Commit Graph

9330 Commits

Author SHA1 Message Date
Raphael Mitsch
749e446ee3 Merge branch 'master' into sync/master-into-v4
# Conflicts:
#	.github/azure-steps.yml
2023-03-06 16:27:56 +01:00
Adriane Boyd
0bbc620dd8
Partially work around pending deprecation of pkg_resources (#12368)
* Handle deprecation of pkg_resources

* Replace `pkg_resources` with `importlib_metadata` for `spacy info
--url`
* Remove requirements check from `spacy project` given the lack of
alternatives

* Fix installed model URL method and CI test

* Fix types/handling, simplify catch-all return

* Move imports instead of disabling requirements check

* Format

* Reenable test with ignored deprecation warning

* Fix except

* Fix return
2023-03-06 14:48:57 +01:00
Raphael Mitsch
1ea31552be Merge branch 'master' into sync/master-into-v4
# Conflicts:
#	requirements.txt
#	spacy/pipeline/entity_linker.py
#	spacy/util.py
#	website/docs/api/entitylinker.mdx
2023-03-02 16:24:15 +01:00
Raphael Mitsch
6aa6b86d49
Make generation of empty KnowledgeBase instances configurable in EntityLinker (#12320)
* Make empty_kb() configurable.

* Format.

* Update docs.

* Be more specific in KB serialization test.

* Update KB serialization tests. Update docs.

* Remove doc update for batched candidate generation.

* Fix serialization of subclassed KB in tests.

* Format.

* Update docstring.

* Update docstring.

* Switch from pickle to json for custom field serialization.
2023-03-01 16:02:55 +01:00
Adriane Boyd
da75896ef5
Return Tuple[Span] for all Doc/Span attrs that provide spans (#12288)
* Return Tuple[Span] for all Doc/Span attrs that provide spans

* Update Span types
2023-03-01 16:00:02 +01:00
Sofie Van Landeghem
74cae47bf6
rely on is_empty property instead of __len__ (#12347) 2023-03-01 12:06:07 +01:00
Adriane Boyd
8f058e39bd
Fix error message for displacy auto_select_port (#12343) 2023-02-28 16:36:03 +01:00
TAN Long
071667376a
Add new REL_OPs: >+, >-, <+, and <- (#12334)
* Add immediate left/right child/parent dependency relations

* Add tests for new REL_OPs: `>+`, `>-`, `<+`, and `<-`.

---------

Co-authored-by: Tan Long <tanloong@foxmail.com>
2023-02-28 14:36:33 +01:00
lise-brinck
e2de188cf1
Bugfix/swedish tokenizer (#12315)
* add unittest for explosion#12311

* create punctuation.py for swedish

* removed : from infixes in swedish punctuation.py

* allow : as infix if succeeding char is uppercase
2023-02-27 10:53:45 +01:00
Kevin Humphreys
acdd993071
Matcher performance fix for extension predicates: use shared key function (#12272)
* standardize predicate key format

* single key function

* Make optional args in key function keyword-only

---------

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-02-27 08:35:08 +01:00
Adriane Boyd
df4c069a13
Remove backoff from .vector to .tensor (#12292) 2023-02-23 11:36:50 +01:00
Paul O'Leary McCann
1e8bac99f3
Add tests for projects to master (#12303)
* Add tests for projects to master

* Fix git clone related issues on Windows

* Add stat import
2023-02-23 10:22:57 +01:00
Daniël de Kok
e27c60a702
Reimplement distillation with oracle cut size (#12214)
* Improve the correctness of _parse_patch

* If there are no more actions, do not attempt to make further
  transitions, even if not all states are final.
* Assert that the number of actions for a step is the same as
  the number of states.

* Reimplement distillation with oracle cut size

The code for distillation with an oracle cut size was not reimplemented
after the parser refactor. We did not notice, because we did not have
tests for this functionality. This change brings back the functionality
and adds this to the parser tests.

* Rename states2actions to _states_to_actions for consistency

* Test distillation max cuts in NER

* Mark parser/NER tests as slow

* Typo

* Fix invariant in _states_diff_to_actions

* Rename _init_batch -> _init_batch_from_teacher

* Ninja edit the ninja edit

* Check that we raise an exception when we pass the incorrect number or actions

* Remove unnecessary get

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

* Write out condition more explicitly

---------

Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
2023-02-21 15:47:18 +01:00
Adriane Boyd
80bc140533
Add grc to langs with lexeme norms in spacy-lookups-data (#12287) 2023-02-16 17:57:02 +01:00
Paul O'Leary McCann
dd3f138830
Use tempfile.TemporaryDirectory (#12285) 2023-02-16 11:08:55 +01:00
Adriane Boyd
b95123060a
Make Span.char_span optional args keyword-only (#12257)
* Make Span.char_span optional args keyword-only

* Make kb_id and following kw-only

* Format
2023-02-15 12:34:33 +01:00
Edward
61b8454137
Adjust return type of registry.find (#12227)
* Fix registry find return type

* add dot

* Add type ignore for mypy

* update black formatting version

* add mypy ignore to package cli

* mypy type fix (for real)

* Update find description in spacy/util.py

Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>

* adjust mypy directive

---------

Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
2023-02-15 12:32:53 +01:00
Adriane Boyd
cbc2ae933e
Remove unused Span.char_span(id=) (#12250) 2023-02-08 14:46:07 +01:00
Adriane Boyd
cf85b81f34
Remove names for vectors (#12243)
* Remove names for vectors

Named vectors are basically a carry-over from v2 and aren't used for
anything.

* Format
2023-02-08 14:37:42 +01:00
Adriane Boyd
5089efa2d0
Use the same tuple in Span cmp and hash (#12251) 2023-02-08 14:28:34 +01:00
Daniël de Kok
eec5ccd72f
Language.update: ensure that tok2vec gets updated (#12136)
* `Language.update`: ensure that tok2vec gets updated

The components in a pipeline can be updated independently. However,
tok2vec implementations are an exception to this, since they depend on
listeners for their gradients. The update method of a tok2vec
implementation computes the tok2vec forward and passes this along with a
backprop function to the listeners. This backprop function accumulates
gradients for all the listeners. There are two ways in which the
accumulated gradients can be used to update the tok2vec weights:

1. Call the `finish_update` method of tok2vec *after* the `update`
   method is called on all of the pipes that use a tok2vec listener.
2. Pass an optimizer to the `update` method of tok2vec. In this
   case, tok2vec will give the last listener a special backprop
   function that calls `finish_update` on the tok2vec.

Unfortunately, `Language.update` did neither of these. Instead, it
immediately called `finish_update` on every pipe after `update`. As a
result, the tok2vec weights are updated when no gradients have been
accumulated from listeners yet. And the gradients of the listeners are
only used in the next call to `Language.update` (when `finish_update` is
called on tok2vec again).

This change fixes this issue by passing the optimizer to the `update`
method of trainable pipes, leading to use of the second strategy
outlined above.

The main updating loop in `Language.update` is also simplified by using
the `TrainableComponent` protocol consistently.

* Train loop: `sgd` is `Optional[Optimizer]`, do not pass false

* Language.update: call pipe finish_update after all pipe updates

This does correct and fast updates if multiple components update the
same parameters.

* Add comment why we moved `finish_update` to a separate loop
2023-02-03 15:22:25 +01:00
Sofie Van Landeghem
c47ec5b5c6
Merge pull request #12218 from adrianeboyd/chore/update-v4-from-master-7
Update v4 from master
2023-02-03 12:04:20 +01:00
Paul O'Leary McCann
89f974d4f5
Cleanup/remove backwards compat overwrite settings (#11888)
* Remove backwards-compatible overwrite from Entity Linker

This also adds a docstring about overwrite, since it wasn't present.

* Fix docstring

* Remove backward compat settings in Morphologizer

This also needed a docstring added.

For this component it's less clear what the right overwrite settings
are.

* Remove backward compat from sentencizer

This was simple

* Remove backward compat from senter

Another simple one

* Remove backward compat setting from tagger

* Add docstrings

* Update spacy/pipeline/morphologizer.pyx

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

* Update docs

---------

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-02-02 14:13:38 +01:00
Adriane Boyd
cd95b29053 Merge remote-tracking branch 'upstream/master' into chore/update-v4-from-master-7 2023-02-02 13:06:15 +01:00
Sofie Van Landeghem
79ef6cf0f9
Have logging calls use string formatting types (#12215)
* change logging call for spacy.LookupsDataLoader.v1

* substitutions in language and _util

* various more substitutions

* add string formatting guidelines to contribution guidelines
2023-02-02 11:15:22 +01:00
Paul O'Leary McCann
6920fb7baf
Move Entity Linker v1 to spacy-legacy (#12006)
* Move Entity Linker v1 component to spacy-legacy

This is a follow up to #11889 that moves the component instead of
removing it.

In general, we never import from spacy-legacy in spaCy proper. However,
to use this component, that kind of import will be necessary. I was able
to test this without issues, but is this current import strategy
acceptable? Or should we put the component in a registry?

* Use spacy-legacy pr for CI

This will need to be reverted before merging.

* Add temporary step to log installed spacy-legacy version

* Modify requirements.txt to trigger tests

* Add comment to Python to trigger tests

* TODO REVERT This is a commit with logic changes to trigger tests

* Remove pipe from YAML

Works locally, but possibly this is causing a quoting error or
something.

* Revert "TODO REVERT This is a commit with logic changes to trigger tests"

This reverts commit 689fae71f3.

* Revert "Add comment to Python to trigger tests"

This reverts commit 11840fc598.

* Add more logging

* Try installing directly in workflow

* Try explicitly uninstalling spacy-legacy first

* Cat requirements.txt to confirm contents

In the branch, the thinc version spec is `thinc>=8.1.0,<8.2.0`. But in
the logs, it's clear that a development release of 9.0 is being
installed. It's not clear why that would happen.

* Log requirements at start of build

* TODO REVERT Change thinc spec

Want to see what happens to the installed thinc spec with this change.

* Update thinc requirements

This makes it the same as it was before the merge, >=8.1.0,<8.2.0.

* Use same thinc version as v4 branch

* TODO REVERT Mark dependency check as xfail

spacy-legacy is specified as a git checkout in requirements.txt while
this PR is in progress, which makes the consistency check here fail.

* Remove debugging output / install step

* Revert "Remove debugging output / install step"

This reverts commit 923ea7448b.

* Clean up debugging output

The manual install step with the URL fragment seems to have caused
issues on Windows due to the = in the URL being misinterpreted. On the
other hand, removing it seems to mean the git version of spacy-legacy
isn't actually installed.

This PR removes the URL fragment but keeps the direct command-line
install. Additionally, since it looks like this job is configured to use
the default shell (and not bash), it removes a comment that upsets the
Windows cmd shell.

* Revert "TODO REVERT Mark dependency check as xfail"

This reverts commit d4863ec156.

* Fix requirements.txt, increasing spacy-legacy version

* Raise spacy legacy version in setup.cfg

* Remove azure build workarounds

* make spacy-legacy version explicit in error message

* Remove debugging line

* Suggestions from code review
2023-02-01 09:47:56 +01:00
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
Raphael Mitsch
02af17a5c8
Remove flaky assertions. (#12210) 2023-01-31 16:52:06 +01:00
Daniël de Kok
c6cca4c00a
Language.distill: copy both reference and predicted (#12209)
* Language.distill: copy both reference and predicted

In distillation we also modify the teacher docs (e.g. in tok2vec
components), so we need to copy both the reference and predicted doc.

Problem caught by @shadeMe

* Make new `_copy_examples` args kwonly
2023-01-31 13:19:42 +01:00
Daniël de Kok
fb7f018ded
Add the configuration schema for distillation (#12201)
* Add the configuration schema for distillation

This also adds the default configuration and some tests. The schema will
be used by the training loop and `distill` subcommand.

* Format

* Change distillation shortopt to -d

* Fix descripion of max_epochs

* Rename distillation flag to -dt

* Rename `pipe_map` to `student_to_teacher`
2023-01-31 13:06:02 +01:00
Paul O'Leary McCann
1b5aba9e22
Don't re-download installed models (#12188)
* Don't re-download installed models

When downloading a model, this checks if the same version of the same
model is already installed. If it is then the download is skipped.

This is necessary because pip uses the final download URL for its
caching feature, but because of the way models are hosted on Github,
their URLs change every few minutes.

* Use importlib instead of meta.json

* Use get_package_version

* Add untested, disabled test

---------

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-01-31 11:31:17 +01:00
Daniël de Kok
6b07be2110
Add Language.distill (#12116)
* Add `Language.distill`

This method is the distillation counterpart of `Language.update`.  It
takes a teacher `Language` instance and distills the student pipes on
the teacher pipes.

* Apply suggestions from code review

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

* Clarify that how Example is used in distillation

* Update transition parser distill docstring for examples argument

* Pass optimizer to `TrainablePipe.distill`

* Annotate pipe before update

As discussed internally, we want to let a pipe annotate before doing an
update with gold/silver data. Otherwise, the output may be (too)
informed by the gold/silver data.

* Rename `component_map` to `student_to_teacher`

* Better synopsis in `Language.distill` docstring

* `name` -> `student_name`

* Fix labels type in docstring

* Mark distill test as slow

* Fix `student_to_teacher` type in docs

---------

Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
2023-01-30 12:44:11 +01:00
Adriane Boyd
606273f7e4
Normalize whitespace in evaluate CLI output test (#12157)
* Normalize whitespace in evaluate CLI output test

Depending on terminal settings, lines may be padded to the screen width
so the comparison is too strict with only the command string replacement.

* Move to test util method

* Change to normalization method
2023-01-27 16:13:34 +01:00
Adriane Boyd
ec45f704b1
Drop python 3.6/3.7, remove unneeded compat (#12187)
* Drop python 3.6/3.7, remove unneeded compat

* Remove unused import

* Minimal python 3.8+ docs updates
2023-01-27 15:48:20 +01:00
Adriane Boyd
5f8a398bb9
Add span_id to Span.char_span, update Doc/Span.char_span docs (#12196)
* Add span_id to Span.char_span, update Doc/Span.char_span docs

`Span.char_span(id=)` should be removed in the future.

* Also use Union[int, str] in Doc docstring
2023-01-27 15:09:17 +01:00
Simon Gurcke
774c10fa39
Add alignment_mode argument to Span.char_span() (#12145)
* Add alignment_mode argument to Span.char_span()

* Update website

* Update spacy/tokens/span.pyx

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

* Add test

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-01-27 11:43:40 +01:00
Adriane Boyd
fd911fe2af Format 2023-01-27 08:29:46 +01:00
Adriane Boyd
8548d4d16e Merge remote-tracking branch 'upstream/master' into update-v4-from-master-1 2023-01-27 08:29:09 +01:00
Peter Baumgartner
c68e6b8a96
trainable_lemmatizer in debug data (#11419)
* WIP

* rm ipython embeds

* rm total

* WIP

* cleanup

* cleanup + reword

* rm component function

* remove migration support form

* fix reference dataset for dev data

* additional fixes

- set approach to identifying unique trees
- adjust line length on messages
- add logic for detecting docs without annotations

* use 0 instead of none for no annotation

* partial annotation support

* initial tests for _compile_gold lemma attributes

Using the example data from the edit tree lemmatizer tests for:
- lemmatizer_trees
- partial_lemma_annotations
- n_low_cardinality_lemmas
- no_lemma_annotations

* adds output test for cli app

* switch msg level

* rm unclear uniqueness check

* Revert "rm unclear uniqueness check"

This reverts commit 6ea2b3524b.

* remove good message on uniqueness

* formatting

* use en_vocab fixture

* clarify data set source in messages

* remove unnecessary import

Co-authored-by: svlandeg <svlandeg@github.com>
2023-01-26 17:36:50 +01:00
Daniël de Kok
8d69874afb
Add spacy.PlainTextCorpusReader.v1 (#12122)
* Add `spacy.PlainTextCorpusReader.v1`

This is a corpus reader that reads plain text corpora with the following
format:

- UTF-8 encoding
- One line per document.
- Blank lines are ignored.

It is useful for applications where we deal with very large corpora,
such as distillation, and don't want to deal with the space overhead of
serialized formats. Additionally, many large corpora already use such
a text format, keeping the necessary preprocessing to a minimum.

* Update spacy/training/corpus.py

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

* docs: add version to `PlainTextCorpus`

* Add docstring to registry function

* Add plain text corpus tests

* Only strip newline/carriage return

* Add return type _string_to_tmp_file helper

* Use a temporary directory in place of file name

Different OS auto delete/sharing semantics are just wonky.

* This will be new in 3.5.1 (rather than 4)

* Test improvements from code review

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-01-26 11:33:22 +01:00
Paul O'Leary McCann
de360bc981
Refactor lexeme mem passing (#12125)
* Don't pass mem pool to new lexeme function

* Remove unused mem from function args

Two methods calling _new_lexeme, get and get_by_orth, took mem arguments
just to call the internal method. That's no longer necessary, so this
cleans it up.

* prettier formatting

* Remove more unused mem args
2023-01-25 12:50:21 +09:00
Raphael Mitsch
950fceceb6
Make test_cli_find_threshold() more robust. (#12148) 2023-01-23 14:42:33 +01:00
Richard Hudson
f9e020dd67
Fix speed problem with top_k>1 on CPU in edit tree lemmatizer (#12017)
* Refactor _scores2guesses

* Handle arrays on GPU

* Convert argmax result to raw integer

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

* Use NumpyOps() to copy data to CPU

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

* Changes based on review comments

* Use different _scores2guesses depending on tree_k

* Add tests for corner cases

* Add empty line for consistency

* Improve naming

Co-authored-by: Daniël de Kok <me@github.danieldk.eu>

* Improve naming

Co-authored-by: Daniël de Kok <me@github.danieldk.eu>

Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
Co-authored-by: Daniël de Kok <me@github.danieldk.eu>
2023-01-20 19:34:11 +01:00
Adriane Boyd
1e993d3b03
Merge pull request #12121 from adrianeboyd/chore/v3.5.0-2
Revert "Temporarily skip tests that require models/compat"
2023-01-19 15:59:30 +01:00
Adriane Boyd
3b8918e166
API docs: Rename kb_in_memory to inmemorylookupkb, add to sidebar (#12128)
* 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>
2023-01-19 13:29:17 +01:00
Daniël de Kok
6348a7a4b4
Set version to v4.0.0.dev0 (#12126) 2023-01-19 09:25:34 +01:00
Daniël de Kok
b052b1b47f
Fix batching regression (#12094)
* Fix batching regression

Some time ago, the spaCy v4 branch switched to the new Thinc v9
schedule. However, this introduced an error in how batching is handed.

In the PR, the batchers were changed to keep track of their step,
so that the step can be passed to the schedule. However, the issue
is that the training loop repeatedly calls the batching functions
(rather than using an infinite generator/iterator). So, the step and
therefore the schedule would be reset each epoch. Before the schedule
switch we didn't have this issue, because the old schedules were
stateful.

This PR fixes this issue by reverting the batching functions to use
a (stateful) generator. Their registry functions do accept a `Schedule`
and we convert `Schedule`s to generators.

* Update batcher docs

* Docstring fixes

* Make minibatch take iterables again as well

* Bump thinc requirement to 9.0.0.dev2

* Use type declaration

* Convert another comment into a proper type declaration
2023-01-18 18:28:30 +01:00
Adriane Boyd
dc0f527039 Revert "Temporarily skip tests that require models/compat"
This reverts commit 378db0eb1e.
2023-01-18 12:54:56 +01:00
Daniël de Kok
a183db3cef
Merge the parser refactor into v4 (#10940)
* Try to fix doc.copy

* Set dev version

* Make vocab always own lexemes

* Change version

* Add SpanGroups.copy method

* Fix set_annotations during Parser.update

* Fix dict proxy copy

* Upd version

* Fix copying SpanGroups

* Fix set_annotations in parser.update

* Fix parser set_annotations during update

* Revert "Fix parser set_annotations during update"

This reverts commit eb138c89ed.

* Revert "Fix set_annotations in parser.update"

This reverts commit c6df0eafd0.

* Fix set_annotations during parser update

* Inc version

* Handle final states in get_oracle_sequence

* Inc version

* Try to fix parser training

* Inc version

* Fix

* Inc version

* Fix parser oracle

* Inc version

* Inc version

* Fix transition has_gold

* Inc version

* Try to use real histories, not oracle

* Inc version

* Upd parser

* Inc version

* WIP on rewrite parser

* WIP refactor parser

* New progress on parser model refactor

* Prepare to remove parser_model.pyx

* Convert parser from cdef class

* Delete spacy.ml.parser_model

* Delete _precomputable_affine module

* Wire up tb_framework to new parser model

* Wire up parser model

* Uncython ner.pyx and dep_parser.pyx

* Uncython

* Work on parser model

* Support unseen_classes in parser model

* Support unseen classes in parser

* Cleaner handling of unseen classes

* Work through tests

* Keep working through errors

* Keep working through errors

* Work on parser. 15 tests failing

* Xfail beam stuff. 9 failures

* More xfail. 7 failures

* Xfail. 6 failures

* cleanup

* formatting

* fixes

* pass nO through

* Fix empty doc in update

* Hackishly fix resizing. 3 failures

* Fix redundant test. 2 failures

* Add reference version

* black formatting

* Get tests passing with reference implementation

* Fix missing prints

* Add missing file

* Improve indexing on reference implementation

* Get non-reference forward func working

* Start rigging beam back up

* removing redundant tests, cf #8106

* black formatting

* temporarily xfailing issue 4314

* make flake8 happy again

* mypy fixes

* ensure labels are added upon predict

* cleanup remnants from merge conflicts

* Improve unseen label masking

Two changes to speed up masking by ~10%:

- Use a bool array rather than an array of float32.

- Let the mask indicate whether a label was seen, rather than
  unseen. The mask is most frequently used to index scores for
  seen labels. However, since the mask marked unseen labels,
  this required computing an intermittent flipped mask.

* Write moves costs directly into numpy array (#10163)

This avoids elementwise indexing and the allocation of an additional
array.

Gives a ~15% speed improvement when using batch_by_sequence with size
32.

* Temporarily disable ner and rehearse tests

Until rehearse is implemented again in the refactored parser.

* Fix loss serialization issue (#10600)

* Fix loss serialization issue

Serialization of a model fails with:

TypeError: array(738.3855, dtype=float32) is not JSON serializable

Fix this using float conversion.

* Disable CI steps that require spacy.TransitionBasedParser.v2

After finishing the refactor, TransitionBasedParser.v2 should be
provided for backwards compat.

* Add back support for beam parsing to the refactored parser (#10633)

* Add back support for beam parsing

Beam parsing was already implemented as part of the `BeamBatch` class.
This change makes its counterpart `GreedyBatch`. Both classes are hooked
up in `TransitionModel`, selecting `GreedyBatch` when the beam size is
one, or `BeamBatch` otherwise.

* Use kwarg for beam width

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

* Avoid implicit default for beam_width and beam_density

* Parser.{beam,greedy}_parse: ensure labels are added

* Remove 'deprecated' comments

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

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

* Parser `StateC` optimizations (#10746)

* `StateC`: Optimizations

Avoid GIL acquisition in `__init__`
Increase default buffer capacities on init
Reduce C++ exception overhead

* Fix typo

* Replace `set::count` with `set::find`

* Add exception attribute to c'tor

* Remove unused import

* Use a power-of-two value for initial capacity
Use default-insert to init `_heads` and `_unshiftable`

* Merge `cdef` variable declarations and assignments

* Vectorize `example.get_aligned_parses` (#10789)

* `example`: Vectorize `get_aligned_parse`
Rename `numpy` import

* Convert aligned array to lists before returning

* Revert import renaming

* Elide slice arguments when selecting the entire range

* Tagger/morphologizer alignment performance optimizations (#10798)

* `example`: Unwrap `numpy` scalar arrays before passing them to `StringStore.__getitem__`

* `AlignmentArray`: Use native list as staging buffer for offset calculation

* `example`: Vectorize `get_aligned`

* Hoist inner functions out of `get_aligned`

* Replace inline `if..else` clause in assignment statement

* `AlignmentArray`: Use raw indexing into offset and data `numpy` arrays

* `example`: Replace array unique value check with `groupby`

* `example`: Correctly exclude tokens with no alignment in `_get_aligned_vectorized`
Simplify `_get_aligned_non_vectorized`

* `util`: Update `all_equal` docstring

* Explicitly use `int32_t*`

* Restore C CPU inference in the refactored parser (#10747)

* Bring back the C parsing model

The C parsing model is used for CPU inference and is still faster for
CPU inference than the forward pass of the Thinc model.

* Use C sgemm provided by the Ops implementation

* Make tb_framework module Cython, merge in C forward implementation

* TransitionModel: raise in backprop returned from forward_cpu

* Re-enable greedy parse test

* Return transition scores when forward_cpu is used

* Apply suggestions from code review

Import `Model` from `thinc.api`

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

* Use relative imports in tb_framework

* Don't assume a default for beam_width

* We don't have a direct dependency on BLIS anymore

* Rename forwards to _forward_{fallback,greedy_cpu}

* Require thinc >=8.1.0,<8.2.0

* tb_framework: clean up imports

* Fix return type of _get_seen_mask

* Move up _forward_greedy_cpu

* Style fixes.

* Lower thinc lowerbound to 8.1.0.dev0

* Formatting fix

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

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

* Reimplement parser rehearsal function (#10878)

* Reimplement parser rehearsal function

Before the parser refactor, rehearsal was driven by a loop in the
`rehearse` method itself. For each parsing step, the loops would:

1. Get the predictions of the teacher.
2. Get the predictions and backprop function of the student.
3. Compute the loss and backprop into the student.
4. Move the teacher and student forward with the predictions of
   the student.

In the refactored parser, we cannot perform search stepwise rehearsal
anymore, since the model now predicts all parsing steps at once.
Therefore, rehearsal is performed in the following steps:

1. Get the predictions of all parsing steps from the student, along
   with its backprop function.
2. Get the predictions from the teacher, but use the predictions of
   the student to advance the parser while doing so.
3. Compute the loss and backprop into the student.

To support the second step a new method, `advance_with_actions` is
added to `GreedyBatch`, which performs the provided parsing steps.

* tb_framework: wrap upper_W and upper_b in Linear

Thinc's Optimizer cannot handle resizing of existing parameters. Until
it does, we work around this by wrapping the weights/biases of the upper
layer of the parser model in Linear. When the upper layer is resized, we
copy over the existing parameters into a new Linear instance. This does
not trigger an error in Optimizer, because it sees the resized layer as
a new set of parameters.

* Add test for TransitionSystem.apply_actions

* Better FIXME marker

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

* Fixes from Madeesh

* Apply suggestions from Sofie

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

* Remove useless assignment

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

* Rename some identifiers in the parser refactor (#10935)

* Rename _parseC to _parse_batch

* tb_framework: prefix many auxiliary functions with underscore

To clearly state the intent that they are private.

* Rename `lower` to `hidden`, `upper` to `output`

* Parser slow test fixup

We don't have TransitionBasedParser.{v1,v2} until we bring it back as a
legacy option.

* Remove last vestiges of PrecomputableAffine

This does not exist anymore as a separate layer.

* ner: re-enable sentence boundary checks

* Re-enable test that works now.

* test_ner: make loss test more strict again

* Remove commented line

* Re-enable some more beam parser tests

* Remove unused _forward_reference function

* Update for CBlas changes in Thinc 8.1.0.dev2

Bump thinc dependency to 8.1.0.dev3.

* Remove references to spacy.TransitionBasedParser.{v1,v2}

Since they will not be offered starting with spaCy v4.

* `tb_framework`: Replace references to `thinc.backends.linalg` with `CBlas`

* dont use get_array_module (#11056) (#11293)

Co-authored-by: kadarakos <kadar.akos@gmail.com>

* Move `thinc.extra.search` to `spacy.pipeline._parser_internals` (#11317)

* `search`: Move from `thinc.extra.search`
Fix NPE in `Beam.__dealloc__`

* `pytest`: Add support for executing Cython tests
Move `search` tests from thinc and patch them to run with `pytest`

* `mypy` fix

* Update comment

* `conftest`: Expose `register_cython_tests`

* Remove unused import

* Move `argmax` impls to new `_parser_utils` Cython module (#11410)

* Parser does not have to be a cdef class anymore

This also fixes validation of the initialization schema.

* Add back spacy.TransitionBasedParser.v2

* Fix a rename that was missed in #10878.

So that rehearsal tests pass.

* Remove module from setup.py that got added during the merge

* Bring back support for `update_with_oracle_cut_size` (#12086)

* Bring back support for `update_with_oracle_cut_size`

This option was available in the pre-refactor parser, but was never
implemented in the refactored parser. This option cuts transition
sequences that are longer than `update_with_oracle_cut` size into
separate sequences that have at most `update_with_oracle_cut`
transitions. The oracle (gold standard) transition sequence is used to
determine the cuts and the initial states for the additional sequences.

Applying this cut makes the batches more homogeneous in the transition
sequence lengths, making forward passes (and as a consequence training)
much faster.

Training time 1000 steps on de_core_news_lg:

- Before this change: 149s
- After this change: 68s
- Pre-refactor parser: 81s

* Fix a rename that was missed in #10878.

So that rehearsal tests pass.

* Apply suggestions from @shadeMe

* Use chained conditional

* Test with update_with_oracle_cut_size={0, 1, 5, 100}

And fix a git that occurs with a cut size of 1.

* Fix up some merge fall out

* Update parser distillation for the refactor

In the old parser, we'd iterate over the transitions in the distill
function and compute the loss/gradients on the go. In the refactored
parser, we first let the student model parse the inputs. Then we'll let
the teacher compute the transition probabilities of the states in the
student's transition sequence. We can then compute the gradients of the
student given the teacher.

* Add back spacy.TransitionBasedParser.v1 references

- Accordion in the architecture docs.
- Test in test_parse, but disabled until we have a spacy-legacy release.

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
Co-authored-by: svlandeg <svlandeg@github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: kadarakos <kadar.akos@gmail.com>
2023-01-18 11:27:45 +01:00
Adriane Boyd
794cea6907
Fix comments and examples for levenshtein_compare (#12113) 2023-01-18 08:02:33 +01:00