Commit Graph

115 Commits

Author SHA1 Message Date
Daniël de Kok
81beaea70e Merge remote-tracking branch 'upstream/master' into maintenance/v4-merge-master-20240119 2024-01-19 12:34:29 +01:00
Adriane Boyd
c096c5c0c9
Update for numpy 2.0 deprecations (#13103)
- Replace `np.trapz` with vendored `trapezoid` from scipy
- Replace `np.float_` with `np.float64`
2023-11-06 08:47:53 +01:00
Daniël de Kok
2468742cb8 isort all the things 2023-06-26 11:41:03 +02:00
Daniël de Kok
e2b70df012
Configure isort to use the Black profile, recursively isort the spacy module (#12721)
* Use isort with Black profile

* isort all the things

* Fix import cycles as a result of import sorting

* Add DOCBIN_ALL_ATTRS type definition

* Add isort to requirements

* Remove isort from build dependencies check

* Typo
2023-06-14 17:48:41 +02:00
Daniël de Kok
50c5e9a2dd Merge remote-tracking branch 'upstream/master' into sync-v4-master-20230612 2023-06-12 15:57:10 +02:00
Adriane Boyd
3637148c4d
Add scorer option to return per-component scores (#12540)
* Add scorer option to return per-component scores

Add `per_component` option to `Language.evaluate` and `Scorer.score` to
return scores keyed by `tokenizer` (hard-coded) or by component name.

Add option to `evaluate` CLI to score by component. Per-component scores
can only be saved to JSON.

* Update help text and messages
2023-05-12 15:36:54 +02:00
Edward
360ccf628a
Rename language codes (Icelandic, multi-language) (#12149)
* Init

* fix tests

* Update spacy/errors.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Fix test_blank_languages

* Rename xx to mul in docs

* Format _util with black

* prettier formatting

---------

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-01-31 17:30:43 +01:00
Adriane Boyd
9e0322de1a
Restore v2 token_acc score implementation (#12073)
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.
2023-01-11 08:01:47 +01:00
Sofie Van Landeghem
6d03b04901
Improve score_cats for use with multiple textcat components (#11820)
* 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>
2023-01-09 11:43:48 +01:00
Adriane Boyd
420b1d854b
Update textcat scorer threshold behavior (#11696)
* 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
2022-11-02 15:35:04 +01:00
Daniël de Kok
c90dd6f265
Alignment: use a simplified ragged type for performance (#10319)
* Alignment: use a simplified ragged type for performance

This introduces the AlignmentArray type, which is a simplified version
of Ragged that performs better on the simple(r) indexing performed for
alignment.

* AlignmentArray: raise an error when using unsupported index

* AlignmentArray: move error messages to Errors

* AlignmentArray: remove simlified ... with simplifications

* AlignmentArray: fix typo that broke a[n:n] indexing
2022-04-01 09:02:06 +02:00
Florian Cäsar
86e71e7b19
Fix Scorer.score_cats for missing labels (#9443)
* Fix Scorer.score_cats for missing labels

* Add test case for Scorer.score_cats missing labels

* semantic nitpick

* black formatting

* adjust test to give different results depending on multi_label setting

* fix loss function according to whether or not missing values are supported

* add note to docs

* small fixes

* make mypy happy

* Update spacy/pipeline/textcat.py

Co-authored-by: Florian Cäsar <florian.caesar@pm.me>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: svlandeg <svlandeg@github.com>
2021-12-29 11:04:39 +01:00
Adriane Boyd
a77f50baa4
Allow Scorer.score_spans to handle pred docs with missing annotation (#9701)
If the predicted docs are missing annotation according to
`has_annotation`, treat the docs as having no predictions rather than
raising errors when the annotation is missing.

The motivation for this is a combined tokenization+sents scorer for a
component where the sents annotation is optional. To provide a single
scorer in the component factory, it needs to be possible for the scorer
to continue despite missing sents annotation in the case where the
component is not annotating sents.
2021-11-23 15:17:19 +01:00
Adriane Boyd
e6f91b6f27
Format (#9630) 2021-11-05 09:56:26 +01:00
Adriane Boyd
12974bf4d9
Add micro PRF for morph scoring (#9546)
* Add micro PRF for morph scoring

For pipelines where morph features are added by more than one component
and a reference training corpus may not contain all features, a micro
PRF score is more flexible than a simple accuracy score. An example is
the reading and inflection features added by the Japanese tokenizer.

* Use `morph_micro_f` as the default morph score for Japanese
morphologizers.

* Update docstring

* Fix typo in docstring

* Update Scorer API docs

* Fix results type

* Organize score list by attribute prefix
2021-10-29 10:29:29 +02:00
Adriane Boyd
a803af9dfa Merge remote-tracking branch 'upstream/master' into chore/update-develop-from-master-v3.2-1 2021-10-26 11:53:50 +02:00
Connor Brinton
657af5f91f
🏷 Add Mypy check to CI and ignore all existing Mypy errors (#9167)
* 🚨 Ignore all existing Mypy errors

* 🏗 Add Mypy check to CI

* Add types-mock and types-requests as dev requirements

* Add additional type ignore directives

* Add types packages to dev-only list in reqs test

* Add types-dataclasses for python 3.6

* Add ignore to pretrain

* 🏷 Improve type annotation on `run_command` helper

The `run_command` helper previously declared that it returned an
`Optional[subprocess.CompletedProcess]`, but it isn't actually possible
for the function to return `None`. These changes modify the type
annotation of the `run_command` helper and remove all now-unnecessary
`# type: ignore` directives.

* 🔧 Allow variable type redefinition in limited contexts

These changes modify how Mypy is configured to allow variables to have
their type automatically redefined under certain conditions. The Mypy
documentation contains the following example:

```python
def process(items: List[str]) -> None:
    # 'items' has type List[str]
    items = [item.split() for item in items]
    # 'items' now has type List[List[str]]
    ...
```

This configuration change is especially helpful in reducing the number
of `# type: ignore` directives needed to handle the common pattern of:
* Accepting a filepath as a string
* Overwriting the variable using `filepath = ensure_path(filepath)`

These changes enable redefinition and remove all `# type: ignore`
directives rendered redundant by this change.

* 🏷 Add type annotation to converters mapping

* 🚨 Fix Mypy error in convert CLI argument verification

* 🏷 Improve type annotation on `resolve_dot_names` helper

* 🏷 Add type annotations for `Vocab` attributes `strings` and `vectors`

* 🏷 Add type annotations for more `Vocab` attributes

* 🏷 Add loose type annotation for gold data compilation

* 🏷 Improve `_format_labels` type annotation

* 🏷 Fix `get_lang_class` type annotation

* 🏷 Loosen return type of `Language.evaluate`

* 🏷 Don't accept `Scorer` in `handle_scores_per_type`

* 🏷 Add `string_to_list` overloads

* 🏷 Fix non-Optional command-line options

* 🙈 Ignore redefinition of `wandb_logger` in `loggers.py`

*  Install `typing_extensions` in Python 3.8+

The `typing_extensions` package states that it should be used when
"writing code that must be compatible with multiple Python versions".
Since SpaCy needs to support multiple Python versions, it should be used
when newer `typing` module members are required. One example of this is
`Literal`, which is available starting with Python 3.8.

Previously SpaCy tried to import `Literal` from `typing`, falling back
to `typing_extensions` if the import failed. However, Mypy doesn't seem
to be able to understand what `Literal` means when the initial import
means. Therefore, these changes modify how `compat` imports `Literal` by
always importing it from `typing_extensions`.

These changes also modify how `typing_extensions` is installed, so that
it is a requirement for all Python versions, including those greater
than or equal to 3.8.

* 🏷 Improve type annotation for `Language.pipe`

These changes add a missing overload variant to the type signature of
`Language.pipe`. Additionally, the type signature is enhanced to allow
type checkers to differentiate between the two overload variants based
on the `as_tuple` parameter.

Fixes #8772

*  Don't install `typing-extensions` in Python 3.8+

After more detailed analysis of how to implement Python version-specific
type annotations using SpaCy, it has been determined that by branching
on a comparison against `sys.version_info` can be statically analyzed by
Mypy well enough to enable us to conditionally use
`typing_extensions.Literal`. This means that we no longer need to
install `typing_extensions` for Python versions greater than or equal to
3.8! 🎉

These changes revert previous changes installing `typing-extensions`
regardless of Python version and modify how we import the `Literal` type
to ensure that Mypy treats it properly.

* resolve mypy errors for Strict pydantic types

* refactor code to avoid missing return statement

* fix types of convert CLI command

* avoid list-set confustion in debug_data

* fix typo and formatting

* small fixes to avoid type ignores

* fix types in profile CLI command and make it more efficient

* type fixes in projects CLI

* put one ignore back

* type fixes for render

* fix render types - the sequel

* fix BaseDefault in language definitions

* fix type of noun_chunks iterator - yields tuple instead of span

* fix types in language-specific modules

* 🏷 Expand accepted inputs of `get_string_id`

`get_string_id` accepts either a string (in which case it returns its 
ID) or an ID (in which case it immediately returns the ID). These 
changes extend the type annotation of `get_string_id` to indicate that 
it can accept either strings or IDs.

* 🏷 Handle override types in `combine_score_weights`

The `combine_score_weights` function allows users to pass an `overrides` 
mapping to override data extracted from the `weights` argument. Since it 
allows `Optional` dictionary values, the return value may also include 
`Optional` dictionary values.

These changes update the type annotations for `combine_score_weights` to 
reflect this fact.

* 🏷 Fix tokenizer serialization method signatures in `DummyTokenizer`

* 🏷 Fix redefinition of `wandb_logger`

These changes fix the redefinition of `wandb_logger` by giving a 
separate name to each `WandbLogger` version. For 
backwards-compatibility, `spacy.train` still exports `wandb_logger_v3` 
as `wandb_logger` for now.

* more fixes for typing in language

* type fixes in model definitions

* 🏷 Annotate `_RandomWords.probs` as `NDArray`

* 🏷 Annotate `tok2vec` layers to help Mypy

* 🐛 Fix `_RandomWords.probs` type annotations for Python 3.6

Also remove an import that I forgot to move to the top of the module 😅

* more fixes for matchers and other pipeline components

* quick fix for entity linker

* fixing types for spancat, textcat, etc

* bugfix for tok2vec

* type annotations for scorer

* add runtime_checkable for Protocol

* type and import fixes in tests

* mypy fixes for training utilities

* few fixes in util

* fix import

* 🐵 Remove unused `# type: ignore` directives

* 🏷 Annotate `Language._components`

* 🏷 Annotate `spacy.pipeline.Pipe`

* add doc as property to span.pyi

* small fixes and cleanup

* explicit type annotations instead of via comment

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: svlandeg <svlandeg@github.com>
2021-10-14 15:21:40 +02:00
Adriane Boyd
f99d6d5e39
Refactor scoring methods to use registered functions (#8766)
* Add scorer option to components

Add an optional `scorer` parameter to all pipeline components. If a
scoring function is provided, it overrides the default scoring method
for that component.

* Add registered scorers for all components

* Add `scorers` registry
* Move all scoring methods outside of components as independent
  functions and register
* Use the registered scoring methods as defaults in configs and inits

Additional:

* The scoring methods no longer have access to the full component, so
  use settings from `cfg` as default scorer options to handle settings
  such as `labels`, `threshold`, and `positive_label`
* The `attribute_ruler` scoring method no longer has access to the
  patterns, so all scoring methods are called
* Bug fix: `spancat` scoring method is updated to set `allow_overlap` to
  score overlapping spans correctly

* Update Russian lemmatizer to use direct score method

* Check type of cfg in Pipe.score

* Fix check

* Update spacy/pipeline/sentencizer.pyx

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Remove validate_examples from scoring functions

* Use Pipe.labels instead of Pipe.cfg["labels"]

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2021-08-10 15:13:39 +02:00
Adriane Boyd
5eeb25f043 Tidy up code 2021-06-28 12:08:15 +02:00
Sofie Van Landeghem
204c2f116b
Extend score_spans for overlapping & non-labeled spans (#7209)
* extend span scorer with consider_label and allow_overlap

* unit test for spans y2x overlap

* add score_spans unit test

* docs for new fields in scorer.score_spans

* rename to include_label

* spell out if-else for clarity

* rename to 'labeled'

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2021-04-08 12:19:17 +02:00
graue70
81fd595223
Fix __add__ method of PRFScore (#7557)
* Add failing test for PRFScore

* Fix erroneous implementation of __add__

* Simplify constructor

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2021-04-08 17:34:14 +10:00
svlandeg
248339039e fix type in docs 2021-02-26 14:27:10 +01:00
Sofie Van Landeghem
113e8d082b
only evaluate named entities for NEL if there is a corresponding gold span (#7074) 2021-02-22 11:06:50 +11:00
Ines Montani
d0c3775712 Replace links to nightly docs [ci skip] 2021-01-30 20:09:38 +11:00
Ines Montani
c0926c9088
WIP: Various small training changes (#6818)
* Allow output_path to be None during training

* Fix cat scoring (?)

* Improve error message for weighted None score

* Improve messages

So we can call this in other places etc.

* FIx output path check

* Use latest wasabi

* Revert "Improve error message for weighted None score"

This reverts commit 7059926763.

* Exclude None scores from final score by default

It's otherwise very difficult to keep track of the score weights if we modify a config programmatically, source components etc.

* Update warnings and use logger.warning
2021-01-26 14:51:52 +11:00
Sofie Van Landeghem
afc5714d32
multi-label textcat component (#6474)
* multi-label textcat component

* formatting

* fix comment

* cleanup

* fix from #6481

* random edit to push the tests

* add explicit error when textcat is called with multi-label gold data

* fix error nr

* small fix
2021-01-06 13:07:14 +11:00
Ines Montani
991669c934 Tidy up and auto-format 2021-01-05 13:41:53 +11:00
Adriane Boyd
31ec9a906e
Clean up 3rd party license info (#6478)
Move scikit-learn license from `Scorer` to
`licenses/3rd_party_licenses.txt`.
2020-12-02 10:15:23 +01:00
Ines Montani
de6453940e
Merge pull request #6305 from svlandeg/feature/score-docs [ci skip] 2020-11-10 02:52:11 +01:00
Adriane Boyd
a4b32b9552
Handle missing reference values in scorer (#6286)
* Handle missing reference values in scorer

Handle missing values in reference doc during scoring where it is
possible to detect an unset state for the attribute. If no reference
docs contain annotation, `None` is returned instead of a score. `spacy
evaluate` displays `-` for missing scores and the missing scores are
saved as `None`/`null` in the metrics.

Attributes without unset states:

* `token.head`: relies on `token.dep` to recognize unset values
* `doc.cats`: unable to handle missing annotation

Additional changes:

* add optional `has_annotation` check to `score_scans` to replace
`doc.sents` hack
* update `score_token_attr_per_feat` to handle missing and empty morph
representations
* fix bug in `Doc.has_annotation` for normalization of `IS_SENT_START`
vs. `SENT_START`

* Fix import

* Update return types
2020-11-03 15:47:18 +01:00
svlandeg
080066ae74 remove TODO note 2020-10-26 10:37:25 +01:00
Sofie Van Landeghem
75a202ce65
TextCat updates and fixes (#6263)
* small fix in example imports

* throw error when train_corpus or dev_corpus is not a string

* small fix in custom logger example

* limit macro_auc to labels with 2 annotations

* fix typo

* also create parents of output_dir if need be

* update documentation of textcat scores

* refactor TextCatEnsemble

* fix tests for new AUC definition

* bump to 3.0.0a42

* update docs

* rename to spacy.TextCatEnsemble.v2

* spacy.TextCatEnsemble.v1 in legacy

* cleanup

* small fix

* update to 3.0.0rc2

* fix import that got lost in merge

* cursed IDE

* fix two typos
2020-10-18 14:50:41 +02:00
Ines Montani
bcd52e5486 Tidy up errors and warnings 2020-10-04 11:16:31 +02:00
Ines Montani
fa47f87924 Tidy up and auto-format 2020-09-29 21:39:28 +02:00
Adriane Boyd
50f20cf722 Revert changes to Scorer.score_spans 2020-09-25 08:21:47 +02:00
Matthew Honnibal
16475528f7
Fix skipped documents in entity scorer (#6137)
* Fix skipped documents in entity scorer

* Add back the skipping of unannotated entities

* Update spacy/scorer.py

* Use more specific NER scorer

* Fix import

* Fix get_ner_prf

* Add scorer

* Fix scorer

Co-authored-by: Ines Montani <ines@ines.io>
2020-09-24 20:38:57 +02:00
Sofie Van Landeghem
c7eedd3534
updates to NEL functionality (#6132)
* NEL: read sentences and ents from reference

* fiddling with sent_start annotations

* add KB serialization test

* KB write additional file with strings.json

* score_links function to calculate NEL P/R/F

* formatting

* documentation
2020-09-24 16:53:59 +02:00
Sofie Van Landeghem
c645c4e7ce
fix micro PRF for textcat (#6130)
* fix micro PRF for textcat

* small fix
2020-09-24 10:31:17 +02:00
Matthew Honnibal
bbdb5f62b7
Temporary work-around for scoring a subset of components (#6090)
* Try hacking the scorer to work around sentence boundaries

* Upd scorer

* Set dev version

* Upd scorer hack

* Fix version

* Improve comment on hack
2020-09-18 14:26:42 +02:00
Sofie Van Landeghem
8e7557656f
Renaming gold & annotation_setter (#6042)
* version bump to 3.0.0a16

* rename "gold" folder to "training"

* rename 'annotation_setter' to 'set_extra_annotations'

* formatting
2020-09-09 10:31:03 +02:00
Ines Montani
ab1bb421ed Update docs links in codebase 2020-09-04 12:58:50 +02:00
Ines Montani
34146750d4 Use frozen list with custom errors
We don't want to break backwards compatibility too much but we also want to provide the best possible UX
2020-08-29 15:20:11 +02:00
Adriane Boyd
43c61da209 Set macro AUC score in Scorer.score_cats 2020-08-26 10:49:30 +02:00
Matthew Honnibal
2771e4f2b3
Fix the git "sparse checkout" functionality (#5973)
* Fix the git sparse checkout functionality

* Format
2020-08-26 04:00:14 +02:00
Matthew Honnibal
ef43152af4 Update scorer 2020-08-25 02:42:47 +02:00
Matthew Honnibal
8038b87f04
Various small tweaks to project CLI (#5965)
* 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
2020-08-25 00:30:52 +02:00
Matthew Honnibal
f232d8db96 Report p/r/f out of 100 2020-08-24 17:17:23 +02:00
Ines Montani
3ae5e02f4f Update docs, types and API consistency 2020-08-17 16:45:24 +02:00
Ines Montani
3eaeb73342 Tidy up and auto-format 2020-08-09 22:36:23 +02:00
Matthew Honnibal
d4525816ef
Be less choosy about reporting textcat scores (#5879)
* Set textcat scores more consistently

* Refactor textcat scores

* Fixes to scorer

* Add comments

* Add threshold

* Rename just 'f' to micro_f in textcat scorer

* Fix textcat score for two-class

* Fix syntax

* Fix textcat score

* Fix docstring
2020-08-06 16:24:13 +02:00