spaCy/spacy/tests/pipeline/test_tok2vec.py

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import pytest
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from numpy.testing import assert_array_equal
from thinc.api import Config, get_current_ops
from spacy import util
from spacy.lang.en import English
from spacy.ml.models.tok2vec import (
MaxoutWindowEncoder,
MultiHashEmbed,
build_Tok2Vec_model,
)
from spacy.pipeline.tok2vec import Tok2Vec, Tok2VecListener
from spacy.tokens import Doc
from spacy.training import Example
from spacy.util import registry
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from spacy.vocab import Vocab
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from ..util import add_vecs_to_vocab, get_batch, make_tempdir
def test_empty_doc():
width = 128
embed_size = 2000
vocab = Vocab()
doc = Doc(vocab, words=[])
tok2vec = build_Tok2Vec_model(
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MultiHashEmbed(
width=width,
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rows=[embed_size, embed_size, embed_size, embed_size],
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include_static_vectors=False,
attrs=["NORM", "PREFIX", "SUFFIX", "SHAPE"],
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),
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MaxoutWindowEncoder(width=width, depth=4, window_size=1, maxout_pieces=3),
)
tok2vec.initialize()
vectors, backprop = tok2vec.begin_update([doc])
assert len(vectors) == 1
assert vectors[0].shape == (0, width)
@pytest.mark.parametrize(
"batch_size,width,embed_size", [[1, 128, 2000], [2, 128, 2000], [3, 8, 63]]
)
def test_tok2vec_batch_sizes(batch_size, width, embed_size):
batch = get_batch(batch_size)
Default settings to configurations (#4995) * fix grad_clip naming * cleaning up pretrained_vectors out of cfg * further refactoring Model init's * move Model building out of pipes * further refactor to require a model config when creating a pipe * small fixes * making cfg in nn_parser more consistent * fixing nr_class for parser * fixing nn_parser's nO * fix printing of loss * architectures in own file per type, consistent naming * convenience methods default_tagger_config and default_tok2vec_config * let create_pipe access default config if available for that component * default_parser_config * move defaults to separate folder * allow reading nlp from package or dir with argument 'name' * architecture spacy.VocabVectors.v1 to read static vectors from file * cleanup * default configs for nel, textcat, morphologizer, tensorizer * fix imports * fixing unit tests * fixes and clean up * fixing defaults, nO, fix unit tests * restore parser IO * fix IO * 'fix' serialization test * add *.cfg to manifest * fix example configs with additional arguments * replace Morpohologizer with Tagger * add IO bit when testing overfitting of tagger (currently failing) * fix IO - don't initialize when reading from disk * expand overfitting tests to also check IO goes OK * remove dropout from HashEmbed to fix Tagger performance * add defaults for sentrec * update thinc * always pass a Model instance to a Pipe * fix piped_added statement * remove obsolete W029 * remove obsolete errors * restore byte checking tests (work again) * clean up test * further test cleanup * convert from config to Model in create_pipe * bring back error when component is not initialized * cleanup * remove calls for nlp2.begin_training * use thinc.api in imports * allow setting charembed's nM and nC * fix for hardcoded nM/nC + unit test * formatting fixes * trigger build
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tok2vec = build_Tok2Vec_model(
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MultiHashEmbed(
width=width,
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rows=[embed_size] * 4,
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include_static_vectors=False,
attrs=["NORM", "PREFIX", "SUFFIX", "SHAPE"],
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),
MaxoutWindowEncoder(width=width, depth=4, window_size=1, maxout_pieces=3),
Default settings to configurations (#4995) * fix grad_clip naming * cleaning up pretrained_vectors out of cfg * further refactoring Model init's * move Model building out of pipes * further refactor to require a model config when creating a pipe * small fixes * making cfg in nn_parser more consistent * fixing nr_class for parser * fixing nn_parser's nO * fix printing of loss * architectures in own file per type, consistent naming * convenience methods default_tagger_config and default_tok2vec_config * let create_pipe access default config if available for that component * default_parser_config * move defaults to separate folder * allow reading nlp from package or dir with argument 'name' * architecture spacy.VocabVectors.v1 to read static vectors from file * cleanup * default configs for nel, textcat, morphologizer, tensorizer * fix imports * fixing unit tests * fixes and clean up * fixing defaults, nO, fix unit tests * restore parser IO * fix IO * 'fix' serialization test * add *.cfg to manifest * fix example configs with additional arguments * replace Morpohologizer with Tagger * add IO bit when testing overfitting of tagger (currently failing) * fix IO - don't initialize when reading from disk * expand overfitting tests to also check IO goes OK * remove dropout from HashEmbed to fix Tagger performance * add defaults for sentrec * update thinc * always pass a Model instance to a Pipe * fix piped_added statement * remove obsolete W029 * remove obsolete errors * restore byte checking tests (work again) * clean up test * further test cleanup * convert from config to Model in create_pipe * bring back error when component is not initialized * cleanup * remove calls for nlp2.begin_training * use thinc.api in imports * allow setting charembed's nM and nC * fix for hardcoded nM/nC + unit test * formatting fixes * trigger build
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)
Update spaCy for thinc 8.0.0 (#4920) * Add load_from_config function * Add train_from_config script * Merge configs and expose via spacy.config * Fix script * Suggest create_evaluation_callback * Hard-code for NER * Fix errors * Register command * Add TODO * Update train-from-config todos * Fix imports * Allow delayed setting of parser model nr_class * Get train-from-config working * Tidy up and fix scores and printing * Hide traceback if cancelled * Fix weighted score formatting * Fix score formatting * Make output_path optional * Add Tok2Vec component * Tidy up and add tok2vec_tensors * Add option to copy docs in nlp.update * Copy docs in nlp.update * Adjust nlp.update() for set_annotations * Don't shuffle pipes in nlp.update, decruft * Support set_annotations arg in component update * Support set_annotations in parser update * Add get_gradients method * Add get_gradients to parser * Update errors.py * Fix problems caused by merge * Add _link_components method in nlp * Add concept of 'listeners' and ControlledModel * Support optional attributes arg in ControlledModel * Try having tok2vec component in pipeline * Fix tok2vec component * Fix config * Fix tok2vec * Update for Example * Update for Example * Update config * Add eg2doc util * Update and add schemas/types * Update schemas * Fix nlp.update * Fix tagger * Remove hacks from train-from-config * Remove hard-coded config str * Calculate loss in tok2vec component * Tidy up and use function signatures instead of models * Support union types for registry models * Minor cleaning in Language.update * Make ControlledModel specifically Tok2VecListener * Fix train_from_config * Fix tok2vec * Tidy up * Add function for bilstm tok2vec * Fix type * Fix syntax * Fix pytorch optimizer * Add example configs * Update for thinc describe changes * Update for Thinc changes * Update for dropout/sgd changes * Update for dropout/sgd changes * Unhack gradient update * Work on refactoring _ml * Remove _ml.py module * WIP upgrade cli scripts for thinc * Move some _ml stuff to util * Import link_vectors from util * Update train_from_config * Import from util * Import from util * Temporarily add ml.component_models module * Move ml methods * Move typedefs * Update load vectors * Update gitignore * Move imports * Add PrecomputableAffine * Fix imports * Fix imports * Fix imports * Fix missing imports * Update CLI scripts * Update spacy.language * Add stubs for building the models * Update model definition * Update create_default_optimizer * Fix import * Fix comment * Update imports in tests * Update imports in spacy.cli * Fix import * fix obsolete thinc imports * update srsly pin * from thinc to ml_datasets for example data such as imdb * update ml_datasets pin * using STATE.vectors * small fix * fix Sentencizer.pipe * black formatting * rename Affine to Linear as in thinc * set validate explicitely to True * rename with_square_sequences to with_list2padded * rename with_flatten to with_list2array * chaining layernorm * small fixes * revert Optimizer import * build_nel_encoder with new thinc style * fixes using model's get and set methods * Tok2Vec in component models, various fixes * fix up legacy tok2vec code * add model initialize calls * add in build_tagger_model * small fixes * setting model dims * fixes for ParserModel * various small fixes * initialize thinc Models * fixes * consistent naming of window_size * fixes, removing set_dropout * work around Iterable issue * remove legacy tok2vec * util fix * fix forward function of tok2vec listener * more fixes * trying to fix PrecomputableAffine (not succesful yet) * alloc instead of allocate * add morphologizer * rename residual * rename fixes * Fix predict function * Update parser and parser model * fixing few more tests * Fix precomputable affine * Update component model * Update parser model * Move backprop padding to own function, for test * Update test * Fix p. affine * Update NEL * build_bow_text_classifier and extract_ngrams * Fix parser init * Fix test add label * add build_simple_cnn_text_classifier * Fix parser init * Set gpu off by default in example * Fix tok2vec listener * Fix parser model * Small fixes * small fix for PyTorchLSTM parameters * revert my_compounding hack (iterable fixed now) * fix biLSTM * Fix uniqued * PyTorchRNNWrapper fix * small fixes * use helper function to calculate cosine loss * small fixes for build_simple_cnn_text_classifier * putting dropout default at 0.0 to ensure the layer gets built * using thinc util's set_dropout_rate * moving layer normalization inside of maxout definition to optimize dropout * temp debugging in NEL * fixed NEL model by using init defaults ! * fixing after set_dropout_rate refactor * proper fix * fix test_update_doc after refactoring optimizers in thinc * Add CharacterEmbed layer * Construct tagger Model * Add missing import * Remove unused stuff * Work on textcat * fix test (again :)) after optimizer refactor * fixes to allow reading Tagger from_disk without overwriting dimensions * don't build the tok2vec prematuraly * fix CharachterEmbed init * CharacterEmbed fixes * Fix CharacterEmbed architecture * fix imports * renames from latest thinc update * one more rename * add initialize calls where appropriate * fix parser initialization * Update Thinc version * Fix errors, auto-format and tidy up imports * Fix validation * fix if bias is cupy array * revert for now * ensure it's a numpy array before running bp in ParserStepModel * no reason to call require_gpu twice * use CupyOps.to_numpy instead of cupy directly * fix initialize of ParserModel * remove unnecessary import * fixes for CosineDistance * fix device renaming * use refactored loss functions (Thinc PR 251) * overfitting test for tagger * experimental settings for the tagger: avoid zero-init and subword normalization * clean up tagger overfitting test * use previous default value for nP * remove toy config * bringing layernorm back (had a bug - fixed in thinc) * revert setting nP explicitly * remove setting default in constructor * restore values as they used to be * add overfitting test for NER * add overfitting test for dep parser * add overfitting test for textcat * fixing init for linear (previously affine) * larger eps window for textcat * ensure doc is not None * Require newer thinc * Make float check vaguer * Slop the textcat overfit test more * Fix textcat test * Fix exclusive classes for textcat * fix after renaming of alloc methods * fixing renames and mandatory arguments (staticvectors WIP) * upgrade to thinc==8.0.0.dev3 * refer to vocab.vectors directly instead of its name * rename alpha to learn_rate * adding hashembed and staticvectors dropout * upgrade to thinc 8.0.0.dev4 * add name back to avoid warning W020 * thinc dev4 * update srsly * using thinc 8.0.0a0 ! Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com> Co-authored-by: Ines Montani <ines@ines.io>
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tok2vec.initialize()
vectors, backprop = tok2vec.begin_update(batch)
assert len(vectors) == len(batch)
for doc_vec, doc in zip(vectors, batch):
assert doc_vec.shape == (len(doc), width)
@pytest.mark.slow
@pytest.mark.parametrize("width", [8])
@pytest.mark.parametrize(
"embed_arch,embed_config",
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# fmt: off
[
("spacy.MultiHashEmbed.v1", {"rows": [100, 100], "attrs": ["SHAPE", "LOWER"], "include_static_vectors": False}),
("spacy.MultiHashEmbed.v1", {"rows": [100, 20], "attrs": ["ORTH", "PREFIX"], "include_static_vectors": False}),
("spacy.CharacterEmbed.v1", {"rows": 100, "nM": 64, "nC": 8, "include_static_vectors": False}),
("spacy.CharacterEmbed.v1", {"rows": 100, "nM": 16, "nC": 2, "include_static_vectors": False}),
],
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# fmt: on
)
@pytest.mark.parametrize(
"tok2vec_arch,encode_arch,encode_config",
# fmt: off
[
("spacy.Tok2Vec.v1", "spacy.MaxoutWindowEncoder.v1", {"window_size": 1, "maxout_pieces": 3, "depth": 2}),
("spacy.Tok2Vec.v2", "spacy.MaxoutWindowEncoder.v2", {"window_size": 1, "maxout_pieces": 3, "depth": 2}),
("spacy.Tok2Vec.v1", "spacy.MishWindowEncoder.v1", {"window_size": 1, "depth": 6}),
("spacy.Tok2Vec.v2", "spacy.MishWindowEncoder.v2", {"window_size": 1, "depth": 6}),
],
# fmt: on
)
def test_tok2vec_configs(
width, tok2vec_arch, embed_arch, embed_config, encode_arch, encode_config
):
embed = registry.get("architectures", embed_arch)
encode = registry.get("architectures", encode_arch)
tok2vec_model = registry.get("architectures", tok2vec_arch)
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embed_config["width"] = width
encode_config["width"] = width
docs = get_batch(3)
tok2vec = tok2vec_model(embed(**embed_config), encode(**encode_config))
tok2vec.initialize(docs)
vectors, backprop = tok2vec.begin_update(docs)
assert len(vectors) == len(docs)
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assert vectors[0].shape == (len(docs[0]), width)
backprop(vectors)
def test_init_tok2vec():
# Simple test to initialize the default tok2vec
nlp = English()
tok2vec = nlp.add_pipe("tok2vec")
assert tok2vec.listeners == []
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nlp.initialize()
assert tok2vec.model.get_dim("nO")
cfg_string = """
[nlp]
lang = "en"
pipeline = ["tok2vec","tagger"]
[components]
[components.tagger]
factory = "tagger"
[components.tagger.model]
@architectures = "spacy.Tagger.v2"
nO = null
[components.tagger.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.tok2vec]
factory = "tok2vec"
[components.tok2vec.model]
@architectures = "spacy.Tok2Vec.v2"
[components.tok2vec.model.embed]
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@architectures = "spacy.MultiHashEmbed.v1"
width = ${components.tok2vec.model.encode.width}
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rows = [2000, 1000, 1000, 1000]
attrs = ["NORM", "PREFIX", "SUFFIX", "SHAPE"]
include_static_vectors = false
[components.tok2vec.model.encode]
@architectures = "spacy.MaxoutWindowEncoder.v2"
width = 96
depth = 4
window_size = 1
maxout_pieces = 3
"""
TRAIN_DATA = [
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(
"I like green eggs",
{"tags": ["N", "V", "J", "N"], "cats": {"preference": 1.0, "imperative": 0.0}},
),
(
"Eat blue ham",
{"tags": ["V", "J", "N"], "cats": {"preference": 0.0, "imperative": 1.0}},
),
]
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@pytest.mark.parametrize("with_vectors", (False, True))
def test_tok2vec_listener(with_vectors):
orig_config = Config().from_str(cfg_string)
orig_config["components"]["tok2vec"]["model"]["embed"][
"include_static_vectors"
] = with_vectors
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
if with_vectors:
ops = get_current_ops()
vectors = [
("apple", ops.asarray([1, 2, 3])),
("orange", ops.asarray([-1, -2, -3])),
("and", ops.asarray([-1, -1, -1])),
("juice", ops.asarray([5, 5, 10])),
("pie", ops.asarray([7, 6.3, 8.9])),
]
add_vecs_to_vocab(nlp.vocab, vectors)
assert nlp.pipe_names == ["tok2vec", "tagger"]
tagger = nlp.get_pipe("tagger")
tok2vec = nlp.get_pipe("tok2vec")
tagger_tok2vec = tagger.model.get_ref("tok2vec")
assert isinstance(tok2vec, Tok2Vec)
assert isinstance(tagger_tok2vec, Tok2VecListener)
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
for tag in t[1]["tags"]:
tagger.add_label(tag)
# Check that the Tok2Vec component finds its listeners
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optimizer = nlp.initialize(lambda: train_examples)
assert tok2vec.listeners == [tagger_tok2vec]
for i in range(5):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
doc = nlp("Running the pipeline as a whole.")
doc_tensor = tagger_tok2vec.predict([doc])[0]
ops = get_current_ops()
assert_array_equal(ops.to_numpy(doc.tensor), ops.to_numpy(doc_tensor))
# test with empty doc
doc = nlp("")
# TODO: should this warn or error?
nlp.select_pipes(disable="tok2vec")
assert nlp.pipe_names == ["tagger"]
nlp("Running the pipeline with the Tok2Vec component disabled.")
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def test_tok2vec_listener_callback():
orig_config = Config().from_str(cfg_string)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
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assert nlp.pipe_names == ["tok2vec", "tagger"]
tagger = nlp.get_pipe("tagger")
tok2vec = nlp.get_pipe("tok2vec")
docs = [nlp.make_doc("A random sentence")]
tok2vec.model.initialize(X=docs)
gold_array = [[1.0 for tag in ["V", "Z"]] for word in docs]
label_sample = [tagger.model.ops.asarray(gold_array, dtype="float32")]
tagger.model.initialize(X=docs, Y=label_sample)
docs = [nlp.make_doc("Another entirely random sentence")]
tok2vec.update([Example.from_dict(x, {}) for x in docs])
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Y, get_dX = tagger.model.begin_update(docs)
# assure that the backprop call works (and doesn't hit a 'None' callback)
assert get_dX(Y) is not None
def test_tok2vec_listener_overfitting():
"""Test that a pipeline with a listener properly overfits, even if 'tok2vec' is in the annotating components"""
orig_config = Config().from_str(cfg_string)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
optimizer = nlp.initialize(get_examples=lambda: train_examples)
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses, annotates=["tok2vec"])
assert losses["tagger"] < 0.00001
# test the trained model
test_text = "I like blue eggs"
doc = nlp(test_text)
assert doc[0].tag_ == "N"
assert doc[1].tag_ == "V"
assert doc[2].tag_ == "J"
assert doc[3].tag_ == "N"
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:
nlp.to_disk(tmp_dir)
nlp2 = util.load_model_from_path(tmp_dir)
doc2 = nlp2(test_text)
assert doc2[0].tag_ == "N"
assert doc2[1].tag_ == "V"
assert doc2[2].tag_ == "J"
assert doc2[3].tag_ == "N"
def test_tok2vec_frozen_not_annotating():
"""Test that a pipeline with a frozen tok2vec raises an error when the tok2vec is not annotating"""
orig_config = Config().from_str(cfg_string)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
optimizer = nlp.initialize(get_examples=lambda: train_examples)
for i in range(2):
losses = {}
with pytest.raises(
ValueError, match=r"the tok2vec embedding layer is not updated"
):
nlp.update(
train_examples, sgd=optimizer, losses=losses, exclude=["tok2vec"]
)
def test_tok2vec_frozen_overfitting():
"""Test that a pipeline with a frozen & annotating tok2vec can still overfit"""
orig_config = Config().from_str(cfg_string)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
optimizer = nlp.initialize(get_examples=lambda: train_examples)
for i in range(100):
losses = {}
nlp.update(
train_examples,
sgd=optimizer,
losses=losses,
exclude=["tok2vec"],
annotates=["tok2vec"],
)
assert losses["tagger"] < 0.0001
# test the trained model
test_text = "I like blue eggs"
doc = nlp(test_text)
assert doc[0].tag_ == "N"
assert doc[1].tag_ == "V"
assert doc[2].tag_ == "J"
assert doc[3].tag_ == "N"
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:
nlp.to_disk(tmp_dir)
nlp2 = util.load_model_from_path(tmp_dir)
doc2 = nlp2(test_text)
assert doc2[0].tag_ == "N"
assert doc2[1].tag_ == "V"
assert doc2[2].tag_ == "J"
assert doc2[3].tag_ == "N"
def test_replace_listeners():
orig_config = Config().from_str(cfg_string)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
examples = [Example.from_dict(nlp.make_doc("x y"), {"tags": ["V", "Z"]})]
nlp.initialize(lambda: examples)
tok2vec = nlp.get_pipe("tok2vec")
tagger = nlp.get_pipe("tagger")
assert isinstance(tagger.model.layers[0], Tok2VecListener)
assert tok2vec.listener_map["tagger"][0] == tagger.model.layers[0]
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assert (
nlp.config["components"]["tok2vec"]["model"]["@architectures"]
== "spacy.Tok2Vec.v2"
)
assert (
nlp.config["components"]["tagger"]["model"]["tok2vec"]["@architectures"]
== "spacy.Tok2VecListener.v1"
)
nlp.replace_listeners("tok2vec", "tagger", ["model.tok2vec"])
assert not isinstance(tagger.model.layers[0], Tok2VecListener)
t2v_cfg = nlp.config["components"]["tok2vec"]["model"]
assert t2v_cfg["@architectures"] == "spacy.Tok2Vec.v2"
assert nlp.config["components"]["tagger"]["model"]["tok2vec"] == t2v_cfg
with pytest.raises(ValueError):
nlp.replace_listeners("invalid", "tagger", ["model.tok2vec"])
with pytest.raises(ValueError):
nlp.replace_listeners("tok2vec", "parser", ["model.tok2vec"])
with pytest.raises(ValueError):
nlp.replace_listeners("tok2vec", "tagger", ["model.yolo"])
with pytest.raises(ValueError):
nlp.replace_listeners("tok2vec", "tagger", ["model.tok2vec", "model.yolo"])
# attempt training with the new pipeline
optimizer = nlp.initialize(lambda: examples)
for i in range(2):
losses = {}
nlp.update(examples, sgd=optimizer, losses=losses)
assert losses["tok2vec"] == 0.0
assert losses["tagger"] > 0.0
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cfg_string_multi = """
[nlp]
lang = "en"
pipeline = ["tok2vec","tagger", "ner"]
[components]
[components.tagger]
factory = "tagger"
[components.tagger.model]
@architectures = "spacy.Tagger.v2"
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nO = null
[components.tagger.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.ner]
factory = "ner"
[components.ner.model]
Merge the parser refactor into `v4` (#10940) * Try to fix doc.copy * Set dev version * Make vocab always own lexemes * Change version * Add SpanGroups.copy method * Fix set_annotations during Parser.update * Fix dict proxy copy * Upd version * Fix copying SpanGroups * Fix set_annotations in parser.update * Fix parser set_annotations during update * Revert "Fix parser set_annotations during update" This reverts commit eb138c89edb306608826dca50619ea8a60de2b14. * Revert "Fix set_annotations in parser.update" This reverts commit c6df0eafd0046179c1c9fb7840074edf04e4721d. * Fix set_annotations during parser update * Inc version * Handle final states in get_oracle_sequence * Inc version * Try to fix parser training * Inc version * Fix * Inc version * Fix parser oracle * Inc version * Inc version * Fix transition has_gold * Inc version * Try to use real histories, not oracle * Inc version * Upd parser * Inc version * WIP on rewrite parser * WIP refactor parser * New progress on parser model refactor * Prepare to remove parser_model.pyx * Convert parser from cdef class * Delete spacy.ml.parser_model * Delete _precomputable_affine module * Wire up tb_framework to new parser model * Wire up parser model * Uncython ner.pyx and dep_parser.pyx * Uncython * Work on parser model * Support unseen_classes in parser model * Support unseen classes in parser * Cleaner handling of unseen classes * Work through tests * Keep working through errors * Keep working through errors * Work on parser. 15 tests failing * Xfail beam stuff. 9 failures * More xfail. 7 failures * Xfail. 6 failures * cleanup * formatting * fixes * pass nO through * Fix empty doc in update * Hackishly fix resizing. 3 failures * Fix redundant test. 2 failures * Add reference version * black formatting * Get tests passing with reference implementation * Fix missing prints * Add missing file * Improve indexing on reference implementation * Get non-reference forward func working * Start rigging beam back up * removing redundant tests, cf #8106 * black formatting * temporarily xfailing issue 4314 * make flake8 happy again * mypy fixes * ensure labels are added upon predict * cleanup remnants from merge conflicts * Improve unseen label masking Two changes to speed up masking by ~10%: - Use a bool array rather than an array of float32. - Let the mask indicate whether a label was seen, rather than unseen. The mask is most frequently used to index scores for seen labels. However, since the mask marked unseen labels, this required computing an intermittent flipped mask. * Write moves costs directly into numpy array (#10163) This avoids elementwise indexing and the allocation of an additional array. Gives a ~15% speed improvement when using batch_by_sequence with size 32. * Temporarily disable ner and rehearse tests Until rehearse is implemented again in the refactored parser. * Fix loss serialization issue (#10600) * Fix loss serialization issue Serialization of a model fails with: TypeError: array(738.3855, dtype=float32) is not JSON serializable Fix this using float conversion. * Disable CI steps that require spacy.TransitionBasedParser.v2 After finishing the refactor, TransitionBasedParser.v2 should be provided for backwards compat. * Add back support for beam parsing to the refactored parser (#10633) * Add back support for beam parsing Beam parsing was already implemented as part of the `BeamBatch` class. This change makes its counterpart `GreedyBatch`. Both classes are hooked up in `TransitionModel`, selecting `GreedyBatch` when the beam size is one, or `BeamBatch` otherwise. * Use kwarg for beam width Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Avoid implicit default for beam_width and beam_density * Parser.{beam,greedy}_parse: ensure labels are added * Remove 'deprecated' comments Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Parser `StateC` optimizations (#10746) * `StateC`: Optimizations Avoid GIL acquisition in `__init__` Increase default buffer capacities on init Reduce C++ exception overhead * Fix typo * Replace `set::count` with `set::find` * Add exception attribute to c'tor * Remove unused import * Use a power-of-two value for initial capacity Use default-insert to init `_heads` and `_unshiftable` * Merge `cdef` variable declarations and assignments * Vectorize `example.get_aligned_parses` (#10789) * `example`: Vectorize `get_aligned_parse` Rename `numpy` import * Convert aligned array to lists before returning * Revert import renaming * Elide slice arguments when selecting the entire range * Tagger/morphologizer alignment performance optimizations (#10798) * `example`: Unwrap `numpy` scalar arrays before passing them to `StringStore.__getitem__` * `AlignmentArray`: Use native list as staging buffer for offset calculation * `example`: Vectorize `get_aligned` * Hoist inner functions out of `get_aligned` * Replace inline `if..else` clause in assignment statement * `AlignmentArray`: Use raw indexing into offset and data `numpy` arrays * `example`: Replace array unique value check with `groupby` * `example`: Correctly exclude tokens with no alignment in `_get_aligned_vectorized` Simplify `_get_aligned_non_vectorized` * `util`: Update `all_equal` docstring * Explicitly use `int32_t*` * Restore C CPU inference in the refactored parser (#10747) * Bring back the C parsing model The C parsing model is used for CPU inference and is still faster for CPU inference than the forward pass of the Thinc model. * Use C sgemm provided by the Ops implementation * Make tb_framework module Cython, merge in C forward implementation * TransitionModel: raise in backprop returned from forward_cpu * Re-enable greedy parse test * Return transition scores when forward_cpu is used * Apply suggestions from code review Import `Model` from `thinc.api` Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Use relative imports in tb_framework * Don't assume a default for beam_width * We don't have a direct dependency on BLIS anymore * Rename forwards to _forward_{fallback,greedy_cpu} * Require thinc >=8.1.0,<8.2.0 * tb_framework: clean up imports * Fix return type of _get_seen_mask * Move up _forward_greedy_cpu * Style fixes. * Lower thinc lowerbound to 8.1.0.dev0 * Formatting fix Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Reimplement parser rehearsal function (#10878) * Reimplement parser rehearsal function Before the parser refactor, rehearsal was driven by a loop in the `rehearse` method itself. For each parsing step, the loops would: 1. Get the predictions of the teacher. 2. Get the predictions and backprop function of the student. 3. Compute the loss and backprop into the student. 4. Move the teacher and student forward with the predictions of the student. In the refactored parser, we cannot perform search stepwise rehearsal anymore, since the model now predicts all parsing steps at once. Therefore, rehearsal is performed in the following steps: 1. Get the predictions of all parsing steps from the student, along with its backprop function. 2. Get the predictions from the teacher, but use the predictions of the student to advance the parser while doing so. 3. Compute the loss and backprop into the student. To support the second step a new method, `advance_with_actions` is added to `GreedyBatch`, which performs the provided parsing steps. * tb_framework: wrap upper_W and upper_b in Linear Thinc's Optimizer cannot handle resizing of existing parameters. Until it does, we work around this by wrapping the weights/biases of the upper layer of the parser model in Linear. When the upper layer is resized, we copy over the existing parameters into a new Linear instance. This does not trigger an error in Optimizer, because it sees the resized layer as a new set of parameters. * Add test for TransitionSystem.apply_actions * Better FIXME marker Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> * Fixes from Madeesh * Apply suggestions from Sofie Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Remove useless assignment Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Rename some identifiers in the parser refactor (#10935) * Rename _parseC to _parse_batch * tb_framework: prefix many auxiliary functions with underscore To clearly state the intent that they are private. * Rename `lower` to `hidden`, `upper` to `output` * Parser slow test fixup We don't have TransitionBasedParser.{v1,v2} until we bring it back as a legacy option. * Remove last vestiges of PrecomputableAffine This does not exist anymore as a separate layer. * ner: re-enable sentence boundary checks * Re-enable test that works now. * test_ner: make loss test more strict again * Remove commented line * Re-enable some more beam parser tests * Remove unused _forward_reference function * Update for CBlas changes in Thinc 8.1.0.dev2 Bump thinc dependency to 8.1.0.dev3. * Remove references to spacy.TransitionBasedParser.{v1,v2} Since they will not be offered starting with spaCy v4. * `tb_framework`: Replace references to `thinc.backends.linalg` with `CBlas` * dont use get_array_module (#11056) (#11293) Co-authored-by: kadarakos <kadar.akos@gmail.com> * Move `thinc.extra.search` to `spacy.pipeline._parser_internals` (#11317) * `search`: Move from `thinc.extra.search` Fix NPE in `Beam.__dealloc__` * `pytest`: Add support for executing Cython tests Move `search` tests from thinc and patch them to run with `pytest` * `mypy` fix * Update comment * `conftest`: Expose `register_cython_tests` * Remove unused import * Move `argmax` impls to new `_parser_utils` Cython module (#11410) * Parser does not have to be a cdef class anymore This also fixes validation of the initialization schema. * Add back spacy.TransitionBasedParser.v2 * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Remove module from setup.py that got added during the merge * Bring back support for `update_with_oracle_cut_size` (#12086) * Bring back support for `update_with_oracle_cut_size` This option was available in the pre-refactor parser, but was never implemented in the refactored parser. This option cuts transition sequences that are longer than `update_with_oracle_cut` size into separate sequences that have at most `update_with_oracle_cut` transitions. The oracle (gold standard) transition sequence is used to determine the cuts and the initial states for the additional sequences. Applying this cut makes the batches more homogeneous in the transition sequence lengths, making forward passes (and as a consequence training) much faster. Training time 1000 steps on de_core_news_lg: - Before this change: 149s - After this change: 68s - Pre-refactor parser: 81s * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Apply suggestions from @shadeMe * Use chained conditional * Test with update_with_oracle_cut_size={0, 1, 5, 100} And fix a git that occurs with a cut size of 1. * Fix up some merge fall out * Update parser distillation for the refactor In the old parser, we'd iterate over the transitions in the distill function and compute the loss/gradients on the go. In the refactored parser, we first let the student model parse the inputs. Then we'll let the teacher compute the transition probabilities of the states in the student's transition sequence. We can then compute the gradients of the student given the teacher. * Add back spacy.TransitionBasedParser.v1 references - Accordion in the architecture docs. - Test in test_parse, but disabled until we have a spacy-legacy release. Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com> Co-authored-by: svlandeg <svlandeg@github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: kadarakos <kadar.akos@gmail.com>
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@architectures = "spacy.TransitionBasedParser.v3"
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[components.ner.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.tok2vec]
factory = "tok2vec"
[components.tok2vec.model]
@architectures = "spacy.Tok2Vec.v2"
[components.tok2vec.model.embed]
@architectures = "spacy.MultiHashEmbed.v1"
width = ${components.tok2vec.model.encode.width}
rows = [2000, 1000, 1000, 1000]
attrs = ["NORM", "PREFIX", "SUFFIX", "SHAPE"]
include_static_vectors = false
[components.tok2vec.model.encode]
@architectures = "spacy.MaxoutWindowEncoder.v2"
width = 96
depth = 4
window_size = 1
maxout_pieces = 3
"""
def test_replace_listeners_from_config():
orig_config = Config().from_str(cfg_string_multi)
nlp = util.load_model_from_config(orig_config, auto_fill=True)
annots = {"tags": ["V", "Z"], "entities": [(0, 1, "A"), (1, 2, "B")]}
examples = [Example.from_dict(nlp.make_doc("x y"), annots)]
nlp.initialize(lambda: examples)
tok2vec = nlp.get_pipe("tok2vec")
tagger = nlp.get_pipe("tagger")
ner = nlp.get_pipe("ner")
assert tok2vec.listening_components == ["tagger", "ner"]
assert any(isinstance(node, Tok2VecListener) for node in ner.model.walk())
assert any(isinstance(node, Tok2VecListener) for node in tagger.model.walk())
with make_tempdir() as dir_path:
nlp.to_disk(dir_path)
base_model = str(dir_path)
new_config = {
"nlp": {
"lang": "en",
"pipeline": ["tok2vec", "tagger2", "ner3", "tagger4"],
},
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"components": {
"tok2vec": {"source": base_model},
"tagger2": {
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"source": base_model,
"component": "tagger",
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"replace_listeners": ["model.tok2vec"],
},
"ner3": {
"source": base_model,
"component": "ner",
},
"tagger4": {
"source": base_model,
"component": "tagger",
},
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},
}
new_nlp = util.load_model_from_config(new_config, auto_fill=True)
new_nlp.initialize(lambda: examples)
tok2vec = new_nlp.get_pipe("tok2vec")
tagger = new_nlp.get_pipe("tagger2")
ner = new_nlp.get_pipe("ner3")
assert "ner" not in new_nlp.pipe_names
assert "tagger" not in new_nlp.pipe_names
assert tok2vec.listening_components == ["ner3", "tagger4"]
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assert any(isinstance(node, Tok2VecListener) for node in ner.model.walk())
assert not any(isinstance(node, Tok2VecListener) for node in tagger.model.walk())
t2v_cfg = new_nlp.config["components"]["tok2vec"]["model"]
assert t2v_cfg["@architectures"] == "spacy.Tok2Vec.v2"
assert new_nlp.config["components"]["tagger2"]["model"]["tok2vec"] == t2v_cfg
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assert (
new_nlp.config["components"]["ner3"]["model"]["tok2vec"]["@architectures"]
== "spacy.Tok2VecListener.v1"
)
assert (
new_nlp.config["components"]["tagger4"]["model"]["tok2vec"]["@architectures"]
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== "spacy.Tok2VecListener.v1"
)
cfg_string_multi_textcat = """
[nlp]
lang = "en"
pipeline = ["tok2vec","textcat_multilabel","tagger"]
[components]
[components.textcat_multilabel]
factory = "textcat_multilabel"
[components.textcat_multilabel.model]
@architectures = "spacy.TextCatEnsemble.v2"
nO = null
[components.textcat_multilabel.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.textcat_multilabel.model.linear_model]
@architectures = "spacy.TextCatBOW.v1"
exclusive_classes = false
ngram_size = 1
no_output_layer = false
[components.tagger]
factory = "tagger"
[components.tagger.model]
@architectures = "spacy.Tagger.v2"
nO = null
[components.tagger.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.tok2vec]
factory = "tok2vec"
[components.tok2vec.model]
@architectures = "spacy.Tok2Vec.v2"
[components.tok2vec.model.embed]
@architectures = "spacy.MultiHashEmbed.v1"
width = ${components.tok2vec.model.encode.width}
rows = [2000, 1000, 1000, 1000]
attrs = ["NORM", "PREFIX", "SUFFIX", "SHAPE"]
include_static_vectors = false
[components.tok2vec.model.encode]
@architectures = "spacy.MaxoutWindowEncoder.v2"
width = 96
depth = 4
window_size = 1
maxout_pieces = 3
"""
def test_tok2vec_listeners_textcat():
orig_config = Config().from_str(cfg_string_multi_textcat)
nlp = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
assert nlp.pipe_names == ["tok2vec", "textcat_multilabel", "tagger"]
tagger = nlp.get_pipe("tagger")
textcat = nlp.get_pipe("textcat_multilabel")
tok2vec = nlp.get_pipe("tok2vec")
tagger_tok2vec = tagger.model.get_ref("tok2vec")
textcat_tok2vec = textcat.model.get_ref("tok2vec")
assert isinstance(tok2vec, Tok2Vec)
assert isinstance(tagger_tok2vec, Tok2VecListener)
assert isinstance(textcat_tok2vec, Tok2VecListener)
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
optimizer = nlp.initialize(lambda: train_examples)
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
docs = list(nlp.pipe(["Eat blue ham", "I like green eggs"]))
cats0 = docs[0].cats
assert cats0["preference"] < 0.1
assert cats0["imperative"] > 0.9
cats1 = docs[1].cats
assert cats1["preference"] > 0.1
assert cats1["imperative"] < 0.9
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assert [t.tag_ for t in docs[0]] == ["V", "J", "N"]
assert [t.tag_ for t in docs[1]] == ["N", "V", "J", "N"]
cfg_string_distillation = """
[nlp]
lang = "en"
pipeline = ["tok2vec","tagger"]
[components]
[components.tagger]
factory = "tagger"
[components.tagger.model]
@architectures = "spacy.Tagger.v2"
nO = null
[components.tagger.model.tok2vec]
@architectures = "spacy.Tok2VecListener.v1"
width = ${components.tok2vec.model.encode.width}
[components.tok2vec]
factory = "tok2vec"
[components.tok2vec.model]
@architectures = "spacy.Tok2Vec.v2"
[components.tok2vec.model.embed]
@architectures = "spacy.MultiHashEmbed.v2"
width = ${components.tok2vec.model.encode.width}
rows = [2000, 1000, 1000, 1000]
attrs = ["NORM", "PREFIX", "SUFFIX", "SHAPE"]
include_static_vectors = false
[components.tok2vec.model.encode]
@architectures = "spacy.MaxoutWindowEncoder.v2"
width = 96
depth = 4
window_size = 1
maxout_pieces = 3
"""
def test_tok2vec_distillation_teacher_annotations():
orig_config = Config().from_str(cfg_string_distillation)
teacher_nlp = util.load_model_from_config(
orig_config, auto_fill=True, validate=True
)
student_nlp = util.load_model_from_config(
orig_config, auto_fill=True, validate=True
)
train_examples_teacher = []
train_examples_student = []
for t in TRAIN_DATA:
train_examples_teacher.append(
Example.from_dict(teacher_nlp.make_doc(t[0]), t[1])
)
train_examples_student.append(
Example.from_dict(student_nlp.make_doc(t[0]), t[1])
)
optimizer = teacher_nlp.initialize(lambda: train_examples_teacher)
student_nlp.initialize(lambda: train_examples_student)
# Since Language.distill creates a copy of the examples to use as
# its internal teacher/student docs, we'll need to monkey-patch the
# tok2vec pipe's distill method.
student_tok2vec = student_nlp.get_pipe("tok2vec")
student_tok2vec._old_distill = student_tok2vec.distill
def tok2vec_distill_wrapper(
self,
teacher_pipe,
examples,
**kwargs,
):
assert all(not eg.reference.tensor.any() for eg in examples)
out = self._old_distill(teacher_pipe, examples, **kwargs)
assert all(eg.reference.tensor.any() for eg in examples)
return out
student_tok2vec.distill = tok2vec_distill_wrapper.__get__(student_tok2vec, Tok2Vec)
student_nlp.distill(teacher_nlp, train_examples_student, sgd=optimizer, losses={})
def test_tok2vec_listener_source_link_name():
"""The component's internal name and the tok2vec listener map correspond
to the most recently modified pipeline.
"""
orig_config = Config().from_str(cfg_string_multi)
nlp1 = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
assert nlp1.get_pipe("tok2vec").listening_components == ["tagger", "ner"]
nlp2 = English()
nlp2.add_pipe("tok2vec", source=nlp1)
nlp2.add_pipe("tagger", name="tagger2", source=nlp1)
# there is no way to have the component have the right name for both
# pipelines, right now the most recently modified pipeline is prioritized
assert nlp1.get_pipe("tagger").name == nlp2.get_pipe("tagger2").name == "tagger2"
# there is no way to have the tok2vec have the right listener map for both
# pipelines, right now the most recently modified pipeline is prioritized
assert nlp2.get_pipe("tok2vec").listening_components == ["tagger2"]
nlp2.add_pipe("ner", name="ner3", source=nlp1)
assert nlp2.get_pipe("tok2vec").listening_components == ["tagger2", "ner3"]
nlp2.remove_pipe("ner3")
assert nlp2.get_pipe("tok2vec").listening_components == ["tagger2"]
nlp2.remove_pipe("tagger2")
assert nlp2.get_pipe("tok2vec").listening_components == []
# at this point the tok2vec component corresponds to nlp2
assert nlp1.get_pipe("tok2vec").listening_components == []
# modifying the nlp1 pipeline syncs the tok2vec listener map back to nlp1
nlp1.add_pipe("sentencizer")
assert nlp1.get_pipe("tok2vec").listening_components == ["tagger", "ner"]
# modifying nlp2 syncs it back to nlp2
nlp2.add_pipe("sentencizer")
assert nlp1.get_pipe("tok2vec").listening_components == []
def test_tok2vec_listener_source_replace_listeners():
orig_config = Config().from_str(cfg_string_multi)
nlp1 = util.load_model_from_config(orig_config, auto_fill=True, validate=True)
assert nlp1.get_pipe("tok2vec").listening_components == ["tagger", "ner"]
nlp1.replace_listeners("tok2vec", "tagger", ["model.tok2vec"])
assert nlp1.get_pipe("tok2vec").listening_components == ["ner"]
nlp2 = English()
nlp2.add_pipe("tok2vec", source=nlp1)
assert nlp2.get_pipe("tok2vec").listening_components == []
nlp2.add_pipe("tagger", source=nlp1)
assert nlp2.get_pipe("tok2vec").listening_components == []
nlp2.add_pipe("ner", name="ner2", source=nlp1)
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assert nlp2.get_pipe("tok2vec").listening_components == ["ner2"]