Unable to pass the pytests

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.linear_assignment_ import linear_assignment
E ModuleNotFoundError: No module named 'sklearn.utils.linear_assignment_'
________________________ ERROR collecting tests/test_dict_field.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_wic_reader.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 ==============================
`