Commit Graph

530 Commits

Author SHA1 Message Date
Adriane Boyd
b841248589
Add Span index boundary checks (#5861)
* Add Span index boundary checks

* Return Span-specific IndexError in all cases

* Simplify and fix if/else
2020-08-04 13:35:25 +02:00
Adriane Boyd
a77c4c3465
Add strings and ENT_KB_ID to Doc serialization (#5691)
* Add strings for all writeable Token attributes to `Doc.to/from_bytes()`.
* Add ENT_KB_ID to default attributes.
2020-07-02 17:11:57 +02:00
Adriane Boyd
d94e961f14
Fix polarity of Token.is_oov and Lexeme.is_oov (#5634)
Fix `Token.is_oov` and `Lexeme.is_oov` so they return `True` when the
lexeme does **not** have a vector.
2020-06-23 13:29:51 +02:00
Adriane Boyd
e1b7cbd197 Remove MorphAnalysis __str__ and __repr__ 2020-05-29 14:33:47 +02:00
Adriane Boyd
71fe61fdcd Disallow merging 0-length spans 2020-05-22 10:14:34 +02:00
adrianeboyd
a5cd203284
Reduce stored lexemes data, move feats to lookups (#5238)
* Reduce stored lexemes data, move feats to lookups

* Move non-derivable lexemes features (`norm / cluster / prob`) to
`spacy-lookups-data` as lookups
  * Get/set `norm` in both lookups and `LexemeC`, serialize in lookups
  * Remove `cluster` and `prob` from `LexemesC`, get/set/serialize in
    lookups only
* Remove serialization of lexemes data as `vocab/lexemes.bin`
  * Remove `SerializedLexemeC`
  * Remove `Lexeme.to_bytes/from_bytes`
* Modify normalization exception loading:
  * Always create `Vocab.lookups` table `lexeme_norm` for
    normalization exceptions
  * Load base exceptions from `lang.norm_exceptions`, but load
    language-specific exceptions from lookups
  * Set `lex_attr_getter[NORM]` including new lookups table in
    `BaseDefaults.create_vocab()` and when deserializing `Vocab`
* Remove all cached lexemes when deserializing vocab to override
  existing normalizations with the new normalizations (as a replacement
  for the previous step that replaced all lexemes data with the
  deserialized data)

* Skip English normalization test

Skip English normalization test because the data is now in
`spacy-lookups-data`.

* Remove norm exceptions

Moved to spacy-lookups-data.

* Move norm exceptions test to spacy-lookups-data

* Load extra lookups from spacy-lookups-data lazily

Load extra lookups (currently for cluster and prob) lazily from the
entry point `lg_extra` as `Vocab.lookups_extra`.

* Skip creating lexeme cache on load

To improve model loading times, do not create the full lexeme cache when
loading. The lexemes will be created on demand when processing.

* Identify numeric values in Lexeme.set_attrs()

With the removal of a special case for `PROB`, also identify `float` to
avoid trying to convert it with the `StringStore`.

* Skip lexeme cache init in from_bytes

* Unskip and update lookups tests for python3.6+

* Update vocab pickle to include lookups_extra

* Update vocab serialization tests

Check strings rather than lexemes since lexemes aren't initialized
automatically, account for addition of "_SP".

* Re-skip lookups test because of python3.5

* Skip PROB/float values in Lexeme.set_attrs

* Convert is_oov from lexeme flag to lex in vectors

Instead of storing `is_oov` as a lexeme flag, `is_oov` reports whether
the lexeme has a vector.

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-05-19 15:59:14 +02:00
adrianeboyd
e63880e081
Use Token.sent_start for Span.sent (#5439)
Use `Token.sent_start` for sentence boundaries in `Span.sent` so that
`Doc.sents` and `Span.sent` return the same sentence boundaries.
2020-05-14 18:22:51 +02:00
Vishnu Priya VR
9ce059dd06
Limiting noun_chunks for specific languages (#5396)
* Limiting noun_chunks for specific langauges

* Limiting noun_chunks for specific languages

Contributor Agreement

* Addressing review comments

* Removed unused fixtures and imports

* Add fa_tokenizer in test suite

* Use fa_tokenizer in test

* Undo extraneous reformatting

Co-authored-by: adrianeboyd <adrianeboyd@gmail.com>
2020-05-14 12:58:06 +02:00
adrianeboyd
3f43c73d37
Normalize TokenC.sent_start values for Matcher (#5346)
Normalize TokenC.sent_start values to booleans for the `Matcher`.
2020-04-29 12:57:30 +02:00
Ines Montani
efec28ce70
Merge pull request #5367 from adrianeboyd/feature/simplify-warnings-v2 2020-04-29 12:55:37 +02:00
adrianeboyd
a6e521cd79
Add is_sent_end token property (#5375)
Reconstruction of the original PR #4697 by @MiniLau.

Removes unused `SENT_END` symbol and `IS_SENT_END` from `Matcher` schema
because the Matcher is only going to be able to support `IS_SENT_START`.
2020-04-29 12:53:16 +02:00
Adriane Boyd
bc39f97e11 Simplify warnings 2020-04-28 13:37:37 +02:00
adrianeboyd
f8ac5b9f56
bugfix in span similarity (#5155) (#5358)
* bugfix in span similarity

* also rewrite doc.pyx for clarity

* formatting

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2020-04-27 16:51:27 +02:00
svlandeg
1724a4f75b additional information if doc is empty 2020-03-09 18:08:18 +01:00
Sofie Van Landeghem
1a2b8fc264
set vector of merged entity (#5085)
* merge_entities sets the vector in the vocab for the merged token

* add unit test

* import unicode_literals

* move code to _merge function

* only set vector if vocab has non-zero vectors
2020-03-06 14:45:28 +01:00
adrianeboyd
9be90dbca3
Improve token head verification (#5079)
* Improve token head verification

Improve the verification for valid token heads when heads are set:

* in `Token.head`: heads come from the same document
* in `Doc.from_array()`: head indices are within the bounds of the
document

* Improve error message
2020-03-03 21:44:51 +01:00
adrianeboyd
d078b47c81
Break out of infinite loop as intended (#5077) 2020-03-03 12:29:05 +01:00
Sofie Van Landeghem
c6b12ab02a
Bugfix/get doc (#5049)
* new (broken) unit test

* fixing get_doc method
2020-03-02 11:49:28 +01:00
Ines Montani
4440a072d2
Merge pull request #5006 from svlandeg/bugfix/multiproc-underscore
load Underscore state when multiprocessing
2020-02-25 14:46:02 +01:00
Tom Keefe
ddf63b97a8
make idx available via to_array (#5030) 2020-02-22 14:13:06 +01:00
adrianeboyd
3b22eb651b
Sync Span __eq__ and __hash__ (#5005)
* Sync Span __eq__ and __hash__

Use the same tuple for `__eq__` and `__hash__`, including all attributes
except `vector` and `vector_norm`.

* Update entity comparison in tests

Update `assert_docs_equal()` test util to compare `Span` properties for
ents rather than `Span` objects.
2020-02-16 17:20:36 +01:00
adrianeboyd
5b102963bf
Require HEAD for is_parsed in Doc.from_array() (#5011)
Modify flag settings so that `DEP` is not sufficient to set `is_parsed`
and only run `set_children_from_heads()` if `HEAD` is provided.

Then the combination `[SENT_START, DEP]` will set deps and not clobber
sent starts with a lot of one-word sentences.
2020-02-16 17:17:09 +01:00
svlandeg
ecbb9c4b9f load Underscore state when multiprocessing 2020-02-12 11:50:42 +01:00
Sofie Van Landeghem
a1b22e90cd serialize ENT_ID (#4852)
* expand serialization test for custom token attribute

* add failing test for issue 4849

* define ENT_ID as attr and use in doc serialization

* fix few typos
2020-01-06 14:57:34 +01:00
Anastasiia Iurshina
1830a12578 Fixes typos (#4843)
* Fixes typos

* Fixes typo

* Contributor agreement
2019-12-29 14:24:13 +01:00
tamuhey
1707e77c5e add char_span to Span (#4793) 2019-12-13 15:54:58 +01:00
adrianeboyd
676e75838f Include Doc.cats in serialization of Doc and DocBin (#4774)
* Include Doc.cats in to_bytes()

* Include Doc.cats in DocBin serialization

* Add tests for serialization of cats

Test serialization of cats for Doc and DocBin.
2019-12-06 14:07:39 +01:00
adrianeboyd
2d8c6e1124 Iterate over lr_edges until sents are correct (#4702)
Iterate over lr_edges until all heads are within the current sentence.
Instead of iterating over them for a fixed number of iterations, check
whether the sentence boundaries are correct for the heads and stop when
all are correct. Stop after a maximum of 10 iterations, providing a
warning in this case since the sentence boundaries may not be correct.
2019-11-25 13:06:36 +01:00
adrianeboyd
91f89f9693 Fix realloc in retokenizer.split() (#4606)
Always realloc to a size larger than `doc.max_length` in
`retokenizer.split()` (or cymem will throw errors).
2019-11-11 16:26:46 +01:00
Ines Montani
a90025b277
Fix serialization of extension attr values in DocBin (#4540) 2019-10-28 16:02:13 +01:00
Ines Montani
6dd2832438 Use numpy.frombuffer instead of fromstring
Deprecation warning says we should do this
2019-10-24 16:18:41 +02:00
Sofie Van Landeghem
48886afc78 prevent zero-length mem alloc (#4429)
* raise specific error when removing a matcher rule that doesn't exist

* rephrasing

* goldparse init: allocate fields only if doc is not empty

* avoid zero length alloc in saving tokenizer cache

* avoid allocating zero length mem in matcher

* asserts to avoid allocating zero length mem

* fix zero-length allocation in matcher

* bump cymem version

* revert cymem version bump
2019-10-22 16:54:33 +02:00
Sofie Van Landeghem
4e7259c6cf Bugfix initializing DocBin with attributes (#4368)
* docbin init fix + documentation fix + unit tests

* newline

* try with zlib instead of gzip (python 2 incompatibilities)
2019-10-03 14:48:45 +02:00
Ines Montani
f7d1736241 Skip duplicate spans in Doc.retokenize (#4339) 2019-09-30 12:43:48 +02:00
Matthew Honnibal
46c02d25b1 Merge changes to test_ner 2019-09-18 21:41:24 +02:00
Sofie Van Landeghem
de5a9ecdf3 Distinction between outside, missing and blocked NER annotations (#4307)
* remove duplicate unit test

* unit test (currently failing) for issue 4267

* bugfix: ensure doc.ents preserves kb_id annotations

* fix in setting doc.ents with empty label

* rename

* test for presetting an entity to a certain type

* allow overwriting Outside + blocking presets

* fix actions when previous label needs to be kept

* fix default ent_iob in set entities

* cleaner solution with U- action

* remove debugging print statements

* unit tests with explicit transitions and is_valid testing

* remove U- from move_names explicitly

* remove unit tests with pre-trained models that don't work

* remove (working) unit tests with pre-trained models

* clean up unit tests

* move unit tests

* small fixes

* remove two TODO's from doc.ents comments
2019-09-18 21:37:17 +02:00
Moshe Hazoom
72463b062f Improve speed of _merge method (#4300)
* make merge more efficient

* fix offsets

* merge works with relative indices

* remove printing

* Add the SCA

* fix SCA date

* more cythonize _retokenize.pyx

* more cythonize _retokenize.pyx

* fix only declaration in _retokenize.pyx

* switch back to absolute head

* switch back to absolute head

* fix comment

* merge from origin repo
2019-09-18 21:34:34 +02:00
Ines Montani
dd1810f05a Update DocBin and add docs 2019-09-18 20:23:21 +02:00
Ines Montani
0f7fe5e7a7 Auto-format and fix typo and consistency 2019-09-18 19:18:30 +02:00
Matthew Honnibal
e53b86751f DocPallet -> DocBin 2019-09-18 15:15:37 +02:00
Matthew Honnibal
fa9a283128 Fix name 2019-09-18 13:40:03 +02:00
Matthew Honnibal
88a23cf49a Fix name 2019-09-18 13:38:29 +02:00
Matthew Honnibal
3507943b15 Add docstring for DocPallet 2019-09-18 13:25:47 +02:00
Matthew Honnibal
1c8de6b2e5 Rename DocBox->DocPallet 2019-09-18 13:13:51 +02:00
Matthew Honnibal
84c65f9455 Merge branch 'master' into develop 2019-09-16 22:12:20 +02:00
Matthew Honnibal
47055d5988 Fix type declarations in _merge method 2019-09-16 22:10:13 +02:00
Sofie Van Landeghem
03ac29f437 Ensure that doc.ents preserves kb_id annotations (#4294)
* bugfix: ensure doc.ents preserves kb_id annotations

* fix backward compatibility

* additional test
2019-09-16 15:18:37 +02:00
Ines Montani
bab9976d9a
💫 Adjust Table API and add docs (#4289)
* Adjust Table API and add docs

* Add attributes and update description [ci skip]

* Use strings.get_string_id instead of hash_string

* Fix table method calls

* Make orth arg in Lemmatizer.lookup optional

Fall back to string, which is now handled by Table.__contains__ out-of-the-box

* Fix method name

* Auto-format
2019-09-15 22:08:13 +02:00
Ines Montani
3c3658ef9f Merge branch 'master' into develop 2019-09-12 18:03:01 +02:00
Paul O'Leary McCann
7d8df69158 Bloom-filter backed Lookup Tables (#4268)
* Improve load_language_data helper

* WIP: Add Lookups implementation

* Start moving lemma data over to JSON

* WIP: move data over for more languages

* Convert more languages

* Fix lemmatizer fixtures in tests

* Finish conversion

* Auto-format JSON files

* Fix test for now

* Make sure tables are stored on instance

* Update docstrings

* Update docstrings and errors

* Update test

* Add Lookups.__len__

* Add serialization methods

* Add Lookups.remove_table

* Use msgpack for serialization to disk

* Fix file exists check

* Try using OrderedDict for everything

* Update .flake8 [ci skip]

* Try fixing serialization

* Update test_lookups.py

* Update test_serialize_vocab_strings.py

* Lookups / Tables now work

This implements the stubs in the Lookups/Table classes. Currently this
is in Cython but with no type declarations, so that could be improved.

* Add lookups to setup.py

* Actually add lookups pyx

The previous commit added the old py file...

* Lookups work-in-progress

* Move from pyx back to py

* Add string based lookups, fix serialization

* Update tests, language/lemmatizer to work with string lookups

There are some outstanding issues here:

- a pickling-related test fails due to the bloom filter
- some custom lemmatizers (fr/nl at least) have issues

More generally, there's a question of how to deal with the case where
you have a string but want to use the lookup table. Currently the table
allows access by string or id, but that's getting pretty awkward.

* Change lemmatizer lookup method to pass (orth, string)

* Fix token lookup

* Fix French lookup

* Fix lt lemmatizer test

* Fix Dutch lemmatizer

* Fix lemmatizer lookup test

This was using a normal dict instead of a Table, so checks for the
string instead of an integer key failed.

* Make uk/nl/ru lemmatizer lookup methods consistent

The mentioned tokenizers all have their own implementation of the
`lookup` method, which accesses a `Lookups` table. The way that was
called in `token.pyx` was changed so this should be updated to have the
same arguments as `lookup` in `lemmatizer.py` (specificially (orth/id,
string)).

Prior to this change tests weren't failing, but there would probably be
issues with normal use of a model. More tests should proably be added.

Additionally, the language-specific `lookup` implementations seem like
they might not be needed, since they handle things like lower-casing
that aren't actually language specific.

* Make recently added Greek method compatible

* Remove redundant class/method

Leftovers from a merge not cleaned up adequately.
2019-09-12 17:26:11 +02:00