The doc/token extension serialization tests add extensions that are not
serializable with pickle. This didn't cause issues before due to the
implicit run order of tests. However, test ordering has changed with
pytest 8.0.0, leading to failed tests in test_language.
Update the fixtures in the extension serialization tests to do proper
teardown and remove the extensions.
* Use isort with Black profile
* isort all the things
* Fix import cycles as a result of import sorting
* Add DOCBIN_ALL_ATTRS type definition
* Add isort to requirements
* Remove isort from build dependencies check
* Typo
* Address upcoming numpy v1.25 deprecations in test suite
* Temporarily test most recent numpy prerelease in CI
* Revert "Temporarily test most recent numpy prerelease in CI"
This reverts commit d75a66e55e.
* 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.
* Change enable/disable behavior so that arguments take precedence over config options. Extend error message on conflict. Add warning message in case of overwriting config option with arguments.
* Fix tests in test_serialize_pipeline.py to reflect changes to handling of enable/disable.
* Fix type issue.
* Move comment.
* Move comment.
* Issue UserWarning instead of printing wasabi message. Adjust test.
* Added pytest.warns(UserWarning) for expected warning to fix tests.
* Update warning message.
* Move type handling out of fetch_pipes_status().
* Add global variable for default value. Use id() to determine whether used values are default value.
* Fix default value for disable.
* Rename DEFAULT_PIPE_STATUS to _DEFAULT_EMPTY_PIPES.
* fix: De/Serialize `SpanGroups` including the SpanGroup keys
This prevents the loss of `SpanGroup`s that have the same .name as other `SpanGroup`s within the same `SpanGroups` object (upon de/serialization of the `SpanGroups`).
Fixes#10685
* Maintain backwards compatibility for serialized `SpanGroups`
(serialized as: a list of `SpanGroup`s, or b'')
* Add tests for `SpanGroups` deserialization backwards-compatibility
* Move a `SpanGroups` de/serialization test (test_issue10685)
to tests/serialize/test_serialize_spangroups.py
* Output a warning if deserializing a `SpanGroups` with duplicate .name-d `SpanGroup`s
* Minor refactor
* `SpanGroups.from_bytes` handles only `list` and `dict` types with
`dict` as the expected default
* For lists, keep first rather than last value encountered
* Update error message
* Rename and update tests
* Update to preserve list serialization of SpanGroups
To avoid breaking compatibility of serialized `Doc` and `DocBin` with
earlier versions of spacy v3, revert back to a list-only serialization,
but update the names just for serialization so that the SpanGroups keys
override the SpanGroup names.
* Preserve object identity and current key overwrite
* Preserve SpanGroup object identity
* Preserve last rather than first span group from SpanGroup list
format without SpanGroups keys
* Update inline comments
* Fix types
* Add type info for SpanGroup.copy
* Deserialize `SpanGroup`s as copies
when a single SpanGroup is the value for more than 1 `SpanGroups` key.
This is because we serialize `SpanGroups` as dicts (to maintain backward-
and forward-compatibility) and we can't assume `SpanGroup`s with the same
bytes/serialization were the same (identical) object, pre-serialization.
* Update spacy/tokens/_dict_proxies.py
* Add more SpanGroups serialization tests
Test that serialized SpanGroups maintain their Span order
* small clarification on older spaCy version
* Update spacy/tests/serialize/test_serialize_span_groups.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add tokenizer option to allow Matcher handling for all rules
Add tokenizer option `with_faster_rules_heuristics` that determines
whether the special cases applied by the internal `Matcher` are filtered
by whether they contain affixes or space. If `True` (default), the rules
are filtered to prioritize speed over rare edge cases. If `False`, all
rules are included in the final `Matcher`-based pass over the doc.
* Reset all caches when reloading special cases
* Revert "Reset all caches when reloading special cases"
This reverts commit 4ef6bd171d.
* Initialize max_length properly
* Add new tag to API docs
* Rename to faster heuristics
* Tagger: use unnormalized probabilities for inference
Using unnormalized softmax avoids use of the relatively expensive exp function,
which can significantly speed up non-transformer models (e.g. I got a speedup
of 27% on a German tagging + parsing pipeline).
* Add spacy.Tagger.v2 with configurable normalization
Normalization of probabilities is disabled by default to improve
performance.
* Update documentation, models, and tests to spacy.Tagger.v2
* Move Tagger.v1 to spacy-legacy
* docs/architectures: run prettier
* Unnormalized softmax is now a Softmax_v2 option
* Require thinc 8.0.14 and spacy-legacy 3.0.9
* Migrate regressions 1-1000
* Move serialize test to correct file
* Remove tests that won't work in v3
* Migrate regressions 1000-1500
Removed regression test 1250 because v3 doesn't support the old LEX
scheme anymore.
* Add missing imports in serializer tests
* Migrate tests 1500-2000
* Migrate regressions from 2000-2500
* Migrate regressions from 2501-3000
* Migrate regressions from 3000-3501
* Migrate regressions from 3501-4000
* Migrate regressions from 4001-4500
* Migrate regressions from 4501-5000
* Migrate regressions from 5001-5501
* Migrate regressions from 5501 to 7000
* Migrate regressions from 7001 to 8000
* Migrate remaining regression tests
* Fixing missing imports
* Update docs with new system [ci skip]
* Update CONTRIBUTING.md
- Fix formatting
- Update wording
* Remove lemmatizer tests in el lang
* Move a few tests into the general tokenizer
* Separate Doc and DocBin tests
* Add support for fasttext-bloom hash-only vectors
Overview:
* Extend `Vectors` to have two modes: `default` and `ngram`
* `default` is the default mode and equivalent to the current
`Vectors`
* `ngram` supports the hash-only ngram tables from `fasttext-bloom`
* Extend `spacy.StaticVectors.v2` to handle both modes with no changes
for `default` vectors
* Extend `spacy init vectors` to support ngram tables
The `ngram` mode **only** supports vector tables produced by this
fork of fastText, which adds an option to represent all vectors using
only the ngram buckets table and which uses the exact same ngram
generation algorithm and hash function (`MurmurHash3_x64_128`).
`fasttext-bloom` produces an additional `.hashvec` table, which can be
loaded by `spacy init vectors --fasttext-bloom-vectors`.
https://github.com/adrianeboyd/fastText/tree/feature/bloom
Implementation details:
* `Vectors` now includes the `StringStore` as `Vectors.strings` so that
the API can stay consistent for both `default` (which can look up from
`str` or `int`) and `ngram` (which requires `str` to calculate the
ngrams).
* In ngram mode `Vectors` uses a default `Vectors` object as a cache
since the ngram vectors lookups are relatively expensive.
* The default cache size is the same size as the provided ngram vector
table.
* Once the cache is full, no more entries are added. The user is
responsible for managing the cache in cases where the initial
documents are not representative of the texts.
* The cache can be resized by setting `Vectors.ngram_cache_size` or
cleared with `vectors._ngram_cache.clear()`.
* The API ends up a bit split between methods for `default` and for
`ngram`, so functions that only make sense for `default` or `ngram`
include warnings with custom messages suggesting alternatives where
possible.
* `Vocab.vectors` becomes a property so that the string stores can be
synced when assigning vectors to a vocab.
* `Vectors` serializes its own config settings as `vectors.cfg`.
* The `Vectors` serialization methods have added support for `exclude`
so that the `Vocab` can exclude the `Vectors` strings while serializing.
Removed:
* The `minn` and `maxn` options and related code from
`Vocab.get_vector`, which does not work in a meaningful way for default
vector tables.
* The unused `GlobalRegistry` in `Vectors`.
* Refactor to use reduce_mean
Refactor to use reduce_mean and remove the ngram vectors cache.
* Rename to floret
* Rename to floret in error messages
* Use --vectors-mode in CLI, vector init
* Fix vectors mode in init
* Remove unused var
* Minor API and docstrings adjustments
* Rename `--vectors-mode` to `--mode` in `init vectors` CLI
* Rename `Vectors.get_floret_vectors` to `Vectors.get_batch` and support
both modes.
* Minor updates to Vectors docstrings.
* Update API docs for Vectors and init vectors CLI
* Update types for StaticVectors
* 🚨 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>
* Pass excludes when serializing vocab
Additional minor bug fix:
* Deserialize vocab in `EntityLinker.from_disk`
* Add test for excluding strings on load
* Fix formatting
* Support a cfg field in transition system
* Make NER 'has gold' check use right alignment for span
* Pass 'negative_samples_key' property into NER transition system
* Add field for negative samples to NER transition system
* Check neg_key in NER has_gold
* Support negative examples in NER oracle
* Test for negative examples in NER
* Fix name of config variable in NER
* Remove vestiges of old-style partial annotation
* Remove obsolete tests
* Add comment noting lack of support for negative samples in parser
* Additions to "neg examples" PR (#8201)
* add custom error and test for deprecated format
* add test for unlearning an entity
* add break also for Begin's cost
* add negative_samples_key property on Parser
* rename
* extend docs & fix some older docs issues
* add subclass constructors, clean up tests, fix docs
* add flaky test with ValueError if gold parse was not found
* remove ValueError if n_gold == 0
* fix docstring
* Hack in environment variables to try out training
* Remove hack
* Remove NER hack, and support 'negative O' samples
* Fix O oracle
* Fix transition parser
* Remove 'not O' from oracle
* Fix NER oracle
* check for spans in both gold.ents and gold.spans and raise if so, to prevent memory access violation
* use set instead of list in consistency check
Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix tokenizer cache flushing
Fix/simplify tokenizer init detection in order to fix cache flushing
when properties are modified.
* Remove init reloading logic
* Remove logic disabling `_reload_special_cases` on init
* Setting `rules` last in `__init__` (as before) means that setting
other properties doesn't reload any special cases
* Reset `rules` first in `from_bytes` so that setting other properties
during deserialization doesn't reload any special cases
unnecessarily
* Reset all properties in `Tokenizer.from_bytes` to allow any settings
to be `None`
* Also reset special matcher when special cache is flushed
* Remove duplicate special case validation
* Add test for special cases flushing
* Extend test for tokenizer deserialization of None values
* Make vocab update in get_docs deterministic
The attribute `DocBin.strings` is a set. In `DocBin.get_docs`
a given vocab is updated by iterating over this set.
Iteration over a python set produces an arbitrary ordering,
therefore vocab is updated non-deterministically.
When training (fine-tuning) a spacy model, the base model's
vocabulary will be updated with the new vocabulary in the
training data in exactly the way described above. After
serialization, the file `model/vocab/strings.json` will
be sorted in an arbitrary way. This prevents reproducible
model training.
* Revert "Make vocab update in get_docs deterministic"
This reverts commit d6b87a2f55.
* Sort strings in StringStore serialization
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* initialize NLP with train corpus
* add more pretraining tests
* more tests
* function to fetch tok2vec layer for pretraining
* clarify parameter name
* test different objectives
* formatting
* fix check for static vectors when using vectors objective
* clarify docs
* logger statement
* fix init_tok2vec and proc.initialize order
* test training after pretraining
* add init_config tests for pretraining
* pop pretraining block to avoid config validation errors
* custom errors
* Override language defaults for null token and URL match
When the serialized `token_match` or `url_match` is `None`, override the
language defaults to preserve `None` on deserialization.
* Fix fixtures in tests
* Draft out initial Spans data structure
* Initial span group commit
* Basic span group support on Doc
* Basic test for span group
* Compile span_group.pyx
* Draft addition of SpanGroup to DocBin
* Add deserialization for SpanGroup
* Add tests for serializing SpanGroup
* Fix serialization of SpanGroup
* Add EdgeC and GraphC structs
* Add draft Graph data structure
* Compile graph
* More work on Graph
* Update GraphC
* Upd graph
* Fix walk functions
* Let Graph take nodes and edges on construction
* Fix walking and getting
* Add graph tests
* Fix import
* Add module with the SpanGroups dict thingy
* Update test
* Rename 'span_groups' attribute
* Try to fix c++11 compilation
* Fix test
* Update DocBin
* Try to fix compilation
* Try to fix graph
* Improve SpanGroup docstrings
* Add doc.spans to documentation
* Fix serialization
* Tidy up and add docs
* Update docs [ci skip]
* Add SpanGroup.has_overlap
* WIP updated Graph API
* Start testing new Graph API
* Update Graph tests
* Update Graph
* Add docstring
Co-authored-by: Ines Montani <ines@ines.io>
* multi-label textcat component
* formatting
* fix comment
* cleanup
* fix from #6481
* random edit to push the tests
* add explicit error when textcat is called with multi-label gold data
* fix error nr
* small fix
* Get basic beam tests working
* Get basic beam tests working
* Compile _beam_utils
* Remove prints
* Test beam density
* Beam parser seems to train
* Draft beam NER
* Upd beam
* Add hypothesis as dev dependency
* Implement missing is-gold-parse method
* Implement early update
* Fix state hashing
* Fix test
* Fix test
* Default to non-beam in parser constructor
* Improve oracle for beam
* Start refactoring beam
* Update test
* Refactor beam
* Update nn
* Refactor beam and weight by cost
* Update ner beam settings
* Update test
* Add __init__.pxd
* Upd test
* Fix test
* Upd test
* Fix test
* Remove ring buffer history from StateC
* WIP change arc-eager transitions
* Add state tests
* Support ternary sent start values
* Fix arc eager
* Fix NER
* Pass oracle cut size for beam
* Fix ner test
* Fix beam
* Improve StateC.clone
* Improve StateClass.borrow
* Work directly with StateC, not StateClass
* Remove print statements
* Fix state copy
* Improve state class
* Refactor parser oracles
* Fix arc eager oracle
* Fix arc eager oracle
* Use a vector to implement the stack
* Refactor state data structure
* Fix alignment of sent start
* Add get_aligned_sent_starts method
* Add test for ae oracle when bad sentence starts
* Fix sentence segment handling
* Avoid Reduce that inserts illegal sentence
* Update preset SBD test
* Fix test
* Remove prints
* Fix sent starts in Example
* Improve python API of StateClass
* Tweak comments and debug output of arc eager
* Upd test
* Fix state test
* Fix state test
* define new architectures for the pretraining objective
* add loss function as attr of the omdel
* cleanup
* cleanup
* shorten name
* fix typo
* remove unused error
* 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
Daniël de Kok