spaCy/spacy/tests/regression/test_issue1501-2000.py
Matthew Honnibal 8c29268749
Improve spacy.gold (no GoldParse, no json format!) (#5555)
* Update errors

* Remove beam for now (maybe)

Remove beam_utils

Update setup.py

Remove beam

* Remove GoldParse

WIP on removing goldparse

Get ArcEager compiling after GoldParse excise

Update setup.py

Get spacy.syntax compiling after removing GoldParse

Rename NewExample -> Example and clean up

Clean html files

Start updating tests

Update Morphologizer

* fix error numbers

* fix merge conflict

* informative error when calling to_array with wrong field

* fix error catching

* fixing language and scoring tests

* start testing get_aligned

* additional tests for new get_aligned function

* Draft create_gold_state for arc_eager oracle

* Fix import

* Fix import

* Remove TokenAnnotation code from nonproj

* fixing NER one-to-many alignment

* Fix many-to-one IOB codes

* fix test for misaligned

* attempt to fix cases with weird spaces

* fix spaces

* test_gold_biluo_different_tokenization works

* allow None as BILUO annotation

* fixed some tests + WIP roundtrip unit test

* add spaces to json output format

* minibatch utiltiy can deal with strings, docs or examples

* fix augment (needs further testing)

* various fixes in scripts - needs to be further tested

* fix test_cli

* cleanup

* correct silly typo

* add support for MORPH in to/from_array, fix morphologizer overfitting test

* fix tagger

* fix entity linker

* ensure test keeps working with non-linked entities

* pipe() takes docs, not examples

* small bug fix

* textcat bugfix

* throw informative error when running the components with the wrong type of objects

* fix parser tests to work with example (most still failing)

* fix BiluoPushDown parsing entities

* small fixes

* bugfix tok2vec

* fix renames and simple_ner labels

* various small fixes

* prevent writing dummy values like deps because that could interfer with sent_start values

* fix the fix

* implement split_sent with aligned SENT_START attribute

* test for split sentences with various alignment issues, works

* Return ArcEagerGoldParse from ArcEager

* Update parser and NER gold stuff

* Draft new GoldCorpus class

* add links to to_dict

* clean up

* fix test checking for variants

* Fix oracles

* Start updating converters

* Move converters under spacy.gold

* Move things around

* Fix naming

* Fix name

* Update converter to produce DocBin

* Update converters

* Allow DocBin to take list of Doc objects.

* Make spacy convert output docbin

* Fix import

* Fix docbin

* Fix compile in ArcEager

* Fix import

* Serialize all attrs by default

* Update converter

* Remove jsonl converter

* Add json2docs converter

* Draft Corpus class for DocBin

* Work on train script

* Update Corpus

* Update DocBin

* Allocate Doc before starting to add words

* Make doc.from_array several times faster

* Update train.py

* Fix Corpus

* Fix parser model

* Start debugging arc_eager oracle

* Update header

* Fix parser declaration

* Xfail some tests

* Skip tests that cause crashes

* Skip test causing segfault

* Remove GoldCorpus

* Update imports

* Update after removing GoldCorpus

* Fix module name of corpus

* Fix mimport

* Work on parser oracle

* Update arc_eager oracle

* Restore ArcEager.get_cost function

* Update transition system

* Update test_arc_eager_oracle

* Remove beam test

* Update test

* Unskip

* Unskip tests

* add links to to_dict

* clean up

* fix test checking for variants

* Allow DocBin to take list of Doc objects.

* Fix compile in ArcEager

* Serialize all attrs by default

Move converters under spacy.gold

Move things around

Fix naming

Fix name

Update converter to produce DocBin

Update converters

Make spacy convert output docbin

Fix import

Fix docbin

Fix import

Update converter

Remove jsonl converter

Add json2docs converter

* Allocate Doc before starting to add words

* Make doc.from_array several times faster

* Start updating converters

* Work on train script

* Draft Corpus class for DocBin

Update Corpus

Fix Corpus

* Update DocBin

Add missing strings when serializing

* Update train.py

* Fix parser model

* Start debugging arc_eager oracle

* Update header

* Fix parser declaration

* Xfail some tests

Skip tests that cause crashes

Skip test causing segfault

* Remove GoldCorpus

Update imports

Update after removing GoldCorpus

Fix module name of corpus

Fix mimport

* Work on parser oracle

Update arc_eager oracle

Restore ArcEager.get_cost function

Update transition system

* Update tests

Remove beam test

Update test

Unskip

Unskip tests

* Add get_aligned_parse method in Example

Fix Example.get_aligned_parse

* Add kwargs to Corpus.dev_dataset to match train_dataset

* Update nonproj

* Use get_aligned_parse in ArcEager

* Add another arc-eager oracle test

* Remove Example.doc property

Remove Example.doc

Remove Example.doc

Remove Example.doc

Remove Example.doc

* Update ArcEager oracle

Fix Break oracle

* Debugging

* Fix Corpus

* Fix eg.doc

* Format

* small fixes

* limit arg for Corpus

* fix test_roundtrip_docs_to_docbin

* fix test_make_orth_variants

* fix add_label test

* Update tests

* avoid writing temp dir in json2docs, fixing 4402 test

* Update test

* Add missing costs to NER oracle

* Update test

* Work on Example.get_aligned_ner method

* Clean up debugging

* Xfail tests

* Remove prints

* Remove print

* Xfail some tests

* Replace unseen labels for parser

* Update test

* Update test

* Xfail test

* Fix Corpus

* fix imports

* fix docs_to_json

* various small fixes

* cleanup

* Support gold_preproc in Corpus

* Support gold_preproc

* Pass gold_preproc setting into corpus

* Remove debugging

* Fix gold_preproc

* Fix json2docs converter

* Fix convert command

* Fix flake8

* Fix import

* fix output_dir (converted to Path by typer)

* fix var

* bugfix: update states after creating golds to avoid out of bounds indexing

* Improve efficiency of ArEager oracle

* pull merge_sent into iob2docs to avoid Doc creation for each line

* fix asserts

* bugfix excl Span.end in iob2docs

* Support max_length in Corpus

* Fix arc_eager oracle

* Filter out uannotated sentences in NER

* Remove debugging in parser

* Simplify NER alignment

* Fix conversion of NER data

* Fix NER init_gold_batch

* Tweak efficiency of precomputable affine

* Update onto-json default

* Update gold test for NER

* Fix parser test

* Update test

* Add NER data test

* Fix convert for single file

* Fix test

* Hack scorer to avoid evaluating non-nered data

* Fix handling of NER data in Example

* Output unlabelled spans from O biluo tags in iob_utils

* Fix unset variable

* Return kept examples from init_gold_batch

* Return examples from init_gold_batch

* Dont return Example from init_gold_batch

* Set spaces on gold doc after conversion

* Add test

* Fix spaces reading

* Improve NER alignment

* Improve handling of missing values in NER

* Restore the 'cutting' in parser training

* Add assertion

* Print epochs

* Restore random cuts in parser/ner training

* Implement Doc.copy

* Implement Example.copy

* Copy examples at the start of Language.update

* Don't unset example docs

* Tweak parser model slightly

* attempt to fix _guess_spaces

* _add_entities_to_doc first, so that links don't get overwritten

* fixing get_aligned_ner for one-to-many

* fix indexing into x_text

* small fix biluo_tags_from_offsets

* Add onto-ner config

* Simplify NER alignment

* Fix NER scoring for partially annotated documents

* fix indexing into x_text

* fix test_cli failing tests by ignoring spans in doc.ents with empty label

* Fix limit

* Improve NER alignment

* Fix count_train

* Remove print statement

* fix tests, we're not having nothing but None

* fix clumsy fingers

* Fix tests

* Fix doc.ents

* Remove empty docs in Corpus and improve limit

* Update config

Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 19:34:12 +02:00

350 lines
11 KiB
Python

import pytest
import gc
import numpy
import copy
from spacy.gold import Example
from spacy.lang.en import English
from spacy.lang.en.stop_words import STOP_WORDS
from spacy.lang.lex_attrs import is_stop
from spacy.vectors import Vectors
from spacy.vocab import Vocab
from spacy.language import Language
from spacy.pipeline.defaults import default_ner, default_tagger
from spacy.tokens import Doc, Span, Token
from spacy.pipeline import Tagger, EntityRecognizer
from spacy.attrs import HEAD, DEP
from spacy.matcher import Matcher
from ..util import make_tempdir
def test_issue1506():
def string_generator():
for _ in range(10001):
yield "It's sentence produced by that bug."
for _ in range(10001):
yield "I erase some hbdsaj lemmas."
for _ in range(10001):
yield "I erase lemmas."
for _ in range(10001):
yield "It's sentence produced by that bug."
for _ in range(10001):
yield "It's sentence produced by that bug."
nlp = English()
for i, d in enumerate(nlp.pipe(string_generator())):
# We should run cleanup more than one time to actually cleanup data.
# In first run — clean up only mark strings as «not hitted».
if i == 10000 or i == 20000 or i == 30000:
gc.collect()
for t in d:
str(t.lemma_)
def test_issue1518():
"""Test vectors.resize() works."""
vectors = Vectors(shape=(10, 10))
vectors.add("hello", row=2)
vectors.resize((5, 9))
def test_issue1537():
"""Test that Span.as_doc() doesn't segfault."""
string = "The sky is blue . The man is pink . The dog is purple ."
doc = Doc(Vocab(), words=string.split())
doc[0].sent_start = True
for word in doc[1:]:
if word.nbor(-1).text == ".":
word.sent_start = True
else:
word.sent_start = False
sents = list(doc.sents)
sent0 = sents[0].as_doc()
sent1 = sents[1].as_doc()
assert isinstance(sent0, Doc)
assert isinstance(sent1, Doc)
# TODO: Currently segfaulting, due to l_edge and r_edge misalignment
# def test_issue1537_model():
# nlp = load_spacy('en')
# doc = nlp('The sky is blue. The man is pink. The dog is purple.')
# sents = [s.as_doc() for s in doc.sents]
# print(list(sents[0].noun_chunks))
# print(list(sents[1].noun_chunks))
def test_issue1539():
"""Ensure vectors.resize() doesn't try to modify dictionary during iteration."""
v = Vectors(shape=(10, 10), keys=[5, 3, 98, 100])
v.resize((100, 100))
def test_issue1547():
"""Test that entity labels still match after merging tokens."""
words = ["\n", "worda", ".", "\n", "wordb", "-", "Biosphere", "2", "-", " \n"]
doc = Doc(Vocab(), words=words)
doc.ents = [Span(doc, 6, 8, label=doc.vocab.strings["PRODUCT"])]
with doc.retokenize() as retokenizer:
retokenizer.merge(doc[5:7])
assert [ent.text for ent in doc.ents]
def test_issue1612(en_tokenizer):
doc = en_tokenizer("The black cat purrs.")
span = doc[1:3]
assert span.orth_ == span.text
def test_issue1654():
nlp = Language(Vocab())
assert not nlp.pipeline
nlp.add_pipe(lambda doc: doc, name="1")
nlp.add_pipe(lambda doc: doc, name="2", after="1")
nlp.add_pipe(lambda doc: doc, name="3", after="2")
assert nlp.pipe_names == ["1", "2", "3"]
nlp2 = Language(Vocab())
assert not nlp2.pipeline
nlp2.add_pipe(lambda doc: doc, name="3")
nlp2.add_pipe(lambda doc: doc, name="2", before="3")
nlp2.add_pipe(lambda doc: doc, name="1", before="2")
assert nlp2.pipe_names == ["1", "2", "3"]
@pytest.mark.parametrize("text", ["test@example.com", "john.doe@example.co.uk"])
def test_issue1698(en_tokenizer, text):
doc = en_tokenizer(text)
assert len(doc) == 1
assert not doc[0].like_url
def test_issue1727():
"""Test that models with no pretrained vectors can be deserialized
correctly after vectors are added."""
data = numpy.ones((3, 300), dtype="f")
vectors = Vectors(data=data, keys=["I", "am", "Matt"])
tagger = Tagger(Vocab(), default_tagger())
tagger.add_label("PRP")
with pytest.warns(UserWarning):
tagger.begin_training()
assert tagger.cfg.get("pretrained_dims", 0) == 0
tagger.vocab.vectors = vectors
with make_tempdir() as path:
tagger.to_disk(path)
tagger = Tagger(Vocab(), default_tagger()).from_disk(path)
assert tagger.cfg.get("pretrained_dims", 0) == 0
def test_issue1757():
"""Test comparison against None doesn't cause segfault."""
doc = Doc(Vocab(), words=["a", "b", "c"])
assert not doc[0] < None
assert not doc[0] is None
assert doc[0] >= None
assert not doc[:2] < None
assert not doc[:2] is None
assert doc[:2] >= None
assert not doc.vocab["a"] is None
assert not doc.vocab["a"] < None
def test_issue1758(en_tokenizer):
"""Test that "would've" is handled by the English tokenizer exceptions."""
tokens = en_tokenizer("would've")
assert len(tokens) == 2
assert tokens[0].tag_ == "MD"
assert tokens[1].lemma_ == "have"
def test_issue1773(en_tokenizer):
"""Test that spaces don't receive a POS but no TAG. This is the root cause
of the serialization issue reported in #1773."""
doc = en_tokenizer("\n")
if doc[0].pos_ == "SPACE":
assert doc[0].tag_ != ""
def test_issue1799():
"""Test sentence boundaries are deserialized correctly, even for
non-projective sentences."""
heads_deps = numpy.asarray(
[
[1, 397],
[4, 436],
[2, 426],
[1, 402],
[0, 8206900633647566924],
[18446744073709551615, 440],
[18446744073709551614, 442],
],
dtype="uint64",
)
doc = Doc(Vocab(), words="Just what I was looking for .".split())
doc.vocab.strings.add("ROOT")
doc = doc.from_array([HEAD, DEP], heads_deps)
assert len(list(doc.sents)) == 1
def test_issue1807():
"""Test vocab.set_vector also adds the word to the vocab."""
vocab = Vocab(vectors_name="test_issue1807")
assert "hello" not in vocab
vocab.set_vector("hello", numpy.ones((50,), dtype="f"))
assert "hello" in vocab
def test_issue1834():
"""Test that sentence boundaries & parse/tag flags are not lost
during serialization."""
string = "This is a first sentence . And another one"
doc = Doc(Vocab(), words=string.split())
doc[6].sent_start = True
new_doc = Doc(doc.vocab).from_bytes(doc.to_bytes())
assert new_doc[6].sent_start
assert not new_doc.is_parsed
assert not new_doc.is_tagged
doc.is_parsed = True
doc.is_tagged = True
new_doc = Doc(doc.vocab).from_bytes(doc.to_bytes())
assert new_doc.is_parsed
assert new_doc.is_tagged
def test_issue1868():
"""Test Vocab.__contains__ works with int keys."""
vocab = Vocab()
lex = vocab["hello"]
assert lex.orth in vocab
assert lex.orth_ in vocab
assert "some string" not in vocab
int_id = vocab.strings.add("some string")
assert int_id not in vocab
def test_issue1883():
matcher = Matcher(Vocab())
matcher.add("pat1", [[{"orth": "hello"}]])
doc = Doc(matcher.vocab, words=["hello"])
assert len(matcher(doc)) == 1
new_matcher = copy.deepcopy(matcher)
new_doc = Doc(new_matcher.vocab, words=["hello"])
assert len(new_matcher(new_doc)) == 1
@pytest.mark.parametrize("word", ["the"])
def test_issue1889(word):
assert is_stop(word, STOP_WORDS) == is_stop(word.upper(), STOP_WORDS)
@pytest.mark.skip(reason="obsolete with the config refactor of v.3")
def test_issue1915():
cfg = {"hidden_depth": 2} # should error out
nlp = Language()
nlp.add_pipe(nlp.create_pipe("ner"))
nlp.get_pipe("ner").add_label("answer")
with pytest.raises(ValueError):
nlp.begin_training(**cfg)
def test_issue1945():
"""Test regression in Matcher introduced in v2.0.6."""
matcher = Matcher(Vocab())
matcher.add("MWE", [[{"orth": "a"}, {"orth": "a"}]])
doc = Doc(matcher.vocab, words=["a", "a", "a"])
matches = matcher(doc) # we should see two overlapping matches here
assert len(matches) == 2
assert matches[0][1:] == (0, 2)
assert matches[1][1:] == (1, 3)
def test_issue1963(en_tokenizer):
"""Test that doc.merge() resizes doc.tensor"""
doc = en_tokenizer("a b c d")
doc.tensor = numpy.ones((len(doc), 128), dtype="f")
with doc.retokenize() as retokenizer:
retokenizer.merge(doc[0:2])
assert len(doc) == 3
assert doc.tensor.shape == (3, 128)
@pytest.mark.parametrize("label", ["U-JOB-NAME"])
def test_issue1967(label):
config = {
"learn_tokens": False,
"min_action_freq": 30,
"beam_width": 1,
"beam_update_prob": 1.0,
}
ner = EntityRecognizer(Vocab(), default_ner(), **config)
example = Example.from_dict(
Doc(ner.vocab, words=["word"]),
{
"ids": [0],
"words": ["word"],
"tags": ["tag"],
"heads": [0],
"deps": ["dep"],
"entities": [label],
},
)
assert "JOB-NAME" in ner.moves.get_actions(examples=[example])[1]
def test_issue1971(en_vocab):
# Possibly related to #2675 and #2671?
matcher = Matcher(en_vocab)
pattern = [
{"ORTH": "Doe"},
{"ORTH": "!", "OP": "?"},
{"_": {"optional": True}, "OP": "?"},
{"ORTH": "!", "OP": "?"},
]
Token.set_extension("optional", default=False)
matcher.add("TEST", [pattern])
doc = Doc(en_vocab, words=["Hello", "John", "Doe", "!"])
# We could also assert length 1 here, but this is more conclusive, because
# the real problem here is that it returns a duplicate match for a match_id
# that's not actually in the vocab!
matches = matcher(doc)
assert all([match_id in en_vocab.strings for match_id, start, end in matches])
def test_issue_1971_2(en_vocab):
matcher = Matcher(en_vocab)
pattern1 = [{"ORTH": "EUR", "LOWER": {"IN": ["eur"]}}, {"LIKE_NUM": True}]
pattern2 = [{"LIKE_NUM": True}, {"ORTH": "EUR"}] # {"IN": ["EUR"]}}]
doc = Doc(en_vocab, words=["EUR", "10", "is", "10", "EUR"])
matcher.add("TEST1", [pattern1, pattern2])
matches = matcher(doc)
assert len(matches) == 2
def test_issue_1971_3(en_vocab):
"""Test that pattern matches correctly for multiple extension attributes."""
Token.set_extension("a", default=1, force=True)
Token.set_extension("b", default=2, force=True)
doc = Doc(en_vocab, words=["hello", "world"])
matcher = Matcher(en_vocab)
matcher.add("A", [[{"_": {"a": 1}}]])
matcher.add("B", [[{"_": {"b": 2}}]])
matches = sorted((en_vocab.strings[m_id], s, e) for m_id, s, e in matcher(doc))
assert len(matches) == 4
assert matches == sorted([("A", 0, 1), ("A", 1, 2), ("B", 0, 1), ("B", 1, 2)])
def test_issue_1971_4(en_vocab):
"""Test that pattern matches correctly with multiple extension attribute
values on a single token.
"""
Token.set_extension("ext_a", default="str_a", force=True)
Token.set_extension("ext_b", default="str_b", force=True)
matcher = Matcher(en_vocab)
doc = Doc(en_vocab, words=["this", "is", "text"])
pattern = [{"_": {"ext_a": "str_a", "ext_b": "str_b"}}] * 3
matcher.add("TEST", [pattern])
matches = matcher(doc)
# Uncommenting this caused a segmentation fault
assert len(matches) == 1
assert matches[0] == (en_vocab.strings["TEST"], 0, 3)