* 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>
Add official support for the `DependencyMatcher`. Redesign the pattern
specification. Fix and extend operator implementations. Update API docs
and add usage docs.
Patterns
--------
Refactor pattern structure to:
```
{
"LEFT_ID": str,
"REL_OP": str,
"RIGHT_ID": str,
"RIGHT_ATTRS": dict,
}
```
The first node contains only `RIGHT_ID` and `RIGHT_ATTRS` and all
subsequent nodes contain all four keys.
New operators
-------------
Because of the way patterns are constructed from left to right, it's
helpful to have `follows` operators along with `precedes` operators. Add
operators for simple precedes / follows alongside immediate precedes /
follows.
* `.*`: precedes
* `;`: immediately follows
* `;*`: follows
Operator fixes
--------------
* `<` and `<<` do not include the node itself
* Fix reversed order for all operators involving linear precedence (`.`,
all sibling operators)
* Linear precedence operators do not match nodes outside the same parse
Additional fixes
----------------
* Use v3 Matcher API
* Support `get` and `remove`
* Support pickling
* rename to spacy-transformers.TransformerListener
* add some more tok2vec tests
* use select_pipes
* fix docs - annotation setter was not changed in the end
* Add AttributeRuler.score
Add scoring for TAG / POS / MORPH / LEMMA if these are present in the
assigned token attributes.
Add default score weights (that don't really make a lot of sense) so
that the scores are in the default config in some form.
* Update docs
- Accept any case for label names in ents and colors option, even if actual predicted label uses different casing
- Don't text-transform: uppercase visually, if it's important to users that the label is represented as-is in the UI
* 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
* 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
* 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`.
* 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
* 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
* 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>
* Add version number to DocBin
Add a version number to DocBin for future use.
* Add POS to all attributes in DocBin
* Add morph string to strings in DocBin
* Update DocBin API
* Add string for ENT_KB_ID in DocBin
Very minor fix in docs, specifically in this part:
```
matcher = PhraseMatcher(nlp.vocab)
> for doc in matcher.pipe(texts, batch_size=50):
> pass
```
`texts` suggests the input is an iterable of strings. I replaced it for `docs`.
Very minor fix in docs, specifically in this part:
```
matcher = PhraseMatcher(nlp.vocab)
> for doc in matcher.pipe(texts, batch_size=50):
> pass
```
`texts` suggests the input is an iterable of strings. I replaced it for `docs`.
* Update website models for v2.3.0
* Add docs for Chinese word segmentation
* Tighten up Chinese docs section
* Merge branch 'master' into docs/v2.3.0 [ci skip]
* Merge branch 'master' into docs/v2.3.0 [ci skip]
* Auto-format and update version
* Update matcher.md
* Update languages and sorting
* Typo in landing page
* Infobox about token_match behavior
* Add meta and basic docs for Japanese
* POS -> TAG in models table
* Add info about lookups for normalization
* Updates to API docs for v2.3
* Update adding norm exceptions for adding languages
* Add --omit-extra-lookups to CLI API docs
* Add initial draft of "What's New in v2.3"
* Add new in v2.3 tags to Chinese and Japanese sections
* Add tokenizer to migration section
* Add new in v2.3 flags to init-model
* Typo
* More what's new in v2.3
Co-authored-by: Ines Montani <ines@ines.io>
* 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
* 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>
To fix the slow tokenizer URL (#4374) and allow `token_match` to take
priority over prefixes and suffixes by default, introduce a new
tokenizer option for a token match pattern that's applied after prefixes
and suffixes but before infixes.
* `debug-data`: determine coverage of provided vectors
* `evaluate`: support `blank:lg` model to make it possible to just evaluate
tokenization
* `init-model`: add option to truncate vectors to N most frequent vectors
from word2vec file
* `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
Reconstruction of the original PR #4697 by @MiniLau.
Removes unused `SENT_END` symbol and `IS_SENT_END` from `Matcher` schema
because the Matcher is only going to be able to support `IS_SENT_START`.
* add lemma option to displacy 'dep' visualiser
* more compact list comprehension
* add option to doc
* fix test and add lemmas to util.get_doc
* fix capital
* remove lemma from get_doc
* cleanup
* Update token.md
documentation is confusing: A '?' is a right punct, but '¿' is a left punct
* Update token.md
add quotations around parentheses in `is_left_punct` and `is_right_punct` for clarrification, ensuring the question mark that follows is not percieved as an example of left and right punctuation
* Move quotes into code block [ci skip]
* Expose tokenizer rules as a property
Expose the tokenizer rules property in the same way as the other core
properties. (The cache resetting is overkill, but consistent with
`from_bytes` for now.)
Add tests and update Tokenizer API docs.
* Update Hungarian punctuation to remove empty string
Update Hungarian punctuation definitions so that `_units` does not match
an empty string.
* Use _load_special_tokenization consistently
Use `_load_special_tokenization()` and have it to handle `None` checks.
* Fix precedence of `token_match` vs. special cases
Remove `token_match` check from `_split_affixes()` so that special cases
have precedence over `token_match`. `token_match` is checked only before
infixes are split.
* Add `make_debug_doc()` to the Tokenizer
Add `make_debug_doc()` to the Tokenizer as a working implementation of
the pseudo-code in the docs.
Add a test (marked as slow) that checks that `nlp.tokenizer()` and
`nlp.tokenizer.make_debug_doc()` return the same non-whitespace tokens
for all languages that have `examples.sentences` that can be imported.
* Update tokenization usage docs
Update pseudo-code and algorithm description to correspond to
`nlp.tokenizer.make_debug_doc()` with example debugging usage.
Add more examples for customizing tokenizers while preserving the
existing defaults.
Minor edits / clarifications.
* Revert "Update Hungarian punctuation to remove empty string"
This reverts commit f0a577f7a5.
* Rework `make_debug_doc()` as `explain()`
Rework `make_debug_doc()` as `explain()`, which returns a list of
`(pattern_string, token_string)` tuples rather than a non-standard
`Doc`. Update docs and tests accordingly, leaving the visualization for
future work.
* Handle cases with bad tokenizer patterns
Detect when tokenizer patterns match empty prefixes and suffixes so that
`explain()` does not hang on bad patterns.
* Remove unused displacy image
* Add tokenizer.explain() to usage docs
* Add arch for MishWindowEncoder
* Support mish in tok2vec and conv window >=2
* Pass new tok2vec settings from parser
* Syntax error
* Fix tok2vec setting
* Fix registration of MishWindowEncoder
* Fix receptive field setting
* Fix mish arch
* Pass more options from parser
* Support more tok2vec options in pretrain
* Require thinc 7.3
* Add docs [ci skip]
* Require thinc 7.3.0.dev0 to run CI
* Run black
* Fix typo
* Update Thinc version
Co-authored-by: Ines Montani <ines@ines.io>
* Implement new API for {Phrase}Matcher.add (backwards-compatible)
* Update docs
* Also update DependencyMatcher.add
* Update internals
* Rewrite tests to use new API
* Add basic check for common mistake
Raise error with suggestion if user likely passed in a pattern instead of a list of patterns
* Fix typo [ci skip]
* Update English tag_map
Update English tag_map based on this conversion table:
https://universaldependencies.org/tagset-conversion/en-penn-uposf.html
* Update German tag_map
Update German tag_map based on this conversion table:
https://universaldependencies.org/tagset-conversion/de-stts-uposf.html
* Add missing Tiger dependencies to glossary
* Add quotes to definition of TO
* Update POS/TAG tables in docs
Update POS/TAG tables for English and German docs using current
information generated from the tag_maps and GLOSSARY.
* Update warning that -PRON- is specific to English
* Revert docs to default JSON output with convert
* Revert "Revert docs to default JSON output with convert"
This reverts commit 6b78c048f1.
* 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
* Move test
* Allow default in Lookups.get_table
* Start with blank tables in Lookups.from_bytes
* Refactor lemmatizer to hold instance of Lookups
* Get lookups table within the lemmatization methods to make sure it references the correct table (even if the table was replaced or modified, e.g. when loading a model from disk)
* Deprecate other arguments on Lemmatizer.__init__ and expect Lookups for consistency
* Remove old and unsupported Lemmatizer.load classmethod
* Refactor language-specific lemmatizers to inherit as much as possible from base class and override only what they need
* Update tests and docs
* Fix more tests
* Fix lemmatizer
* Upgrade pytest to try and fix weird CI errors
* Try pytest 4.6.5
* Allow vectors name to be specified in init-model
* Document --vectors-name argument to init-model
* Update website/docs/api/cli.md
Co-Authored-By: Ines Montani <ines@ines.io>
* 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>
* Adjust Table API and add docs
* Add attributes and update description [ci skip]
* Use strings.get_string_id instead of hash_string
* Fix table method calls
* Make orth arg in Lemmatizer.lookup optional
Fall back to string, which is now handled by Table.__contains__ out-of-the-box
* Fix method name
* Auto-format
* Allow copying the user_data with as_doc + unit test
* add option to docs
* add typing
* import fix
* workaround to avoid bool clashing ...
* bint instead of bool
* document token ent_kb_id
* document span kb_id
* update pipeline documentation
* prior and context weights as bool's instead
* entitylinker api documentation
* drop for both models
* finish entitylinker documentation
* small fixes
* documentation for KB
* candidate documentation
* links to api pages in code
* small fix
* frequency examples as counts for consistency
* consistent documentation about tensors returned by predict
* add entity linking to usage 101
* add entity linking infobox and KB section to 101
* entity-linking in linguistic features
* small typo corrections
* training example and docs for entity_linker
* predefined nlp and kb
* revert back to similarity encodings for simplicity (for now)
* set prior probabilities to 0 when excluded
* code clean up
* bugfix: deleting kb ID from tokens when entities were removed
* refactor train el example to use either model or vocab
* pretrain_kb example for example kb generation
* add to training docs for KB + EL example scripts
* small fixes
* error numbering
* ensure the language of vocab and nlp stay consistent across serialization
* equality with =
* avoid conflict in errors file
* add error 151
* final adjustements to the train scripts - consistency
* update of goldparse documentation
* small corrections
* push commit
* typo fix
* add candidate API to kb documentation
* update API sidebar with EntityLinker and KnowledgeBase
* remove EL from 101 docs
* remove entity linker from 101 pipelines / rephrase
* custom el model instead of existing model
* set version to 2.2 for EL functionality
* update documentation for 2 CLI scripts
* Updates/bugfixes for NER/IOB converters
* Converter formats `ner` and `iob` use autodetect to choose a converter if
possible
* `iob2json` is reverted to handle sentence-per-line data like
`word1|pos1|ent1 word2|pos2|ent2`
* Fix bug in `merge_sentences()` so the second sentence in each batch isn't
skipped
* `conll_ner2json` is made more general so it can handle more formats with
whitespace-separated columns
* Supports all formats where the first column is the token and the final
column is the IOB tag; if present, the second column is the POS tag
* As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O`
separates documents
* Add option for segmenting sentences (new flag `-s`)
* Parser-based sentence segmentation with a provided model, otherwise with
sentencizer (new option `-b` to specify model)
* Can group sentences into documents with `n_sents` as long as sentence
segmentation is available
* Only applies automatic segmentation when there are no existing delimiters
in the data
* Provide info about settings applied during conversion with warnings and
suggestions if settings conflict or might not be not optimal.
* Add tests for common formats
* Add '(default)' back to docs for -c auto
* Add document count back to output
* Revert changes to converter output message
* Use explicit tabs in convert CLI test data
* Adjust/add messages for n_sents=1 default
* Add sample NER data to training examples
* Update README
* Add links in docs to example NER data
* Define msg within converters
* add `words`
* update name of entity list to `ner`
I think it might be a bit more consistent to have `ner` named `entities`
or `ents` (and `ents` is actually set somewhere to `None`, which is a
bit confusing), but it looks like renaming it would be a non-trivial
decision.
* Update pretrain to prevent unintended overwriting of weight files for #3859
* Add '--epoch-start' to pretrain docs
* Add mising pretrain arguments to bash example
* Update doc tag for v2.1.5
* Perserve flags in EntityRuler
The EntityRuler (explosion/spaCy#3526) does not preserve
overwrite flags (or `ent_id_sep`) when serialized. This
commit adds support for serialization/deserialization preserving
overwrite and ent_id_sep flags.
* add signed contributor agreement
* flake8 cleanup
mostly blank line issues.
* mark test from the issue as needing a model
The test from the issue needs some language model for serialization
but the test wasn't originally marked correctly.
* Adds `phrase_matcher_attr` to allow args to PhraseMatcher
This is an added arg to pass to the `PhraseMatcher`. For example,
this allows creation of a case insensitive phrase matcher when the
`EntityRuler` is created. References explosion/spaCy#3822
* remove unneeded model loading
The model didn't need to be loaded, and I replaced it with
a change that doesn't require it (using existings fixtures)
* updated docstring for new argument
* updated docs to reflect new argument to the EntityRuler constructor
* change tempdir handling to be compatible with python 2.7
* return conflicted code to entityruler
Some stuff got cut out because of merge conflicts, this
returns that code for the phrase_matcher_attr.
* fixed typo in the code added back after conflicts
* flake8 compliance
When I deconflicted the branch there were some flake8 issues
introduced. This resolves the spacing problems.
* test changes: attempts to fix flaky test in python3.5
These tests seem to be alittle flaky in 3.5 so I changed the check to avoid
the comparisons that seem to be fail sometimes.
* Add error to `get_vectors_loss` for unsupported loss function of `pretrain`
* Add missing "--loss-func" argument to pretrain docs. Update pretrain plac annotations to match docs.
* Add missing quotation marks
* Update tokenizer.md for construction example
Self contained example. You should really say what nlp is so that the example will work as is
* Update CONTRIBUTOR_AGREEMENT.md
* Restore contributor agreement
* Adjust construction examples
* Add check for empty input file to CLI pretrain
* Raise error if JSONL is not a dict or contains neither `tokens` nor `text` key
* Skip empty values for correct pretrain keys and log a counter as warning
* Add tests for CLI pretrain core function make_docs.
* Add a short hint for the `tokens` key to the CLI pretrain docs
* Add success message to CLI pretrain
* Update model loading to fix the tests
* Skip empty values and do not create docs out of it
<!--- Provide a general summary of your changes in the title. -->
When using `spacy pretrain`, the model is saved only after every epoch. But each epoch can be very big since `pretrain` is used for language modeling tasks. So I added a `--save-every` option in the CLI to save after every `--save-every` batches.
## Description
<!--- Use this section to describe your changes. If your changes required
testing, include information about the testing environment and the tests you
ran. If your test fixes a bug reported in an issue, don't forget to include the
issue number. If your PR is still a work in progress, that's totally fine – just
include a note to let us know. -->
To test...
Save this file to `sample_sents.jsonl`
```
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
```
Then run `--save-every 2` when pretraining.
```bash
spacy pretrain sample_sents.jsonl en_core_web_md here -nw 1 -bs 1 -i 10 --save-every 2
```
And it should save the model to the `here/` folder after every 2 batches. The models that are saved during an epoch will have a `.temp` appended to the save name.
At the end the training, you should see these files (`ls here/`):
```bash
config.json model2.bin model5.bin model8.bin
log.jsonl model2.temp.bin model5.temp.bin model8.temp.bin
model0.bin model3.bin model6.bin model9.bin
model0.temp.bin model3.temp.bin model6.temp.bin model9.temp.bin
model1.bin model4.bin model7.bin
model1.temp.bin model4.temp.bin model7.temp.bin
```
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
This is a new feature to `spacy pretrain`.
🌵 **Unfortunately, I haven't been able to test this because compiling from source is not working (cythonize error).**
```
Processing matcher.pyx
[Errno 2] No such file or directory: '/Users/mwu/github/spaCy/spacy/matcher.pyx'
Traceback (most recent call last):
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 169, in <module>
run(args.root)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 158, in run
process(base, filename, db)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 124, in process
preserve_cwd(base, process_pyx, root + ".pyx", root + ".cpp")
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 87, in preserve_cwd
func(*args)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 63, in process_pyx
raise Exception("Cython failed")
Exception: Cython failed
Traceback (most recent call last):
File "setup.py", line 276, in <module>
setup_package()
File "setup.py", line 209, in setup_package
generate_cython(root, "spacy")
File "setup.py", line 132, in generate_cython
raise RuntimeError("Running cythonize failed")
RuntimeError: Running cythonize failed
```
Edit: Fixed! after deleting all `.cpp` files: `find spacy -name "*.cpp" | xargs rm`
## 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.
* fix(util): fix decaying function output
* fix(util): better test and adhere to code standards
* fix(util): correct variable name, pytestify test, update website text
* Fix code for bag-of-words feature extraction
The _ml.py module had a redundant copy of a function to extract unigram
bag-of-words features, except one had a bug that set values to 0.
Another function allowed extraction of bigram features. Replace all three
with a new function that supports arbitrary ngram sizes and also allows
control of which attribute is used (e.g. ORTH, LOWER, etc).
* Support 'bow' architecture for TextCategorizer
This allows efficient ngram bag-of-words models, which are better when
the classifier needs to run quickly, especially when the texts are long.
Pass architecture="bow" to use it. The extra arguments ngram_size and
attr are also available, e.g. ngram_size=2 means unigram and bigram
features will be extracted.
* Fix size limits in train_textcat example
* Explain architectures better in docs
Add and document CLI options for batch size, max doc length, min doc length for `spacy pretrain`.
Also improve CLI output.
Closes#3216
## 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.
* Add component_cfg kwarg to begin_training
* Document component_cfg arg to begin_training
* Update docs and auto-format
* Support component_cfg across Language
* Format
* Update docs and docstrings [ci skip]
* Fix begin_training
* Make serialization methods consistent
exclude keyword argument instead of random named keyword arguments and deprecation handling
* Update docs and add section on serialization fields
* Use default return instead of else
* Add Doc.is_nered to indicate if entities have been set
* Add properties in Doc.to_json if they were set, not if they're available
This way, if a processed Doc exports "pos": None, it means that the tag was explicitly unset. If it exports "ents": [], it means that entity annotations are available but that this document doesn't contain any entities. Before, this would have been unclear and problematic for training.
<!--- Provide a general summary of your changes in the title. -->
## Description
* tidy up and adjust Cython code to code style
* improve docstrings and make calling `help()` nicer
* add URLs to new docs pages to docstrings wherever possible, mostly to user-facing objects
* fix various typos and inconsistencies in docs
### Types of change
enhancement, docs
## 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.
* 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.
<!--- Provide a general summary of your changes in the title. -->
## Description
This PR adds the abilility to override custom extension attributes during merging. This will only work for attributes that are writable, i.e. attributes registered with a default value like `default=False` or attribute that have both a getter *and* a setter implemented.
```python
Token.set_extension('is_musician', default=False)
doc = nlp("I like David Bowie.")
with doc.retokenize() as retokenizer:
attrs = {"LEMMA": "David Bowie", "_": {"is_musician": True}}
retokenizer.merge(doc[2:4], attrs=attrs)
assert doc[2].text == "David Bowie"
assert doc[2].lemma_ == "David Bowie"
assert doc[2]._.is_musician
```
### 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.
<!--- Provide a general summary of your changes in the title. -->
## Description
The new website is implemented using [Gatsby](https://www.gatsbyjs.org) with [Remark](https://github.com/remarkjs/remark) and [MDX](https://mdxjs.com/). This allows authoring content in **straightforward Markdown** without the usual limitations. Standard elements can be overwritten with powerful [React](http://reactjs.org/) components and wherever Markdown syntax isn't enough, JSX components can be used. Hopefully, this update will also make it much easier to contribute to the docs. Once this PR is merged, I'll implement auto-deployment via [Netlify](https://netlify.com) on a specific branch (to avoid building the website on every PR). There's a bunch of other cool stuff that the new setup will allow us to do – including writing front-end tests, service workers, offline support, implementing a search and so on.
This PR also includes various new docs pages and content.
Resolves#3270. Resolves#3222. Resolves#2947. Resolves#2837.
### 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.
