Commit Graph

2565 Commits

Author SHA1 Message Date
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
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
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
Daniël de Kok
5e297aa20e
Add TrainablePipe.{distill,get_teacher_student_loss} (#12016)
* Add `TrainablePipe.{distill,get_teacher_student_loss}`

This change adds two methods:

- `TrainablePipe::distill` which performs a training step of a
   student pipe on a teacher pipe, giving a batch of `Doc`s.
- `TrainablePipe::get_teacher_student_loss` computes the loss
  of a student relative to the teacher.

The `distill` or `get_teacher_student_loss` methods are also implemented
in the tagger, edit tree lemmatizer, and parser pipes, to enable
distillation in those pipes and as an example for other pipes.

* Fix stray `Beam` import

* Fix incorrect import

* Apply suggestions from code review

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

* Apply suggestions from code review

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

* TrainablePipe.distill: use `Iterable[Example]`

* Add Pipe.is_distillable method

* Add `validate_distillation_examples`

This first calls `validate_examples` and then checks that the
student/teacher tokens are the same.

* Update distill documentation

* Add distill documentation for all pipes that support distillation

* Fix incorrect identifier

* Apply suggestions from code review

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

* Add comment to explain `is_distillable`

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2023-01-16 10:25:53 +01:00
Daniël de Kok
dda7331da3
Handle missing annotations in the edit tree lemmatizer (#12098)
The losses/gradients of missing annotations were not correctly masked
out. Fix this and check the masking in the partial data test.
2023-01-12 12:13:55 +01:00
Daniël de Kok
319eb508b5
Add a spacy benchmark speed subcommand (#11902)
* 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`
2023-01-12 11:55:21 +01:00
svlandeg
fc2723925b update tests from master to follow v4 principles (2) 2023-01-11 19:04:06 +01:00
svlandeg
6ff5eb256c update tests from master to follow v4 principles 2023-01-11 18:57:50 +01:00
svlandeg
b2fd9490e3 Merge branch 'copy_master' into copy_v4 2023-01-11 18:40:55 +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
Kevin Humphreys
19650ebb52
Enable fuzzy text matching in Matcher (#11359)
* 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>
2023-01-10 10:36:17 +01:00
Zhangrp
eb8bb35c13
improve ux for displacy when the serve port is in use (#11948)
* 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>
2023-01-10 15:52:57 +09:00
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
Sofie Van Landeghem
7f6c638c3a
fix processing of "auto" in convert (#12050)
* 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
2023-01-05 10:21:00 +01:00
svlandeg
6852adc8b7 Merge branch 'copy_master' into copy_v4 2023-01-03 13:34:05 +01:00
github-actions[bot]
abb0ab109d
Auto-format code with black (#12035)
Co-authored-by: explosion-bot <explosion-bot@users.noreply.github.com>
2023-01-02 11:59:57 +01:00
Adriane Boyd
ef9e504eac
Rename modified textcat scorer to v2 (#11971)
As a follow-up to #11696, rename the modified scorer to v2 and move the
v1 scorer to `spacy-legacy`.
2022-12-29 14:01:08 +01:00
Daniël de Kok
207565a788 Merge remote-tracking branch 'upstream/master' into chore/v4-merge-master-20221222 2022-12-22 10:08:54 +01:00
Raphael Mitsch
eef3d950b4
Fix SpanGroup and Span typing (#12009)
* Correct Span.label, Span.kb_id types. Fix SpanGroup.__iter__().

* Extend test.

* Rename test. Fix typo.

* Add comment.

* Fix types for Span.label, Span.kb_id, Span.char_span().

* Update spacy/tests/doc/test_span_group.py

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

* Update docs.

* Fix typo.

* Update spacy/tokens/span_group.pyx

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

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-12-21 18:54:27 +01:00
kadarakos
c223cd7a86
Add apply CLI (#11376)
* annotate cli first try

* add batch-size and n_process

* rename to apply

* typing fix

* handle file suffixes

* walk directories

* support jsonl

* typing fix

* remove debug

* make suffix optional for walk

* revert unrelated

* don't warn but raise

* better error message

* minor touch up

* Update spacy/tests/test_cli.py

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

* Update spacy/cli/apply.py

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

* Update spacy/cli/apply.py

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

* update tests and bugfix

* add force_overwrite

* typo

* fix adding .spacy suffix

* Update spacy/cli/apply.py

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

* Update spacy/cli/apply.py

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

* Update spacy/cli/apply.py

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

* store user data and rename cmd arg

* include test for user attr

* rename cmd arg

* better help message

* documentation

* prettier

* black

* link fix

* Update spacy/cli/apply.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update website/docs/api/cli.md

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update website/docs/api/cli.md

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update website/docs/api/cli.md

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* addressing reviews

* dont quit but warn

* prettier

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
2022-12-20 17:11:33 +01:00
Daniël de Kok
f9308aae13
Fix v4 branch to build against Thinc v9 (#11921)
* Move `thinc.extra.search` to `spacy.pipeline._parser_internals`

Backport of:
https://github.com/explosion/spaCy/pull/11317

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

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

Backport of:
https://github.com/explosion/spaCy/pull/11292

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

* Use cross entropy from `thinc.legacy`

* Require thinc>=9.0.0.dev0,<9.1.0

Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
2022-12-17 14:32:19 +01:00
Edward
ca75190a3d
Custom extensions for spans with equal boundaries (#11429)
* Init

* Fix return type for mypy

* adjust types and improve setting new attributes

* Add underscore changes to json conversion

* Add test and underscore changes to from_docs

* add underscore changes and test to span.to_doc

* update return values

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

* Add types to function

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

* adjust formatting

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

* shorten return type

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

* add helper function to improve readability

* Improve code and add comments

* rerun azure tests

* Fix tests for json conversion

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-12-12 08:55:53 +01:00
Adriane Boyd
0591e67265
Cast to uint64 for all array-based doc representations (#11933)
* 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
2022-12-12 08:45:35 +01:00
github-actions[bot]
f22fc7a113
Auto-format code with black (#11955)
Co-authored-by: explosion-bot <explosion-bot@users.noreply.github.com>
2022-12-09 10:15:52 +01:00
Paul O'Leary McCann
6b9af38eeb
Remove all references to "begin_training" (#11943)
When v3 was released, `begin_training` was renamed to `initialize`.
There were warnings in the code and docs about that. This PR removes
them.
2022-12-08 11:43:52 +01:00
Daniël de Kok
27fac7df2e
EditTreeLemmatizer: correctly add strings when initializing from labels (#11934)
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.
2022-12-07 13:53:41 +09:00
Zhangrp
23085ffef4
Fix interpolation in directory names, see #11235. (#11914) 2022-12-06 17:42:12 +09:00
svlandeg
04fea09ffd Merge branch 'copy_master' into copy_v4 2022-12-05 08:56:15 +01:00
Adriane Boyd
445c670a2d
Fix spancat for zero suggestions (#11860)
* Add test for spancat predict with zero suggestions

* Fix spancat for zero suggestions

* Undo changes to extract_spans

* Use .sum() as in update
2022-12-02 09:33:52 +01:00
Adriane Boyd
6f9d630f7e
Replace Pipe type with Callable in Language (#11803)
* Replace Pipe type with Callable in Language

* Use Callable[[Doc], Doc] in the docstrings
2022-11-29 13:20:08 +01:00
Adriane Boyd
e0d43557b7
Merge pull request #11871 from adrianeboyd/chore/v3.5.0
Prepare for v3.5.0
2022-11-29 11:41:32 +01:00
Adriane Boyd
1ebe7db07c
Support local filesystem remotes for projects (#11762)
* 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
2022-11-29 11:40:58 +01:00
Paul O'Leary McCann
f54bfb56c9
Don't throw an error if using displacy on an unset span key (#11845)
* Don't throw an error if using displacy on an unset span key

* List available keys in W117
2022-11-28 10:01:09 +01:00
Adriane Boyd
681ec20914
Add smart_open requirement, update deprecated options (#11864)
* Switch from deprecated `ignore_ext` to `compression`
* Add upload/download test for local files
2022-11-25 13:00:57 +01:00
Adriane Boyd
378db0eb1e Temporarily skip tests that require models/compat 2022-11-25 12:05:25 +01:00
Raphael Mitsch
c0fd8a2e71
find-threshold: CLI command for multi-label classifier threshold tuning (#11280)
* Add foundation for find-threshold CLI functionality.

* Finish first draft for find-threshold.

* Add tests.

* Revert adjusted import statements.

* Fix mypy errors.

* Fix imports.

* Harmonize arguments with spacy evaluate command.

* Generalize component and threshold handling. Harmonize arguments with 'spacy evaluate' CLI.

* Fix Spancat test.

* Add beta parameter to Scorer and PRFScore.

* Make beta a component scorer setting.

* Remove beta.

* Update nlp.config (workaround).

* Reload pipeline on threshold change. Adjust tests. Remove confection reference.

* Remove assumption of component being a Pipe object or having a .cfg attribute.

* Adjust test output and reference values.

* Remove beta references. Delete universe.json.

* Reverting unnecessary changes. Removing unused default values. Renaming variables in find-cli tests.

* Update spacy/cli/find_threshold.py

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

* Remove adding labels in tests.

* Remove unused error

* Undo changes to PRFScorer

* Change default value for n_trials. Log table iteratively.

* Add warnings for pointless applications of find_threshold().

* Fix imports.

* Adjust type check of TextCategorizer to exclude subclasses.

* Change check of if there's only one unique value in scores.

* Update spacy/cli/find_threshold.py

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

* Incorporate feedback.

* Fix test issue. Update docstring.

* Update docs & docstring.

* Update spacy/tests/test_cli.py

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

* Add examples to docs. Rename _nlp to nlp in tests.

* Update spacy/cli/find_threshold.py

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

* Update spacy/cli/find_threshold.py

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

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-11-25 11:44:55 +01:00
Adriane Boyd
30d31fd335
Update Russian and Ukrainian lemmatizers (#11811)
* 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>
2022-11-25 11:12:46 +01:00
Madeesh Kannan
5ea14af32b
Add training.before_update callback (#11739)
* 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>
2022-11-23 17:54:58 +01:00
Edward
e79910d57e
Remove sentiment extension (#11722)
* remove sentiment attribute

* remove sentiment from docs

* add test for backwards compatibility

* replace from_disk with from_bytes

* Fix docs and format file

* Fix formatting
2022-11-23 13:09:32 +01:00
Marco Edward Gorelli
f0d8309a28
fix comparison of constants (#11834)
Co-authored-by: MarcoGorelli <>
2022-11-21 08:12:03 +01:00
Paul O'Leary McCann
75bb7ad541
Check textcat values for validity (#11763)
* 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
2022-11-17 10:25:01 +01:00
Paul O'Leary McCann
c0c54e44bc
Add equality definition for vectors (#11806)
* 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>
2022-11-16 09:44:42 +01:00
Adriane Boyd
03eebe9d1c
Update warning, add tests for project requirements check (#11777)
* 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
2022-11-09 10:59:28 +01:00
Raphael Mitsch
20bbbe3e44
Revert disable/disabled merging behavior (#11745)
* Merge disable with disabled. Adjust warnings, errors and tests.

* Replace any() with set operation.

* Update spacy/tests/pipeline/test_pipe_methods.py

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

* Update docs.

* Remve reference to config entry nlp.enabled from docs.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-11-08 14:58:10 +01:00
Adriane Boyd
40e1000db0
Restore Doc attr getter values in Doc.to_json (#11700) 2022-11-03 11:49:08 +01:00