* 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
* rename to spacy-transformers.TransformerListener
* add some more tok2vec tests
* use select_pipes
* fix docs - annotation setter was not changed in the end
* Fix up/download of http and local paths
* Support git_sparse_checkout for assets
* Fix scorer
* Handle already-present directories for git assets
* Improve convert command
* Fix support for existant files in git assets
* Support branches in git sparse checkout
* Format
* Fix git assets
* Document git block in assets
* Fix test
* Fix test
* Revert "Fix test"
This reverts commit cf3097260f.
* Revert "Fix test"
This reverts commit 964d636e27.
* Dont multiply p/r/f by 100
* Display scores * 100 during training
- As much as I dislike YAML, it seemed like a better format here because it allows us to add comments if we want to explain the different recommendations
- Don't include the generated JS in the repo by default and build it on the fly when running or deploying the site. This ensures it's always up to date.
- Simplify jinja_to_js script and use fewer dependencies
* 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
Move timing into `Language.evaluate` so that only the processing is
timing, not processing + scoring. `Language.evaluate` returns
`scores["speed"]` as words per second, which should be identical to how
the speed was added to the scores previously. Also add the speed to the
evaluate CLI output.
Add and update `score` methods, provided `scores`, and default weights
`default_score_weights` for pipeline components.
* `scores` provides all top-level keys returned by `score` (merely informative, similar to `assigns`).
* `default_score_weights` provides the default weights for a default config.
* The keys from `default_score_weights` determine which values will be
shown in the `spacy train` output, so keys with weight `0.0` will be
displayed but not counted toward the overall score.
* Provide top-level score as `attr_score`
* Provide a description of the score as `attr_score_desc`
* Provide all potential scores keys, setting unused keys to `None`
* Update CLI evaluate accordingly
* Refactor the Scorer to improve flexibility
Refactor the `Scorer` to improve flexibility for arbitrary pipeline
components.
* Individual pipeline components provide their own `evaluate` methods
that score a list of `Example`s and return a dictionary of scores
* `Scorer` is initialized either:
* with a provided pipeline containing components to be scored
* with a default pipeline containing the built-in statistical
components (senter, tagger, morphologizer, parser, ner)
* `Scorer.score` evaluates a list of `Example`s and returns a dictionary
of scores referring to the scores provided by the components in the
pipeline
Significant differences:
* `tags_acc` is renamed to `tag_acc` to be consistent with `token_acc`
and the new `morph_acc`, `pos_acc`, and `lemma_acc`
* Scoring is no longer cumulative: `Scorer.score` scores a list of
examples rather than a single example and does not retain any state
about previously scored examples
* PRF values in the returned scores are no longer multiplied by 100
* Add kwargs to Morphologizer.evaluate
* Create generalized scoring methods in Scorer
* Generalized static scoring methods are added to `Scorer`
* Methods require an attribute (either on Token or Doc) that is
used to key the returned scores
Naming differences:
* `uas`, `las`, and `las_per_type` in the scores dict are renamed to
`dep_uas`, `dep_las`, and `dep_las_per_type`
Scoring differences:
* `Doc.sents` is now scored as spans rather than on sentence-initial
token positions so that `Doc.sents` and `Doc.ents` can be scored with
the same method (this lowers scores since a single incorrect sentence
start results in two incorrect spans)
* Simplify / extend hasattr check for eval method
* Add hasattr check to tokenizer scoring
* Simplify to hasattr check for component scoring
* Reset Example alignment if docs are set
Reset the Example alignment if either doc is set in case the
tokenization has changed.
* Add PRF tokenization scoring for tokens as spans
Add PRF scores for tokens as character spans. The scores are:
* token_acc: # correct tokens / # gold tokens
* token_p/r/f: PRF for (token.idx, token.idx + len(token))
* Add docstring to Scorer.score_tokenization
* Rename component.evaluate() to component.score()
* Update Scorer API docs
* Update scoring for positive_label in textcat
* Fix TextCategorizer.score kwargs
* Update Language.evaluate docs
* Update score names in default config
* 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>
* Improve tag map initialization and updating
Generalize tag map initialization and updating so that the tag map can
be loaded correctly prior to loading a `Corpus` with `spacy debug-data`
and `spacy train`.
* normalize provided tag map as necessary
* use the same method for initializing and updating the tag map
* Replace rather than update tag map
Replace rather than update tag map when loading a custom tag map.
Updating the tag map is problematic due to the sorted list of tag names
and the fact that the tag map will contain lingering/unwanted tags from
the default tag map.
* Update CLI scripts
* Reinitialize cache after loading new tag map
Reinitialize the cache with the right size after loading a new tag map.
* Improve tag map initialization and updating
Generalize tag map initialization and updating so that a provided tag
map can be loaded correctly in the CLI.
* normalize provided tag map as necessary
* use the same method for initializing and overwriting the tag map
* Reinitialize cache after loading new tag map
Reinitialize the cache with the right size after loading a new tag map.
* adding debug-model to print the internals for debugging purposes
* expend debug-model script with 4 stages: before, init, train, predict
* avoid enforcing to have a seed in the train script
* small fixes
* Update project CLI hashes, directories, skipping
* Improve clone success message
* Remove unused context args
* Move project-specific utils to project utils
The hashing/checksum functions may not end up being general-purpose functions and are more designed for the projects, so they shouldn't live in spacy.util
* Improve run help and add workflows
* Add note re: directory checksum speed
* Fix cloning from subdirectories and output messages
* Remove hard-coded dirs
* Make project command a submodule
* Update with WIP
* Add helper for joining commands
* Update docstrins, formatting and types
* Update assets and add support for copying local files
* Fix type
* Update success messages
* 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
* Use cosine loss in Cloze multitask
* Fix char_embed for gpu
* Call resume_training for base model in train CLI
* Fix bilstm_depth default in pretrain command
* Implement character-based pretraining objective
* Use chars loss in ClozeMultitask
* Add method to decode predicted characters
* Fix number characters
* Rescale gradients for mlm
* Fix char embed+vectors in ml
* Fix pipes
* Fix pretrain args
* Move get_characters_loss
* Fix import
* Fix import
* Mention characters loss option in pretrain
* Remove broken 'self attention' option in pretrain
* Revert "Remove broken 'self attention' option in pretrain"
This reverts commit 56b820f6af.
* Document 'characters' objective of pretrain
* Tell convert CLI to store user data for Doc
* Remove assert
* Add has_unknwon_spaces flag on Doc
* Do not tokenize docs with unknown spaces in Corpus
* Handle conversion of unknown spaces in Example
* Fixes
* Fixes
* Draft has_known_spaces support in DocBin
* Add test for serialize has_unknown_spaces
* Fix DocBin serialization when has_unknown_spaces
* Use serialization in test
* 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
Updates from #5362 and fix from #5387:
* `train`:
* if training on GPU, only run evaluation/timing on CPU in the first
iteration
* if training is aborted, exit with a non-0 exit status
