* 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
* 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
* moving syntax folder to _parser_internals
* moving nn_parser and transition_system
* move nn_parser and transition_system out of internals folder
* moving nn_parser code into transition_system file
* rename transition_system to transition_parser
* moving parser_model and _state to ml
* move _state back to internals
* The Parser now inherits from Pipe!
* small code fixes
* removing unnecessary imports
* remove link_vectors_to_models
* transition_system to internals folder
* little bit more cleanup
* newlines
* 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>
* 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
* entity linker training example: model loading changed according to issue 5668 (https://github.com/explosion/spaCy/issues/5668) + vocab_path is a required argument
* contributor agreement
* 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
* 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>
* 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
* 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
* 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>
* 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>
* Draft layer for BILUO actions
* Fixes to biluo layer
* WIP on BILUO layer
* Add tests for BILUO layer
* Format
* Fix transitions
* Update test
* Link in the simple_ner
* Update BILUO tagger
* Update __init__
* Import simple_ner
* Update test
* Import
* Add files
* Add config
* Fix label passing for BILUO and tagger
* Fix label handling for simple_ner component
* Update simple NER test
* Update config
* Hack train script
* Update BILUO layer
* Fix SimpleNER component
* Update train_from_config
* Add biluo_to_iob helper
* Add IOB layer
* Add IOBTagger model
* Update biluo layer
* Update SimpleNER tagger
* Update BILUO
* Read random seed in train-from-config
* Update use of normal_init
* Fix normalization of gradient in SimpleNER
* Update IOBTagger
* Remove print
* Tweak masking in BILUO
* Add dropout in SimpleNER
* Update thinc
* Tidy up simple_ner
* Fix biluo model
* Unhack train-from-config
* Update setup.cfg and requirements
* Add tb_framework.py for parser model
* Try to avoid memory leak in BILUO
* Move ParserModel into spacy.ml, avoid need for subclass.
* Use updated parser model
* Remove incorrect call to model.initializre in PrecomputableAffine
* Update parser model
* Avoid divide by zero in tagger
* Add extra dropout layer in tagger
* Refine minibatch_by_words function to avoid oom
* Fix parser model after refactor
* Try to avoid div-by-zero in SimpleNER
* Fix infinite loop in minibatch_by_words
* Use SequenceCategoricalCrossentropy in Tagger
* Fix parser model when hidden layer
* Remove extra dropout from tagger
* Add extra nan check in tagger
* Fix thinc version
* Update tests and imports
* Fix test
* Update test
* Update tests
* Fix tests
* Fix test
Co-authored-by: Ines Montani <ines@ines.io>
Sofie Van Landeghem