Unable to pass the pytests

[YalingQing]

Hi,

I tried to set up the environment following the guidance in the readme. But after running all commands, I still fail the tests. This is the error I got. I wonder how to solve this problem. Thanks!

` ========================================== ERRORS ========================================== __ ERROR collecting tests/test_bert_pretraining_reader.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_bert_pretraining_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_bert_pretraining_reader.py:2: in from kb.bert_pretraining_reader import BertPreTrainingReader, \ kb/bert_pretraining_reader.py:15: in from kb.bert_tokenizer_and_candidate_generator import TokenizerAndCandidateGenerator, start_token, sep_token kb/bert_tokenizer_and_candidate_generator.py:14: in from kb.common import MentionGenerator, get_empty_candidates kb/common.py:11: in from allennlp.training.metrics.metric import Metric ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/training/init.py:1: in from allennlp.training.trainer import Trainer ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/training/trainer.py:22: in from allennlp.models.model import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory __ ERROR collecting tests/test_bert_tokenizer_and_candidate_generator.py _____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_bert_tokenizer_and_candidate_generator.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_bert_tokenizer_and_candidate_generator.py:4: in from kb.bert_tokenizer_and_candidate_generator import BertTokenizerAndCandidateGenerator kb/bert_tokenizer_and_candidate_generator.py:14: in from kb.common import MentionGenerator, get_empty_candidates kb/common.py:11: in from allennlp.training.metrics.metric import Metric ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/training/metrics/init.py:12: in from allennlp.training.metrics.conll_coref_scores import ConllCorefScores ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/training/metrics/conll_coref_scores.py:5: in from sklearn.utils.linearassignment import linear_assignment E ModuleNotFoundError: No module named 'sklearn.utils.linearassignment' __ ERROR collecting tests/test_dictfield.py ____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_dict_field.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_dict_field.py:12: in from kb.entity_linking import TokenCharactersIndexerTokenizer kb/entity_linking.py:77: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory __ ERROR collecting tests/test_entity_linking.py _____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_entity_linking.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_entity_linking.py:9: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ____ ERROR collecting tests/test_kg_embedding.py ____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_kg_embedding.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_kg_embedding.py:5: in from kb.kg_embedding import KGTupleReader, get_labels_tensor_from_indices, \ kb/kg_embedding.py:13: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory __ ERROR collecting tests/test_kg_probe_reader.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_kg_probe_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_kg_probe_reader.py:10: in from kb.wordnet import WordNetCandidateMentionGenerator kb/wordnet.py:25: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ____ ERROR collecting tests/test_knowbert.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_knowbert.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_knowbert.py:10: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ____ ERROR collecting tests/test_wiki_reader.py ____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_wiki_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_wiki_reader.py:4: in from allennlp.common.testing.test_case import AllenNlpTestCase ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/common/testing/init.py:5: in from allennlp.common.testing.model_test_case import ModelTestCase ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/common/testing/model_test_case.py:7: in from allennlp.commands.train import train_model_from_file ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/commands/init.py:8: in from allennlp.commands.configure import Configure ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/commands/configure.py:27: in from allennlp.service.config_explorer import make_app ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/service/config_explorer.py:24: in from allennlp.common.configuration import configure, choices ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/common/configuration.py:21: in from allennlp.modules.seq2seq_encoders import _Seq2SeqWrapper ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory __ ERROR collecting tests/test_wordnet.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/test_wordnet.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_wordnet.py:7: in from kb.wordnet import WordNetFineGrainedSenseDisambiguationReader kb/wordnet.py:25: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory _____ ERROR collecting tests/evaluation/test_semeval2010_task8.py ____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/evaluation/test_semeval2010_task8.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/evaluation/test_semeval2010_task8.py:3: in from kb.include_all import SemEval2010Task8Reader, SemEval2010Task8Metric kb/include_all.py:2: in from kb.kg_embedding import KGTupleReader, KGTupleModel kb/kg_embedding.py:13: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ____ ERROR collecting tests/evaluation/test_simple_classifier.py ____ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/evaluation/test_simple_classifier.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/evaluation/test_simple_classifier.py:3: in from kb.include_all import SimpleClassifier, F1Metric kb/include_all.py:2: in from kb.kg_embedding import KGTupleReader, KGTupleModel kb/kg_embedding.py:13: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ____ ERROR collecting tests/evaluation/test_tacred_reader.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/evaluation/test_tacred_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/evaluation/test_tacred_reader.py:10: in from kb.wordnet import WordNetCandidateMentionGenerator kb/wordnet.py:25: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory _ ERROR collecting tests/evaluation/test_ultra_fine_reader.py __ ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/evaluation/test_ultra_fine_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/evaluation/test_ultra_fine_reader.py:7: in from kb.include_all import UltraFineReader kb/include_all.py:2: in from kb.kg_embedding import KGTupleReader, KGTupleModel kb/kg_embedding.py:13: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory _ ERROR collecting tests/evaluation/test_wicreader.py ImportError while importing test module '/work/08582/yqing/maverick2/kb/tests/evaluation/test_wic_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../miniconda3/envs/knowbert2/lib/python3.6/importlib/init.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/evaluation/test_wic_reader.py:3: in from kb.include_all import WicDatasetReader kb/include_all.py:2: in from kb.kg_embedding import KGTupleReader, KGTupleModel kb/kg_embedding.py:13: in from allennlp.models import Model ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/init.py:8: in from allennlp.models.biattentive_classification_network import BiattentiveClassificationNetwork ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/models/biattentive_classification_network.py:12: in from allennlp.modules import Elmo, FeedForward, Maxout, Seq2SeqEncoder, TextFieldEmbedder ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/init.py:9: in from allennlp.modules.elmo import Elmo ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/allennlp/modules/elmo.py:12: in import h5py /opt/apps/intel18/impi18_0/python2/2.7.16/lib/python2.7/site-packages/h5py/init.py:26: in from . import _errors E ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory ===================================== warnings summary ===================================== ../miniconda3/envs/knowbert2/lib/python3.6/site-packages/plac_ext.py:6 /work/08582/yqing/maverick2/miniconda3/envs/knowbert2/lib/python3.6/site-packages/plac_ext.py:6: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp

../miniconda3/envs/knowbert2/lib/python3.6/site-packages/google/auth/crypt/_cryptography_rsa.py:22 /work/08582/yqing/maverick2/miniconda3/envs/knowbert2/lib/python3.6/site-packages/google/auth/crypt/_cryptography_rsa.py:22: CryptographyDeprecationWarning: Python 3.6 is no longer supported by the Python core team. Therefore, support for it is deprecated in cryptography and will be removed in a future release. import cryptography.exceptions

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================================= short test summary info ================================== ERROR tests/test_bert_pretraining_reader.py ERROR tests/test_bert_tokenizer_and_candidate_generator.py ERROR tests/test_dict_field.py ERROR tests/test_entity_linking.py ERROR tests/test_kg_embedding.py ERROR tests/test_kg_probe_reader.py ERROR tests/test_knowbert.py ERROR tests/test_wiki_reader.py ERROR tests/test_wordnet.py ERROR tests/evaluation/test_semeval2010_task8.py ERROR tests/evaluation/test_simple_classifier.py ERROR tests/evaluation/test_tacred_reader.py ERROR tests/evaluation/test_ultra_fine_reader.py ERROR tests/evaluation/test_wic_reader.py !!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 14 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!! ============================= 2 warnings, 14 errors in 24.48s ============================== `

[gpiat]

Hello, First, could you please reformat your errors as code? It will make them easier to read. Second, there's clearly in issue with you h5py package. For some reason it seems like you have a python2 version of h5py. Since it's a dependency of AllenNLP and this is a common issue, I suspect the issue is with your version of AllenNLP. Can you check your version? The discussion in issue #39 may help you if you have trouble finding and installing the correct versions of dependencies.

[fatanehfarahani]

try to run the code in Linux, the errors will solve. or you can delete _ in the name of files for example instead of test_wic_reader.py , you can remane with testwicreader.py by this way errors will solve.