* Convert Candidate from Cython to Python class.
* Format.
* Fix .entity_ typo in _add_activations() usage.
* Change type for mentions to look up entity candidates for to SpanGroup from Iterable[Span].
* Update docs.
* Update spacy/kb/candidate.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Update doc string of BaseCandidate.__init__().
* Update spacy/kb/candidate.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Rename Candidate to InMemoryCandidate, BaseCandidate to Candidate.
* Adjust Candidate to support and mandate numerical entity IDs.
* Format.
* Fix docstring and docs.
* Update website/docs/api/kb.mdx
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Rename alias -> mention.
* Refactor Candidate attribute names. Update docs and tests accordingly.
* Refacor Candidate attributes and their usage.
* Format.
* Fix mypy error.
* Update error code in line with v4 convention.
* Reverse erroneous changes during merge.
* Update return type in EL tests.
* Re-add Candidate to setup.py.
* Format updated docs.
---------
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Make empty_kb() configurable.
* Format.
* Update docs.
* Be more specific in KB serialization test.
* Update KB serialization tests. Update docs.
* Remove doc update for batched candidate generation.
* Fix serialization of subclassed KB in tests.
* Format.
* Update docstring.
* Update docstring.
* Switch from pickle to json for custom field serialization.
* Remove backwards-compatible overwrite from Entity Linker
This also adds a docstring about overwrite, since it wasn't present.
* Fix docstring
* Remove backward compat settings in Morphologizer
This also needed a docstring added.
For this component it's less clear what the right overwrite settings
are.
* Remove backward compat from sentencizer
This was simple
* Remove backward compat from senter
Another simple one
* Remove backward compat setting from tagger
* Add docstrings
* Update spacy/pipeline/morphologizer.pyx
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update docs
---------
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Move Entity Linker v1 component to spacy-legacy
This is a follow up to #11889 that moves the component instead of
removing it.
In general, we never import from spacy-legacy in spaCy proper. However,
to use this component, that kind of import will be necessary. I was able
to test this without issues, but is this current import strategy
acceptable? Or should we put the component in a registry?
* Use spacy-legacy pr for CI
This will need to be reverted before merging.
* Add temporary step to log installed spacy-legacy version
* Modify requirements.txt to trigger tests
* Add comment to Python to trigger tests
* TODO REVERT This is a commit with logic changes to trigger tests
* Remove pipe from YAML
Works locally, but possibly this is causing a quoting error or
something.
* Revert "TODO REVERT This is a commit with logic changes to trigger tests"
This reverts commit 689fae71f3.
* Revert "Add comment to Python to trigger tests"
This reverts commit 11840fc598.
* Add more logging
* Try installing directly in workflow
* Try explicitly uninstalling spacy-legacy first
* Cat requirements.txt to confirm contents
In the branch, the thinc version spec is `thinc>=8.1.0,<8.2.0`. But in
the logs, it's clear that a development release of 9.0 is being
installed. It's not clear why that would happen.
* Log requirements at start of build
* TODO REVERT Change thinc spec
Want to see what happens to the installed thinc spec with this change.
* Update thinc requirements
This makes it the same as it was before the merge, >=8.1.0,<8.2.0.
* Use same thinc version as v4 branch
* TODO REVERT Mark dependency check as xfail
spacy-legacy is specified as a git checkout in requirements.txt while
this PR is in progress, which makes the consistency check here fail.
* Remove debugging output / install step
* Revert "Remove debugging output / install step"
This reverts commit 923ea7448b.
* Clean up debugging output
The manual install step with the URL fragment seems to have caused
issues on Windows due to the = in the URL being misinterpreted. On the
other hand, removing it seems to mean the git version of spacy-legacy
isn't actually installed.
This PR removes the URL fragment but keeps the direct command-line
install. Additionally, since it looks like this job is configured to use
the default shell (and not bash), it removes a comment that upsets the
Windows cmd shell.
* Revert "TODO REVERT Mark dependency check as xfail"
This reverts commit d4863ec156.
* Fix requirements.txt, increasing spacy-legacy version
* Raise spacy legacy version in setup.cfg
* Remove azure build workarounds
* make spacy-legacy version explicit in error message
* Remove debugging line
* Suggestions from code review
* Store activations in Doc when `store_activations` is enabled
This change adds the new `activations` attribute to `Doc`. This
attribute can be used by trainable pipes to store their activations,
probabilities, and guesses for downstream users.
As an example, this change modifies the `tagger` and `senter` pipes to
add an `store_activations` option. When this option is enabled, the
probabilities and guesses are stored in `set_annotations`.
* Change type of `store_activations` to `Union[bool, List[str]]`
When the value is:
- A bool: all activations are stored when set to `True`.
- A List[str]: the activations named in the list are stored
* Formatting fixes in Tagger
* Support store_activations in spancat and morphologizer
* Make Doc.activations type visible to MyPy
* textcat/textcat_multilabel: add store_activations option
* trainable_lemmatizer/entity_linker: add store_activations option
* parser/ner: do not currently support returning activations
* Extend tagger and senter tests
So that they, like the other tests, also check that we get no
activations if no activations were requested.
* Document `Doc.activations` and `store_activations` in the relevant pipes
* Start errors/warnings at higher numbers to avoid merge conflicts
Between the master and v4 branches.
* Add `store_activations` to docstrings.
* Replace store_activations setter by set_store_activations method
Setters that take a different type than what the getter returns are still
problematic for MyPy. Replace the setter by a method, so that type inference
works everywhere.
* Use dict comprehension suggested by @svlandeg
* Revert "Use dict comprehension suggested by @svlandeg"
This reverts commit 6e7b958f70.
* EntityLinker: add type annotations to _add_activations
* _store_activations: make kwarg-only, remove doc_scores_lens arg
* set_annotations: add type annotations
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* TextCat.predict: return dict
* Make the `TrainablePipe.store_activations` property a bool
This means that we can also bring back `store_activations` setter.
* Remove `TrainablePipe.activations`
We do not need to enumerate the activations anymore since `store_activations` is
`bool`.
* Add type annotations for activations in predict/set_annotations
* Rename `TrainablePipe.store_activations` to `save_activations`
* Error E1400 is not used anymore
This error was used when activations were still `Union[bool, List[str]]`.
* Change wording in API docs after store -> save change
* docs: tag (save_)activations as new in spaCy 4.0
* Fix copied line in morphologizer activations test
* Don't train in any test_save_activations test
* Rename activations
- "probs" -> "probabilities"
- "guesses" -> "label_ids", except in the edit tree lemmatizer, where
"guesses" -> "tree_ids".
* Remove unused W400 warning.
This warning was used when we still allowed the user to specify
which activations to save.
* Formatting fixes
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Replace "kb_ids" by a constant
* spancat: replace a cast by an assertion
* Fix EOF spacing
* Fix comments in test_save_activations tests
* Do not set RNG seed in activation saving tests
* Revert "spancat: replace a cast by an assertion"
This reverts commit 0bd5730d16.
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix TODO about typing
Fix was simple: just request an array2f.
* Add type ignore
Maxout has a more restrictive type than the residual layer expects (only
Floats2d vs any Floats).
* Various cleanup
This moves a lot of lines around but doesn't change any functionality.
Details:
1. use `continue` to reduce indentation
2. move sentence doc building inside conditional since it's otherwise
unused
3. reduces some temporary assignments
* Add failing test
* Partial fix for issue
This kind of works. The issue with token length mismatches is gone. The
problem is that when you get empty lists of encodings to compare, it
fails because the sizes are not the same, even though they're both zero:
(0, 3) vs (0,). Not sure why that happens...
* Short circuit on empties
* Remove spurious check
The check here isn't needed now the the short circuit is fixed.
* Update spacy/tests/pipeline/test_entity_linker.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Use "eg", not "example"
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* 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>
* 🚨 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>
* Add overwrite settings for more components
For pipeline components where it's relevant and not already implemented,
add an explicit `overwrite` setting that controls whether
`set_annotations` overwrites existing annotation.
For the `morphologizer`, add an additional setting `extend`, which
controls whether the existing features are preserved.
* +overwrite, +extend: overwrite values of existing features, add any new
features
* +overwrite, -extend: overwrite completely, removing any existing
features
* -overwrite, +extend: keep values of existing features, add any new
features
* -overwrite, -extend: do not modify the existing value if set
In all cases an unset value will be set by `set_annotations`.
Preserve current overwrite defaults:
* True: morphologizer, entity linker
* False: tagger, sentencizer, senter
* Add backwards compat overwrite settings
* Put empty line back
Removed by accident in last commit
* Set backwards-compatible defaults in __init__
Because the `TrainablePipe` serialization methods update `cfg`, there's
no straightforward way to detect whether models serialized with a
previous version are missing the overwrite settings.
It would be possible in the sentencizer due to its separate
serialization methods, however to keep the changes parallel, this also
sets the default in `__init__`.
* Remove traces
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Add scorer option to components
Add an optional `scorer` parameter to all pipeline components. If a
scoring function is provided, it overrides the default scoring method
for that component.
* Add registered scorers for all components
* Add `scorers` registry
* Move all scoring methods outside of components as independent
functions and register
* Use the registered scoring methods as defaults in configs and inits
Additional:
* The scoring methods no longer have access to the full component, so
use settings from `cfg` as default scorer options to handle settings
such as `labels`, `threshold`, and `positive_label`
* The `attribute_ruler` scoring method no longer has access to the
patterns, so all scoring methods are called
* Bug fix: `spancat` scoring method is updated to set `allow_overlap` to
score overlapping spans correctly
* Update Russian lemmatizer to use direct score method
* Check type of cfg in Pipe.score
* Fix check
* Update spacy/pipeline/sentencizer.pyx
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Remove validate_examples from scoring functions
* Use Pipe.labels instead of Pipe.cfg["labels"]
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Pass excludes when serializing vocab
Additional minor bug fix:
* Deserialize vocab in `EntityLinker.from_disk`
* Add test for excluding strings on load
* Fix formatting
* unit test for pickling KB
* add pickling test for NEL
* KB to_bytes and from_bytes
* NEL to_bytes and from_bytes
* xfail pickle tests for now
* fix docs
* cleanup
* Replace negative rows with 0 in StaticVectors
Replace negative row indices with 0-vectors in `StaticVectors`.
* Increase versions related to StaticVectors
* Increase versions of all architctures and layers related to
`StaticVectors`
* Improve efficiency of 0-vector operations
Parallel `spacy-legacy` PR: https://github.com/explosion/spacy-legacy/pull/5
* Update config defaults to new versions
* Update docs
* add error handler for pipe methods
* add unit tests
* remove pipe method that are the same as their base class
* have Language keep track of a default error handler
* cleanup
* formatting
* small refactor
* add documentation
* rename Pipe to TrainablePipe
* split functionality between Pipe and TrainablePipe
* remove unnecessary methods from certain components
* cleanup
* hasattr(component, "pipe") should be sufficient again
* remove serialization and vocab/cfg from Pipe
* unify _ensure_examples and validate_examples
* small fixes
* hasattr checks for self.cfg and self.vocab
* make is_resizable and is_trainable properties
* serialize strings.json instead of vocab
* fix KB IO + tests
* fix typos
* more typos
* _added_strings as a set
* few more tests specifically for _added_strings field
* bump to 3.0.0a36
* NEL: read sentences and ents from reference
* fiddling with sent_start annotations
* add KB serialization test
* KB write additional file with strings.json
* score_links function to calculate NEL P/R/F
* formatting
* documentation
