Commit Graph

16264 Commits

Author SHA1 Message Date
Raphael Mitsch
304b9331e6
Modify EL batching to doc-wise streaming approach (#12367)
* Convert Candidate from Cython to Python class.

* Format.

* Fix .entity_ typo in _add_activations() usage.

* Change type for mentions to look up entity candidates for to SpanGroup from Iterable[Span].

* Update docs.

* Update spacy/kb/candidate.py

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

* Update doc string of BaseCandidate.__init__().

* Update spacy/kb/candidate.py

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

* Rename Candidate to InMemoryCandidate, BaseCandidate to Candidate.

* Adjust Candidate to support and mandate numerical entity IDs.

* Format.

* Fix docstring and docs.

* Update website/docs/api/kb.mdx

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

* Rename alias -> mention.

* Refactor Candidate attribute names. Update docs and tests accordingly.

* Refacor Candidate attributes and their usage.

* Format.

* Fix mypy error.

* Update error code in line with v4 convention.

* Modify EL batching system.

* Update leftover get_candidates() mention in docs.

* Format docs.

* Format.

* Update spacy/kb/candidate.py

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

* Updated error code.

* Simplify interface for int/str representations.

* Update website/docs/api/kb.mdx

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

* Rename 'alias' to 'mention'.

* Port Candidate and InMemoryCandidate to Cython.

* Remove redundant entry in setup.py.

* Add abstract class check.

* Drop storing mention.

* Update spacy/kb/candidate.pxd

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

* Fix entity_id refactoring problems in docstrings.

* Drop unused InMemoryCandidate._entity_hash.

* Update docstrings.

* Move attributes out of Candidate.

* Partially fix alias/mention terminology usage. Convert Candidate to interface.

* Remove prior_prob from supported properties in Candidate. Introduce KnowledgeBase.supports_prior_probs().

* Update docstrings related to prior_prob.

* Update alias/mention usage in doc(strings).

* Update spacy/ml/models/entity_linker.py

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

* Update spacy/ml/models/entity_linker.py

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

* Mention -> alias renaming. Drop Candidate.mentions(). Drop InMemoryLookupKB.get_alias_candidates() from docs.

* Update docstrings.

* Fix InMemoryCandidate attribute names.

* Update spacy/kb/kb.pyx

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

* Update spacy/ml/models/entity_linker.py

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

* Update W401 test.

* Update spacy/errors.py

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

* Update spacy/kb/kb.pyx

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

* Use Candidate output type for toy generators in the test suite to mimick best practices

* fix docs

* fix import

* Fix merge leftovers.

* Update spacy/kb/kb.pyx

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

* Update spacy/kb/kb.pyx

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

* Update website/docs/api/kb.mdx

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

* Update website/docs/api/entitylinker.mdx

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

* Update spacy/kb/kb_in_memory.pyx

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

* Update website/docs/api/inmemorylookupkb.mdx

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

* Update get_candidates() docstring.

* Reformat imports in entity_linker.py.

* Drop valid_ent_idx_per_doc.

* Update docs.

* Format.

* Simplify doc loop in predict().

* Remove E1044 comment.

* Fix merge errors.

* Format.

* Format.

* Format.

* Fix merge error & tests.

* Format.

* Apply suggestions from code review

Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>

* Use type alias.

* isort.

* isort.

* Lint.

* Add typedefs.pyx.

* Fix typedef import.

* Fix type aliases.

* Format.

* Update docstring and type usage.

* Add info on get_candidates(), get_candidates_batched().

* Readd get_candidates info to v3 changelog.

* Update website/docs/api/entitylinker.mdx

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

* Update factory functions for backwards compatibility.

* Format.

* Ignore mypy error.

* Fix mypy error.

* Format.

* Add test for multiple docs with multiple entities.

---------

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
Co-authored-by: svlandeg <svlandeg@github.com>
2024-04-09 11:39:18 +02:00
Adriane Boyd
afb22ad491
Remove debug data normalization for span analysis (#13203)
* Remove debug data normalization for span analysis

As a result of this normalization, `debug data` could show a user tokens
that do not exist in their data.

* Update spacy/cli/debug_data.py

---------

Co-authored-by: svlandeg <svlandeg@github.com>
2024-02-06 14:14:55 +01:00
Daniël de Kok
1052cba9f3
Merge pull request #13299 from danieldk/copy/master
Sync main with latests changes from master (v3)
2024-02-04 15:40:55 +01:00
Daniël de Kok
2d4067d021 Test if closing explicitly solves recursive lock issues 2024-02-02 11:39:07 +01:00
Daniël de Kok
d84068e460
Run slow tests: v4 -> main (#13290)
* Run slow tests: v4 -> main

* Also update the branch in GPU tests
2024-01-30 13:58:28 +01:00
Sofie Van Landeghem
89a43f39b7
update universe description (#13291) 2024-01-30 13:49:49 +01:00
Daniël de Kok
68d7841df5
Extension serialization attr tests: add teardown (#13284)
The doc/token extension serialization tests add extensions that are not
serializable with pickle. This didn't cause issues before due to the
implicit run order of tests. However, test ordering has changed with
pytest 8.0.0, leading to failed tests in test_language.

Update the fixtures in the extension serialization tests to do proper
teardown and remove the extensions.
2024-01-29 13:51:56 +01:00
Eliana Vornov
00e938a7c3
add custom code support to CLI speed benchmark (#13247)
* add custom code support to CLI speed benchmark

* sort imports

* better copying for warmup docs
2024-01-26 13:29:22 +01:00
Sofie Van Landeghem
68b85ea950
Clarify data_path loading for apply CLI command (#13272)
* attempt to clarify additional annotations on .spacy file

* suggestion by Daniël

* pipeline instead of pipe
2024-01-26 12:10:05 +01:00
Sofie Van Landeghem
7496e03a2c
Clarify vocab docs (#13273)
* add line to ensure that apple is in fact in the vocab

* add that the vocab may be empty
2024-01-26 10:58:48 +01:00
Daniël de Kok
70e2f2a14a
Update spacy-legacy dependency to 4.0.0.dev1 (#13270)
This release is compatible with the parser refactor backout.
2024-01-25 18:24:22 +01:00
Daniël de Kok
ce9ea9629f
Set version to v4.0.0.dev2 (#13269) 2024-01-25 12:54:23 +01:00
Daniël de Kok
bbf38d4d0f
Merge pull request #13250 from danieldk/maintenance/v4-merge-master-20240119
Merge `master` into `v4`
2024-01-24 19:30:23 +01:00
Daniël de Kok
9e97c730be Fix up requirements test
To account for buil dependencies being removed from `setup.cfg`.
2024-01-24 17:18:49 +01:00
Daniël de Kok
36ee709390 Remove setup_requires from setup.cfg 2024-01-24 15:02:02 +01:00
Daniël de Kok
e722284ff4 Construct TextCatEnsemble.v2 using helper function 2024-01-24 14:59:01 +01:00
Daniël de Kok
ce4ea5ffa7 Py_UNICODE is not compatible with 3.12 2024-01-24 13:08:56 +01:00
Daniël de Kok
c621e251b8 Typing fixes 2024-01-24 12:20:01 +01:00
Sofie Van Landeghem
a493981163
fix typo (#13254) 2024-01-24 09:29:57 +01:00
Daniël de Kok
82ef6783a8 Merge remote-tracking branch 'upstream/master' into maintenance/v4-merge-master-20240119 2024-01-24 09:09:01 +01:00
Daniël de Kok
a8894a8946
Merge pull request #13240 from mauricesvp/patch-1
Fix typo in method name
2024-01-23 20:49:21 +01:00
Daniël de Kok
afac7fb650
test_find_available_port: use port 5001 (#13255)
macOS now uses port 5000 for the AirPlay receiver functionality, so this
test will always fail on a macOS desktop (unless AirPlay receiver
functionality is disabled like in CI).
2024-01-23 20:11:16 +01:00
Daniël de Kok
5a2ad4af4b Merge remote-tracking branch 'upstream/master' into patch-1 2024-01-23 19:53:20 +01:00
Daniël de Kok
128197a5fc
Properly clean up pipe multiprocessing workers (#13259)
Before this change, the workers of pipe call with n_process != 1 were
stopped by calling `terminate` on the processes. However, terminating a
process can leave queues, pipes, and other concurrent data structures in
an invalid state.

With this change, we stop using terminate and take the following approach
instead:

* When the all documents are processed, the parent process puts a
  sentinel in the queue of each worker.
* The parent process then calls `join` on each worker process to
  let them finish up gracefully.
* Worker processes break from the queue processing loop when the
  sentinel is encountered, so that they exit.

We need special handling when one of the workers encounters an error and
the error handler is set to raise an exception. In this case, we cannot
rely on the sentinel to finish all workers -- the queue is a FIFO queue
and there may be other work queued up before the sentinel. We use the
following approach to handle error scenarios:

* The parent puts the end-of-work sentinel in the queue of each worker.
* The parent closes the reading-end of the channel of each worker.
* Then:
  - If the worker was waiting for work, it will encounter the sentinel
    and break from the processing loop.
  - If the worker was processing a batch, it will attempt to write
    results to the channel. This will fail because the channel was
    closed by the parent and the worker will break from the processing
    loop.
2024-01-23 18:33:04 +01:00
Raphael Mitsch
3b3b5cdc63
Merge pull request #13253 from explosion/chore/sync-master-with-llm_main
Sync `master` with `docs/llm_main`
2024-01-19 16:50:43 +01:00
Raphael Mitsch
575c405ae3 Fix LLM docs on task factories. 2024-01-19 16:48:54 +01:00
Raphael Mitsch
256468c414 Merge branch 'docs/llm_main' into chore/sync-master-with-llm_main
# Conflicts:
#	website/docs/api/large-language-models.mdx
2024-01-19 16:34:35 +01:00
Raphael Mitsch
91c24c0285
Merge pull request #13251 from explosion/docs/llm_develop
Sync `docs/llm_main` with `docs/llm_develop`
2024-01-19 12:56:38 +01:00
Daniël de Kok
81beaea70e Merge remote-tracking branch 'upstream/master' into maintenance/v4-merge-master-20240119 2024-01-19 12:34:29 +01:00
Daniël de Kok
2891e27421
Merge pull request #13191 from explosion/maintenance/revert-parser-refactor
Revert the parser refactor
2024-01-18 17:06:41 +01:00
Daniël de Kok
9972333ef9 Temporily xfail local remote storage test 2024-01-17 10:20:40 +01:00
maurice
c608baeecc
Fix typo in method name 2024-01-16 21:54:54 +01:00
Daniël de Kok
7351f6bbeb Update thinc dependency to 9.0.0.dev4 2024-01-16 15:56:09 +01:00
Raphael Mitsch
0062c22c35
Updated docs w.r.t. infinite doc length changes (#13214)
* Updated docs w.r.t. infinite doc length.

* Fix typo.

* fix typo's

* Fix table formatting.

* Update formatting.

---------

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2024-01-05 14:20:58 +01:00
Daniël de Kok
e2a3952de5
Add spacy.TextCatParametricAttention.v1 (#13201)
* Add spacy.TextCatParametricAttention.v1

This layer provides is a simplification of the ensemble classifier that
only uses paramteric attention. We have found empirically that with a
sufficient amount of training data, using the ensemble classifier with
BoW does not provide significant improvement in classifier accuracy.
However, plugging in a BoW classifier does reduce GPU training and
inference performance substantially, since it uses a GPU-only kernel.

* Fix merge fallout
2024-01-02 10:03:06 +01:00
Daniël de Kok
7718886fa3
TransitionBasedParser.v2 in run example output
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-12-21 11:14:35 +01:00
Daniël de Kok
7ebba86402
Add TextCatReduce.v1 (#13181)
* Add TextCatReduce.v1

This is a textcat classifier that pools the vectors generated by a
tok2vec implementation and then applies a classifier to the pooled
representation. Three reductions are supported for pooling: first, max,
and mean. When multiple reductions are enabled, the reductions are
concatenated before providing them to the classification layer.

This model is a generalization of the TextCatCNN model, which only
supports mean reductions and is a bit of a misnomer, because it can also
be used with transformers. This change also reimplements TextCatCNN.v2
using the new TextCatReduce.v1 layer.

* Doc fixes

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

* Fully specify `TextCatCNN` <-> `TextCatReduce` equivalence

* Move TextCatCNN docs to legacy, in prep for moving to spacy-legacy

* Add back a test for TextCatCNN.v2

* Replace TextCatCNN in pipe configurations and templates

* Add an infobox to the `TextCatReduce` section with an `TextCatCNN` anchor

* Add last reduction (`use_reduce_last`)

* Remove non-working TextCatCNN Netlify redirect

* Revert layer changes for the quickstart

* Revert one more quickstart change

* Remove unused import

* Fix docstring

* Fix setting name in error message

---------

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-12-21 11:00:06 +01:00
Daniël de Kok
532225b955 Fix parser distillation test seed
The test would sometimes fail. Rather than increasing test by increasing
training iterations, use a known-good seed.
2023-12-21 10:06:28 +01:00
Daniël de Kok
7b689bde44 No need for Literal compat, since we only support >= 3.8 2023-12-21 09:47:38 +01:00
Daniël de Kok
57203fa0fc Fix TransitionBasedParser version in transformer embeddings docs 2023-12-19 09:28:20 +01:00
Daniël de Kok
5e8bafa5bb Bring back W401 2023-12-18 20:17:24 +01:00
Daniël de Kok
9b36729cbd Fix Cython lints 2023-12-18 20:02:15 +01:00
Steven Crowther
764be103bc
update README to include links to GPU processing, LLM's, and the spaCy blog. (#13197)
* Update README.md to include links for GPU processing, LLM, and spaCy's blog.

* Create ojo4f3.md

* corrected README to most current version with links to GPU processing, LLM's, and the spaCy blog.

* Delete .github/contributors/ojo4f3.md

* changed LLM icon

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

* Apply suggestions from code review

---------

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-12-18 09:49:07 +01:00
Sofie Van Landeghem
56fc3bc0f3
Type documentation fixes for Doc (#13187)
* correct char_span output type - can be None

* unify type of exclude parameter

* black

* further fixes to from_dict and to_dict

* formatting
2023-12-18 09:00:47 +01:00
Ines Montani
7df328fbfe
Update README.md [ci skip] 2023-12-12 10:19:57 +01:00
Raphael Mitsch
d56ee65ddf
Document spacy-llm's TranslationTask (#13183)
* Describe translation task.

* Fix references to examples and template.

* Format.
2023-12-11 17:41:04 +01:00
Raphael Mitsch
e79a9c5acd
Document spacy-llm's RawTask (#13180)
* Add section on RawTask.

* Fix API docs.

* Update website/docs/api/large-language-models.mdx

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

---------

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2023-12-11 17:14:12 +01:00
Ines Montani
8cfccdd2f8
Update links [ci skip] 2023-12-11 15:51:43 +01:00
Ines Montani
f78b91c03b
Update links [ci skip] 2023-12-11 15:51:01 +01:00
Daniël de Kok
42fe4edfd7 Add distillation tests with max cut size
And fix endless loop when the max cut size is 0 or 1.
2023-12-08 20:38:01 +01:00