selection_partitioner (mvpa2.tests.test_splitter.SplitterTests) ... ok test_nfold_random_counted_selection_partitioner_huge (mvpa2.tests.test_splitter.SplitterTests) ... ok test_odd_even_split (mvpa2.tests.test_splitter.SplitterTests) ... FAIL test_reprs (mvpa2.tests.test_splitter.SplitterTests) ... ok test_simplest_cv_pat_gen (mvpa2.tests.test_splitter.SplitterTests) ... FAIL test_slicing (mvpa2.tests.test_splitter.SplitterTests) ... ok test_splitattr_deprecation (mvpa2.tests.test_splitter.SplitterTests) ... ok mvpa2.tests.test_generators.test_splitter ... FAIL mvpa2.tests.test_generators.test_partitionmapper ... ok mvpa2.tests.test_generators.test_attrpermute ... ok mvpa2.tests.test_generators.test_balancer ... FAIL mvpa2.tests.test_generators.test_repeater ... ok mvpa2.tests.test_generators.test_sifter ... ok mvpa2.tests.test_generators.test_exclude_targets_combinations ... ok mvpa2.tests.test_eepdataset.test_eep_load ... ok mvpa2.tests.test_eepdataset.test_eep_bin ... ok mvpa2.tests.test_erdataset.test_erdataset ... ok mvpa2.tests.test_multiclf.test_multiclass_ties ... ok mvpa2.tests.test_neighborhood.test_distances ... ok mvpa2.tests.test_neighborhood.test_sphere ... ok mvpa2.tests.test_neighborhood.test_sphere_distance_func ... ok mvpa2.tests.test_neighborhood.test_sphere_scaled ... ok mvpa2.tests.test_neighborhood.test_hollowsphere_basic ... ok Test either we sustain empty neighborhoods ... WARNING: HollowSphere(radius=1, inner_radius=0, element_sizes=(3, 3, 3)) defines no neighbors ok mvpa2.tests.test_neighborhood.test_query_engine ... ok Test cached query engine ... ERROR Do some extended testing of OneWayAnova ... ok Testing null dist probability ... ok mvpa2.tests.test_mapper.test_flatten ... ok mvpa2.tests.test_mapper.test_subset ... ok mvpa2.tests.test_mapper.test_subset_filler ... ok mvpa2.tests.test_mapper.test_repr ... ok mvpa2.tests.test_mapper.test_chainmapper ... ok mvpa2.tests.test_mapper.test_sampleslicemapper ... ok mvpa2.tests.test_mapper.test_strip_boundary ... ok mvpa2.tests.test_arraymapper.test_forward_dense_array_mapper ... ok mvpa2.tests.test_arraymapper.test_reverse_dense_array_mapper ... ok mvpa2.tests.test_arraymapper.test_mapper_aliases ... ok mvpa2.tests.test_arraymapper.test_selects ... ok mvpa2.tests.test_boxcarmapper.test_simpleboxcar ... ok mvpa2.tests.test_boxcarmapper.test_datasetmapping ... ok test_size (mvpa2.tests.test_prototypemapper.PrototypeMapperTests) ... ok test_size_random_prototypes (mvpa2.tests.test_prototypemapper.PrototypeMapperTests) ... ok test_streamline_equal_mapper (mvpa2.tests.test_prototypemapper.PrototypeMapperTests) ... ok test_streamline_random_mapper (mvpa2.tests.test_prototypemapper.PrototypeMapperTests) ... ok test_symmetry (mvpa2.tests.test_prototypemapper.PrototypeMapperTests) ... ok mvpa2.tests.test_fxmapper.test_samplesgroup_mapper ... FAIL mvpa2.tests.test_fxmapper.test_fx_native_calls ... ok mvpa2.tests.test_fxmapper.test_featuregroup_mapper ... FAIL mvpa2.tests.test_fxmapper.test_fxmapper ... ok mvpa2.tests.test_fxmapper.test_features01 ... ok Test by comparing to results of elderly z-score function ... ok mvpa2.tests.test_zscoremapper.test_zcore_repr ... ok Test z-scoring transformation ... WARNING: Z-scoring chunk-wise having a chunk with less than three samples will set features in these samples to either zero (with 1 sample in a chunk) or -1/+1 (with 2 samples in a chunk). You have chunks with following number of samples: {0: 1, 1: 1} WARNING: Z-scoring chunk-wise having a chunk with less than three samples will set features in these samples to either zero (with 1 sample in a chunk) or -1/+1 (with 2 samples in a chunk). You have chunks with following number of samples: {0: 2, 1: 2} WARNING: Z-scoring chunk-wise having a chunk with only 3 samples is 'discouraged'. You have chunks with following number of samples: {0: 3, 1: 3} ok Disabled the test since we have no SpAM yet ... SKIP: skipped SPaM since no SPaM test_cached_kernel (mvpa2.tests.test_kernel.KernelTests) ... ok Euclidean distance kernel testing ... ok Simplistic testing of linear kernel ... ok test_pnorm_w (mvpa2.tests.test_kernel.KernelTests) ... ok Statistic Kernels ... ok mvpa2.tests.test_senses.test_splitclf_sensitivities ... ok test_noise_classification (mvpa2.tests.test_clfcrossval.CrossValidationTests) ... ok test_simple_n_minus_one_cv (mvpa2.tests.test_clfcrossval.CrossValidationTests) ... ok Simple testing of reading RTC files from BrainVoyager ... ok test_column_data_from_file (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_fsl_ev (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_fsl_ev2 (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_fsl_glm_design (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_read_fsl_design (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_samples_attributes (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok test_sensor_locations (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok Simple testing of helper Design2Labels ... ok testlabels2chunks (mvpa2.tests.test_iohelpers.IOHelperTests) ... ok Test AUC computation ... ok test_confusion_based_error (mvpa2.tests.test_transerror.ErrorsTests) ... ok test_confusion_call (mvpa2.tests.test_transerror.ErrorsTests) ... ok test_confusion_matrix (mvpa2.tests.test_transerror.ErrorsTests) ... WARNING: ROC was asked to be evaluated on data with 0 labels which is a degenerate case. ok test_confusion_matrix_acc (mvpa2.tests.test_transerror.ErrorsTests) ... SKIP: External scipy is not present thus tests battery skipped Test confusions addition inconsistent results (GH #51) ... ok test_confusion_matrix_with_mappings (mvpa2.tests.test_transerror.ErrorsTests) ... ok Basic test of confusion plot ... ok test_confusion_plot2 (mvpa2.tests.test_transerror.ErrorsTests) ... ok test_confusionmatrix_nulldist (mvpa2.tests.test_transerror.ErrorsTests) ... ok test_degenerate_confusion (mvpa2.tests.test_transerror.ErrorsTests) ... WARNING: ROC was asked to be evaluated on data with 1 labels which is a degenerate case. WARNING: ROC was asked to be evaluated on data with 1 labels which is a degenerate case. WARNING: ROC was asked to be evaluated on data with 1 labels which is a degenerate case. WARNING: ROC was asked to be evaluated on data with 1 labels which is a degenerate case. ok test_null_dist_prob (mvpa2.tests.test_transerror.ErrorsTests) ... ok Test analyzers in split classifier ... ok Additional aspects of OnewayAnova ... ok test_basic (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ERROR test_clf_transfer_measure (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok Test combination of the selectors in a single function ... ok test_linear_svm_weights (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok test_linear_svm_weights_per_class (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok Test sensitivity of the mapped classifier ... ok test_pseudo_cv_measure (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok test_repeated_features (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok test_split_featurewise_dataset_measure (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok test_transfer_measure (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok test_union_feature_selection (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ... ok mvpa2.tests.test_misc.test_dual_gaussian ... SKIP: 1 tests were skipped in testing test_dual_gaussian Failure: SkipTest () ... SKIP Failure: SkipTest (External scipy is not present thus tests battery skipped) ... SKIP: External scipy is not present thus tests battery skipped Failure: SkipTest (External scipy is not present thus tests battery skipped) ... SKIP: External scipy is not present thus tests battery skipped Failure: SkipTest (External pywt is not present thus tests battery skipped) ... SKIP: External pywt is not present thus tests battery skipped Failure: SkipTest (External mdp is not present thus tests battery skipped) ... SKIP: External mdp is not present thus tests battery skipped Failure: SkipTest (External scipy is not present thus tests battery skipped) ... SKIP: External scipy is not present thus tests battery skipped Failure: SkipTest (External elasticnet is not present thus tests battery skipped) ... SKIP: External elasticnet is not present thus tests battery skipped Failure: SkipTest (External lars is not present thus tests battery skipped) ... SKIP: External lars is not present thus tests battery skipped Failure: SkipTest (External glmnet is not present thus tests battery skipped) ... SKIP: External glmnet is not present thus tests battery skipped Failure: SkipTest (External shogun is not present thus tests battery skipped) ... SKIP: External shogun is not present thus tests battery skipped Failure: SkipTest (External scipy is not present thus tests battery skipped) ... SKIP: External scipy is not present thus tests battery skipped Failure: SkipTest (External h5py is not present thus tests battery skipped) ... SKIP: External h5py is not present thus tests battery skipped Failure: SkipTest (External h5py is not present thus tests battery skipped) ... SKIP: External h5py is not present thus tests battery skipped ====================================================================== ERROR: test_simple_som (mvpa2.tests.test_som.SOMMapperTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_som.py", line 31, in test_simple_som som.train(colors) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 131, in train result = self._train(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/types.py", line 36, in extract_samples return fx(obj, data) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/mappers/som.py", line 127, in _train unit_deltas += infl[:,:,np.newaxis] * (s - self._K) ValueError: operands could not be broadcast together with shapes (9,5,1) (10,5,3) ====================================================================== ERROR: test_parametrized (mvpa2.tests.test_state.StateTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_state.py", line 292, in test_parametrized a2_str = repr(a2) NameError: global name 'a2' is not defined ====================================================================== ERROR: Test our ad-hoc SmartVersion ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_support.py", line 222, in test_smart_version self.assertTrue(SV(v1) < SV(v2), File "/usr/lib/python3.2/distutils/version.py", line 58, in __lt__ c = self._cmp(other) AttributeError: 'SmartVersion' object has no attribute '_cmp' ====================================================================== ERROR: Test if MappedClassifier could handle a mapper altering number of samples ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_clf.py", line 1015, in test_gideon_weird_case errors.append(np.asscalar(te(ds_meaned))) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 237, in __call__ return super(Learner, self).__call__(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/node.py", line 80, in __call__ result = self._call(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/base.py", line 548, in _call dstrain = next(dsgen) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/generators/splitters.py", line 102, in generate cfgs = splattr.unique File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/collections.py", line 237, in unique self._unique_values = np.unique(arrvalue) File "/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py", line 191, in unique ar.sort() ValueError: operands could not be broadcast together with shapes (9) (90) ====================================================================== ERROR: Basic tests for TreeClassifier ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_clf.py", line 584, in test_tree_classifier cverror = cv(ds).samples.squeeze() File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 237, in __call__ return super(Learner, self).__call__(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/node.py", line 80, in __call__ result = self._call(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/base.py", line 467, in _call return super(CrossValidation, self)._call(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/base.py", line 300, in _call result = node(sds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 237, in __call__ return super(Learner, self).__call__(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/node.py", line 80, in __call__ result = self._call(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/base.py", line 555, in _call measure.train(dstrain) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 121, in train result = self._train(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/clfs/meta.py", line 866, in _train clf.train(ds_group) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 121, in train result = self._train(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/clfs/plr.py", line 75, in _train %(set(d),)) ValueError: Regressors for logistic regression should be [0,1]. Got {'L2', 'L3'} ====================================================================== ERROR: test_multivariate (mvpa2.tests.test_svm.SVMTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_svm.py", line 31, in test_multivariate l_clf = clfswh['linear', 'svm'][0] IndexError: list index out of range ====================================================================== ERROR: test_regression_with_additional_sa (mvpa2.tests.test_searchlight.SearchlightTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_searchlight.py", line 320, in test_regression_with_additional_sa regr = regrswh[:][0] IndexError: list index out of range ====================================================================== ERROR: test_usecase_concordancesl (mvpa2.tests.test_searchlight.SearchlightTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_searchlight.py", line 389, in test_usecase_concordancesl ds_both = vstack((ds1, ds2))# join 2 images into a single dataset File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/dataset.py", line 675, in vstack [ds.sa[attr].value for ds in datasets], axis=0) ValueError: arrays must have same number of dimensions ====================================================================== ERROR: test_james_problem (mvpa2.tests.test_rfe.RFETests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_rfe.py", line 385, in test_james_problem rfesvm_split = LinearCSVMC() NameError: global name 'LinearCSVMC' is not defined ====================================================================== ERROR: test_james_problem_multiclass (mvpa2.tests.test_rfe.RFETests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_rfe.py", line 433, in test_james_problem_multiclass rfesvm_split = LinearCSVMC() NameError: global name 'LinearCSVMC' is not defined ====================================================================== ERROR: mvpa2.tests.test_dataset_formats.test_format_lightsvm_basic ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_dataset_formats.py", line 26, in test_format_lightsvm_basic am = to_lightsvm_format(ds, f) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/datasets/formats.py", line 116, in to_lightsvm_format for i,v in zip(list(range(1, dataset.nfeatures+1)), s)))) TypeError: a float is required ====================================================================== ERROR: Test cached query engine ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_neighborhood.py", line 238, in test_cached_query_engine res_kw = [q(myspace=x) for x in ds.fa.myspace] File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_neighborhood.py", line 238, in <listcomp> res_kw = [q(myspace=x) for x in ds.fa.myspace] File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/misc/neighborhood.py", line 330, in __call__ return self.query(**kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/misc/neighborhood.py", line 652, in query v = self._lookup.get(k, None) TypeError: unhashable type: 'numpy.ndarray' ====================================================================== ERROR: test_basic (mvpa2.tests.test_datameasure.SensitivityAnalysersTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/sweepargs.py", line 67, in do_sweep method(*args_, **kwargs_) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_datameasure.py", line 79, in test_basic self.assertTrue(f[0] > 0.1) # some reasonably large value TypeError: unorderable types: Dataset() > float() ====================================================================== FAIL: test_id_hash (mvpa2.tests.test_support.SupportFxTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/sweepargs.py", line 133, in do_sweep raise AssertionError(estr).with_traceback(etb) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_support.py", line 159, in test_id_hash self.assertTrue(a_1 != a_2, msg="Idhash must change") AssertionError: Single scenario lead to failures of unittest test_id_hash: on pair=(array([[ -8.67732246e-01, 2.30164844e-01, -1.42720211e+00, 3.14619183e-01, 1.76 ... : False is not true : Idhash must change ====================================================================== FAIL: Tests both generic and GNBSearchlight ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/sweepargs.py", line 133, in do_sweep raise AssertionError(estr).with_traceback(etb) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/sweepargs.py", line 133, in do_sweep raise AssertionError(estr).with_traceback(etb) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_searchlight.py", line 105, in test_spatial_searchlight results = sl(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/learner.py", line 237, in __call__ return super(Learner, self).__call__(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/base/node.py", line 80, in __call__ result = self._call(ds) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/searchlight.py", line 122, in _call results, roi_sizes = self._sl_call(dataset, roi_ids, nproc) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/measures/gnbsearchlight.py", line 372, in _sl_call assert(block_labels.dtype.kind is 'i') AssertionError: Single scenario lead to failures of unittest test_spatial_searchlight: on common_variance=True : Single scenario lead to failures of unittest test_spatial_searchlight: on do_roi=False ====================================================================== FAIL: test_docstrings (mvpa2.tests.test_suite.SuiteTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_suite.py", line 93, in test_docstrings self.fail('\n'.join(sfailures)) AssertionError: Some items have missing docstrings: functions: isSequenceType ====================================================================== FAIL: mvpa2.tests.test_attrmap.test_attrmap ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_attrmap.py", line 30, in test_attrmap assert_array_equal(am.to_numeric(literal), num_default) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (mismatch 100.0%) x: array(['eins', 'zwei', 'sieben', 'eins', 'sieben', 'eins'], dtype='<U6') y: array([0, 2, 1, 0, 1, 0]) ====================================================================== FAIL: mvpa2.tests.test_datasetng.test_idhash ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_datasetng.py", line 665, in test_idhash msg="Changing value in attribute should change idhash") File "/usr/lib/python3/dist-packages/nose/tools.py", line 25, in ok_ assert expr, msg AssertionError: Changing value in attribute should change idhash ====================================================================== FAIL: test_counted_splitting (mvpa2.tests.test_splitter.SplitterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 323, in test_counted_splitting self.assertEqual(chosenchunks, list(range(target))) AssertionError: Lists differ: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,... != [0, 1, 2, 3, 4, 5, 6, 7, 8, 9,... First differing element 1: 0 1 Diff is 1284 characters long. Set self.maxDiff to None to see it. ====================================================================== FAIL: test_custom_split (mvpa2.tests.test_splitter.SplitterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 248, in test_custom_split self.assertTrue( p[0].nsamples == 50 ) AssertionError: False is not true ====================================================================== FAIL: test_half_split (mvpa2.tests.test_splitter.SplitterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 105, in test_half_split assert_array_equal(splits[0][1].sa['chunks'].unique, [0, 1, 2, 3, 4]) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 600, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (shapes (50,), (5,) mismatch) x: array([ 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2. , 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3. , 3.1, 3.2,... y: array([0, 1, 2, 3, 4]) ====================================================================== FAIL: Test NGroupSplitter alongside with the reversal of the ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 138, in test_n_group_split [0, 1, 2, 3, 4]) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 600, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (shapes (50,), (5,) mismatch) x: array([ 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2. , 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3. , 3.1, 3.2,... y: array([0, 1, 2, 3, 4]) ====================================================================== FAIL: test_odd_even_split (mvpa2.tests.test_splitter.SplitterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 79, in test_odd_even_split assert_array_equal(splits[0][1].sa['chunks'].unique, [1, 3, 5, 7, 9]) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 600, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (shapes (50,), (5,) mismatch) x: array([ 0.1, 0.3, 0.5, 0.7, 0.9, 1.1, 1.3, 1.5, 1.7, 1.9, 2.1, 2.3, 2.5, 2.7, 2.9, 3.1, 3.3, 3.5, 3.7, 3.9, 4.1, 4.3, 4.5, 4.7, 4.9, 5.1, 5.3, 5.5, 5.7, 5.9, 6.1, 6.3, 6.5,... y: array([1, 3, 5, 7, 9]) ====================================================================== FAIL: test_simplest_cv_pat_gen (mvpa2.tests.test_splitter.SplitterTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_splitter.py", line 57, in test_simplest_cv_pat_gen self.assertTrue( len(xvpat) == 10 ) AssertionError: False is not true ====================================================================== FAIL: mvpa2.tests.test_generators.test_splitter ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_generators.py", line 62, in test_splitter assert_equal(len(split.sa['chunks'].unique), 10) AssertionError: 25 != 10 ====================================================================== FAIL: mvpa2.tests.test_generators.test_balancer ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/testing/tools.py", line 158, in newfunc return func(*arg, **kwargs) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_generators.py", line 165, in test_balancer assert_almost_equal(np.mean(res.sa.balanced_set), 0.8) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 468, in assert_almost_equal raise AssertionError(msg) AssertionError: Arrays are not almost equal to 7 decimals ACTUAL: 1.0 DESIRED: 0.8 ====================================================================== FAIL: mvpa2.tests.test_fxmapper.test_samplesgroup_mapper ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_fxmapper.py", line 56, in test_samplesgroup_mapper assert_array_equal(mapped.targets, clabels) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 600, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (shapes (4, 2), (4,) mismatch) x: array([[0, 0], [1, 1], [0, 0], [1, 1]]) y: array([0, 1, 0, 1]) ====================================================================== FAIL: mvpa2.tests.test_fxmapper.test_featuregroup_mapper ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/tiziano/git/PyMVPA/build/py3k/mvpa2/tests/test_fxmapper.py", line 83, in test_featuregroup_mapper assert_array_equal(mds.fa.roi, np.unique([0, 1] * 4)) File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/usr/lib/python3/dist-packages/numpy/testing/utils.py", line 600, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (shapes (2, 4), (2,) mismatch) x: array([[0, 0, 0, 0], [1, 1, 1, 1]]) y: array([0, 1]) ---------------------------------------------------------------------- Ran 284 tests in 18.166s FAILED (SKIP=18, errors=13, failures=15) make: *** [unittest-py3] Error 1
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