Commit Graph

263 Commits

Author SHA1 Message Date
Adriane Boyd
b927893309
Merge branch 'develop' into feature/dependency-matcher-v3 2020-09-04 13:03:30 +02:00
Ines Montani
ab1bb421ed Update docs links in codebase 2020-09-04 12:58:50 +02:00
Ines Montani
595f9dc2e4 Make displacy color registry consistent with others
This was the only registry that expected the registered objects to be dictionaries instead of functions that return something. We can still support plain dicts but we should also support functions for consistency
2020-09-03 23:05:41 +02:00
Adriane Boyd
960d9cfadc Officially support DependencyMatcher
Add official support for the `DependencyMatcher`. Redesign the pattern
specification. Fix and extend operator implementations. Update API docs
and add usage docs.

Patterns
--------

Refactor pattern structure to:

```
{
  "LEFT_ID": str,
  "REL_OP": str,
  "RIGHT_ID": str,
  "RIGHT_ATTRS": dict,
}
```

The first node contains only `RIGHT_ID` and `RIGHT_ATTRS` and all
subsequent nodes contain all four keys.

New operators
-------------

Because of the way patterns are constructed from left to right, it's
helpful to have `follows` operators along with `precedes` operators. Add
operators for simple precedes / follows alongside immediate precedes /
follows.

* `.*`: precedes
* `;`: immediately follows
* `;*`: follows

Operator fixes
--------------

* `<` and `<<` do not include the node itself
* Fix reversed order for all operators involving linear precedence (`.`,
  all sibling operators)
* Linear precedence operators do not match nodes outside the same parse

Additional fixes
----------------

* Use v3 Matcher API
* Support `get` and `remove`
* Support pickling
2020-09-02 17:45:29 +02:00
Adriane Boyd
9130094199
Prevent Tagger model init with 0 labels (#5984)
* Prevent Tagger model init with 0 labels

Raise an error before trying to initialize a tagger model with 0 labels.

* Add dummy tagger label for test

* Remove tagless tagger model initializiation

* Fix error number after merge

* Add dummy tagger label to test

* Fix formatting

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-31 21:24:33 +02:00
Ines Montani
add9de5487 Deprecate (Phrase)Matcher.pipe 2020-08-31 17:01:24 +02:00
Adriane Boyd
216efaf5f5 Restrict tokenizer exceptions to ORTH and NORM 2020-08-31 09:55:01 +02:00
Ines Montani
45f46a5c85
Merge pull request #5993 from explosion/feature/disabled-components 2020-08-29 15:58:41 +02:00
Ines Montani
34146750d4 Use frozen list with custom errors
We don't want to break backwards compatibility too much but we also want to provide the best possible UX
2020-08-29 15:20:11 +02:00
Ines Montani
10da74382f Raise if disabled components are removed before DisabledPipes.restore 2020-08-28 20:35:26 +02:00
Ines Montani
cad988da7f Allow component decorators to re-run with same function 2020-08-28 16:27:22 +02:00
Matthew Honnibal
2d520d3b45 Remove unused error 2020-08-26 15:41:14 +02:00
Sofie Van Landeghem
358cbb21e3
Define candidate generator in EL config (#5876)
* candidate generator as separate part of EL config

* update comment

* ent instead of str as input for candidate generation

* Span instead of str: correct type indication

* fix types

* unit test to create new candidate generator

* fix replace_pipe argument passing

* move error message, general cleanup

* add vocab back to KB constructor

* provide KB as callable from Vocab arg

* rename to kb_loader, fix KB serialization as part of the EL pipe

* fix typo

* reformatting

* cleanup

* fix comment

* fix wrongly duplicated code from merge conflict

* rename dump to to_disk

* from_disk instead of load_bulk

* update test after recent removal of set_morphology in tagger

* remove old doc
2020-08-18 16:10:36 +02:00
Sofie Van Landeghem
688e77562b
Train CLI script fixes (#5931)
* fix dash replacement in overrides arguments

* perform interpolation on training config

* make sure only .spacy files are read
2020-08-18 16:06:37 +02:00
Ines Montani
db2dbc8e59 Remove unused warning 2020-08-14 14:58:03 +02:00
Ines Montani
950832f087
Tidy up pipes (#5906)
* Tidy up pipes

* Fix init, defaults and raise custom errors

* Update docs

* Update docs [ci skip]

* Apply suggestions from code review

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>

* Tidy up error handling and validation, fix consistency

* Simplify get_examples check

* Remove unused import [ci skip]

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-11 23:29:31 +02:00
Adriane Boyd
e962784531
Add Lemmatizer and simplify related components (#5848)
* Add Lemmatizer and simplify related components

* Add `Lemmatizer` pipe with `lookup` and `rule` modes using the
`Lookups` tables.
* Reduce `Tagger` to a simple tagger that sets `Token.tag` (no pos or lemma)
* Reduce `Morphology` to only keep track of morph tags (no tag map, lemmatizer,
or morph rules)
* Remove lemmatizer from `Vocab`
* Adjust many many tests

Differences:

* No default lookup lemmas
* No special treatment of TAG in `from_array` and similar required
* Easier to modify labels in a `Tagger`
* No extra strings added from morphology / tag map

* Fix test

* Initial fix for Lemmatizer config/serialization

* Adjust init test to be more generic

* Adjust init test to force empty Lookups

* Add simple cache to rule-based lemmatizer

* Convert language-specific lemmatizers

Convert language-specific lemmatizers to component lemmatizers. Remove
previous lemmatizer class.

* Fix French and Polish lemmatizers

* Remove outdated UPOS conversions

* Update Russian lemmatizer init in tests

* Add minimal init/run tests for custom lemmatizers

* Add option to overwrite existing lemmas

* Update mode setting, lookup loading, and caching

* Make `mode` an immutable property
* Only enforce strict `load_lookups` for known supported modes
* Move caching into individual `_lemmatize` methods

* Implement strict when lang is not found in lookups

* Fix tables/lookups in make_lemmatizer

* Reallow provided lookups and allow for stricter checks

* Add lookups asset to all Lemmatizer pipe tests

* Rename lookups in lemmatizer init test

* Clean up merge

* Refactor lookup table loading

* Add helper from `load_lemmatizer_lookups` that loads required and
optional lookups tables based on settings provided by a config.

Additional slight refactor of lookups:

* Add `Lookups.set_table` to set a table from a provided `Table`
* Reorder class definitions to be able to specify type as `Table`

* Move registry assets into test methods

* Refactor lookups tables config

Use class methods within `Lemmatizer` to provide the config for
particular modes and to load the lookups from a config.

* Add pipe and score to lemmatizer

* Simplify Tagger.score

* Add missing import

* Clean up imports and auto-format

* Remove unused kwarg

* Tidy up and auto-format

* Update docstrings for Lemmatizer

Update docstrings for Lemmatizer.

Additionally modify `is_base_form` API to take `Token` instead of
individual features.

* Update docstrings

* Remove tag map values from Tagger.add_label

* Update API docs

* Fix relative link in Lemmatizer API docs
2020-08-07 15:27:13 +02:00
svlandeg
0b4d1e1bc4 'debug data' instead of 'debug-data' 2020-08-06 15:47:31 +02:00
Ines Montani
0881455a5d Update error message 2020-08-05 23:15:05 +02:00
Ines Montani
2a1fa86a0d Add better error for failed model shortcut loading 2020-08-05 23:10:29 +02:00
Ines Montani
823e533dc1
Add config callbacks for modifying nlp object before and after init (#5866)
* WIP: Concept for modifying nlp object before and after init

* Make callbacks return nlp object

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>

* Raise if callbacks don't return correct type

* Rename, update types, add after_pipeline_creation

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-05 19:47:54 +02:00
Adriane Boyd
4193402c47
Add warning when Matcher subpattern is discarded (#5873)
* Add a warning when a subpattern is not processed and discarded

* Normalize subpattern attribute/operator keys to upper case like
top-level attributes
2020-08-05 14:56:14 +02:00
Ines Montani
b795f02fbd
Allow adding pipeline components from source model (#5857)
* Allow adding pipeline components from source model

* Config: name -> component

* Improve error messages

* Fix error and test

* Add frozen components and exclude logic

* Remove exclude from Language.evaluate

* Init sourced components with current vocab

* Fix error codes
2020-08-04 23:39:19 +02:00
Adriane Boyd
fa79a0db9f
Add AttributeRuler for token attribute exceptions (#5842)
* Add AttributeRuler for token attribute exceptions

Add the `AttributeRuler` to handle exceptions for token-level
attributes. The `AttributeRuler` uses `Matcher` patterns to identify
target spans and applies the specified attributes to the token at the
provided index in the matched span. A negative index can be used to
index from the end of the matched span. The retokenizer is used to
"merge" the individual tokens and assign them the provided attributes.

Helper functions can import existing tag maps and morph rules to the
corresponding `Matcher` patterns.

There is an additional minor bug fix for `MORPH` attributes in the
retokenizer to correctly normalize the values and to handle `MORPH`
alongside `_` in an attrs dict.

* Fix default name

* Update name in error message

* Extend AttributeRuler functionality

* Add option to initialize with a dict of AttributeRuler patterns

* Instead of silently discarding overlapping matches (the default
behavior for the retokenizer if only the attrs differ), split the
matches into disjoint sets and retokenize each set separately. This
allows, for instance, one pattern to set the POS and another pattern to
set the lemma. (If two matches modify the same attribute, it looks like
the attrs are applied in the order they were added, but it may not be
deterministic?)

* Improve types

* Sort spans before processing

* Fix index boundaries in Span

* Refactor retokenizer to separate attrs methods

Add top-level `normalize_token_attrs` and `set_token_attrs` methods.

* Update AttributeRuler to use refactored methods

Update `AttributeRuler` to replace use of full retokenizer with only the
relevant methods for normalizing and setting attributes for a single
token.

* Update spacy/pipeline/attributeruler.py

Co-authored-by: Ines Montani <ines@ines.io>

* Make API more similar to EntityRuler

* Add `AttributeRuler.add_patterns` to add patterns from a list of dicts
* Return list of dicts as property `AttributeRuler.patterns`

* Make attrs_unnormed private

* Add test loading patterns from assets

* Revert "Fix index boundaries in Span"

This reverts commit 8f8a5c3386.

* Add Span index boundary checks (#5861)

* Add Span index boundary checks

* Return Span-specific IndexError in all cases

* Simplify and fix if/else

Co-authored-by: Ines Montani <ines@ines.io>
2020-08-04 17:02:39 +02:00
Sofie Van Landeghem
492d1ec5de
Prevent alignment when texts don't match (#5867)
* remove empty gold.pyx

* add alignment unit test (to be used in docs)

* ensure that Alignment is only used on equal texts

* additional test using example.alignment

* formatting

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-04 16:29:18 +02:00
Sofie Van Landeghem
82347110f5
Default empty KB in EL component (#5872)
* EL field documentation

* documentation consistent with docs

* default empty KB, initialize vocab separately

* formatting

* add test for changing the default entity vector length

* update comment
2020-08-04 14:34:09 +02:00
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
Ines Montani
b40f44419b Simplify pipe analysis
- remove unused code
- don't print by default
- integrate attrs info into analysis output
2020-08-01 13:40:06 +02:00
Sofie Van Landeghem
40c995b1be
Option for returning only greedy matches (#5771)
* add "greedy" option for match pattern

* distinction between greedy FIRST or LONGEST

* check for proper values, throw custom warning otherwise

* unxfail one more test

* add comment in docstring

* add test that LONGEST also prefers first match if equal length

* use c arrays for more efficient processing

* rename 'greediness' to 'greedy'
2020-07-29 11:04:43 +02:00
Ines Montani
ba22111ff4 Move error to Errors 2020-07-28 16:24:14 +02:00
svlandeg
61068e0fb1 util function dot_to_object and corresponding unit test 2020-07-27 17:50:12 +02:00
Ines Montani
e92df281ce Tidy up, autoformat, add types 2020-07-25 15:01:15 +02:00
Ines Montani
c003d26b94 Tidy up 2020-07-25 12:21:37 +02:00
Ines Montani
b9aaa4e457 Improve vocab data integration and warning 2020-07-25 11:51:30 +02:00
Ines Montani
14d7d46f89 Merge branch 'develop' into feature/language-data-config 2020-07-22 22:18:53 +02:00
Ines Montani
d0c6d1efc5
@factories -> factory (#5801) 2020-07-22 17:29:31 +02:00
Adriane Boyd
038ff1a811
Improve warnings around normalization tables (#5794)
Provide more customized normalization table warnings when training a new
model. Only suggest installing `spacy-lookups-data` if it's not already
installed and it includes a table for this language (currently checked
in a hard-coded list).
2020-07-22 16:04:58 +02:00
Ines Montani
945f795a3e WIP: move more language data to config 2020-07-22 15:59:37 +02:00
Ines Montani
43b960c01b
Refactor pipeline components, config and language data (#5759)
* Update with WIP

* Update with WIP

* Update with pipeline serialization

* Update types and pipe factories

* Add deep merge, tidy up and add tests

* Fix pipe creation from config

* Don't validate default configs on load

* Update spacy/language.py

Co-authored-by: Ines Montani <ines@ines.io>

* Adjust factory/component meta error

* Clean up factory args and remove defaults

* Add test for failing empty dict defaults

* Update pipeline handling and methods

* provide KB as registry function instead of as object

* small change in test to make functionality more clear

* update example script for EL configuration

* Fix typo

* Simplify test

* Simplify test

* splitting pipes.pyx into separate files

* moving default configs to each component file

* fix batch_size type

* removing default values from component constructors where possible (TODO: test 4725)

* skip instead of xfail

* Add test for config -> nlp with multiple instances

* pipeline.pipes -> pipeline.pipe

* Tidy up, document, remove kwargs

* small cleanup/generalization for Tok2VecListener

* use DEFAULT_UPSTREAM field

* revert to avoid circular imports

* Fix tests

* Replace deprecated arg

* Make model dirs require config

* fix pickling of keyword-only arguments in constructor

* WIP: clean up and integrate full config

* Add helper to handle function args more reliably

Now also includes keyword-only args

* Fix config composition and serialization

* Improve config debugging and add visual diff

* Remove unused defaults and fix type

* Remove pipeline and factories from meta

* Update spacy/default_config.cfg

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Update spacy/default_config.cfg

* small UX edits

* avoid printing stack trace for debug CLI commands

* Add support for language-specific factories

* specify the section of the config which holds the model to debug

* WIP: add Language.from_config

* Update with language data refactor WIP

* Auto-format

* Add backwards-compat handling for Language.factories

* Update morphologizer.pyx

* Fix morphologizer

* Update and simplify lemmatizers

* Fix Japanese tests

* Port over tagger changes

* Fix Chinese and tests

* Update to latest Thinc

* WIP: xfail first Russian lemmatizer test

* Fix component-specific overrides

* fix nO for output layers in debug_model

* Fix default value

* Fix tests and don't pass objects in config

* Fix deep merging

* Fix lemma lookup data registry

Only load the lookups if an entry is available in the registry (and if spacy-lookups-data is installed)

* Add types

* Add Vocab.from_config

* Fix typo

* Fix tests

* Make config copying more elegant

* Fix pipe analysis

* Fix lemmatizers and is_base_form

* WIP: move language defaults to config

* Fix morphology type

* Fix vocab

* Remove comment

* Update to latest Thinc

* Add morph rules to config

* Tidy up

* Remove set_morphology option from tagger factory

* Hack use_gpu

* Move [pipeline] to top-level block and make [nlp.pipeline] list

Allows separating component blocks from component order – otherwise, ordering the config would mean a changed component order, which is bad. Also allows initial config to define more components and not use all of them

* Fix use_gpu and resume in CLI

* Auto-format

* Remove resume from config

* Fix formatting and error

* [pipeline] -> [components]

* Fix types

* Fix tagger test: requires set_morphology?

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-07-22 13:42:59 +02:00
Sofie Van Landeghem
c9da9605f7
Test suite clean up (#5781)
* step_through tests: skip instead of xfail

* test_empty_doc should be fixed with new Thinc version

* remove outdated test (there are other misaligned tests now)

* xfail reason

* fix test according to french exceptions

* clarified some skipped tests

* skip ukranian test instead of xfail

* skip instead of xfail

* skip + reason instead of xfail

* removed obsolete tests referring to removed "set_frozen" functionality

* fix test 999

* remove unused AlignmentError

* remove xfail where possible, skip otherwise

* increment thinc release for empty_doc test
2020-07-20 14:49:54 +02:00
Adriane Boyd
39ebcd9ec9
Refactor Chinese tokenizer configuration (#5736)
* Refactor Chinese tokenizer configuration

Refactor `ChineseTokenizer` configuration so that it uses a single
`segmenter` setting to choose between character segmentation, jieba, and
pkuseg.

* replace `use_jieba`, `use_pkuseg`, `require_pkuseg` with the setting
`segmenter` with the supported values: `char`, `jieba`, `pkuseg`
* make the default segmenter plain character segmentation `char` (no
additional libraries required)

* Fix Chinese serialization test to use char default

* Warn if attempting to customize other segmenter

Add a warning if `Chinese.pkuseg_update_user_dict` is called when
another segmenter is selected.
2020-07-19 13:34:37 +02:00
Adriane Boyd
5228920e2f
Clarify warning W030 for misaligned BILUO tags (#5761) 2020-07-14 14:09:48 +02:00
Ines Montani
5f6f4ff594 Remove object subclassing 2020-07-12 14:03:23 +02:00
Sofie Van Landeghem
dd207a28be
cleanup components API (#5726)
* add keyword separator for update functions and drop unused "state"

* few more Example tests and various small fixes

* consistently return losses after update call

* eliminate unused tensors field across pipe components

* fix name

* fix arg name
2020-07-09 19:43:39 +02:00
Sofie Van Landeghem
a39a110c4e
Few more Example unit tests (#5720)
* small fixes in Example, UX

* add gold tests for aligned_spans and get_aligned_parse

* sentencizer unnecessary
2020-07-07 18:46:00 +02:00
Ines Montani
412dbb1f38
Remove dead and/or deprecated code (#5710)
* Remove dead and/or deprecated code

* Remove n_threads

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-07-06 13:06:25 +02:00
Sofie Van Landeghem
fcbf899b08
Feature/example only (#5707)
* remove _convert_examples

* fix test_gold, raise TypeError if tuples are used instead of Example's

* throwing proper errors when the wrong type of objects are passed

* fix deprectated format in tests

* fix deprectated format in parser tests

* fix tests for NEL, morph, senter, tagger, textcat

* update regression tests with new Example format

* use make_doc

* more fixes to nlp.update calls

* few more small fixes for rehearse and evaluate

* only import ml_datasets if really necessary
2020-07-06 13:02:36 +02:00
Jan Jessewitsch
e4dcac4a4b
Merging multiple docs into one (#5032)
* Add static method to Doc to allow merging of multiple docs.

* Add error description for the error that occurs if docs with different
vocabs (from different languages) are merged in Doc.from_docs().

* Add test for Doc.from_docs() implementation.

* Fix using numpy's concatenate in Doc.from_docs.

* Replace typing's type annotations in from_docs.

* Simply remove type annotations in from_docs.

* Add documentation for Doc.from_docs to api.

* Simplify from_docs, its test and the api doc for codebase consistency.

* Fix merging of Doc objects that end with whitespaces (Achieved by simply not setting the SPACY attribute on whitespace tokens). Remove two unnecessary imports of attributes.

* Add merging of user data from Doc objects in from_docs. Add user data test case to corresponding test. Add applicable warning messages.

* Fix incorrect setting of tokens idx by using concatenated spaces (again). Add test case to corresponding test.

* Add MORPH to attrs

* Update warnings calls

* Remove out-dated error from merge

* Rename space_delimiter to ensure_whitespace

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2020-07-03 11:32:42 +02:00
svlandeg
04ed4d60a8 raise error when links are not aligned to tokens 2020-07-02 13:57:35 +02:00
svlandeg
f503817623 fix parsing entity links in new gold format 2020-07-02 13:48:11 +02:00
svlandeg
60f97bc519 add custom warning when run_command fails 2020-06-30 17:28:43 +02:00
svlandeg
ff233d5743 print details on error msg (e.g. PermissionError on specific file) 2020-06-29 18:22:33 +02:00
svlandeg
894b8e7ff6 throw warning (instead of crashing) when temp dir can't be cleaned 2020-06-29 18:16:39 +02:00
Sofie Van Landeghem
8d3c0306e1
refactor fixes (#5664)
* fixes in ud_train, UX for morphs

* update pyproject with new version of thinc

* fixes in debug_data script

* cleanup of old unused error messages

* remove obsolete TempErrors

* move error messages to errors.py

* add ENT_KB_ID to default DocBin serialization

* few fixes to simple_ner

* fix tags
2020-06-29 14:33:00 +02:00
Matthew Honnibal
8c29268749
Improve spacy.gold (no GoldParse, no json format!) (#5555)
* Update errors

* Remove beam for now (maybe)

Remove beam_utils

Update setup.py

Remove beam

* Remove GoldParse

WIP on removing goldparse

Get ArcEager compiling after GoldParse excise

Update setup.py

Get spacy.syntax compiling after removing GoldParse

Rename NewExample -> Example and clean up

Clean html files

Start updating tests

Update Morphologizer

* fix error numbers

* fix merge conflict

* informative error when calling to_array with wrong field

* fix error catching

* fixing language and scoring tests

* start testing get_aligned

* additional tests for new get_aligned function

* Draft create_gold_state for arc_eager oracle

* Fix import

* Fix import

* Remove TokenAnnotation code from nonproj

* fixing NER one-to-many alignment

* Fix many-to-one IOB codes

* fix test for misaligned

* attempt to fix cases with weird spaces

* fix spaces

* test_gold_biluo_different_tokenization works

* allow None as BILUO annotation

* fixed some tests + WIP roundtrip unit test

* add spaces to json output format

* minibatch utiltiy can deal with strings, docs or examples

* fix augment (needs further testing)

* various fixes in scripts - needs to be further tested

* fix test_cli

* cleanup

* correct silly typo

* add support for MORPH in to/from_array, fix morphologizer overfitting test

* fix tagger

* fix entity linker

* ensure test keeps working with non-linked entities

* pipe() takes docs, not examples

* small bug fix

* textcat bugfix

* throw informative error when running the components with the wrong type of objects

* fix parser tests to work with example (most still failing)

* fix BiluoPushDown parsing entities

* small fixes

* bugfix tok2vec

* fix renames and simple_ner labels

* various small fixes

* prevent writing dummy values like deps because that could interfer with sent_start values

* fix the fix

* implement split_sent with aligned SENT_START attribute

* test for split sentences with various alignment issues, works

* Return ArcEagerGoldParse from ArcEager

* Update parser and NER gold stuff

* Draft new GoldCorpus class

* add links to to_dict

* clean up

* fix test checking for variants

* Fix oracles

* Start updating converters

* Move converters under spacy.gold

* Move things around

* Fix naming

* Fix name

* Update converter to produce DocBin

* Update converters

* Allow DocBin to take list of Doc objects.

* Make spacy convert output docbin

* Fix import

* Fix docbin

* Fix compile in ArcEager

* Fix import

* Serialize all attrs by default

* Update converter

* Remove jsonl converter

* Add json2docs converter

* Draft Corpus class for DocBin

* Work on train script

* Update Corpus

* Update DocBin

* Allocate Doc before starting to add words

* Make doc.from_array several times faster

* Update train.py

* Fix Corpus

* Fix parser model

* Start debugging arc_eager oracle

* Update header

* Fix parser declaration

* Xfail some tests

* Skip tests that cause crashes

* Skip test causing segfault

* Remove GoldCorpus

* Update imports

* Update after removing GoldCorpus

* Fix module name of corpus

* Fix mimport

* Work on parser oracle

* Update arc_eager oracle

* Restore ArcEager.get_cost function

* Update transition system

* Update test_arc_eager_oracle

* Remove beam test

* Update test

* Unskip

* Unskip tests

* add links to to_dict

* clean up

* fix test checking for variants

* Allow DocBin to take list of Doc objects.

* Fix compile in ArcEager

* Serialize all attrs by default

Move converters under spacy.gold

Move things around

Fix naming

Fix name

Update converter to produce DocBin

Update converters

Make spacy convert output docbin

Fix import

Fix docbin

Fix import

Update converter

Remove jsonl converter

Add json2docs converter

* Allocate Doc before starting to add words

* Make doc.from_array several times faster

* Start updating converters

* Work on train script

* Draft Corpus class for DocBin

Update Corpus

Fix Corpus

* Update DocBin

Add missing strings when serializing

* Update train.py

* Fix parser model

* Start debugging arc_eager oracle

* Update header

* Fix parser declaration

* Xfail some tests

Skip tests that cause crashes

Skip test causing segfault

* Remove GoldCorpus

Update imports

Update after removing GoldCorpus

Fix module name of corpus

Fix mimport

* Work on parser oracle

Update arc_eager oracle

Restore ArcEager.get_cost function

Update transition system

* Update tests

Remove beam test

Update test

Unskip

Unskip tests

* Add get_aligned_parse method in Example

Fix Example.get_aligned_parse

* Add kwargs to Corpus.dev_dataset to match train_dataset

* Update nonproj

* Use get_aligned_parse in ArcEager

* Add another arc-eager oracle test

* Remove Example.doc property

Remove Example.doc

Remove Example.doc

Remove Example.doc

Remove Example.doc

* Update ArcEager oracle

Fix Break oracle

* Debugging

* Fix Corpus

* Fix eg.doc

* Format

* small fixes

* limit arg for Corpus

* fix test_roundtrip_docs_to_docbin

* fix test_make_orth_variants

* fix add_label test

* Update tests

* avoid writing temp dir in json2docs, fixing 4402 test

* Update test

* Add missing costs to NER oracle

* Update test

* Work on Example.get_aligned_ner method

* Clean up debugging

* Xfail tests

* Remove prints

* Remove print

* Xfail some tests

* Replace unseen labels for parser

* Update test

* Update test

* Xfail test

* Fix Corpus

* fix imports

* fix docs_to_json

* various small fixes

* cleanup

* Support gold_preproc in Corpus

* Support gold_preproc

* Pass gold_preproc setting into corpus

* Remove debugging

* Fix gold_preproc

* Fix json2docs converter

* Fix convert command

* Fix flake8

* Fix import

* fix output_dir (converted to Path by typer)

* fix var

* bugfix: update states after creating golds to avoid out of bounds indexing

* Improve efficiency of ArEager oracle

* pull merge_sent into iob2docs to avoid Doc creation for each line

* fix asserts

* bugfix excl Span.end in iob2docs

* Support max_length in Corpus

* Fix arc_eager oracle

* Filter out uannotated sentences in NER

* Remove debugging in parser

* Simplify NER alignment

* Fix conversion of NER data

* Fix NER init_gold_batch

* Tweak efficiency of precomputable affine

* Update onto-json default

* Update gold test for NER

* Fix parser test

* Update test

* Add NER data test

* Fix convert for single file

* Fix test

* Hack scorer to avoid evaluating non-nered data

* Fix handling of NER data in Example

* Output unlabelled spans from O biluo tags in iob_utils

* Fix unset variable

* Return kept examples from init_gold_batch

* Return examples from init_gold_batch

* Dont return Example from init_gold_batch

* Set spaces on gold doc after conversion

* Add test

* Fix spaces reading

* Improve NER alignment

* Improve handling of missing values in NER

* Restore the 'cutting' in parser training

* Add assertion

* Print epochs

* Restore random cuts in parser/ner training

* Implement Doc.copy

* Implement Example.copy

* Copy examples at the start of Language.update

* Don't unset example docs

* Tweak parser model slightly

* attempt to fix _guess_spaces

* _add_entities_to_doc first, so that links don't get overwritten

* fixing get_aligned_ner for one-to-many

* fix indexing into x_text

* small fix biluo_tags_from_offsets

* Add onto-ner config

* Simplify NER alignment

* Fix NER scoring for partially annotated documents

* fix indexing into x_text

* fix test_cli failing tests by ignoring spans in doc.ents with empty label

* Fix limit

* Improve NER alignment

* Fix count_train

* Remove print statement

* fix tests, we're not having nothing but None

* fix clumsy fingers

* Fix tests

* Fix doc.ents

* Remove empty docs in Corpus and improve limit

* Update config

Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 19:34:12 +02:00
Ines Montani
52728d8fa3 Merge branch 'develop' into master-tmp 2020-06-20 15:52:00 +02:00
Adriane Boyd
c482f20778
Fix and add warnings related to spacy-lookups-data (#5588)
* Fix warning message for lemmatization tables

* Add a warning when the `lexeme_norm` table is empty. (Given the
relatively lang-specific loading for `Lookups`, it seemed like too much
overhead to dynamically extract the list of languages, so for now it's
hard-coded.)
2020-06-15 14:56:04 +02:00
Sofie Van Landeghem
c0f4a1e43b
train is from-config by default (#5575)
* verbose and tag_map options

* adding init_tok2vec option and only changing the tok2vec that is specified

* adding omit_extra_lookups and verifying textcat config

* wip

* pretrain bugfix

* add replace and resume options

* train_textcat fix

* raw text functionality

* improve UX when KeyError or when input data can't be parsed

* avoid unnecessary access to goldparse in TextCat pipe

* save performance information in nlp.meta

* add noise_level to config

* move nn_parser's defaults to config file

* multitask in config - doesn't work yet

* scorer offering both F and AUC options, need to be specified in config

* add textcat verification code from old train script

* small fixes to config files

* clean up

* set default config for ner/parser to allow create_pipe to work as before

* two more test fixes

* small fixes

* cleanup

* fix NER pickling + additional unit test

* create_pipe as before
2020-06-12 02:02:07 +02:00
Ines Montani
d93cbeb14f
Add warning for loose version constraints (#5536)
* Add warning for loose version constraints

* Update wording [ci skip]

* Tweak error message

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-06-05 12:42:15 +02:00
Matthew Honnibal
8411d4f4e6
Merge pull request #5543 from svlandeg/feature/pretrain-config
pretrain from config
2020-06-04 19:07:12 +02:00
svlandeg
ffe0451d09 pretrain from config 2020-06-03 14:45:00 +02:00
Ines Montani
810fce3bb1 Merge branch 'develop' into master-tmp 2020-06-03 14:36:59 +02:00
svlandeg
03c58b488c prevent infinite loop, custom warning 2020-06-03 10:00:21 +02:00
Adriane Boyd
bbc1836581 Add rudimentary version checks on model load 2020-06-02 17:33:48 +02:00
Ines Montani
dc186afdc5 Add warning 2020-05-30 15:34:54 +02:00
svlandeg
291483157d prevent loading a pretrained Tok2Vec layer AND pretrained components 2020-05-29 17:38:33 +02:00
Ines Montani
5d3806e059 unicode -> str consistency 2020-05-24 17:20:58 +02:00
Adriane Boyd
71fe61fdcd Disallow merging 0-length spans 2020-05-22 10:14:34 +02:00
Ines Montani
891fa59009 Use backwards-compatible super() 2020-05-21 20:52:48 +02:00
Ines Montani
24f72c669c Merge branch 'develop' into master-tmp 2020-05-21 18:39:06 +02:00
Ines Montani
d8f3190c0a Tidy up and auto-format 2020-05-21 14:14:01 +02:00
Sofie Van Landeghem
7f5715a081
Various fixes to NEL functionality, Example class etc (#5460)
* setting KB in the EL constructor, similar to how the model is passed on

* removing wikipedia example files - moved to projects

* throw an error when nlp.update is called with 2 positional arguments

* rewriting the config logic in create pipe to accomodate for other objects (e.g. KB) in the config

* update config files with new parameters

* avoid training pipeline components that don't have a model (like sentencizer)

* various small fixes + UX improvements

* small fixes

* set thinc to 8.0.0a9 everywhere

* remove outdated comment
2020-05-20 11:41:12 +02:00
adrianeboyd
40e65d6f63
Fix most_similar for vectors with unused rows (#5348)
* Fix most_similar for vectors with unused rows

Address issues related to the unused rows in the vector table and
`most_similar`:

* Update `most_similar()` to search only through rows that are in use
according to `key2row`.

* Raise an error when `most_similar(n=n)` is larger than the number of
vectors in the table.

* Set and restore `_unset` correctly when vectors are added or
deserialized so that new vectors are added in the correct row.

* Set data and keys to the same length in `Vocab.prune_vectors()` to
avoid spurious entries in `key2row`.

* Fix regression test using `most_similar`

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-05-19 16:41:26 +02:00
adrianeboyd
70da1fd2d6
Add warning for misaligned character offset spans (#5007)
* Add warning for misaligned character offset spans

* Resolve conflict

* Filter warnings in example scripts

Filter warnings in example scripts to show warnings once, in particular
warnings about misaligned entities.

Co-authored-by: Ines Montani <ines@ines.io>
2020-05-19 16:01:18 +02:00
Sofie Van Landeghem
0d94737857
Feature toggle_pipes (#5378)
* make disable_pipes deprecated in favour of the new toggle_pipes

* rewrite disable_pipes statements

* update documentation

* remove bin/wiki_entity_linking folder

* one more fix

* remove deprecated link to documentation

* few more doc fixes

* add note about name change to the docs

* restore original disable_pipes

* small fixes

* fix typo

* fix error number to W096

* rename to select_pipes

* also make changes to the documentation

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-05-18 22:27:10 +02:00
svlandeg
e0fda2bd81 throw warning when model_cfg is None 2020-05-15 11:02:10 +02:00
Ilia Ivanov
712d9d4820 fixup! Fix ErrorsWithCodes().__class__ return value 2020-05-14 15:45:58 +02:00
Ilia Ivanov
a987e9e45d Fix ErrorsWithCodes().__class__ return value 2020-05-14 14:14:15 +02:00
adrianeboyd
113e7981d0
Check that row is within bounds when adding vector (#5430)
Check that row is within bounds for the vector data array when adding a
vector.

Don't add vectors with rank OOV_RANK in `init-model` (change is due to
shift from OOV as 0 to OOV as OOV_RANK).
2020-05-13 22:08:28 +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
84e06f9fb7
Improve GoldParse NER alignment (#5335)
Improve GoldParse NER alignment by including all cases where the start
and end of the NER span can be aligned, regardless of internal
tokenization differences.

To do this, convert BILUO tags to character offsets, check start/end
alignment with `doc.char_span()`, and assign the BILUO tags for the
aligned spans. Alignment for `O/-` tags is handled through the
one-to-one and multi alignments.
2020-04-23 16:58:23 +02:00
Paolo Arduin
1ca32d8f9c
Matcher support for Span as well as Doc (#5113)
* Matcher support for Span, as well as Doc #5056

* Removes an import unused

* Signed contributors agreement

* Code optimization and better test

* Add error message for bad Matcher call argument

* Fix merging
2020-04-15 13:51:33 +02:00
adrianeboyd
3d2c308906
Add Doc init from list of words and text (#5251)
* Add Doc init from list of words and text

Add an option to initialize a `Doc` from a text and list of words where
the words may or may not include all whitespace tokens. If the text and
words are mismatched, raise an error.

* Fix error code

* Remove all whitespace before aligning words/text

* Move words/text init to util function

* Update error message

* Rename to get_words_and_spaces

* Fix formatting
2020-04-14 19:15:52 +02:00
adrianeboyd
d107afcffb
Raise error for inplace resize with new vector dim (#5228)
Raise an error if there is an attempt to resize the vectors in place with
a different vector dimension.
2020-04-02 10:43:13 +02:00
adrianeboyd
963bd890c1
Modify Vector.resize to work with cupy and improve resizing (#5216)
* Modify Vector.resize to work with cupy

Modify `Vectors.resize` to work with cupy. Modify behavior when resizing
to a different vector dimension so that individual vectors are truncated
or extended with zeros instead of having the original values filled into
the new shape without regard for the original axes.

* Update spacy/tests/vocab_vectors/test_vectors.py

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

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-03-29 13:51:20 +02:00
Ines Montani
46568f40a7 Merge branch 'master' into tmp/sync 2020-03-26 13:38:14 +01:00
Ines Montani
828acffc12 Tidy up and auto-format 2020-03-25 12:28:12 +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
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
7efaa76168 Update errors.py 2020-02-28 12:23:31 +01:00
Ines Montani
37691e6d5d Simplify warnings 2020-02-28 12:20:23 +01:00
Sofie Van Landeghem
06f0a8daa0
Default settings to configurations (#4995)
* fix grad_clip naming

* cleaning up pretrained_vectors out of cfg

* further refactoring Model init's

* move Model building out of pipes

* further refactor to require a model config when creating a pipe

* small fixes

* making cfg in nn_parser more consistent

* fixing nr_class for parser

* fixing nn_parser's nO

* fix printing of loss

* architectures in own file per type, consistent naming

* convenience methods default_tagger_config and default_tok2vec_config

* let create_pipe access default config if available for that component

* default_parser_config

* move defaults to separate folder

* allow reading nlp from package or dir with argument 'name'

* architecture spacy.VocabVectors.v1 to read static vectors from file

* cleanup

* default configs for nel, textcat, morphologizer, tensorizer

* fix imports

* fixing unit tests

* fixes and clean up

* fixing defaults, nO, fix unit tests

* restore parser IO

* fix IO

* 'fix' serialization test

* add *.cfg to manifest

* fix example configs with additional arguments

* replace Morpohologizer with Tagger

* add IO bit when testing overfitting of tagger (currently failing)

* fix IO - don't initialize when reading from disk

* expand overfitting tests to also check IO goes OK

* remove dropout from HashEmbed to fix Tagger performance

* add defaults for sentrec

* update thinc

* always pass a Model instance to a Pipe

* fix piped_added statement

* remove obsolete W029

* remove obsolete errors

* restore byte checking tests (work again)

* clean up test

* further test cleanup

* convert from config to Model in create_pipe

* bring back error when component is not initialized

* cleanup

* remove calls for nlp2.begin_training

* use thinc.api in imports

* allow setting charembed's nM and nC

* fix for hardcoded nM/nC + unit test

* formatting fixes

* trigger build
2020-02-27 18:42:27 +01:00
Ines Montani
a3335d36b8 Merge branch 'develop' into refactor/remove-symlinks 2020-02-18 17:22:20 +01:00
Ines Montani
09cbeaef27 Remove symlinks, data dir and related stuff 2020-02-18 17:20:17 +01:00
Ines Montani
1278161f47 Tidy up and fix issues 2020-02-18 15:17:03 +01:00
Ines Montani
de11ea753a Merge branch 'master' into develop 2020-02-18 14:47:23 +01:00
adrianeboyd
adc9745718 Modify morphology to support arbitrary features (#4932)
* Restructure tag maps for MorphAnalysis changes

Prepare tag maps for upcoming MorphAnalysis changes that allow
arbritrary features.

* Use default tag map rather than duplicating for ca / uk / vi

* Import tag map into defaults for ga

* Modify tag maps so all morphological fields and features are strings
  * Move features from `"Other"` to the top level
  * Rewrite tuples as strings separated by `","`

* Rewrite morph symbols for fr lemmatizer as strings

* Export MorphAnalysis under spacy.tokens

* Modify morphology to support arbitrary features

Modify `Morphology` and `MorphAnalysis` so that arbitrary features are
supported.

* Modify `MorphAnalysisC` so that it can support arbitrary features and
multiple values per field. `MorphAnalysisC` is redesigned to contain:
  * key: hash of UD FEATS string of morphological features
  * array of `MorphFeatureC` structs that each contain a hash of `Field`
and `Field=Value` for a given morphological feature, which makes it
possible to:
    * find features by field
    * represent multiple values for a given field

* `get_field()` is renamed to `get_by_field()` and is no longer `nogil`.
Instead a new helper function `get_n_by_field()` is `nogil` and returns
`n` features by field.

* `MorphAnalysis.get()` returns all possible values for a field as a
list of individual features such as `["Tense=Pres", "Tense=Past"]`.

* `MorphAnalysis`'s `str()` and `repr()` are the UD FEATS string.

* `Morphology.feats_to_dict()` converts a UD FEATS string to a dict
where:
  * Each field has one entry in the dict
  * Multiple values remain separated by a separator in the value string

* `Token.morph_` returns the UD FEATS string and you can set
`Token.morph_` with a UD FEATS string or with a tag map dict.

* Modify get_by_field to use np.ndarray

Modify `get_by_field()` to use np.ndarray. Remove `max_results` from
`get_n_by_field()` and always iterate over all the fields.

* Rewrite without MorphFeatureC

* Add shortcut for existing feats strings as keys

Add shortcut for existing feats strings as keys in `Morphology.add()`.

* Check for '_' as empty analysis when adding morphs

* Extend helper converters in Morphology

Add and extend helper converters that convert and normalize between:

* UD FEATS strings (`"Case=dat,gen|Number=sing"`)
* per-field dict of feats (`{"Case": "dat,gen", "Number": "sing"}`)
* list of individual features (`["Case=dat", "Case=gen",
"Number=sing"]`)

All converters sort fields and values where applicable.
2020-01-23 22:01:54 +01:00
Sofie Van Landeghem
6e9b61b49d add warning in debug_data for punctuation in entities (#4853) 2020-01-06 14:59:28 +01:00