Commit Graph

53 Commits

Author SHA1 Message Date
Ines Montani 8128e5eb35 Replace lexeme_norm warning with logging 2020-08-14 15:00:52 +02:00
Ines Montani ef2c67cca5
Add DocBin to/from_disk methods and update docs (#5892)
* Add DocBin to/from_disk methods and update docs

* Use DocBin.from_disk in Corpus
2020-08-07 14:30:59 +02:00
Ines Montani e68459296d Tidy up and auto-format 2020-08-05 16:00:59 +02:00
Sofie Van Landeghem 34873c4911
Example Dict format consistency (#5858)
* consistently use upper-case IDS in token_annotation format and for get_aligned

* remove ID from to_dict (not used in from_dict either)

* fix test

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-04 22:22:26 +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
Matthew Honnibal ecb3c4e8f4
Create corpus iterator and batcher from registry during training (#5865)
* Move batchers into their own module (and registry)

* Update CLI

* Update Corpus and batcher

* Update tests

* Update one config

* Merge 'evaluation' block back under [training]

* Import batchers in gold __init__

* Fix batchers

* Update config

* Update schema

* Update util

* Don't assume train and dev are actually paths

* Update onto-joint config

* Fix missing import

* Format

* Format

* Update spacy/gold/corpus.py

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

* Fix name

* Update default config

* Fix get_length option in batchers

* Update test

* Add comment

* Pass path into Corpus

* Update docstring

* Update schema and configs

* Update config

* Fix test

* Fix paths

* Fix print

* Fix create_train_batches

* [training.read_train] -> [training.train_corpus]

* Update onto-joint config

Co-authored-by: Ines Montani <ines@ines.io>
2020-08-04 15:09:37 +02:00
Adriane Boyd b7e3018d97
Recalculate alignment if tokenization differs (#5868)
* Recalculate alignment if tokenization differs

* Refactor cached alignment data
2020-08-04 14:31:32 +02:00
Ines Montani e92df281ce Tidy up, autoformat, add types 2020-07-25 15:01:15 +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 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
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
Matthew Honnibal cc477be952
Improve gold-standard alignment (#5711)
* Remove previous alignment

* Implement better alignment, using ragged data structure

* Use pytokenizations for alignment

* Fixes

* Fixes

* Fix overlapping entities in alignment

* Fix align split_sents

* Update test

* Commit align.py

* Try to appease setuptools

* Fix flake8

* use realistic entities for testing

* Update tests for better alignment

* Improve alignment heuristic

Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-07-06 17:39:31 +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
Ines Montani 37c3bb35e2 Auto-format 2020-07-04 16:25:34 +02:00
Sofie Van Landeghem fc3cb1fa9e
NER align tests (#5656)
* one_to_man works better. misalignment doesn't yet.

* fix tests

* restore example

* xfail alignment tests
2020-06-29 13:59:17 +02:00
Matthw Honnibal 1d672e0c12 Revert "attempt to fix _guess_spaces"
This reverts commit 5b6ed05752.
2020-06-26 23:42:41 +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 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
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
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
adrianeboyd 521f361052
Switch to new gold.align method (#5334)
* Switch from original `_align` to new simpler alignment algorithm from
  #4526

* Remove alignment normalizations beyond whitespace and lowercasing
2020-04-21 19:31:03 +02:00
adrianeboyd ce0e538068
Check whether doc is instantiated in Example.get_gold_parses() (#5167)
* Check whether doc is instantiated

When creating docs to pair with gold parses, modify test to check
whether a doc is unset rather than whether it contains tokens.

* Restore test of evaluate on an empty doc

* Set a minimal gold.orig for the scorer

Without a minimal gold.orig the scorer can't evaluate empty docs. This
is the v3 equivalent of #4925.
2020-03-29 13:57:00 +02:00
adrianeboyd 06b251dd1e Add support for pos/morphs/lemmas in training data (#4941)
Add support for pos/morphs/lemmas throughout `GoldParse`, `Example`, and
`docs_to_json()`.
2020-01-28 11:36:29 +01:00
Ines Montani db55577c45
Drop Python 2.7 and 3.5 (#4828)
* Remove unicode declarations

* Remove Python 3.5 and 2.7 from CI

* Don't require pathlib

* Replace compat helpers

* Remove OrderedDict

* Use f-strings

* Set Cython compiler language level

* Fix typo

* Re-add OrderedDict for Table

* Update setup.cfg

* Revert CONTRIBUTING.md

* Revert lookups.md

* Revert top-level.md

* Small adjustments and docs [ci skip]
2019-12-22 01:53:56 +01:00
adrianeboyd 79ba1a3b92 Add lemmas to GoldParse / Example / docs_to_json (#4726) 2019-11-28 14:53:44 +01:00
adrianeboyd 0c9640ced3 Replace old gold alignment with new gold alignment (#4710)
Replace old gold alignment that allowed for some noise in the alignment between raw and orth with the new simpler alignment that requires that the raw and orth strings are identical except for whitespace and capitalization.

* Replace old alignment with new alignment, removing `_align.pyx` and
its tests
* Remove all quote normalizations
* Enable test for new align
  * Modify test case for quote normalization
2019-11-25 23:13:26 +01:00
adrianeboyd 392c4880d9 Restructure Example with merged sents as default (#4632)
* Switch to train_dataset() function in train CLI

* Fixes for pipe() methods in pipeline components

* Don't clobber `examples` variable with `as_example` in pipe() methods
* Remove unnecessary traversals of `examples`

* Update Parser.pipe() for Examples

* Add `as_examples` kwarg to `pipe()` with implementation to return
`Example`s

* Accept `Doc` or `Example` in `pipe()` with `_get_doc()` (copied from
`Pipe`)

* Fixes to Example implementation in spacy.gold

* Move `make_projective` from an attribute of Example to an argument of
`Example.get_gold_parses()`

* Head of 0 are not treated as unset

* Unset heads are set to self rather than `None` (which causes problems
while projectivizing)

* Check for `Doc` (not just not `None`) when creating GoldParses for
pre-merged example

* Don't clobber `examples` variable in `iter_gold_docs()`

* Add/modify gold tests for handling projectivity

* In JSON roundtrip compare results from `dev_dataset` rather than
`train_dataset` to avoid projectivization (and other potential
modifications)

* Add test for projective train vs. nonprojective dev versions of the
same `Doc`

* Handle ignore_misaligned as arg rather than attr

Move `ignore_misaligned` from an attribute of `Example` to an argument
to `Example.get_gold_parses()`, which makes it parallel to
`make_projective`.

Add test with old and new align that checks whether `ignore_misaligned`
errors are raised as expected (only for new align).

* Remove unused attrs from gold.pxd

Remove `ignore_misaligned` and `make_projective` from `gold.pxd`

* Restructure Example with merged sents as default

An `Example` now includes a single `TokenAnnotation` that includes all
the information from one `Doc` (=JSON `paragraph`). If required, the
individual sentences can be returned as a list of examples with
`Example.split_sents()` with no raw text available.

* Input/output a single `Example.token_annotation`

* Add `sent_starts` to `TokenAnnotation` to handle sentence boundaries

* Replace `Example.merge_sents()` with `Example.split_sents()`

* Modify components to use a single `Example.token_annotation`

  * Pipeline components
  * conllu2json converter

* Rework/rename `add_token_annotation()` and `add_doc_annotation()` to
`set_token_annotation()` and `set_doc_annotation()`, functions that set
rather then appending/extending.

* Rename `morphology` to `morphs` in `TokenAnnotation` and `GoldParse`

* Add getters to `TokenAnnotation` to supply default values when a given
attribute is not available

* `Example.get_gold_parses()` in `spacy.gold._make_golds()` is only
applied on single examples, so the `GoldParse` is returned saved in the
provided `Example` rather than creating a new `Example` with no other
internal annotation

* Update tests for API changes and `merge_sents()` vs. `split_sents()`

* Refer to Example.goldparse in iter_gold_docs()

Use `Example.goldparse` in `iter_gold_docs()` instead of `Example.gold`
because a `None` `GoldParse` is generated with ignore_misaligned and
generating it on-the-fly can raise an unwanted AlignmentError

* Fix make_orth_variants()

Fix bug in make_orth_variants() related to conversion from multiple to
one TokenAnnotation per Example.

* Add basic test for make_orth_variants()

* Replace try/except with conditionals

* Replace default morph value with set
2019-11-25 16:03:28 +01:00
adrianeboyd 44829950ba Fix Example details for train CLI / pipeline components (#4624)
* Switch to train_dataset() function in train CLI

* Fixes for pipe() methods in pipeline components

* Don't clobber `examples` variable with `as_example` in pipe() methods
* Remove unnecessary traversals of `examples`

* Update Parser.pipe() for Examples

* Add `as_examples` kwarg to `pipe()` with implementation to return
`Example`s

* Accept `Doc` or `Example` in `pipe()` with `_get_doc()` (copied from
`Pipe`)

* Fixes to Example implementation in spacy.gold

* Move `make_projective` from an attribute of Example to an argument of
`Example.get_gold_parses()`

* Head of 0 are not treated as unset

* Unset heads are set to self rather than `None` (which causes problems
while projectivizing)

* Check for `Doc` (not just not `None`) when creating GoldParses for
pre-merged example

* Don't clobber `examples` variable in `iter_gold_docs()`

* Add/modify gold tests for handling projectivity

* In JSON roundtrip compare results from `dev_dataset` rather than
`train_dataset` to avoid projectivization (and other potential
modifications)

* Add test for projective train vs. nonprojective dev versions of the
same `Doc`

* Handle ignore_misaligned as arg rather than attr

Move `ignore_misaligned` from an attribute of `Example` to an argument
to `Example.get_gold_parses()`, which makes it parallel to
`make_projective`.

Add test with old and new align that checks whether `ignore_misaligned`
errors are raised as expected (only for new align).

* Remove unused attrs from gold.pxd

Remove `ignore_misaligned` and `make_projective` from `gold.pxd`

* Refer to Example.goldparse in iter_gold_docs()

Use `Example.goldparse` in `iter_gold_docs()` instead of `Example.gold`
because a `None` `GoldParse` is generated with ignore_misaligned and
generating it on-the-fly can raise an unwanted AlignmentError

* Update test for ignore_misaligned
2019-11-23 14:32:15 +01:00
Ines Montani 74b951fe61
Fix xpassing tests (#4657)
* Ignore internal warnings

* Un-xfail passing tests

* Skip instead of xfail
2019-11-16 20:20:53 +01:00
Sofie Van Landeghem e48a09df4e Example class for training data (#4543)
* OrigAnnot class instead of gold.orig_annot list of zipped tuples

* from_orig to replace from_annot_tuples

* rename to RawAnnot

* some unit tests for GoldParse creation and internal format

* removing orig_annot and switching to lists instead of tuple

* rewriting tuples to use RawAnnot (+ debug statements, WIP)

* fix pop() changing the data

* small fixes

* pop-append fixes

* return RawAnnot for existing GoldParse to have uniform interface

* clean up imports

* fix merge_sents

* add unit test for 4402 with new structure (not working yet)

* introduce DocAnnot

* typo fixes

* add unit test for merge_sents

* rename from_orig to from_raw

* fixing unit tests

* fix nn parser

* read_annots to produce text, doc_annot pairs

* _make_golds fix

* rename golds_to_gold_annots

* small fixes

* fix encoding

* have golds_to_gold_annots use DocAnnot

* missed a spot

* merge_sents as function in DocAnnot

* allow specifying only part of the token-level annotations

* refactor with Example class + underlying dicts

* pipeline components to work with Example objects (wip)

* input checking

* fix yielding

* fix calls to update

* small fixes

* fix scorer unit test with new format

* fix kwargs order

* fixes for ud and conllu scripts

* fix reading data for conllu script

* add in proper errors (not fixed numbering yet to avoid merge conflicts)

* fixing few more small bugs

* fix EL script
2019-11-11 17:35:27 +01:00
Matthew Honnibal a927b3a21e Put new alignment behind flag for v2.2.2 release (#4541)
* Xfail new tokenization test

* Put new alignment behind feature flag

* Move USE_ALIGN to top of the file [ci skip]


Co-authored-by: Ines Montani <ines@ines.io>
2019-10-28 16:12:32 +01:00
tamuhey df293f3894 modified gold.align to handle space tokens (#4537)
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2019-10-28 15:44:28 +01:00
Ines Montani c5e41247e8 Tidy up and auto-format 2019-10-28 12:43:55 +01:00
tamuhey 554850206c [#4525] fix gold.align (#4526)
* fix: gold.align

* fix align

* remove old align
2019-10-27 13:38:04 +01:00
Ines Montani cc05d9dad6 Auto-format [ci skip] 2019-10-24 16:21:08 +02:00
adrianeboyd 8516e9d53b Support train dict format as JSONL (#4471)
* Support train dict format as JSONL

* Add (overly simple) check for dict vs. tuple to read JSONL lines as
either train dicts or train tuples

* Extend JSON/JSONL roundtrip conversion tests using `docs_to_json()`
and `GoldCorpus.train_tuples`

* Revert docs to default JSON output with convert
2019-10-23 16:01:44 +02:00
adrianeboyd f5c551a43a Checks/errors related to ill-formed IOB input in CLI convert and debug-data (#4487)
* Error for ill-formed input to iob_to_biluo()

Check for empty label in iob_to_biluo(), which can result from
ill-formed input.

* Check for empty NER label in debug-data
2019-10-21 12:20:28 +02:00
Ines Montani 3d8fd4b461 Revert #4334 2019-09-29 17:32:12 +02:00
Ines Montani c9cd516d96 Move tests out of package (#4334)
* Move tests out of package

* Fix typo
2019-09-28 18:05:00 +02:00
adrianeboyd b5d999e510 Add textcat to train CLI (#4226)
* Add doc.cats to spacy.gold at the paragraph level

Support `doc.cats` as `"cats": [{"label": string, "value": number}]` in
the spacy JSON training format at the paragraph level.

* `spacy.gold.docs_to_json()` writes `docs.cats`

* `GoldCorpus` reads in cats in each `GoldParse`

* Update instances of gold_tuples to handle cats

Update iteration over gold_tuples / gold_parses to handle addition of
cats at the paragraph level.

* Add textcat to train CLI

* Add textcat options to train CLI
* Add textcat labels in `TextCategorizer.begin_training()`
* Add textcat evaluation to `Scorer`:
  * For binary exclusive classes with provided label: F1 for label
  * For 2+ exclusive classes: F1 macro average
  * For multilabel (not exclusive): ROC AUC macro average (currently
relying on sklearn)
* Provide user info on textcat evaluation settings, potential
incompatibilities
* Provide pipeline to Scorer in `Language.evaluate` for textcat config
* Customize train CLI output to include only metrics relevant to current
pipeline
* Add textcat evaluation to evaluate CLI

* Fix handling of unset arguments and config params

Fix handling of unset arguments and model confiug parameters in Scorer
initialization.

* Temporarily add sklearn requirement

* Remove sklearn version number

* Improve Scorer handling of models without textcats

* Fixing Scorer handling of models without textcats

* Update Scorer output for python 2.7

* Modify inf in Scorer for python 2.7

* Auto-format

Also make small adjustments to make auto-formatting with black easier and produce nicer results

* Move error message to Errors

* Update documentation

* Add cats to annotation JSON format [ci skip]

* Fix tpl flag and docs [ci skip]

* Switch to internal roc_auc_score

Switch to internal `roc_auc_score()` adapted from scikit-learn.

* Add AUCROCScore tests and improve errors/warnings

* Add tests for AUCROCScore and roc_auc_score
* Add missing error for only positive/negative values
* Remove unnecessary warnings and errors

* Make reduced roc_auc_score functions private

Because most of the checks and warnings have been stripped for the
internal functions and access is only intended through `ROCAUCScore`,
make the functions for roc_auc_score adapted from scikit-learn private.

* Check that data corresponds with multilabel flag

Check that the training instances correspond with the multilabel flag,
adding the multilabel flag if required.

* Add textcat score to early stopping check

* Add more checks to debug-data for textcat

* Add example training data for textcat

* Add more checks to textcat train CLI

* Check configuration when extending base model
* Fix typos

* Update textcat example data

* Provide licensing details and licenses for data
* Remove two labels with no positive instances from jigsaw-toxic-comment
data.


Co-authored-by: Ines Montani <ines@ines.io>
2019-09-15 22:31:31 +02:00
Ines Montani 009280fbc5 Tidy up and auto-format 2019-08-18 15:09:16 +02:00
Ziming He eea7d4f4a8 biluo_tags_from_offsets throw exception for overlapping entities (#4021)
* Check whether two entities overlap

- biluo_gold_biluo_overlap now throw exception when entities passed in have overlaps
- added unit test

* SCA agreement
2019-08-15 18:13:32 +02:00
Ines Montani 9b62639d19 Auto-format [ci skip] 2019-02-27 14:24:55 +01:00
Matthew Honnibal f1d77eb140
💫 Improve handling of missing NER tags (closes #2603) (#3341)
* Improve handling of missing NER tags

GoldParse can accept missing NER tags, if entities is provided
in BILUO format (rather than as spans). Missing tags can be provided
as None values.

Fix bug that occurred when first tag was a None value. Closes #2603.

* Document specification of missing NER tags.
2019-02-27 12:06:32 +01:00
Ines Montani f25bd9f5e4 Add gold.spans_from_biluo_tags helper (#3227) 2019-02-06 21:50:26 +11:00
Ines Montani 37c7c85a86 💫 New JSON helpers, training data internals & CLI rewrite (#2932)
* Support nowrap setting in util.prints

* Tidy up and fix whitespace

* Simplify script and use read_jsonl helper

* Add JSON schemas (see #2928)

* Deprecate Doc.print_tree

Will be replaced with Doc.to_json, which will produce a unified format

* Add Doc.to_json() method (see #2928)

Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space.

* Remove outdated test

* Add write_json and write_jsonl helpers

* WIP: Update spacy train

* Tidy up spacy train

* WIP: Use wasabi for formatting

* Add GoldParse helpers for JSON format

* WIP: add debug-data command

* Fix typo

* Add missing import

* Update wasabi pin

* Add missing import

* 💫 Refactor CLI (#2943)

To be merged into #2932.

## Description
- [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi)
- [x] use [`black`](https://github.com/ambv/black) for auto-formatting
- [x] add `flake8` config
- [x] move all messy UD-related scripts to `cli.ud`
- [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO)

### Types of change
enhancement

## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.

* Update wasabi pin

* Delete old test

* Update errors

* Fix typo

* Tidy up and format remaining code

* Fix formatting

* Improve formatting of messages

* Auto-format remaining code

* Add tok2vec stuff to spacy.train

* Fix typo

* Update wasabi pin

* Fix path checks for when train() is called as function

* Reformat and tidy up pretrain script

* Update argument annotations

* Raise error if model language doesn't match lang

* Document new train command
2018-11-30 20:16:14 +01:00