Merge branch 'develop' of https://github.com/explosion/spaCy into develop

spacy/about.py

@@ -1,6 +1,6 @@
 # fmt: off
 __title__ = "spacy-nightly"
-__version__ = "3.0.0a23"
+__version__ = "3.0.0a24"
 __release__ = True
 __download_url__ = "https://github.com/explosion/spacy-models/releases/download"
 __compatibility__ = "https://raw.githubusercontent.com/explosion/spacy-models/master/compatibility.json"

spacy/cli/download.py

@@ -88,7 +88,6 @@ def get_compatibility() -> dict:
 
 
 def get_version(model: str, comp: dict) -> str:
-    model = get_base_version(model)
     if model not in comp:
         msg.fail(
             f"No compatible package found for '{model}' (spaCy v{about.__version__})",

spacy/cli/info.py

@@ -91,7 +91,9 @@ def info_model(model: str, *, silent: bool = True) -> Dict[str, Any]:
         meta["source"] = str(model_path.resolve())
     else:
         meta["source"] = str(model_path)
-    return {k: v for k, v in meta.items() if k not in ("accuracy", "speed")}
+    return {
+        k: v for k, v in meta.items() if k not in ("accuracy", "performance", "speed")
+    }
 
 
 def get_markdown(data: Dict[str, Any], title: Optional[str] = None) -> str:

spacy/cli/train.py

@@ -97,6 +97,7 @@ def train(
     dev_corpus = dot_to_object(config, T_cfg["dev_corpus"])
     batcher = T_cfg["batcher"]
     train_logger = T_cfg["logger"]
+    before_to_disk = create_before_to_disk_callback(T_cfg["before_to_disk"])
     # Components that shouldn't be updated during training
     frozen_components = T_cfg["frozen_components"]
     # Sourced components that require resume_training
@@ -167,6 +168,7 @@ def train(
                     with nlp.select_pipes(disable=frozen_components):
                         update_meta(T_cfg, nlp, info)
                     with nlp.use_params(optimizer.averages):
+                        nlp = before_to_disk(nlp)
                         nlp.to_disk(output_path / "model-best")
                 progress = tqdm.tqdm(total=T_cfg["eval_frequency"], leave=False)
                 progress.set_description(f"Epoch {info['epoch']}")
@@ -179,6 +181,7 @@ def train(
                 f"Aborting and saving the final best model. "
                 f"Encountered exception: {str(e)}"
             )
+            nlp = before_to_disk(nlp)
             nlp.to_disk(output_path / "model-final")
         raise e
     finally:
@@ -233,6 +236,21 @@ def create_evaluation_callback(
     return evaluate
 
 
+def create_before_to_disk_callback(
+    callback: Optional[Callable[[Language], Language]]
+) -> Callable[[Language], Language]:
+    def before_to_disk(nlp: Language) -> Language:
+        if not callback:
+            return nlp
+        modified_nlp = callback(nlp)
+        if not isinstance(modified_nlp, Language):
+            err = Errors.E914.format(name="before_to_disk", value=type(modified_nlp))
+            raise ValueError(err)
+        return modified_nlp
+
+    return before_to_disk
+
+
 def train_while_improving(
     nlp: Language,
     optimizer: Optimizer,

spacy/default_config.cfg

@@ -72,6 +72,8 @@ frozen_components = []
 dev_corpus = "corpora.dev"
 # Location in the config where the train corpus is defined
 train_corpus = "corpora.train"
+# Optional callback before nlp object is saved to disk after training
+before_to_disk = null
 
 [training.logger]
 @loggers = "spacy.ConsoleLogger.v1"

spacy/errors.py

@@ -480,6 +480,9 @@ class Errors:
     E201 = ("Span index out of range.")
 
     # TODO: fix numbering after merging develop into master
+    E914 = ("Executing {name} callback failed. Expected the function to "
+            "return the nlp object but got: {value}. Maybe you forgot to return "
+            "the modified object in your function?")
     E915 = ("Can't use score '{name}' to calculate final weighted score. Expected "
             "float or int but got: {score_type}. To exclude the score from the "
             "final score, set its weight to null in the [training.score_weights] "
@@ -693,6 +696,12 @@ class Errors:
     E1009 = ("String for hash '{val}' not found in StringStore. Set the value "
              "through token.morph_ instead or add the string to the "
              "StringStore with `nlp.vocab.strings.add(string)`.")
+    E1010 = ("Unable to set entity information for token {i} which is included "
+             "in more than one span in entities, blocked, missing or outside.")
+    E1011 = ("Unsupported default '{default}' in doc.set_ents. Available "
+             "options: {modes}")
+    E1012 = ("Entity spans and blocked/missing/outside spans should be "
+             "provided to doc.set_ents as lists of `Span` objects.")
 
 
 @add_codes

spacy/schemas.py

@@ -182,8 +182,7 @@ class ModelMetaSchema(BaseModel):
     sources: Optional[Union[List[StrictStr], List[Dict[str, str]]]] = Field(None, title="Training data sources")
     vectors: Dict[str, Any] = Field({}, title="Included word vectors")
     labels: Dict[str, List[str]] = Field({}, title="Component labels, keyed by component name")
-    accuracy: Dict[str, Union[float, Dict[str, float]]] = Field({}, title="Accuracy numbers")
+    performance: Dict[str, Union[float, Dict[str, float]]] = Field({}, title="Accuracy and speed numbers")
-    speed: Dict[str, Union[float, int]] = Field({}, title="Speed evaluation numbers")
     spacy_git_version: StrictStr = Field("", title="Commit of spaCy version used")
     # fmt: on
 
@@ -217,6 +216,7 @@ class ConfigSchemaTraining(BaseModel):
     optimizer: Optimizer = Field(..., title="The optimizer to use")
     logger: Logger = Field(..., title="The logger to track training progress")
     frozen_components: List[str] = Field(..., title="Pipeline components that shouldn't be updated during training")
+    before_to_disk: Optional[Callable[["Language"], "Language"]] = Field(..., title="Optional callback to modify nlp object after training, before it's saved to disk")
     # fmt: on
 
     class Config:

spacy/tests/doc/test_add_entities.py

@@ -29,10 +29,10 @@ def test_doc_add_entities_set_ents_iob(en_vocab):
     ner.begin_training(lambda: [_ner_example(ner)])
     ner(doc)
 
-    doc.ents = [(doc.vocab.strings["ANIMAL"], 3, 4)]
+    doc.ents = [("ANIMAL", 3, 4)]
     assert [w.ent_iob_ for w in doc] == ["O", "O", "O", "B"]
 
-    doc.ents = [(doc.vocab.strings["WORD"], 0, 2)]
+    doc.ents = [("WORD", 0, 2)]
     assert [w.ent_iob_ for w in doc] == ["B", "I", "O", "O"]
 
 

spacy/tests/doc/test_doc_api.py

@@ -152,7 +152,7 @@ def test_doc_api_set_ents(en_tokenizer):
     assert len(tokens.ents) == 0
     tokens.ents = [(tokens.vocab.strings["PRODUCT"], 2, 4)]
     assert len(list(tokens.ents)) == 1
-    assert [t.ent_iob for t in tokens] == [0, 0, 3, 1, 0, 0, 0, 0]
+    assert [t.ent_iob for t in tokens] == [2, 2, 3, 1, 2, 2, 2, 2]
     assert tokens.ents[0].label_ == "PRODUCT"
     assert tokens.ents[0].start == 2
     assert tokens.ents[0].end == 4
@@ -427,7 +427,7 @@ def test_has_annotation(en_vocab):
     doc[0].lemma_ = "a"
     doc[0].dep_ = "dep"
     doc[0].head = doc[1]
-    doc.ents = [Span(doc, 0, 1, label="HELLO")]
+    doc.set_ents([Span(doc, 0, 1, label="HELLO")], default="missing")
 
     for attr in attrs:
         assert doc.has_annotation(attr)
@@ -457,7 +457,74 @@ def test_is_flags_deprecated(en_tokenizer):
         doc.is_sentenced
 
 
-def test_doc_set_ents():
+def test_doc_set_ents(en_tokenizer):
+    # set ents
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents([Span(doc, 0, 1, 10), Span(doc, 1, 3, 11)])
+    assert [t.ent_iob for t in doc] == [3, 3, 1, 2, 2]
+    assert [t.ent_type for t in doc] == [10, 11, 11, 0, 0]
+
+    # add ents, invalid IOB repaired
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents([Span(doc, 0, 1, 10), Span(doc, 1, 3, 11)])
+    doc.set_ents([Span(doc, 0, 2, 12)], default="unmodified")
+    assert [t.ent_iob for t in doc] == [3, 1, 3, 2, 2]
+    assert [t.ent_type for t in doc] == [12, 12, 11, 0, 0]
+
+    # missing ents
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents([Span(doc, 0, 1, 10), Span(doc, 1, 3, 11)], missing=[doc[4:5]])
+    assert [t.ent_iob for t in doc] == [3, 3, 1, 2, 0]
+    assert [t.ent_type for t in doc] == [10, 11, 11, 0, 0]
+
+    # outside ents
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents(
+        [Span(doc, 0, 1, 10), Span(doc, 1, 3, 11)],
+        outside=[doc[4:5]],
+        default="missing",
+    )
+    assert [t.ent_iob for t in doc] == [3, 3, 1, 0, 2]
+    assert [t.ent_type for t in doc] == [10, 11, 11, 0, 0]
+
+    # blocked ents
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents([], blocked=[doc[1:2], doc[3:5]], default="unmodified")
+    assert [t.ent_iob for t in doc] == [0, 3, 0, 3, 3]
+    assert [t.ent_type for t in doc] == [0, 0, 0, 0, 0]
+    assert doc.ents == tuple()
+
+    # invalid IOB repaired after blocked
+    doc.ents = [Span(doc, 3, 5, "ENT")]
+    assert [t.ent_iob for t in doc] == [2, 2, 2, 3, 1]
+    doc.set_ents([], blocked=[doc[3:4]], default="unmodified")
+    assert [t.ent_iob for t in doc] == [2, 2, 2, 3, 3]
+
+    # all types
+    doc = en_tokenizer("a b c d e")
+    doc.set_ents(
+        [Span(doc, 0, 1, 10)],
+        blocked=[doc[1:2]],
+        missing=[doc[2:3]],
+        outside=[doc[3:4]],
+        default="unmodified",
+    )
+    assert [t.ent_iob for t in doc] == [3, 3, 0, 2, 0]
+    assert [t.ent_type for t in doc] == [10, 0, 0, 0, 0]
+
+    doc = en_tokenizer("a b c d e")
+    # single span instead of a list
+    with pytest.raises(ValueError):
+        doc.set_ents([], missing=doc[1:2])
+    # invalid default mode
+    with pytest.raises(ValueError):
+        doc.set_ents([], missing=[doc[1:2]], default="none")
+    # conflicting/overlapping specifications
+    with pytest.raises(ValueError):
+        doc.set_ents([], missing=[doc[1:2]], outside=[doc[1:2]])
+
+
+def test_doc_ents_setter():
     """Test that both strings and integers can be used to set entities in
     tuple format via doc.ents."""
     words = ["a", "b", "c", "d", "e"]

spacy/tests/parser/test_ner.py

@@ -168,7 +168,7 @@ def test_accept_blocked_token():
     ner2 = nlp2.create_pipe("ner", config=config)
 
     # set "New York" to a blocked entity
-    doc2.ents = [(0, 3, 5)]
+    doc2.set_ents([], blocked=[doc2[3:5]], default="unmodified")
     assert [token.ent_iob_ for token in doc2] == ["", "", "", "B", "B"]
     assert [token.ent_type_ for token in doc2] == ["", "", "", "", ""]
 
@@ -358,5 +358,5 @@ class BlockerComponent1:
         self.name = name
 
     def __call__(self, doc):
-        doc.ents = [(0, self.start, self.end)]
+        doc.set_ents([], blocked=[doc[self.start:self.end]], default="unmodified")
         return doc

spacy/tokens/doc.pyx

@@ -7,6 +7,8 @@ from libc.stdint cimport int32_t, uint64_t
 
 import copy
 from collections import Counter
+from enum import Enum
+import itertools
 import numpy
 import srsly
 from thinc.api import get_array_module
@@ -86,6 +88,17 @@ cdef attr_t get_token_attr_for_matcher(const TokenC* token, attr_id_t feat_name)
         return get_token_attr(token, feat_name)
 
 
+class SetEntsDefault(str, Enum):
+    blocked = "blocked"
+    missing = "missing"
+    outside = "outside"
+    unmodified = "unmodified"
+
+    @classmethod
+    def values(cls):
+        return list(cls.__members__.keys())
+
+
 cdef class Doc:
     """A sequence of Token objects. Access sentences and named entities, export
     annotations to numpy arrays, losslessly serialize to compressed binary
@@ -660,50 +673,100 @@ cdef class Doc:
             # TODO:
             # 1. Test basic data-driven ORTH gazetteer
             # 2. Test more nuanced date and currency regex
-            tokens_in_ents = {}
+            cdef attr_t entity_type, kb_id
-            cdef attr_t entity_type
+            cdef int ent_start, ent_end
-            cdef attr_t kb_id
+            ent_spans = []
-            cdef int ent_start, ent_end, token_index
             for ent_info in ents:
                 entity_type_, kb_id, ent_start, ent_end = get_entity_info(ent_info)
                 if isinstance(entity_type_, str):
                     self.vocab.strings.add(entity_type_)
-                entity_type = self.vocab.strings.as_int(entity_type_)
+                span = Span(self, ent_start, ent_end, label=entity_type_, kb_id=kb_id)
-                for token_index in range(ent_start, ent_end):
+                ent_spans.append(span)
-                    if token_index in tokens_in_ents:
+            self.set_ents(ent_spans, default=SetEntsDefault.outside)
-                        raise ValueError(Errors.E103.format(
+
-                            span1=(tokens_in_ents[token_index][0],
+    def set_ents(self, entities, *, blocked=None, missing=None, outside=None, default=SetEntsDefault.outside):
-                                   tokens_in_ents[token_index][1],
+        """Set entity annotation.
-                                   self.vocab.strings[tokens_in_ents[token_index][2]]),
+
-                            span2=(ent_start, ent_end, self.vocab.strings[entity_type])))
+        entities (List[Span]): Spans with labels to set as entities.
-                    tokens_in_ents[token_index] = (ent_start, ent_end, entity_type, kb_id)
+        blocked (Optional[List[Span]]): Spans to set as 'blocked' (never an
-            cdef int i
+            entity) for spacy's built-in NER component. Other components may
+            ignore this setting.
+        missing (Optional[List[Span]]): Spans with missing/unknown entity
+            information.
+        outside (Optional[List[Span]]): Spans outside of entities (O in IOB).
+        default (str): How to set entity annotation for tokens outside of any
+            provided spans. Options: "blocked", "missing", "outside" and
+            "unmodified" (preserve current state). Defaults to "outside".
+        """
+        if default not in SetEntsDefault.values():
+            raise ValueError(Errors.E1011.format(default=default, modes=", ".join(SetEntsDefault)))
+
+        # Ignore spans with missing labels
+        entities = [ent for ent in entities if ent.label > 0]
+
+        if blocked is None:
+            blocked = tuple()
+        if missing is None:
+            missing = tuple()
+        if outside is None:
+            outside = tuple()
+
+        # Find all tokens covered by spans and check that none are overlapping
+        cdef int i
+        seen_tokens = set()
+        for span in itertools.chain.from_iterable([entities, blocked, missing, outside]):
+            if not isinstance(span, Span):
+                raise ValueError(Errors.E1012.format(span=span))
+            for i in range(span.start, span.end):
+                if i in seen_tokens:
+                    raise ValueError(Errors.E1010.format(i=i))
+                seen_tokens.add(i)
+
+        # Set all specified entity information
+        for span in entities:
+            for i in range(span.start, span.end):
+                if i == span.start:
+                    self.c[i].ent_iob = 3
+                else:
+                    self.c[i].ent_iob = 1
+                self.c[i].ent_type = span.label
+                self.c[i].ent_kb_id = span.kb_id
+        for span in blocked:
+            for i in range(span.start, span.end):
+                self.c[i].ent_iob = 3
+                self.c[i].ent_type = 0
+        for span in missing:
+            for i in range(span.start, span.end):
+                self.c[i].ent_iob = 0
+                self.c[i].ent_type = 0
+        for span in outside:
+            for i in range(span.start, span.end):
+                self.c[i].ent_iob = 2
+                self.c[i].ent_type = 0
+
+        # Set tokens outside of all provided spans
+        if default != SetEntsDefault.unmodified:
             for i in range(self.length):
-                # default values
+                if i not in seen_tokens:
-                entity_type = 0
+                    self.c[i].ent_type = 0
-                kb_id = 0
+                    if default == SetEntsDefault.outside:
+                        self.c[i].ent_iob = 2
+                    elif default == SetEntsDefault.missing:
+                        self.c[i].ent_iob = 0
+                    elif default == SetEntsDefault.blocked:
+                        self.c[i].ent_iob = 3
 
-                # Set ent_iob to Missing (0) by default unless this token was nered before
+        # Fix any resulting inconsistent annotation
-                ent_iob = 0
+        for i in range(self.length - 1):
-                if self.c[i].ent_iob != 0:
+            # I must follow B or I: convert I to B
-                    ent_iob = 2
+            if (self.c[i].ent_iob == 0 or self.c[i].ent_iob == 2) and \
-
+                    self.c[i+1].ent_iob == 1:
-                # overwrite if the token was part of a specified entity
+                self.c[i+1].ent_iob = 3
-                if i in tokens_in_ents.keys():
+            # Change of type with BI or II: convert second I to B
-                    ent_start, ent_end, entity_type, kb_id = tokens_in_ents[i]
+            if self.c[i].ent_type != self.c[i+1].ent_type and \
-                    if entity_type is None or entity_type <= 0:
+                    (self.c[i].ent_iob == 3 or self.c[i].ent_iob == 1) and \
-                        # Blocking this token from being overwritten by downstream NER
+                    self.c[i+1].ent_iob == 1:
-                        ent_iob = 3
+                self.c[i+1].ent_iob = 3
-                    elif ent_start == i:
-                        # Marking the start of an entity
-                        ent_iob = 3
-                    else:
-                        # Marking the inside of an entity
-                        ent_iob = 1
-
-                self.c[i].ent_type = entity_type
-                self.c[i].ent_kb_id = kb_id
-                self.c[i].ent_iob = ent_iob
 
     @property
     def noun_chunks(self):

spacy/training/example.pyx

@@ -288,6 +288,7 @@ def _annot2array(vocab, tok_annot, doc_annot):
 
 
 def _add_entities_to_doc(doc, ner_data):
+    print(ner_data)
     if ner_data is None:
         return
     elif ner_data == []:
@@ -303,9 +304,14 @@ def _add_entities_to_doc(doc, ner_data):
             biluo_tags_to_spans(doc, ner_data)
         )
     elif isinstance(ner_data[0], Span):
-        # Ugh, this is super messy. Really hard to set O entities
+        entities = []
-        doc.ents = ner_data
+        missing = []
-        doc.ents = [span for span in ner_data if span.label_]
+        for span in ner_data:
+            if span.label:
+                entities.append(span)
+            else:
+                missing.append(span)
+        doc.set_ents(entities, missing=missing)
     else:
         raise ValueError(Errors.E973)
 

spacy/training/iob_utils.py

@@ -151,9 +151,10 @@ def biluo_tags_to_spans(doc: Doc, tags: Iterable[str]) -> List[Span]:
 
     doc (Doc): The document that the BILUO tags refer to.
     entities (iterable): A sequence of BILUO tags with each tag describing one
-        token. Each tags string will be of the form of either "", "O" or
+        token. Each tag string will be of the form of either "", "O" or
         "{action}-{label}", where action is one of "B", "I", "L", "U".
-    RETURNS (list): A sequence of Span objects.
+    RETURNS (list): A sequence of Span objects. Each token with a missing IOB
+        tag is returned as a Span with an empty label.
     """
     token_offsets = tags_to_entities(tags)
     spans = []
@@ -186,22 +187,18 @@ def tags_to_entities(tags: Iterable[str]) -> List[Tuple[str, int, int]]:
     entities = []
     start = None
     for i, tag in enumerate(tags):
-        if tag is None:
+        if tag is None or tag.startswith("-"):
-            continue
-        if tag.startswith("O"):
             # TODO: We shouldn't be getting these malformed inputs. Fix this.
             if start is not None:
                 start = None
             else:
                 entities.append(("", i, i))
-            continue
+        elif tag.startswith("O"):
-        elif tag == "-":
+            pass
-            continue
         elif tag.startswith("I"):
             if start is None:
                 raise ValueError(Errors.E067.format(start="I", tags=tags[: i + 1]))
-            continue
+        elif tag.startswith("U"):
-        if tag.startswith("U"):
             entities.append((tag[2:], i, i))
         elif tag.startswith("B"):
             start = i

website/docs/api/data-formats.md

@@ -180,26 +180,27 @@ single corpus once and then divide it up into `train` and `dev` partitions.
 This section defines settings and controls for the training and evaluation
 process that are used when you run [`spacy train`](/api/cli#train).
 
-| Name                  | Description                                                                                                                                                                                                  |
+| Name                  | Description                                                                                                                                                                                                                               |
-| --------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `accumulate_gradient` | Whether to divide the batch up into substeps. Defaults to `1`. ~~int~~                                                                                                                                       |
+| `accumulate_gradient` | Whether to divide the batch up into substeps. Defaults to `1`. ~~int~~                                                                                                                                                                    |
-| `batcher`             | Callable that takes an iterator of [`Doc`](/api/doc) objects and yields batches of `Doc`s. Defaults to [`batch_by_words`](/api/top-level#batch_by_words). ~~Callable[[Iterator[Doc], Iterator[List[Doc]]]]~~ |
+| `batcher`             | Callable that takes an iterator of [`Doc`](/api/doc) objects and yields batches of `Doc`s. Defaults to [`batch_by_words`](/api/top-level#batch_by_words). ~~Callable[[Iterator[Doc], Iterator[List[Doc]]]]~~                              |
-| `dev_corpus`          | Dot notation of the config location defining the dev corpus. Defaults to `corpora.dev`. ~~str~~                                                                                                              |
+| `before_to_disk`      | Optional callback to modify `nlp` object right before it is saved to disk during and after training. Can be used to remove or reset config values or disable components. Defaults to `null`. ~~Optional[Callable[[Language], Language]]~~ |
-| `dropout`             | The dropout rate. Defaults to `0.1`. ~~float~~                                                                                                                                                               |
+| `dev_corpus`          | Dot notation of the config location defining the dev corpus. Defaults to `corpora.dev`. ~~str~~                                                                                                                                           |
-| `eval_frequency`      | How often to evaluate during training (steps). Defaults to `200`. ~~int~~                                                                                                                                    |
+| `dropout`             | The dropout rate. Defaults to `0.1`. ~~float~~                                                                                                                                                                                            |
-| `frozen_components`   | Pipeline component names that are "frozen" and shouldn't be updated during training. See [here](/usage/training#config-components) for details. Defaults to `[]`. ~~List[str]~~                              |
+| `eval_frequency`      | How often to evaluate during training (steps). Defaults to `200`. ~~int~~                                                                                                                                                                 |
-| `gpu_allocator`       | Library for cupy to route GPU memory allocation to. Can be `"pytorch"` or `"tensorflow"`. Defaults to variable `${system.gpu_allocator}`. ~~str~~                                                            |
+| `frozen_components`   | Pipeline component names that are "frozen" and shouldn't be updated during training. See [here](/usage/training#config-components) for details. Defaults to `[]`. ~~List[str]~~                                                           |
-| `init_tok2vec`        | Optional path to pretrained tok2vec weights created with [`spacy pretrain`](/api/cli#pretrain). Defaults to variable `${paths.init_tok2vec}`. ~~Optional[str]~~                                              |
+| `gpu_allocator`       | Library for cupy to route GPU memory allocation to. Can be `"pytorch"` or `"tensorflow"`. Defaults to variable `${system.gpu_allocator}`. ~~str~~                                                                                         |
-| `lookups`             | Additional lexeme and vocab data from [`spacy-lookups-data`](https://github.com/explosion/spacy-lookups-data). Defaults to `null`. ~~Optional[Lookups]~~                                                     |
+| `init_tok2vec`        | Optional path to pretrained tok2vec weights created with [`spacy pretrain`](/api/cli#pretrain). Defaults to variable `${paths.init_tok2vec}`. ~~Optional[str]~~                                                                           |
-| `max_epochs`          | Maximum number of epochs to train for. Defaults to `0`. ~~int~~                                                                                                                                              |
+| `lookups`             | Additional lexeme and vocab data from [`spacy-lookups-data`](https://github.com/explosion/spacy-lookups-data). Defaults to `null`. ~~Optional[Lookups]~~                                                                                  |
-| `max_steps`           | Maximum number of update steps to train for. Defaults to `20000`. ~~int~~                                                                                                                                    |
+| `max_epochs`          | Maximum number of epochs to train for. Defaults to `0`. ~~int~~                                                                                                                                                                           |
-| `optimizer`           | The optimizer. The learning rate schedule and other settings can be configured as part of the optimizer. Defaults to [`Adam`](https://thinc.ai/docs/api-optimizers#adam). ~~Optimizer~~                      |
+| `max_steps`           | Maximum number of update steps to train for. Defaults to `20000`. ~~int~~                                                                                                                                                                 |
-| `patience`            | How many steps to continue without improvement in evaluation score. Defaults to `1600`. ~~int~~                                                                                                              |
+| `optimizer`           | The optimizer. The learning rate schedule and other settings can be configured as part of the optimizer. Defaults to [`Adam`](https://thinc.ai/docs/api-optimizers#adam). ~~Optimizer~~                                                   |
-| `raw_text`            | Optional path to a jsonl file with unlabelled text documents for a [rehearsal](/api/language#rehearse) step. Defaults to variable `${paths.raw}`. ~~Optional[str]~~                                          |
+| `patience`            | How many steps to continue without improvement in evaluation score. Defaults to `1600`. ~~int~~                                                                                                                                           |
-| `score_weights`       | Score names shown in metrics mapped to their weight towards the final weighted score. See [here](/usage/training#metrics) for details. Defaults to `{}`. ~~Dict[str, float]~~                                |
+| `raw_text`            | Optional path to a jsonl file with unlabelled text documents for a [rehearsal](/api/language#rehearse) step. Defaults to variable `${paths.raw}`. ~~Optional[str]~~                                                                       |
-| `seed`                | The random seed. Defaults to variable `${system.seed}`. ~~int~~                                                                                                                                              |
+| `score_weights`       | Score names shown in metrics mapped to their weight towards the final weighted score. See [here](/usage/training#metrics) for details. Defaults to `{}`. ~~Dict[str, float]~~                                                             |
-| `train_corpus`        | Dot notation of the config location defining the train corpus. Defaults to `corpora.train`. ~~str~~                                                                                                          |
+| `seed`                | The random seed. Defaults to variable `${system.seed}`. ~~int~~                                                                                                                                                                           |
-| `vectors`             | Name or path of pipeline containing pretrained word vectors to use, e.g. created with [`init vocab`](/api/cli#init-vocab). Defaults to `null`. ~~Optional[str]~~                                             |
+| `train_corpus`        | Dot notation of the config location defining the train corpus. Defaults to `corpora.train`. ~~str~~                                                                                                                                       |
+| `vectors`             | Name or path of pipeline containing pretrained word vectors to use, e.g. created with [`init vocab`](/api/cli#init-vocab). Defaults to `null`. ~~Optional[str]~~                                                                          |
 
 ### pretraining {#config-pretraining tag="section,optional"}
 
@@ -275,8 +276,8 @@ $ python -m spacy convert ./data.json ./output.spacy
 > entity label, prefixed by the BILUO marker. For example `"B-ORG"` describes
 > the first token of a multi-token `ORG` entity and `"U-PERSON"` a single token
 > representing a `PERSON` entity. The
-> [`offsets_to_biluo_tags`](/api/top-level#offsets_to_biluo_tags) function
+> [`offsets_to_biluo_tags`](/api/top-level#offsets_to_biluo_tags) function can
-> can help you convert entity offsets to the right format.
+> help you convert entity offsets to the right format.
 
 ```python
 ### Example structure
@@ -518,7 +519,7 @@ source of truth** used for loading a pipeline.
 >     "ner": ["PERSON", "ORG", "PRODUCT"],
 >     "textcat": ["POSITIVE", "NEGATIVE"]
 >   },
->   "accuracy": {
+>   "performance": {
 >     "ents_f": 82.7300930714,
 >     "ents_p": 82.135523614,
 >     "ents_r": 83.3333333333,

website/docs/api/doc.md

@@ -219,6 +219,30 @@ alignment mode `"strict".
 | `alignment_mode`                     | How character indices snap to token boundaries. Options: `"strict"` (no snapping), `"contract"` (span of all tokens completely within the character span), `"expand"` (span of all tokens at least partially covered by the character span). Defaults to `"strict"`. ~~str~~ |
 | **RETURNS**                          | The newly constructed object or `None`. ~~Optional[Span]~~                                                                                                                                                                                                                   |
 
+## Doc.set_ents {#ents tag="method" new="3"}
+
+Set the named entities in the document.
+
+> #### Example
+>
+> ```python
+> from spacy.tokens import Span
+> doc = nlp("Mr. Best flew to New York on Saturday morning.")
+> doc.set_ents([Span(doc, 0, 2, "PERSON")])
+> ents = list(doc.ents)
+> assert ents[0].label_ == "PERSON"
+> assert ents[0].text == "Mr. Best"
+> ```
+
+| Name           | Description                                                                                                                                                                               |
+| -------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| entities       | Spans with labels to set as entities. ~~List[Span]~~                                                                                                                                      |
+| _keyword-only_ |                                                                                                                                                                                           |
+| blocked        | Spans to set as "blocked" (never an entity) for spacy's built-in NER component. Other components may ignore this setting. ~~Optional[List[Span]]~~                                        |
+| missing        | Spans with missing/unknown entity information. ~~Optional[List[Span]]~~                                                                                                                   |
+| outside        | Spans outside of entities (O in IOB). ~~Optional[List[Span]]~~                                                                                                                            |
+| default        | How to set entity annotation for tokens outside of any provided spans. Options: "blocked", "missing", "outside" and "unmodified" (preserve current state). Defaults to "outside". ~~str~~ |
+
 ## Doc.similarity {#similarity tag="method" model="vectors"}
 
 Make a semantic similarity estimate. The default estimate is cosine similarity
@@ -542,7 +566,6 @@ objects, if the entity recognizer has been applied.
 > ```python
 > doc = nlp("Mr. Best flew to New York on Saturday morning.")
 > ents = list(doc.ents)
-> assert ents[0].label == 346
 > assert ents[0].label_ == "PERSON"
 > assert ents[0].text == "Mr. Best"
 > ```

website/docs/usage/_benchmarks-models.md

@@ -1,13 +1,13 @@
 import { Help } from 'components/typography'; import Link from 'components/link'
 
-<!-- TODO: update, add project template -->
+<!-- TODO: update numbers -->
 
 <figure>
 
-| System                                                     | Parser | Tagger |  NER | WPS<br />CPU <Help>words per second on CPU, higher is better</Help> | WPS<br/>GPU <Help>words per second on GPU, higher is better</Help> |
+| Pipeline                                                   | Parser | Tagger |  NER | WPS<br />CPU <Help>words per second on CPU, higher is better</Help> | WPS<br/>GPU <Help>words per second on GPU, higher is better</Help> |
 | ---------------------------------------------------------- | -----: | -----: | ---: | ------------------------------------------------------------------: | -----------------------------------------------------------------: |
 | [`en_core_web_trf`](/models/en#en_core_web_trf) (spaCy v3) |        |        |      |                                                                     |                                                                 6k |
-| [`en_core_web_lg`](/models/en#en_core_web_lg) (spaCy v3)   |        |        |      |                                                                     |                                                                    |
+| [`en_core_web_lg`](/models/en#en_core_web_lg) (spaCy v3)   |   92.1 |   97.4 | 87.0 |                                                                  7k |                                                                    |
 | `en_core_web_lg` (spaCy v2)                                |   91.9 |   97.2 | 85.9 |                                                                 10k |                                                                    |
 
 <figcaption class="caption">
@@ -21,10 +21,10 @@ import { Help } from 'components/typography'; import Link from 'components/link'
 
 <figure>
 
-| Named Entity Recognition Model                                                 | OntoNotes | CoNLL '03 |
+| Named Entity Recognition System                                                | OntoNotes | CoNLL '03 |
 | ------------------------------------------------------------------------------ | --------: | --------: |
 | spaCy RoBERTa (2020)                                                           |           |      92.2 |
-| spaCy CNN (2020)                                                               |           |      88.4 |
+| spaCy CNN (2020)                                                               |      85.3 |      88.4 |
 | spaCy CNN (2017)                                                               |      86.4 |           |
 | [Stanza](https://stanfordnlp.github.io/stanza/) (StanfordNLP)<sup>1</sup>      |      88.8 |      92.1 |
 | <Link to="https://github.com/flairNLP/flair" hideIcon>Flair</Link><sup>2</sup> |      89.7 |      93.1 |

website/docs/usage/embeddings-transformers.md

@@ -235,8 +235,6 @@ The `Transformer` component sets the
 [`Doc._.trf_data`](/api/transformer#custom_attributes) extension attribute,
 which lets you access the transformers outputs at runtime.
 
-<!-- TODO: update/confirm once we have final models trained -->
-
 ```cli
 $ python -m spacy download en_core_trf_lg
 ```

website/docs/usage/facts-figures.md

@@ -63,7 +63,7 @@ import Benchmarks from 'usage/\_benchmarks-models.md'
 
 <figure>
 
-| System                                                                         |  UAS |  LAS |
+| Dependency Parsing System                                                      |  UAS |  LAS |
 | ------------------------------------------------------------------------------ | ---: | ---: |
 | spaCy RoBERTa (2020)<sup>1</sup>                                               | 96.8 | 95.0 |
 | spaCy CNN (2020)<sup>1</sup>                                                   | 93.7 | 91.8 |

website/docs/usage/linguistic-features.md

@@ -1654,9 +1654,12 @@ The [`SentenceRecognizer`](/api/sentencerecognizer) is a simple statistical
 component that only provides sentence boundaries. Along with being faster and
 smaller than the parser, its primary advantage is that it's easier to train
 because it only requires annotated sentence boundaries rather than full
-dependency parses.
+dependency parses. spaCy's [trained pipelines](/models) include both a parser
-
+and a trained sentence segmenter, which is
-<!-- TODO: update/confirm usage once we have final models trained -->
+[disabled](/usage/processing-pipelines#disabling) by default. If you only need
+sentence boundaries and no parser, you can use the `enable` and `disable`
+arguments on [`spacy.load`](/api/top-level#spacy.load) to enable the senter and
+disable the parser.
 
 > #### senter vs. parser
 >

website/docs/usage/processing-pipelines.md

@@ -253,8 +253,6 @@ different mechanisms you can use:
 Disabled and excluded component names can be provided to
 [`spacy.load`](/api/top-level#spacy.load) as a list.
 
-<!-- TODO: update with info on our models shipped with optional components -->
-
 > #### 💡 Optional pipeline components
 >
 > The `disable` mechanism makes it easy to distribute pipeline packages with
@@ -262,6 +260,11 @@ Disabled and excluded component names can be provided to
 > your pipeline may include a statistical _and_ a rule-based component for
 > sentence segmentation, and you can choose which one to run depending on your
 > use case.
+>
+> For example, spaCy's [trained pipelines](/models) like
+> [`en_core_web_sm`](/models/en#en_core_web_sm) contain both a `parser` and
+> `senter` that perform sentence segmentation, but the `senter` is disabled by
+> default.
 
 ```python
 # Load the pipeline without the entity recognizer

website/docs/usage/projects.md

@@ -733,7 +733,10 @@ workflows, but only one can be tracked by DVC.
 <Infobox title="This section is still under construction" emoji="🚧" variant="warning">
 
 The Prodigy integration will require a nightly version of Prodigy that supports
-spaCy v3+.
+spaCy v3+. You can already use annotations created with Prodigy in spaCy v3 by
+exporting your data with
+[`data-to-spacy`](https://prodi.gy/docs/recipes#data-to-spacy) and running
+[`spacy convert`](/api/cli#convert) to convert it to the binary format.
 
 </Infobox>
 

website/src/templates/models.js

@@ -32,11 +32,17 @@ const MODEL_META = {
     las: 'Labelled dependencies',
     token_acc: 'Tokenization',
     tok: 'Tokenization',
+    lemma: 'Statistical lemmatization',
+    morph: 'Morphological analysis',
     tags_acc: 'Part-of-speech tags (fine grained tags, Token.tag)',
     tag: 'Part-of-speech tags (fine grained tags, Token.tag)',
+    pos: 'Part-of-speech tags (coarse grained tags, Token.pos)',
     ents_f: 'Named entities (F-score)',
     ents_p: 'Named entities (precision)',
     ents_r: 'Named entities (recall)',
+    ner_f: 'Named entities (F-score)',
+    ner_p: 'Named entities (precision)',
+    ner_r: 'Named entities (recall)',
     sent_f: 'Sentence segmentation (F-score)',
     sent_p: 'Sentence segmentation (precision)',
     sent_r: 'Sentence segmentation (recall)',
@@ -88,11 +94,12 @@ function formatVectors(data) {
 }
 
 function formatAccuracy(data) {
+    const exclude = ['speed']
     if (!data) return []
     return Object.keys(data)
         .map(label => {
             const value = data[label]
-            return isNaN(value)
+            return isNaN(value) || exclude.includes(label)
                 ? null
                 : {
                       label,
@@ -109,6 +116,7 @@ function formatModelMeta(data) {
         version: data.version,
         sizeFull: data.size,
         pipeline: data.pipeline,
+        components: data.components,
         notes: data.notes,
         description: data.description,
         sources: data.sources,
@@ -117,7 +125,8 @@ function formatModelMeta(data) {
         license: data.license,
         labels: isEmptyObj(data.labels) ? null : data.labels,
         vectors: formatVectors(data.vectors),
-        accuracy: formatAccuracy(data.accuracy),
+        // TODO: remove accuracy fallback
+        accuracy: formatAccuracy(data.accuracy || data.performance),
     }
 }