* API docs: Rename kb_in_memory to inmemorylookupkb, add to sidebar
* adjust to mdx
* linkout to InMemoryLookupKB at first occurrence in kb.mdx
* fix links to docs
* revert Azure trigger setting (I'll make a separate PR)
Co-authored-by: svlandeg <svlandeg@github.com>
* Add a `spacy evaluate speed` subcommand
This subcommand reports the mean batch performance of a model on a data set with
a 95% confidence interval. For reliability, it first performs some warmup
rounds. Then it will measure performance on batches with randomly shuffled
documents.
To avoid having too many spaCy commands, `speed` is a subcommand of `evaluate`
and accuracy evaluation is moved to its own `evaluate accuracy` subcommand.
* Fix import cycle
* Restore `spacy evaluate`, make `spacy benchmark speed` an alias
* Add documentation for `spacy benchmark`
* CREATES -> PRINTS
* WPS -> words/s
* Disable formatting of benchmark speed arguments
* Fail with an error message when trying to speed bench empty corpus
* Make it clearer that `benchmark accuracy` is a replacement for `evaluate`
* Fix docstring webpage reference
* tests: check `evaluate` output against `benchmark accuracy`
* Clean up displacy port-related error messages, docs
There were some issues in the error messages and docs in #11948.
1. the error messages didn't specify the port argument to displacy.serve correctly
2. the docs didn't mark the auto select argument as new
This addresses those issues.
* Update website/docs/api/top-level.md
Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
* Apply prettier
Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
In the v3 scorer refactoring, `token_acc` was implemented incorrectly.
It should use `precision` instead of `fscore` for the measure of
correctly aligned tokens / number of predicted tokens.
Fix the docs to reflect that the measure uses the number of predicted
tokens rather than the number of gold tokens.
* enable fuzzy matching
* add fuzzy param to EntityMatcher
* include rapidfuzz_capi
not yet used
* fix type
* add FUZZY predicate
* add fuzzy attribute list
* fix type properly
* tidying
* remove unnecessary dependency
* handle fuzzy sets
* simplify fuzzy sets
* case fix
* switch to FUZZYn predicates
use Levenshtein distance.
remove fuzzy param.
remove rapidfuzz_capi.
* revert changes added for fuzzy param
* switch to polyleven
(Python package)
* enable fuzzy matching
* add fuzzy param to EntityMatcher
* include rapidfuzz_capi
not yet used
* fix type
* add FUZZY predicate
* add fuzzy attribute list
* fix type properly
* tidying
* remove unnecessary dependency
* handle fuzzy sets
* simplify fuzzy sets
* case fix
* switch to FUZZYn predicates
use Levenshtein distance.
remove fuzzy param.
remove rapidfuzz_capi.
* revert changes added for fuzzy param
* switch to polyleven
(Python package)
* fuzzy match only on oov tokens
* remove polyleven
* exclude whitespace tokens
* don't allow more edits than characters
* fix min distance
* reinstate FUZZY operator
with length-based distance function
* handle sets inside regex operator
* remove is_oov check
* attempt build fix
no mypy failure locally
* re-attempt build fix
* don't overwrite fuzzy param value
* move fuzzy_match
to its own Python module to allow patching
* move fuzzy_match back inside Matcher
simplify logic and add tests
* Format tests
* Parametrize fuzzyn tests
* Parametrize and merge fuzzy+set tests
* Format
* Move fuzzy_match to a standalone method
* Change regex kwarg type to bool
* Add types for fuzzy_match
- Refactor variable names
- Add test for symmetrical behavior
* Parametrize fuzzyn+set tests
* Minor refactoring for fuzz/fuzzy
* Make fuzzy_match a Matcher kwarg
* Update type for _default_fuzzy_match
* don't overwrite function param
* Rename to fuzzy_compare
* Update fuzzy_compare default argument declarations
* allow fuzzy_compare override from EntityRuler
* define new Matcher keyword arg
* fix type definition
* Implement fuzzy_compare config option for EntityRuler and SpanRuler
* Rename _default_fuzzy_compare to fuzzy_compare, remove from reexported objects
* Use simpler fuzzy_compare algorithm
* Update types
* Increase minimum to 2 in fuzzy_compare to allow one transposition
* Fix predicate keys and matching for SetPredicate with FUZZY and REGEX
* Add FUZZY6..9
* Add initial docs
* Increase default fuzzy to rounded 30% of pattern length
* Update docs for fuzzy_compare in components
* Update EntityRuler and SpanRuler API docs
* Rename EntityRuler and SpanRuler setting to matcher_fuzzy_compare
To having naming similar to `phrase_matcher_attr`, rename
`fuzzy_compare` setting for `EntityRuler` and `SpanRuler` to
`matcher_fuzzy_compare. Organize next to `phrase_matcher_attr` in docs.
* Fix schema aliases
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix typo
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add FUZZY6-9 operators and update tests
* Parameterize test over greedy
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix type for fuzzy_compare to remove Optional
* Rename to spacy.levenshtein_compare.v1, move to spacy.matcher.levenshtein
* Update docs following levenshtein_compare renaming
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* check port in use and add itself
* check port in use and add itself
* Auto switch to nearest available port.
* Use bind to check port instead of connect_ex.
* Reformat.
* Add auto_select_port argument.
* update docs for displacy.serve
* Update spacy/errors.py
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Update website/docs/api/top-level.md
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Update spacy/errors.py
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Add test using multiprocessing
* fix argument name
* Increase sleep times
Want to rule this out as a cause of test failure
* Don't terminate a process that isn't alive
* Refactor port finding logic
This moves all the port logic into its own util function, which can be
tested without having to background a server directly.
* Use with for the server
This ensures the server is closed correctly.
* Pass in the host when checking port availability
* Shorten argument name
* Update error codes following merge
* Add types for arguments, specify docstrings.
* Add typing for arguments with default value.
* Update docstring to match spaCy format.
* Update docstring to match spaCy format.
* Fix docs
Arg name changed from `auto_select_port` to just `auto_select`.
* Revert "Fix docs"
This reverts commit 356966fe84.
Co-authored-by: zhiiw <1302593554@qq.com>
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
* add test for running evaluate on an nlp pipeline with two distinct textcat components
* cleanup
* merge dicts instead of overwrite
* don't add more labels to the given set
* Revert "merge dicts instead of overwrite"
This reverts commit 89bee0ed77.
* Switch tests to separate scorer keys rather than merged dicts
* Revert unrelated edits
* Switch textcat scorers to v2
* formatting
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* fix processing of "auto" in walk_directory
* add check for None
* move AUTO check to convert and fix verification of args
* add specific CLI test with CliRunner
* cleanup
* more cleanup
* update docstring
* Fix inconsistency in displaCy docs about page option
The `page` option, which wraps the output SVG in HTML, is true by
default for `serve` but not for `render`. The `render` docs were wrong
though, so this updates them.
* Update the same statement in more docs
A few renderers used the same language
* Add `ConsoleLogger.v3`
This addition expands the progress bar feature to count up the training/distillation steps to either the next evaluation pass or the maximum number of steps.
* Rename progress bar types
* Add defaults to docs
Minor fixes
* Move comment
* Minor punctuation fixes
* Explicitly check for `None` when validating progress bar type
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Convert all individual values explicitly to uint64 for array-based doc representations
* Temporarily test with latest numpy v1.24.0rc
* Remove unnecessary conversion from attr_t
* Reduce number of individual casts
* Convert specifically from int32 to uint64
* Revert "Temporarily test with latest numpy v1.24.0rc"
This reverts commit eb0e3c5006.
* Also use int32 in tests
Strings in replacement nodes where not added to the `StringStore`
when `EditTreeLemmatizer` was initialized from a set of labels. The
corresponding test did not capture this because it added the strings
through the examples that were passed to the initialization.
This change fixes both this bug in the initialization as the 'shadowing'
of the bug in the test.
If you don't have spacy-transformers installed, but try to use `init
config` with the GPU flag, you'll get an error. The issue is that the
`use_transformers` flag in the config is conflated with the GPU flag,
and then there's an attempt to access transformers config info that may
not exist.
There may be a better way to do this, but this stops the error.
* Support local filesystem remotes for projects
* Fix support for local filesystem remotes for projects
* Use `FluidPath` instead of `Pathy` to support both filesystem and
remote paths
* Create missing parent directories if required for local filesystem
* Add a more general `_file_exists` method to support both `Pathy`,
`Path`, and `smart_open`-compatible URLs
* Add explicit `smart_open` dependency starting with support for
`compression` flag
* Update `pathy` dependency to exclude older versions that aren't
compatible with required `smart_open` version
* Update docs to refer to `Pathy` instead of `smart_open` for project
remotes (technically you can still push to any `smart_open`-compatible
path but you can't pull from them)
* Add tests for local filesystem remotes
* Update pathy for general BlobStat sorting
* Add import
* Remove _file_exists since only Pathy remotes are supported
* Format CLI docs
* Clean up merge
* pymorph2 issues #11620, #11626, #11625:
- #11620: pymorphy2_lookup
- #11626: handle multiple forms pointing to the same normal form + handling empty POS tag
- #11625: matching DET that are labelled as PRON by pymorhp2
* Move lemmatizer algorithm changes back into RussianLemmatizer
* Fix uk pymorphy3_lookup mode init
* Move and update tests for ru/uk lookup lemmatizer modes
* Fix typo
* Remove traces of previous behavior for uninflected POS
* Refactor to private generic-looking pymorphy methods
* Remove xfailed uk lemmatizer cases
* Update spacy/lang/ru/lemmatizer.py
Co-authored-by: Richard Hudson <richard@explosion.ai>
Co-authored-by: Dmytro S Lituiev <d.lituiev@gmail.com>
Co-authored-by: Richard Hudson <richard@explosion.ai>
* Add `training.before_update` callback
This callback can be used to implement training paradigms like gradual (un)freezing of components (e.g: the Transformer) after a certain number of training steps to mitigate catastrophic forgetting during fine-tuning.
* Fix type annotation, default config value
* Generalize arguments passed to the callback
* Update schema
* Pass `epoch` to callback, rename `current_step` to `step`
* Add test
* Simplify test
* Replace config string with `spacy.blank`
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Cleanup imports
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Check textcat values for validity
* Fix error numbers
* Clean up vals reference
* Check category value validity through training
The _validate_categories is called in update, which for multilabel is
inherited from the single label component.
* Formatting
* Add equality definition for vectors
This re-uses the check from sourcing components.
* Use the equality check
* Format
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Fix typos, add couple of new abbreviations, remove nonbreaking spaces
* Remove space from abbreviation
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update warning, add tests for project requirements check
* Make warning more general for differences between PEP 508 and pip
* Add tests for _check_requirements
* Parameterize test
* Add fallback in requirements check, only check once
* Rename to skip_requirements_check
* Update spacy/cli/project/run.py
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
* Fix default parameters for load functions
Some load functions used SimpleFrozenList() directly instead of the
_DEFAULT_EMPTY_PIPES parameter. That mostly worked as intended, but
the changes in #11459 check for equality using identity, not value, so a
warning is incorrectly raised sometimes, as in #11706.
This change just has all the load functions use the singleton value
instead.
* Add test that there are no warnings on module-based load
This will succeed due to changes in this branch, but local tests with
the latest release failed as intended.
* Try reverting commit and see if CI changes
There is an error in CI that is probably unrelated.
Revert "Fix default parameters for load functions"
This reverts commit dc46b35687.
* Revert "Try reverting commit and see if CI changes"
This reverts commit 2514ed07ef.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update textcat scorer threshold behavior
For `textcat` (with exclusive classes) the scorer should always use a
threshold of 0.0 because there should be one predicted label per doc and
the numeric score for that particular label should not matter.
* Rename to test_textcat_multilabel_threshold
* Remove all uses of threshold for multi_label=False
* Update Scorer.score_cats API docs
* Add tests for score_cats with thresholds
* Update textcat API docs
* Fix types
* Convert threshold back to float
* Fix threshold type in docstring
* Improve formatting in Scorer API docs
* Handle docs with no entities
If a whole batch contains no entities it won't make it to the model, but
it's possible for individual Docs to have no entities. Before this
commit, those Docs would cause an error when attempting to concatenate
arrays because the dimensions didn't match.
It turns out the process of preparing the Ragged at the end of the span
maker forward was a little different from list2ragged, which just uses
the flatten function directly. Letting list2ragged do the conversion
avoids the dimension issue.
This did not come up before because in NEL demo projects it's typical
for data with no entities to be discarded before it reaches the NEL
component.
This includes a simple direct test that shows the issue and checks it's
resolved. It doesn't check if there are any downstream changes, so a
more complete test could be added. A full run was tested by adding an
example with no entities to the Emerson sample project.
* Add a blank instance to default training data in tests
Rather than adding a specific test, since not failing on instances with
no entities is basic functionality, it makes sense to add it to the
default set.
* Fix without modifying architecture
If the architecture is modified this would have to be a new version, but
this change isn't big enough to merit that.
* Fix multiple extensions and character offset
* Rename token_start/end to start/end
* Refactor Doc.from_json based on review
* Iterate over user_data items
* Only add non-empty underscore entries
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Fix flag handling in dvc
Prior to this commit, if a flag (--verbose or --quiet) was passed to
DVC, it would be added to the end of the generated dvc command line.
This would result in the command being interpreted as part of the actual
command to run, rather than an argument to dvc. This would result in
command lines like:
spacy project run preprocess --verbose
That would fail with an error that there's no such directory as
`--verbose`.
This change puts the flags at the front of the dvc command so that they
are interpreted correctly. It removes the `run_dvc_commands` function,
which had been reduced to just a for loop and wasn't used elsewhere.
A separate problem is that there's no way to specify the quiet behaviour
to dvc from the command line, though it's unclear if that's a bug.
* Add dvc quiet flag to docs
* Handle case in DVC where no commands are appropriate
If only have commands with no deps or outputs (admittedly unlikely), you
get a weird error about the dvc file not existing. This gives explicit
output instead.
* Add support for quiet flag
* Fix command execution
Commands are strings now because they're joined further up.
* Change enable/disable behavior so that arguments take precedence over config options. Extend error message on conflict. Add warning message in case of overwriting config option with arguments.
* Fix tests in test_serialize_pipeline.py to reflect changes to handling of enable/disable.
* Fix type issue.
* Move comment.
* Move comment.
* Issue UserWarning instead of printing wasabi message. Adjust test.
* Added pytest.warns(UserWarning) for expected warning to fix tests.
* Update warning message.
* Move type handling out of fetch_pipes_status().
* Add global variable for default value. Use id() to determine whether used values are default value.
* Fix default value for disable.
* Rename DEFAULT_PIPE_STATUS to _DEFAULT_EMPTY_PIPES.
* add punctuation to grc
Add support for special editorial punctuation that is common in ancient Greek texts. Ancient Greek texts, as found in digital and print form, have been largely edited by scholars. Restorations and improvements are normally marked with special characters that need to be handled properly by the tokenizer.
* add unit tests
* simplify regex
* move generic quotes to char classes
* rename unit test
* fix regex
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: svlandeg <svlandeg@github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Preserve both `-` and `O` annotation in augmenters rather than relying
on `Example.to_dict`'s default support for one option outside of labeled
entity spans.
This is intended as a temporary workaround for augmenters for v3.4.x.
The behavior of `Example` and related IOB utils could be improved in the
general case for v3.5.
* Remove side effects from Doc.__init__()
* Changes based on review comment
* Readd test
* Change interface of Doc.__init__()
* Simplify test
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update doc.md
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* replicate bug with tok2vec in annotating components
* add overfitting test with a frozen tok2vec
* remove broadcast from predict and check doc.tensor instead
* remove broadcast
* proper error
* slight rephrase of documentation
* Enable Cython<->Python bindings for `Pipe` and `TrainablePipe` methods
* `pipes_with_nvtx_range`: Skip hooking methods whose signature cannot be ascertained
When loading pipelines from a config file, the arguments passed to individual pipeline components is validated by `pydantic` during init. For this, the validation model attempts to parse the function signature of the component's c'tor/entry point so that it can check if all mandatory parameters are present in the config file.
When using the `models_and_pipes_with_nvtx_range` as a `after_pipeline_creation` callback, the methods of all pipeline components get replaced by a NVTX range wrapper **before** the above-mentioned validation takes place. This can be problematic for components that are implemented as Cython extension types - if the extension type is not compiled with Python bindings for its methods, they will have no signatures at runtime. This resulted in `pydantic` matching the *wrapper's* parameters with the those in the config and raising errors.
To avoid this, we now skip applying the wrapper to any (Cython) methods that do not have signatures.
* new error message when 'project run assets'
* new error message when 'project run assets'
* Update spacy/cli/project/run.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Due to problems with the javascript conversion in the website
quickstart, remove the `has_letters` setting to simplify generating
`attrs` for the default `tok2vec`.
Additionally reduce `PREFIX` as in the trained pipelines.
* Add a dry run flag to download
* Remove --dry-run, add --url option to `spacy info` instead
* Make mypy happy
* Print only the URL, so it's easier to use in scripts
* Don't add the egg hash unless downloading an sdist
* Update spacy/cli/info.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add two implementations of requirements
* Clean up requirements sample slightly
This should make mypy happy
* Update URL help string
* Remove requirements option
* Add url option to docs
* Add URL to spacy info model output, when available
* Add types-setuptools to testing reqs
* Add types-setuptools to requirements
* Add "compatible", expand docstring
* Update spacy/cli/info.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Run prettier on CLI docs
* Update docs
Add a sidebar about finding download URLs, with some examples of the new
command.
* Add download URLs to table on model page
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Updates from review
* download url -> download link
* Update docs
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* `Matcher`: Better type checking of values in `SetPredicate`
`SetPredicate`: Emit warning and return `False` on unexpected value types
* Rename `value_type_mismatch` variable
* Inline warning
* Remove unexpected type warning from `_SetPredicate`
* Ensure that `str` values are not interpreted as sequences
Check elements of sequence values for convertibility to `str` or `int`
* Add more `INTERSECT` and `IN` test cases
* Test for inputs with multiple characters
* Return `False` early instead of using a boolean flag
* Remove superfluous `int` check, parentheses
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Appy suggestions from code review
* Clarify test comment
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
