Commit Graph

498 Commits

Author SHA1 Message Date
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
Sofie Van Landeghem
9be4d1c105 Allow copying of user_data in as_doc (#4282)
* Allow copying the user_data with as_doc + unit test

* add option to docs

* add typing

* import fix

* workaround to avoid bool clashing ...

* bint instead of bool
2019-09-12 17:08:14 +02:00
Matthew Honnibal
7d782aa97b Add more docstrings for MorphAnalysis 2019-09-12 16:48:30 +02:00
Matthew Honnibal
1a65c5b7af Update develop from master 2019-09-08 18:21:41 +02:00
adrianeboyd
aec755d3a3 Modify retokenizer to use span root attributes (#4219)
* Modify retokenizer to use span root attributes

* tag/pos/morph are set to root tag/pos/morph

* lemma and norm are reset and end up as orth (not ideal, but better
than orth of first token)

* Also handle individual merge case

* Add test

* Attempt to handle ent_iob and ent_type in merges

* Fix check for whether B-ENT should become I-ENT

* Move IOB consistency check to after attrs

Move all IOB consistency checks after attrs are set and simplify to
check entire document, modifying I to B at the beginning of the document
or if the entity type of the previous token isn't the same.

* Move IOB consistency check for single merge

Move IOB consistency check after the token array is compressed for the
single merge case.

* Update spacy/tokens/_retokenize.pyx

Co-Authored-By: Matthew Honnibal <honnibal+gh@gmail.com>

* Remove single vs. multiple merge distinction

Remove original single-instance `_merge()` and use `_bulk_merge()` (now
renamed `_merge()`) for all merges.

* Add out-of-bound check in previous entity check
2019-09-08 13:04:49 +02:00
Matthew Honnibal
c308cf3e3e
Merge branch 'master' into feature/lemmatizer 2019-08-25 13:52:27 +02:00
Sofie Van Landeghem
73b38c33e4 Small retokenizer fix (#4174) 2019-08-22 12:23:54 +02:00
Sofie Van Landeghem
01c5980187 Serialize POS attribute when doc.is_tagged (#4092)
* fix and unit test for issue 3959

* additional unit test for manifestation of the same (resolved) bug
2019-08-21 21:59:30 +02:00
Matthew Honnibal
bcd08f20af Merge changes from master 2019-08-21 14:18:52 +02:00
Sofie Van Landeghem
0ba1b5eebc CLI scripts for entity linking (wikipedia & generic) (#4091)
* document token ent_kb_id

* document span kb_id

* update pipeline documentation

* prior and context weights as bool's instead

* entitylinker api documentation

* drop for both models

* finish entitylinker documentation

* small fixes

* documentation for KB

* candidate documentation

* links to api pages in code

* small fix

* frequency examples as counts for consistency

* consistent documentation about tensors returned by predict

* add entity linking to usage 101

* add entity linking infobox and KB section to 101

* entity-linking in linguistic features

* small typo corrections

* training example and docs for entity_linker

* predefined nlp and kb

* revert back to similarity encodings for simplicity (for now)

* set prior probabilities to 0 when excluded

* code clean up

* bugfix: deleting kb ID from tokens when entities were removed

* refactor train el example to use either model or vocab

* pretrain_kb example for example kb generation

* add to training docs for KB + EL example scripts

* small fixes

* error numbering

* ensure the language of vocab and nlp stay consistent across serialization

* equality with =

* avoid conflict in errors file

* add error 151

* final adjustements to the train scripts - consistency

* update of goldparse documentation

* small corrections

* push commit

* turn kb_creator into CLI script (wip)

* proper parameters for training entity vectors

* wikidata pipeline split up into two executable scripts

* remove context_width

* move wikidata scripts in bin directory, remove old dummy script

* refine KB script with logs and preprocessing options

* small edits

* small improvements to logging of EL CLI script
2019-08-13 15:38:59 +02:00
Sofie Van Landeghem
963ea5e8d0 Update lemma and vector information after splitting a token (#4097)
* fixing vector and lemma attributes after retokenizer.split

* fixing unit test with mockup tensor

* xp instead of numpy
2019-08-08 15:09:44 +02:00
Sofie Van Landeghem
ad09b0d6f3 fetch norm from lex if necessary for matching (#4080) 2019-08-05 23:51:04 +02:00
Matthew Honnibal
944a66c326 Add span.tensor and token.tensor attributes 2019-08-01 18:30:50 +02:00
Ines Montani
d5bce35fb1 Fix bug in Span.similarity when called via hook 2019-07-27 15:33:27 +02:00
Ines Montani
109b5e1798 Fix bug in Token.similarity when called via hook 2019-07-27 15:26:01 +02:00
Sofie Van Landeghem
ba02957c80 Fix dependency copy for as_doc (#3969)
* failing unit test for issue 3962

* attempt to fix Issue #3962

* create artificial unit test example

* using length instead of self.length

* sp

* reformat with black

* find better ancestor within span and use generic 'dep'

* attach to span.root if there is no appropriate ancestor

* comment span text

* clean up ancestor code

* reconstruct dep tree to keep same number of sentences
2019-07-23 18:28:54 +02:00
Ines Montani
673c864a06
Fix doc.count_by functionality (#3950)
Fix doc.count_by functionality
2019-07-11 13:44:00 +02:00
svlandeg
349107daa3 cleanup 2019-07-11 13:09:22 +02:00
svlandeg
0f0f07318a counter instead of preshcounter 2019-07-11 13:05:53 +02:00
Matthew Honnibal
0491a8e7c8 Reformat 2019-07-11 11:49:36 +02:00
Matthew Honnibal
bd3c3f342b Fix _serialize 2019-07-11 11:48:55 +02:00
svlandeg
e080412385 tracked the bug down to PreshCounter.inc - still unclear what goes wrong 2019-07-11 01:53:06 +02:00
Matthew Honnibal
b94c5443d9 Rename Binder->DocBox, and improve it. 2019-07-10 19:37:20 +02:00
Matthew Honnibal
3d18600c05 Return True from doc.is_... when no ambiguity
* Make doc.is_sentenced return True if len(doc) < 2.

* Make doc.is_nered return True if len(doc) == 0, for consistency.

Closes #3934
2019-07-10 19:21:42 +02:00
Ines Montani
6ba5ddbd5f
Merge pull request #3864 from svlandeg/feature/nel-wiki
Entity linking using Wikipedia & Wikidata
2019-07-10 11:25:41 +02:00
Björn Böing
205c73a589 Update tokenizer and doc init example (#3939)
* Fix Doc.to_json hyperlink

* Update tokenizer and doc init examples

* Change "matchin rules" to "punctuation rules"

* Auto-format
2019-07-10 10:16:48 +02:00
svlandeg
8608685543 ensure Span.as_doc keeps the entity links + unit test 2019-06-25 15:28:51 +02:00
Ines Montani
8baff1c7c0
💫 Improve introspection of custom extension attributes (#3729)
* Add custom __dir__ to Underscore (see #3707)

* Make sure custom extension methods keep their docstrings (see #3707)

* Improve tests

* Prepend note on partial to docstring (see #3707)

* Remove print statement

* Handle cases where docstring is None
2019-05-12 00:53:11 +02:00
Sofie
a4a6bfa4e1
Merge branch 'master' into feature/el-framework 2019-03-26 11:00:02 +01:00
Ines Montani
06bf130890 💫 Add better and serializable sentencizer (#3471)
* Add better serializable sentencizer component

* Replace default factory

* Add tests

* Tidy up

* Pass test

* Update docs
2019-03-23 15:45:02 +01:00
svlandeg
5b1cd49222 error msg and unit tests for setting kb_id on span 2019-03-22 12:05:35 +01:00
svlandeg
feb71e15fd hash the entity name 2019-03-22 11:36:44 +01:00
svlandeg
735fc2a735 annotate kb_id through ents in doc 2019-03-22 11:36:44 +01:00