4 Commits

Author	SHA1	Message	Date
Paul O'Leary McCann	91acc3ea75	Fix entity linker batching (#9669) ... * Partial fix of entity linker batching * Add import * Better name * Add `use_gold_ents` option, docs * Change to v2, create stub v1, update docs etc. * Fix error type Honestly no idea what the right type to use here is. ConfigValidationError seems wrong. Maybe a NotImplementedError? * Make mypy happy * Add hacky fix for init issue * Add legacy pipeline entity linker * Fix references to class name * Add __init__.py for legacy * Attempted fix for loss issue * Remove placeholder V1 * formatting * slightly more interesting train data * Handle batches with no usable examples This adds a test for batches that have docs but not entities, and a check in the component that detects such cases and skips the update step as thought the batch were empty. * Remove todo about data verification Check for empty data was moved further up so this should be OK now - the case in question shouldn't be possible. * Fix gradient calculation The model doesn't know which entities are not in the kb, so it generates embeddings for the context of all of them. However, the loss does know which entities aren't in the kb, and it ignores them, as there's no sensible gradient. This has the issue that the gradient will not be calculated for some of the input embeddings, which causes a dimension mismatch in backprop. That should have caused a clear error, but with numpyops it was causing nans to happen, which is another problem that should be addressed separately. This commit changes the loss to give a zero gradient for entities not in the kb. * add failing test for v1 EL legacy architecture * Add nasty but simple working check for legacy arch * Clarify why init hack works the way it does * Clarify use_gold_ents use case * Fix use gold ents related handling * Add tests for no gold ents and fix other tests * Use aligned ents function (not working) This doesn't actually work because the "aligned" ents are gold-only. But if I have a different function that returns the intersection, *then* this will work as desired. * Use proper matching ent check This changes the process when gold ents are not used so that the intersection of ents in the pred and gold is used. * Move get_matching_ents to Example * Use model attribute to check for legacy arch * Rename flag * bump spacy-legacy to lower 3.0.9 Co-authored-by: svlandeg <svlandeg@github.com>	2022-03-04 09:17:36 +01:00
Adriane Boyd	c9baf9d196	Fix spancat for empty docs and zero suggestions (#9654) ... * Fix spancat for empty docs and zero suggestions * Use ops.xp.zeros in test	2021-11-15 12:40:55 +01:00
Connor Brinton	657af5f91f	🏷 Add Mypy check to CI and ignore all existing Mypy errors (#9167) ... * 🚨 Ignore all existing Mypy errors * 🏗 Add Mypy check to CI * Add types-mock and types-requests as dev requirements * Add additional type ignore directives * Add types packages to dev-only list in reqs test * Add types-dataclasses for python 3.6 * Add ignore to pretrain * 🏷 Improve type annotation on `run_command` helper The `run_command` helper previously declared that it returned an `Optional[subprocess.CompletedProcess]`, but it isn't actually possible for the function to return `None`. These changes modify the type annotation of the `run_command` helper and remove all now-unnecessary `# type: ignore` directives. * 🔧 Allow variable type redefinition in limited contexts These changes modify how Mypy is configured to allow variables to have their type automatically redefined under certain conditions. The Mypy documentation contains the following example: ```python def process(items: List[str]) -> None: # 'items' has type List[str] items = [item.split() for item in items] # 'items' now has type List[List[str]] ... ``` This configuration change is especially helpful in reducing the number of `# type: ignore` directives needed to handle the common pattern of: * Accepting a filepath as a string * Overwriting the variable using `filepath = ensure_path(filepath)` These changes enable redefinition and remove all `# type: ignore` directives rendered redundant by this change. * 🏷 Add type annotation to converters mapping * 🚨 Fix Mypy error in convert CLI argument verification * 🏷 Improve type annotation on `resolve_dot_names` helper * 🏷 Add type annotations for `Vocab` attributes `strings` and `vectors` * 🏷 Add type annotations for more `Vocab` attributes * 🏷 Add loose type annotation for gold data compilation * 🏷 Improve `_format_labels` type annotation * 🏷 Fix `get_lang_class` type annotation * 🏷 Loosen return type of `Language.evaluate` * 🏷 Don't accept `Scorer` in `handle_scores_per_type` * 🏷 Add `string_to_list` overloads * 🏷 Fix non-Optional command-line options * 🙈 Ignore redefinition of `wandb_logger` in `loggers.py` * ➕ Install `typing_extensions` in Python 3.8+ The `typing_extensions` package states that it should be used when "writing code that must be compatible with multiple Python versions". Since SpaCy needs to support multiple Python versions, it should be used when newer `typing` module members are required. One example of this is `Literal`, which is available starting with Python 3.8. Previously SpaCy tried to import `Literal` from `typing`, falling back to `typing_extensions` if the import failed. However, Mypy doesn't seem to be able to understand what `Literal` means when the initial import means. Therefore, these changes modify how `compat` imports `Literal` by always importing it from `typing_extensions`. These changes also modify how `typing_extensions` is installed, so that it is a requirement for all Python versions, including those greater than or equal to 3.8. * 🏷 Improve type annotation for `Language.pipe` These changes add a missing overload variant to the type signature of `Language.pipe`. Additionally, the type signature is enhanced to allow type checkers to differentiate between the two overload variants based on the `as_tuple` parameter. Fixes #8772 * ➖ Don't install `typing-extensions` in Python 3.8+ After more detailed analysis of how to implement Python version-specific type annotations using SpaCy, it has been determined that by branching on a comparison against `sys.version_info` can be statically analyzed by Mypy well enough to enable us to conditionally use `typing_extensions.Literal`. This means that we no longer need to install `typing_extensions` for Python versions greater than or equal to 3.8! 🎉 These changes revert previous changes installing `typing-extensions` regardless of Python version and modify how we import the `Literal` type to ensure that Mypy treats it properly. * resolve mypy errors for Strict pydantic types * refactor code to avoid missing return statement * fix types of convert CLI command * avoid list-set confustion in debug_data * fix typo and formatting * small fixes to avoid type ignores * fix types in profile CLI command and make it more efficient * type fixes in projects CLI * put one ignore back * type fixes for render * fix render types - the sequel * fix BaseDefault in language definitions * fix type of noun_chunks iterator - yields tuple instead of span * fix types in language-specific modules * 🏷 Expand accepted inputs of `get_string_id` `get_string_id` accepts either a string (in which case it returns its ID) or an ID (in which case it immediately returns the ID). These changes extend the type annotation of `get_string_id` to indicate that it can accept either strings or IDs. * 🏷 Handle override types in `combine_score_weights` The `combine_score_weights` function allows users to pass an `overrides` mapping to override data extracted from the `weights` argument. Since it allows `Optional` dictionary values, the return value may also include `Optional` dictionary values. These changes update the type annotations for `combine_score_weights` to reflect this fact. * 🏷 Fix tokenizer serialization method signatures in `DummyTokenizer` * 🏷 Fix redefinition of `wandb_logger` These changes fix the redefinition of `wandb_logger` by giving a separate name to each `WandbLogger` version. For backwards-compatibility, `spacy.train` still exports `wandb_logger_v3` as `wandb_logger` for now. * more fixes for typing in language * type fixes in model definitions * 🏷 Annotate `_RandomWords.probs` as `NDArray` * 🏷 Annotate `tok2vec` layers to help Mypy * 🐛 Fix `_RandomWords.probs` type annotations for Python 3.6 Also remove an import that I forgot to move to the top of the module 😅 * more fixes for matchers and other pipeline components * quick fix for entity linker * fixing types for spancat, textcat, etc * bugfix for tok2vec * type annotations for scorer * add runtime_checkable for Protocol * type and import fixes in tests * mypy fixes for training utilities * few fixes in util * fix import * 🐵 Remove unused `# type: ignore` directives * 🏷 Annotate `Language._components` * 🏷 Annotate `spacy.pipeline.Pipe` * add doc as property to span.pyi * small fixes and cleanup * explicit type annotations instead of via comment Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com> Co-authored-by: svlandeg <svlandeg@github.com>	2021-10-14 15:21:40 +02:00
Matthew Honnibal	f9946154d9	Add SpanCategorizer component (#6747) ... * Draft spancat model * Add spancat model * Add test for extract_spans * Add extract_spans layer * Upd extract_spans * Add spancat model * Add test for spancat model * Upd spancat model * Update spancat component * Upd spancat * Update spancat model * Add quick spancat test * Import SpanCategorizer * Fix SpanCategorizer component * Import SpanGroup * Fix span extraction * Fix import * Fix import * Upd model * Update spancat models * Add scoring, update defaults * Update and add docs * Fix type * Update spacy/ml/extract_spans.py * Auto-format and fix import * Fix comment * Fix type * Fix type * Update website/docs/api/spancategorizer.md * Fix comment Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Better defense Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix labels list Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/extract_spans.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/pipeline/spancat.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Set annotations during update * Set annotations in spancat * fix imports in test * Update spacy/pipeline/spancat.py * replace MaxoutLogistic with LinearLogistic * fix config * various small fixes * remove set_annotations parameter in update * use our beloved tupley format with recent support for doc.spans * bugfix to allow renaming the default span_key (scores weren't showing up) * use different key in docs example * change defaults to better-working parameters from project (WIP) * register spacy.extract_spans.v1 for legacy purposes * Upd dev version so can build wheel * layers instead of architectures for smaller building blocks * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Include additional scores from overrides in combined score weights * Parameterize spans key in scoring Parameterize the `SpanCategorizer` `spans_key` for scoring purposes so that it's possible to evaluate multiple `spancat` components in the same pipeline. * Use the (intentionally very short) default spans key `sc` in the `SpanCategorizer` * Adjust the default score weights to include the default key * Adjust the scorer to use `spans_{spans_key}` as the prefix for the returned score * Revert addition of `attr_name` argument to `score_spans` and adjust the key in the `getter` instead. Note that for `spancat` components with a custom `span_key`, the score weights currently need to be modified manually in `[training.score_weights]` for them to be available during training. To suppress the default score weights `spans_sc_p/r/f` during training, set them to `null` in `[training.score_weights]`. * Update website/docs/api/scorer.md * Fix scorer for spans key containing underscore * Increment version * Add Spans to Evaluate CLI (#8439) * Add Spans to Evaluate CLI * Change to spans_key * Add spans per_type output Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Fix spancat GPU issues (#8455) * Fix GPU issues * Require thinc >=8.0.6 * Switch to glorot_uniform_init * Fix and test ngram suggester * Include final ngram in doc for all sizes * Fix ngrams for docs of the same length as ngram size * Handle batches of docs that result in no ngrams * Add tests Co-authored-by: Ines Montani <ines@ines.io> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Nirant <NirantK@users.noreply.github.com>	2021-06-24 12:35:27 +02:00