import pytest from spacy.cli.evaluate import print_textcats_auc_per_cat, print_prf_per_type from spacy.lang.en import English from spacy.training import Example from spacy.tokens.doc import Doc from spacy.vocab import Vocab from spacy.kb import KnowledgeBase from spacy.pipeline._parser_internals.arc_eager import ArcEager from spacy.util import load_config_from_str, load_config from spacy.cli.init_config import fill_config from thinc.api import Config from wasabi import msg from ..util import make_tempdir @pytest.mark.issue(7019) def test_issue7019(): scores = {"LABEL_A": 0.39829102, "LABEL_B": 0.938298329382, "LABEL_C": None} print_textcats_auc_per_cat(msg, scores) scores = { "LABEL_A": {"p": 0.3420302, "r": 0.3929020, "f": 0.49823928932}, "LABEL_B": {"p": None, "r": None, "f": None}, } print_prf_per_type(msg, scores, name="foo", type="bar") CONFIG_7029 = """ [nlp] lang = "en" pipeline = ["tok2vec", "tagger"] [components] [components.tok2vec] factory = "tok2vec" [components.tok2vec.model] @architectures = "spacy.Tok2Vec.v1" [components.tok2vec.model.embed] @architectures = "spacy.MultiHashEmbed.v1" width = ${components.tok2vec.model.encode:width} attrs = ["NORM","PREFIX","SUFFIX","SHAPE"] rows = [5000,2500,2500,2500] include_static_vectors = false [components.tok2vec.model.encode] @architectures = "spacy.MaxoutWindowEncoder.v1" width = 96 depth = 4 window_size = 1 maxout_pieces = 3 [components.tagger] factory = "tagger" [components.tagger.model] @architectures = "spacy.Tagger.v1" nO = null [components.tagger.model.tok2vec] @architectures = "spacy.Tok2VecListener.v1" width = ${components.tok2vec.model.encode:width} upstream = "*" """ @pytest.mark.issue(7029) def test_issue7029(): """Test that an empty document doesn't mess up an entire batch.""" TRAIN_DATA = [ ("I like green eggs", {"tags": ["N", "V", "J", "N"]}), ("Eat blue ham", {"tags": ["V", "J", "N"]}), ] nlp = English.from_config(load_config_from_str(CONFIG_7029)) 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) texts = ["first", "second", "third", "fourth", "and", "then", "some", ""] docs1 = list(nlp.pipe(texts, batch_size=1)) docs2 = list(nlp.pipe(texts, batch_size=4)) assert [doc[0].tag_ for doc in docs1[:-1]] == [doc[0].tag_ for doc in docs2[:-1]] @pytest.mark.issue(7055) def test_issue7055(): """Test that fill-config doesn't turn sourced components into factories.""" source_cfg = { "nlp": {"lang": "en", "pipeline": ["tok2vec", "tagger"]}, "components": { "tok2vec": {"factory": "tok2vec"}, "tagger": {"factory": "tagger"}, }, } source_nlp = English.from_config(source_cfg) with make_tempdir() as dir_path: # We need to create a loadable source pipeline source_path = dir_path / "test_model" source_nlp.to_disk(source_path) base_cfg = { "nlp": {"lang": "en", "pipeline": ["tok2vec", "tagger", "ner"]}, "components": { "tok2vec": {"source": str(source_path)}, "tagger": {"source": str(source_path)}, "ner": {"factory": "ner"}, }, } base_cfg = Config(base_cfg) base_path = dir_path / "base.cfg" base_cfg.to_disk(base_path) output_path = dir_path / "config.cfg" fill_config(output_path, base_path, silent=True) filled_cfg = load_config(output_path) assert filled_cfg["components"]["tok2vec"]["source"] == str(source_path) assert filled_cfg["components"]["tagger"]["source"] == str(source_path) assert filled_cfg["components"]["ner"]["factory"] == "ner" assert "model" in filled_cfg["components"]["ner"] @pytest.mark.issue(7056) def test_issue7056(): """Test that the Unshift transition works properly, and doesn't cause sentence segmentation errors.""" vocab = Vocab() ae = ArcEager( vocab.strings, ArcEager.get_actions(left_labels=["amod"], right_labels=["pobj"]) ) doc = Doc(vocab, words="Severe pain , after trauma".split()) state = ae.init_batch([doc])[0] ae.apply_transition(state, "S") ae.apply_transition(state, "L-amod") ae.apply_transition(state, "S") ae.apply_transition(state, "S") ae.apply_transition(state, "S") ae.apply_transition(state, "R-pobj") ae.apply_transition(state, "D") ae.apply_transition(state, "D") ae.apply_transition(state, "D") assert not state.eol() def test_partial_links(): # Test that having some entities on the doc without gold links, doesn't crash TRAIN_DATA = [ ( "Russ Cochran his reprints include EC Comics.", { "links": {(0, 12): {"Q2146908": 1.0}}, "entities": [(0, 12, "PERSON")], "sent_starts": [1, -1, 0, 0, 0, 0, 0, 0], }, ) ] nlp = English() vector_length = 3 train_examples = [] for text, annotation in TRAIN_DATA: doc = nlp(text) train_examples.append(Example.from_dict(doc, annotation)) def create_kb(vocab): # create artificial KB mykb = KnowledgeBase(vocab, entity_vector_length=vector_length) mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3]) mykb.add_alias("Russ Cochran", ["Q2146908"], [0.9]) return mykb # Create and train the Entity Linker entity_linker = nlp.add_pipe("entity_linker", last=True) entity_linker.set_kb(create_kb) optimizer = nlp.initialize(get_examples=lambda: train_examples) for i in range(2): losses = {} nlp.update(train_examples, sgd=optimizer, losses=losses) # adding additional components that are required for the entity_linker nlp.add_pipe("sentencizer", first=True) patterns = [ {"label": "PERSON", "pattern": [{"LOWER": "russ"}, {"LOWER": "cochran"}]}, {"label": "ORG", "pattern": [{"LOWER": "ec"}, {"LOWER": "comics"}]}, ] ruler = nlp.add_pipe("entity_ruler", before="entity_linker") ruler.add_patterns(patterns) # this will run the pipeline on the examples and shouldn't crash results = nlp.evaluate(train_examples) assert "PERSON" in results["ents_per_type"] assert "PERSON" in results["nel_f_per_type"] assert "ORG" in results["ents_per_type"] assert "ORG" not in results["nel_f_per_type"] @pytest.mark.issue(7065) def test_issue7065(): text = "Kathleen Battle sang in Mahler 's Symphony No. 8 at the Cincinnati Symphony Orchestra 's May Festival." nlp = English() nlp.add_pipe("sentencizer") ruler = nlp.add_pipe("entity_ruler") patterns = [ { "label": "THING", "pattern": [ {"LOWER": "symphony"}, {"LOWER": "no"}, {"LOWER": "."}, {"LOWER": "8"}, ], } ] ruler.add_patterns(patterns) doc = nlp(text) sentences = [s for s in doc.sents] assert len(sentences) == 2 sent0 = sentences[0] ent = doc.ents[0] assert ent.start < sent0.end < ent.end assert sentences.index(ent.sent) == 0 @pytest.mark.issue(7065) def test_issue7065_b(): # Test that the NEL doesn't crash when an entity crosses a sentence boundary nlp = English() vector_length = 3 nlp.add_pipe("sentencizer") text = "Mahler 's Symphony No. 8 was beautiful." entities = [(0, 6, "PERSON"), (10, 24, "WORK")] links = { (0, 6): {"Q7304": 1.0, "Q270853": 0.0}, (10, 24): {"Q7304": 0.0, "Q270853": 1.0}, } sent_starts = [1, -1, 0, 0, 0, 0, 0, 0, 0] doc = nlp(text) example = Example.from_dict( doc, {"entities": entities, "links": links, "sent_starts": sent_starts} ) train_examples = [example] def create_kb(vocab): # create artificial KB mykb = KnowledgeBase(vocab, entity_vector_length=vector_length) mykb.add_entity(entity="Q270853", freq=12, entity_vector=[9, 1, -7]) mykb.add_alias( alias="No. 8", entities=["Q270853"], probabilities=[1.0], ) mykb.add_entity(entity="Q7304", freq=12, entity_vector=[6, -4, 3]) mykb.add_alias( alias="Mahler", entities=["Q7304"], probabilities=[1.0], ) return mykb # Create the Entity Linker component and add it to the pipeline entity_linker = nlp.add_pipe("entity_linker", last=True) entity_linker.set_kb(create_kb) # train the NEL pipe optimizer = nlp.initialize(get_examples=lambda: train_examples) for i in range(2): losses = {} nlp.update(train_examples, sgd=optimizer, losses=losses) # Add a custom rule-based component to mimick NER patterns = [ {"label": "PERSON", "pattern": [{"LOWER": "mahler"}]}, { "label": "WORK", "pattern": [ {"LOWER": "symphony"}, {"LOWER": "no"}, {"LOWER": "."}, {"LOWER": "8"}, ], }, ] ruler = nlp.add_pipe("entity_ruler", before="entity_linker") ruler.add_patterns(patterns) # test the trained model - this should not throw E148 doc = nlp(text) assert doc