Commit Graph

196 Commits

Author SHA1 Message Date
Ines Montani
8ff73f04db Fix morph in Doc.to_json 2020-10-08 14:44:35 +02:00
Ines Montani
126268ce50 Auto-format [ci skip] 2020-10-05 21:58:18 +02:00
Ines Montani
59deeb7da6 Merge branch 'develop' into master-tmp 2020-10-04 14:52:20 +02:00
Ines Montani
3bc3c05fcc Tidy up and auto-format 2020-10-03 17:20:18 +02:00
Adriane Boyd
f83dfe62da Fix test 2020-10-02 10:17:26 +02:00
Adriane Boyd
86c3ec9c2b
Refactor Token morph setting (#6175)
* Refactor Token morph setting

* Remove `Token.morph_`
* Add `Token.set_morph()`
  * `0` resets `token.c.morph` to unset
  * Any other values are passed to `Morphology.add`

* Add token.morph setter to set from MorphAnalysis
2020-10-01 22:21:46 +02:00
Adriane Boyd
73538782a0
Switch Doc.__init__(ents=) to IOB tags (#6173)
* Switch Doc.__init__(ents=) to IOB tags

* Fix check for "-"

* Allow "" or None as missing IOB tag
2020-10-01 16:22:18 +02:00
Yohei Tamura
3243ddac8f
Fix/span.sent (#6083)
* add fail test

* fix test

* fix span.sent

* Remove incorrect implicit check

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2020-10-01 14:01:52 +02:00
Ines Montani
fa47f87924 Tidy up and auto-format 2020-09-29 21:39:28 +02:00
Ines Montani
ff9a63bfbd begin_training -> initialize 2020-09-28 21:35:09 +02:00
Ines Montani
7e938ed63e Update config resolution to use new Thinc 2020-09-27 22:21:31 +02:00
Adriane Boyd
8eaacaae97 Refactor Doc.ents setter to use Doc.set_ents
Additional changes:

* Entity spans with missing labels are ignored
* Fix ent_kb_id setting in `Doc.set_ents`
2020-09-24 12:36:51 +02:00
Adriane Boyd
e4acb28658
Fix norm in retokenizer split (#6111)
Parallel to behavior in merge, reset norm on original token in
retokenizer split.
2020-09-22 21:53:33 +02:00
Adriane Boyd
535842e483
Merge branch 'develop' into feature/doc-ents-v3-2 2020-09-22 13:45:50 +02:00
Ines Montani
beb766d0a0 Add test 2020-09-22 09:15:57 +02:00
Ines Montani
67fbcb3da5 Tidy up tests and docs 2020-09-21 20:43:54 +02:00
Ines Montani
a5f6ab4943
Merge pull request #6098 from adrianeboyd/feature/doc-init 2020-09-21 18:35:20 +02:00
Adriane Boyd
f212303729 Add sent_starts to Doc.__init__
Add sent_starts to `Doc.__init__`. Officially specify `is_sent_start`
values but also convert to and accept `sent_start` internally.
2020-09-21 17:59:09 +02:00
Adriane Boyd
177df15d89 Implement Doc.set_ents 2020-09-21 15:54:05 +02:00
Adriane Boyd
13fbf6556a Merge remote-tracking branch 'upstream/develop' into feature/doc-ents-v3-2 2020-09-21 14:42:04 +02:00
Ines Montani
1114219ae3 Tidy up and auto-format 2020-09-21 10:59:07 +02:00
Adriane Boyd
a88106e852
Remove W106: HEAD and SENT_START in doc.from_array (#6086)
* Remove W106: HEAD and SENT_START in doc.from_array

This warning was hacky and being triggered too often.

* Fix test
2020-09-18 03:01:29 +02:00
Adriane Boyd
8b650f3a78 Modify setting missing and blocked entity tokens
In order to make it easier to construct `Doc` objects as training data,
modify how missing and blocked entity tokens are set to prioritize
setting `O` and missing entity tokens for training purposes over setting
blocked entity tokens.

* `Doc.ents` setter sets tokens outside entity spans to `O` regardless
of the current state of each token

* For `Doc.ents`, setting a span with a missing label sets the `ent_iob`
to missing instead of blocked

* `Doc.block_ents(spans)` marks spans as hard `O` for use with the
`EntityRecognizer`
2020-09-17 21:27:42 +02:00
Adriane Boyd
7e4cd7575c
Refactor Docs.is_ flags (#6044)
* Refactor Docs.is_ flags

* Add derived `Doc.has_annotation` method

  * `Doc.has_annotation(attr)` returns `True` for partial annotation

  * `Doc.has_annotation(attr, require_complete=True)` returns `True` for
    complete annotation

* Add deprecation warnings to `is_tagged`, `is_parsed`, `is_sentenced`
and `is_nered`

* Add `Doc._get_array_attrs()`, which returns a full list of `Doc` attrs
for use with `Doc.to_array`, `Doc.to_bytes` and `Doc.from_docs`. The
list is the `DocBin` attributes list plus `SPACY` and `LENGTH`.

Notes on `Doc.has_annotation`:

* `HEAD` is converted to `DEP` because heads don't have an unset state

* Accept `IS_SENT_START` as a synonym of `SENT_START`

Additional changes:

* Add `NORM`, `ENT_ID` and `SENT_START` to default attributes for
`DocBin`

* In `Doc.from_array()` the presence of `DEP` causes `HEAD` to override
`SENT_START`

* In `Doc.from_array()` using `attrs` other than
`Doc._get_array_attrs()` (i.e., a user's custom list rather than our
default internal list) with both `HEAD` and `SENT_START` shows a warning
that `HEAD` will override `SENT_START`

* `set_children_from_heads` does not require dependency labels to set
sentence boundaries and sets `sent_start` for all non-sentence starts to
`-1`

* Fix call to set_children_form_heads

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-09-17 00:14:01 +02:00
Adriane Boyd
a119667a36
Clean up spacy.tokens (#6046)
* Clean up spacy.tokens

* Update `set_children_from_heads`:
  * Don't check `dep` when setting lr_* or sentence starts
  * Set all non-sentence starts to `False`

* Use `set_children_from_heads` in `Token.head` setter
  * Reduce similar/duplicate code (admittedly adds a bit of overhead)
  * Update sentence starts consistently

* Remove unused `Doc.set_parse`

* Minor changes:
  * Declare cython variables (to avoid cython warnings)
  * Clean up imports

* Modify set_children_from_heads to set token range

Modify `set_children_from_heads` so that it adjust tokens within a
specified range rather then the whole document.

Modify the `Token.head` setter to adjust only the tokens affected by the
new head assignment.
2020-09-16 20:32:38 +02:00
Adriane Boyd
ab270364f1
Modify Token.morph to enable unsetting (#6043)
Modify `Token.morph` property so that `Token.c.morph` can be reset back
to an internal value of `0`. Allow setting `Token.morph` from a hash as
long as the morph string is already in the `StringStore`, setting it
indirectly through `Token.morph_` so that the value is added to the
morphology. If the hash is not in the `StringStore`, raise an error.
2020-09-13 14:06:07 +02:00
Ines Montani
febb99916d Tidy up and auto-format [ci skip] 2020-09-13 10:55:36 +02:00
Sofie Van Landeghem
8e7557656f
Renaming gold & annotation_setter (#6042)
* version bump to 3.0.0a16

* rename "gold" folder to "training"

* rename 'annotation_setter' to 'set_extra_annotations'

* formatting
2020-09-09 10:31:03 +02:00
Sofie Van Landeghem
60f22e1800
Pipe API (#6034)
* ensure Language passes on valid examples for initialization

* fix tagger model initialization

* check for valid get_examples across components

* assume labels were added before begin_training

* fix senter initialization

* fix morphologizer initialization

* use methods to check arguments

* test textcat init, requires thinc>=8.0.0a31

* fix tok2vec init

* fix entity linker init

* use islice

* fix simple NER

* cleanup debug model

* fix assert statements

* fix tests

* throw error when adding a label if the output layer can't be resized anymore

* fix test

* add failing test for simple_ner

* UX improvements

* morphologizer UX

* assume begin_training gets a representative set and processes the labels

* remove assumptions for output of untrained NER model

* restore test for original purpose
2020-09-08 22:44:25 +02:00
Ines Montani
864a697e63 Merge branch 'develop' into master-tmp 2020-09-04 13:15:36 +02:00
Yohei Tamura
5af432e0f2
fix for empty string (#5936) 2020-09-03 10:09:03 +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
Ines Montani
c099f6eece Add Token.lex 2020-08-10 16:43:52 +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
Ines Montani
e68459296d Tidy up and auto-format 2020-08-05 16:00:59 +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
Adriane Boyd
c62fd878a3
Allow Doc.char_span to snap to token boundaries (#5849)
* Allow Doc.char_span to snap to token boundaries

Add a `mode` option to allow `Doc.char_span` to snap to token
boundaries. The `mode` options:

* `strict`: character offsets must match token boundaries (default, same as
before)
* `inside`: all tokens completely within the character span
* `outside`: all tokens at least partially covered by the character span

Add a new helper function `token_by_char` that returns the token
corresponding to a character position in the text. Update
`token_by_start` and `token_by_end` to use `token_by_char` for more
efficient searching.

* Remove unused import

* Rename mode to alignment_mode

Rename `mode` to `alignment_mode` with the options
`strict`/`contract`/`expand`. Any unrecognized modes are silently
converted to `strict`.
2020-08-04 13:36:32 +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
e92df281ce Tidy up, autoformat, add types 2020-07-25 15:01:15 +02:00
Adriane Boyd
fdb8815ef5
Minor refactor for Morphology and MorphAnalysis (#5804)
* `MorphAnalysis.get` returns only the field values
* Move `_normalize_props` inside `Morphology` as
`Morphology.normalize_attrs` and simplify
  * Simplify POS field detection/conversion
  * Convert all non-POS features to strings
* `Morphology` returns an empty string for a missing morph to align
with the FEATS string returned for an existing morph
* Remove unused `list_to_feats`
2020-07-24 09:28:06 +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
Ines Montani
644074b954 Merge branch 'develop' into master-tmp 2020-07-20 14:58:04 +02:00
Adriane Boyd
2f981d5af1 Remove corpus-specific tag maps
Remove corpus-specific tag maps from the language data for languages
without custom tokenizers. For languages with custom word segmenters
that also provide tags (Japanese and Korean), the tag maps for the
custom tokenizers are kept as the default.

The default tag maps for languages without custom tokenizers are now the
default tag map from `lang/tag_map/py`, UPOS -> UPOS.
2020-07-15 15:58:29 +02:00
Adriane Boyd
a7a7e0d2a6
Add morph to morphology in Doc.from_array (#5762)
* Add morph to morphology in Doc.from_array

Add morphological analyses to morphology table in `Doc.from_array`.

* Use separate vocab in DocBin roundtrip test
2020-07-14 14:07:35 +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
Ines Montani
37c3bb35e2 Auto-format 2020-07-04 16:25:34 +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
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
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