* 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`
* 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>
* detect cycle during projectivize
* not complete test to detect cycle in projectivize
* boolean to int type to propagate error
* use unordered_set instead of set
* moved error message to errors
* removed cycle from test case
* use find instead of count
* cycle check: only perform one lookup
* Return bool again from _has_head_as_ancestor
Communicate presence of cycles through an output argument.
* Switch to returning std::pair to encode presence of a cycle
The has_cycle pointer is too easy to misuse. Ideally, we would have a
sum type like Rust's `Result` here, but C++ is not there yet.
* _is_non_proj_arc: clarify what we are returning
* _has_head_as_ancestor: remove count
We are now explicitly checking for cycles, so the algorithm must always
terminate. Either we encounter the head, we find a root, or a cycle.
* _is_nonproj_arc: simplify condition
* Another refactor using C++ exceptions
* Remove unused error code
* Print graph with cycle on exception
* Include .hh files in source package
* Add FIXME comment
* cycle detection test
* find cycle when starting from problematic vertex
Co-authored-by: Daniël de Kok <me@danieldk.eu>
* fix: De/Serialize `SpanGroups` including the SpanGroup keys
This prevents the loss of `SpanGroup`s that have the same .name as other `SpanGroup`s within the same `SpanGroups` object (upon de/serialization of the `SpanGroups`).
Fixes#10685
* Maintain backwards compatibility for serialized `SpanGroups`
(serialized as: a list of `SpanGroup`s, or b'')
* Add tests for `SpanGroups` deserialization backwards-compatibility
* Move a `SpanGroups` de/serialization test (test_issue10685)
to tests/serialize/test_serialize_spangroups.py
* Output a warning if deserializing a `SpanGroups` with duplicate .name-d `SpanGroup`s
* Minor refactor
* `SpanGroups.from_bytes` handles only `list` and `dict` types with
`dict` as the expected default
* For lists, keep first rather than last value encountered
* Update error message
* Rename and update tests
* Update to preserve list serialization of SpanGroups
To avoid breaking compatibility of serialized `Doc` and `DocBin` with
earlier versions of spacy v3, revert back to a list-only serialization,
but update the names just for serialization so that the SpanGroups keys
override the SpanGroup names.
* Preserve object identity and current key overwrite
* Preserve SpanGroup object identity
* Preserve last rather than first span group from SpanGroup list
format without SpanGroups keys
* Update inline comments
* Fix types
* Add type info for SpanGroup.copy
* Deserialize `SpanGroup`s as copies
when a single SpanGroup is the value for more than 1 `SpanGroups` key.
This is because we serialize `SpanGroups` as dicts (to maintain backward-
and forward-compatibility) and we can't assume `SpanGroup`s with the same
bytes/serialization were the same (identical) object, pre-serialization.
* Update spacy/tokens/_dict_proxies.py
* Add more SpanGroups serialization tests
Test that serialized SpanGroups maintain their Span order
* small clarification on older spaCy version
* Update spacy/tests/serialize/test_serialize_span_groups.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add SpanRuler component
Add a `SpanRuler` component similar to `EntityRuler` that saves a list
of matched spans to `Doc.spans[spans_key]`. The matches from the token
and phrase matchers are deduplicated and sorted before assignment but
are not otherwise filtered.
* Update spacy/pipeline/span_ruler.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix cast
* Add self.key property
* Use number of patterns as length
* Remove patterns kwarg from init
* Update spacy/tests/pipeline/test_span_ruler.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add options for spans filter and setting to ents
* Add `spans_filter` option as a registered function'
* Make `spans_key` optional and if `None`, set to `doc.ents` instead of
`doc.spans[spans_key]`.
* Update and generalize tests
* Add test for setting doc.ents, fix key property type
* Fix typing
* Allow independent doc.spans and doc.ents
* If `spans_key` is set, set `doc.spans` with `spans_filter`.
* If `annotate_ents` is set, set `doc.ents` with `ents_fitler`.
* Use `util.filter_spans` by default as `ents_filter`.
* Use a custom warning if the filter does not work for `doc.ents`.
* Enable use of SpanC.id in Span
* Support id in SpanRuler as Span.id
* Update types
* `id` can only be provided as string (already by `PatternType`
definition)
* Update all uses of Span.id/ent_id in Doc
* Rename Span id kwarg to span_id
* Update types and docs
* Add ents filter to mimic EntityRuler overwrite_ents
* Refactor `ents_filter` to take `entities, spans` args for more
filtering options
* Give registered filters more descriptive names
* Allow registered `filter_spans` filter
(`spacy.first_longest_spans_filter.v1`) to take any number of
`Iterable[Span]` objects as args so it can be used for spans filter
or ents filter
* Implement future entity ruler as span ruler
Implement a compatible `entity_ruler` as `future_entity_ruler` using
`SpanRuler` as the underlying component:
* Add `sort_key` and `sort_reverse` to allow the sorting behavior to be
customized. (Necessary for the same sorting/filtering as in
`EntityRuler`.)
* Implement `overwrite_overlapping_ents_filter` and
`preserve_existing_ents_filter` to support
`EntityRuler.overwrite_ents` settings.
* Add `remove_by_id` to support `EntityRuler.remove` functionality.
* Refactor `entity_ruler` tests to parametrize all tests to test both
`entity_ruler` and `future_entity_ruler`
* Implement `SpanRuler.token_patterns` and `SpanRuler.phrase_patterns`
properties.
Additional changes:
* Move all config settings to top-level attributes to avoid duplicating
settings in the config vs. `span_ruler/cfg`. (Also avoids a lot of
casting.)
* Format
* Fix filter make method name
* Refactor to use same error for removing by label or ID
* Also provide existing spans to spans filter
* Support ids property
* Remove token_patterns and phrase_patterns
* Update docstrings
* Add span ruler docs
* Fix types
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Move sorting into filters
* Check for all tokens in seen tokens in entity ruler filters
* Remove registered sort key
* Set Token.ent_id in a backwards-compatible way in Doc.set_ents
* Remove sort options from API docs
* Update docstrings
* Rename entity ruler filters
* Fix and parameterize scoring
* Add id to Span API docs
* Fix typo in API docs
* Include explicit labeled=True for scorer
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix TODO about typing
Fix was simple: just request an array2f.
* Add type ignore
Maxout has a more restrictive type than the residual layer expects (only
Floats2d vs any Floats).
* Various cleanup
This moves a lot of lines around but doesn't change any functionality.
Details:
1. use `continue` to reduce indentation
2. move sentence doc building inside conditional since it's otherwise
unused
3. reduces some temporary assignments
* 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>
* Update docs for displacy style kwargs
Added "span" to the accepted values for the style kwarg in the displacy.serve and displacy.render top-level functions. These styles are new as of SpaCy 3.3, so I added the "new" tag for that option only
* restored alpha ordering
* Parser: use C saxpy/sgemm provided by the Ops implementation
This is a backport of https://github.com/explosion/spaCy/pull/10747
from the parser refactor branch. It eliminates the explicit calls
to BLIS, instead using the saxpy/sgemm provided by the Ops
implementation.
This allows us to use Accelerate in the parser on M1 Macs (with
an updated thinc-apple-ops).
Performance of the de_core_news_lg pipe:
BLIS 0.7.0, no thinc-apple-ops: 6385 WPS
BLIS 0.7.0, thinc-apple-ops: 36455 WPS
BLIS 0.9.0, no thinc-apple-ops: 19188 WPS
BLIS 0.9.0, thinc-apple-ops: 36682 WPS
This PR, thinc-apple-ops: 38726 WPS
Performance of the de_core_news_lg pipe (only tok2vec -> parser):
BLIS 0.7.0, no thinc-apple-ops: 13907 WPS
BLIS 0.7.0, thinc-apple-ops: 73172 WPS
BLIS 0.9.0, no thinc-apple-ops: 41576 WPS
BLIS 0.9.0, thinc-apple-ops: 72569 WPS
This PR, thinc-apple-ops: 87061 WPS
* Require thinc >=8.1.0,<8.2.0
* Lower thinc lowerbound to 8.1.0.dev0
* Use best CPU ops for CBLAS when the parser model is on the GPU
* Fix another unguarded cblas() call
* Fix: use ops as a shorthand for self.model.ops
Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
This change removes `thinc.util.has_cupy` from the GPU presence check.
Currently `gpu_is_available` already implies `has_cupy`. We also want
to show this warning in the future when a machine has a non-CuPy GPU.
* Make changes to typing
* Correction
* Format with black
* Corrections based on review
* Bumped Thinc dependency version
* Bumped blis requirement
* Correction for older Python versions
* Update spacy/ml/models/textcat.py
Co-authored-by: Daniël de Kok <me@github.danieldk.eu>
* Corrections based on review feedback
* Readd deleted docstring line
Co-authored-by: Daniël de Kok <me@github.danieldk.eu>
* `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*`
