Project dependencies may have API risk issues

[PyDeps]

Hi, In NeuroNER, inappropriate dependency versioning constraints can cause risks.

Below are the dependencies and version constraints that the project is using

matplotlib==3.0.2
networkx==2.2
pycorenlp==0.3.0
scikit-learn==0.20.2
scipy==1.2.0
spacy==2.0.18
tensorflow==1.1.0
numpy==1.16.0

The version constraint == will introduce the risk of dependency conflicts because the scope of dependencies is too strict.
The version constraint No Upper Bound and * will introduce the risk of the missing API Error because the latest version of the dependencies may remove some APIs.

After further analysis, in this project,
The version constraint of dependency matplotlib can be changed to >=1.3.0,<=3.0.3.
The version constraint of dependency networkx can be changed to >=2.0,<=2.8.4.
The version constraint of dependency scikit-learn can be changed to >=0.15.0,<=0.20.4.
The version constraint of dependency spacy can be changed to >=0.100.0,<=3.3.1.

The above modification suggestions can reduce the dependency conflicts as much as possible,
and introduce the latest version as much as possible without calling Error in the projects.

The invocation of the current project includes all the following methods.

The calling methods from the matplotlib

matplotlib.colors.ListedColormap
matplotlib.cm.get_cmap
matplotlib.use

The calling methods from the networkx

max

The calling methods from the scikit-learn

sklearn.preprocessing.LabelBinarizer.fit
sklearn.preprocessing.LabelBinarizer.transform
sklearn.metrics.precision_recall_fscore_support
sklearn.preprocessing.normalize
random.choice
sklearn.metrics.confusion_matrix
sklearn.metrics.classification_report
sklearn.preprocessing.LabelBinarizer
sklearn.metrics.f1_score
sklearn.metrics.accuracy_score

The calling methods from the spacy

spacy.load

The calling methods from the all methods

distutils.util.strtobool
neuroner.conll_to_brat.conll_to_brat
plot_handles.extend
neuroner.neuromodel.fetch_data
numpy.arange
bioes_filepath.utils.get_basename_without_extension.split
self.unique_label_indices_of_interest.append
matplotlib.pyplot.axvline
tensorflow.python.tools.inspect_checkpoint.print_tensors_in_checkpoint_file
tensorflow.contrib.tensorboard.plugins.projector.ProjectorConfig
tensorflow.stack
pprint.pprint
tensorflow.constant
neuroner.utils.get_parameter_to_section_of_configparser
self._parse_dataset
pkg_resources.resource_isdir
collections.OrderedDict
token_dict.split
argparse.ArgumentParser.print_help
get_current_time_in_seconds
sorted.append
input_conll_filepath.utils.get_basename_without_extension.split
annotation_filepath.codecs.open.close
conll_to_brat
numpy.histogram
os.path.abspath
dataset_type.character_indices_padded.append
json.dump
random.choice.split
f.write
neuroner.utils_nlp.is_token_in_pretrained_embeddings
neuroner.utils.get_basename_without_extension
config.sections
p.vertices.mean
time.strftime
self.index_to_label.keys
neuroner.utils_nlp.load_pretrained_token_embeddings
token.split
self.tokens_mapped_to_unk.append
tensorflow.name_scope
type
os.makedirs
codecs.open
os.path.getsize
pretraining_string_to_index.keys
numpy.linspace
str
neuroner.brat_to_conll.check_brat_annotation_and_text_compatibility
matplotlib.pyplot.gca.set_xticklabels
sess.run
matplotlib.pyplot.gca.text
AssertionError
matplotlib.pyplot.clf
json.load
line.str.replace
tensorflow.argmax
neuroner.evaluate.save_results
output_conll_lines_with_bioes
tensorflow.train.Saver.save
neuroner.utils.reverse_dictionary.keys
dataset_filepaths.get
_get_default_param.items
sorted.add
os.path.isfile
pickle.load
dataset_filepaths.keys
support.append
line.split.replace
split_lines.append
all_y_true.extend
shutil.rmtree
matplotlib.pyplot.gcf.set_size_inches
get_sentences_and_tokens_from_stanford.append
neuroner.train.predict_labels
unary_scores.tolist
self.index_to_character.keys
tensorflow.nn.embedding_lookup
tensorflow.square
matplotlib.pyplot.xlabel
entity_lstm.EntityLSTM
neuroner.evaluate.evaluate_model
line.strip
self.dataset_filepaths.update
tensorflow.nn.tanh
tokens.append
sorted.sort
tensorflow.expand_dims
writers.add_summary
tensorflow.zeros
neuroner.train.prediction_step
neuroner.neuromodel.fetch_model
input_filepath.xml.etree.ElementTree.parse.getroot
line.split.strip
matplotlib.pyplot.gca.set_yticks
matplotlib.pyplot.title
vars
matplotlib.pyplot.gca.invert_yaxis
epoch_number.results.append
kwargs.items
self.character_indices.update
labels_bioes.append
neuroner.dataset.Dataset
codecs.open.write
argparse.ArgumentParser
self.token_embedding_weights.assign
self.token_embedding_weights.read_value
neuroner.utils.pad_list
cm2inch
generate_reference_text_file_for_conll
line.strip.replace
writers.flush
labels_bio.append
line.strip.split.strip
os.path.splitext
neuroner.utils_nlp.bioes_to_bio
matplotlib.pyplot.figure
matplotlib.colors.ListedColormap
file_obj.RenameUnpickler.load
self.saver.restore
sklearn.metrics.classification_report
filepath.os.path.basename.replace
datetime.datetime.now
end_current_entity
tensorflow.reduce_mean
dataset_type.token_lengths.append
map
argparse.ArgumentParser.add_argument
self.model.load_pretrained_token_embeddings
remove_bio_from_label_name
self.load_pretrained_token_embeddings
l.rstrip.replace.replace.replace.strip.split
tensorflow.summary.histogram
get_entities_from_brat
self._create_stats_graph_folder
tensorflow.Variable
self.sess.close
self.optimizer.compute_gradients
config.items
round
tag.get
matplotlib.pyplot.ylabel
self.index_to_token.keys
self.load_embeddings_from_pretrained_model
check_validity_of_conll_bioes
tensorflow.summary.FileWriter
get_sentences_and_tokens_from_stanford
os.path.exists
dataset_type.character_indices.append
dataset_types.append
os.path.join
sys.exit
plotMat.append
document_count.str.zfill
shutil.copytree
os.system
pycorenlp.StanfordCoreNLP
token_dict.strip
tensorflow.Session
tensorflow.tile
_get_default_param
ax.yaxis.get_major_ticks
_clean_param_dtypes.items
bio_to_bioes
sorted
matplotlib.pyplot.bar
neuroner.utils_plots.heatmap
tensorflow.variable_scope
labels.y_pred.y_true.sklearn.metrics.precision_recall_fscore_support.tolist
print
line.strip.split.pop
tensorflow.reduce_max
numpy.copy.flatten
pc.update_scalarmappable
matplotlib.pyplot.xlim
output_file.write
bidirectional_LSTM
numpy.fill_diagonal
IOError
tensorflow.contrib.rnn.CoupledInputForgetGateLSTMCell
tensorflow.clip_by_value
neuroner.conll_to_brat.output_brat
all_predictions.extend
line.split
matplotlib.pyplot.plot
os.path.relpath
tensorflow.assign
open
l.rstrip.replace.replace
self.model.restore_from_pretrained_model
self.modeldata.update_dataset
sklearn.metrics.confusion_matrix.tolist
collections.defaultdict.items
self.dataset_brat_folders.update
sorted.remove
assess_model
matplotlib.cm.get_cmap
dataset_type.writers.close
tensorflow.nn.bidirectional_dynamic_rnn
len
_get_config_param
get_stanford_annotations
shutil.copyfile
embedding_weights.read_value
neuroner.neuromodel.load_parameters
xml_to_brat
neuroner.utils_nlp.load_pretrained_token_embeddings.keys
tensorflow.contrib.rnn.LSTMStateTuple
tensorflow.contrib.layers.xavier_initializer
plot_handles.append
token.strip
matplotlib.pyplot.gcf
param_config.items
matplotlib.pyplot.gca.barh
neuroner.utils.convert_configparser_to_dictionary
tensorflow.summary.scalar
dataset_type.token_indices.append
matplotlib.pyplot.subplots
neuroner.brat_to_conll.get_entities_from_brat
numpy.random.rand
self.characters.update
self._get_valid_dataset_filepaths
tensorflow.contrib.crf.viterbi_decode
prepare_pretrained_model_for_restoring
os.listdir
new_token_sequence.append
range
predictions.tolist.tolist
neuroner.neuromodel.NeuroNER.close
dataset_type.characters.append
matplotlib.pyplot.grid
_clean_param_dtypes
pc.get_array
tensorflow.global_variables_initializer
dataset_type.label_indices.append
neuroner.utils.convert_configparser_to_dictionary.items
pretraining_dataset.label_to_index.keys
self.define_training_procedure
labels.append
random.shuffle
tensorflow.reduce_min
pretraining_dataset.index_to_token.values
cmap
tensorflow.nn.xw_plus_b
tensorflow.get_collection
_fetch
neuroner.utils.renamed_load
numpy.copy
entity.replace
neuroner.neuromodel.NeuroNER.fit
prediction_step
configparser.ConfigParser.set
trim_dataset_pickle
matplotlib.pyplot.gca
sklearn.preprocessing.normalize.flatten
sklearn.metrics.f1_score
tensorflow.train.Saver.restore
matplotlib.pyplot.colorbar
sklearn.preprocessing.LabelBinarizer.fit
tensorflow.summary.merge_all
pretraining_dataset.index_to_character.values
trim_model_checkpoint
self.character_indices_padded.update
classification_report.split
l.rstrip.replace.replace.replace.strip
configparser.ConfigParser.read
neuroner.utils_nlp.remove_bio_from_label_name
dataset.token_to_index.keys
neuroner.utils.reverse_dictionary
os.path.dirname
os.remove
self._check_param_compatibility
_clean_param_dtypes.update
labels.copy
show_values
pc.get_facecolors
self.label_vector_indices.update
tensorflow.cast
get_sentences_and_tokens_from_spacy
random.choice
neuroner.train.train_step
operator.itemgetter
parse_arguments.items
tensorflow.get_variable
dictionary.items
self.prediction_count.str.zfill
list
sentence_tokens.append
neuroner.evaluate.remap_labels
int
os.path.basename
numpy.random.uniform
tensorflow.contrib.tensorboard.plugins.projector.visualize_embeddings
token.replace
tensorflow.concat
neuroner.utils_nlp.get_parsed_conll_output
colors.append
copy.copy
pkg_resources.resource_filename
classes.append
neuroner.entity_lstm.EntityLSTM
save_results
tensorflow.train.GradientDescentOptimizer
neuroner.utils_tf.resize_tensor_variable
tensorflow.sqrt
l.rstrip.replace.replace.replace
classification_report.keys
neuroner.neuromodel.NeuroNER
infrequent_token_indices.append
neuroner.utils_plots.plot_classification_report
neuroner.utils_nlp.replace_unicode_whitespaces_with_ascii_whitespace
dataset_type.label_vector_indices.append
dataset_type.f1_dict_all.append
epoch_number.str.zfill
check_param_compatibility
enumerate
os.path.isdir
new_label_sequence.append
neuroner.utils.order_dictionary.get
neuroner.utils.copytree
neuroner.utils.order_dictionary
super
neuroner.brat_to_conll.brat_to_conll
token.lower
min
tensorflow.nn.dropout
class_names.append
numpy.all
argparse.ArgumentParser.parse_args
str.lower
self.label_indices.update
embeddings_projector_config.embeddings.add
collections.defaultdict.keys
ax.xaxis.get_major_ticks
sklearn.metrics.confusion_matrix
conf_parameters.write
spacy.load
join
input_filepath.xml.etree.ElementTree.parse.getroot.findall
token.token.text.replace
max
self.modeldata.load_dataset
spacy_nlp
time.time
tensorflow.train.AdadeltaOptimizer
list.remove
ax.pcolor.append
load_parameters
heatmap
sklearn.preprocessing.LabelBinarizer.transform
embedding_weights.assign
tensorflow.ConfigProto
self.token_indices.update
self.sess.run
cur_line.split.split
matplotlib.use
line.strip.replace.split
matplotlib.pyplot.ylim
tensorflow.train.Saver
codecs.open.readline
plot_f1_vs_epoch
shutil.copy
all
self.unique_labels_of_interest.remove
time.localtime
cur_line.split.strip
warnings.warn
numpy.array
re.sub
tensorflow.variables_initializer
f.read
RenameUnpickler
ValueError
tensorflow.train.AdamOptimizer
format
set
utils.create_folder_if_not_exists
matplotlib.pyplot.gca.set_yticklabels
random.randint
neuroner.utils.get_current_time_in_miliseconds
original_conll_file.readline.strip
neuroner.utils.create_folder_if_not_exists
pickle.dump
collections.defaultdict
neuroner.utils_nlp.convert_conll_from_bio_to_bioes
self.__del__
sklearn.preprocessing.normalize
string.split
sklearn.preprocessing.LabelBinarizer
glob.glob
get_cmap
pretraining_dataset.label_to_index.copy
pycorenlp.StanfordCoreNLP.annotate
main
tensorflow.equal
output_entities
parse_arguments
token_dict.replace
tensorflow.placeholder
input_filepath.xml.etree.ElementTree.parse.getroot.findtext
float
result.update
AUC.flatten.min
get_start_and_end_offset_of_token_from_spacy
self.unique_labels.append
model.saver.save
matplotlib.pyplot.legend
writers.get_logdir
f1.np.asarray.argmax
dataset.__dict__.keys
pc.get_paths
l.rstrip.replace
set.add
dataset_type.result_update.update
remap_labels
abs
index_to_string.items
entities.append
check_bio_bioes_compatibility
tensorflow.nn.softmax_cross_entropy_with_logits
line.strip.split.append
tuple
matplotlib.pyplot.gca.set_xticks
output_filepaths.keys
AUC.flatten.max
self.RenameUnpickler.super.find_class
xml.etree.ElementTree.parse
sklearn.metrics.accuracy_score
self._convert_to_indices
numpy.asarray
line.split.split
self.token_lengths.update
f.read.splitlines
matplotlib.pyplot.axhline
tensorflow.shape
codecs.open.close
l.rstrip
dict
bioes_to_bio
matplotlib.pyplot.gca.pcolor
warnings.filterwarnings
neuroner.conll_to_brat.check_compatibility_between_conll_and_brat_text
json.loads
zip
matplotlib.pyplot.close
shutil.copy2
self.sess.as_default
neuroner.utils_tf.variable_summaries
line.strip.split
self.optimizer.apply_gradients
neuroner.conll_to_brat.output_entities
ax.xaxis.tick_top
tensorflow.contrib.crf.crf_log_likelihood
sklearn.metrics.precision_recall_fscore_support
matplotlib.pyplot.savefig
configparser.ConfigParser
setuptools.setup
results.keys
tensorflow.squeeze

@developer
Could please help me check this issue?
May I pull a request to fix it?
Thank you very much.