* avoid nesting then flattening
* mypy fix
* Apply suggestions from code review
* Add type for indices
* Run full matrix for mypy
* Add back modified type: ignore
* Revert "Run full matrix for mypy"
This reverts commit e218873d04.
---------
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Use `build` instead of `python setup.py sdist`
* Remove in-place build with `setup.py`
* Remove `gpu` parameter and GPU tests
* Keep `architecture` and `num_build_jobs` in azure steps with CI
defaults
* Fix use of `num_build_jobs` parameters
* Remove now-unused `prefix` parameter
* Test imports and CLI before installing test requirements
* Remove `*.egg-info` directory in addition to source directory for an
warning-free `import spacy`
* Switch `thinc-apple-ops` test to python 3.11 (as most recent python
that is tested across platforms)
* 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
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.
After the precomputable affine table of shape [nB, nF, nO, nP] is
computed, padding with shape [1, nF, nO, nP] is assigned to the first
row of the precomputed affine table. However, when we are indexing the
precomputed table, we get a row of shape [nF, nO, nP]. CuPy versions
before 10.0 cannot paper over this shape difference.
This change fixes compatibility with CuPy < 10.0 by squeezing the first
dimension of the padding before assignment.
The `forward` of `precomputable_biaffine` performs matrix multiplication
and then `vstack`s the result with padding. This creates a temporary
array used for the output of matrix concatenation.
This change avoids the temporary by pre-allocating an array that is
large enough for the output of matrix multiplication plus padding and
fills the array in-place.
This gave me a small speedup (a bit over 100 WPS) on de_core_news_lg on
M1 Max (after changing thinc-apple-ops to support in-place gemm as BLIS
does).
* 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>
* 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
* Add failing test
* Partial fix for issue
This kind of works. The issue with token length mismatches is gone. The
problem is that when you get empty lists of encodings to compare, it
fails because the sizes are not the same, even though they're both zero:
(0, 3) vs (0,). Not sure why that happens...
* Short circuit on empties
* Remove spurious check
The check here isn't needed now the the short circuit is fixed.
* Update spacy/tests/pipeline/test_entity_linker.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Use "eg", not "example"
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Rename to spans_key for consistency
* Implement spans length in debug data
* Implement how span bounds and spans are obtained
In this commit, I implemented how span boundaries (the tokens) around a
given span and spans are obtained. I've put them in the compile_gold()
function so that it's accessible later on. I will do the actual
computation of the span and boundary distinctiveness in the main
function above.
* Compute for p_spans and p_bounds
* Add computation for SD and BD
* Fix mypy issues
* Add weighted average computation
* Fix compile_gold conditional logic
* Add test for frequency distribution computation
* Add tests for kl-divergence computation
* Fix weighted average computation
* Make tables more compact by rounding them
* Add more descriptive checks for spans
* Modularize span computation methods
In this commit, I added the _get_span_characteristics and
_print_span_characteristics functions so that they can be reusable
anywhere.
* Remove unnecessary arguments and make fxs more compact
* Update a few parameter arguments
* Add tests for print_span and get_span methods
* Update API to talk about span characteristics in brief
* Add better reporting of spans_length
* Add test for span length reporting
* Update formatting of span length report
Removed '' to indicate that it's not a string, then
sort the n-grams by their length, not by their frequency.
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Show all frequency distribution when -V
In this commit, I displayed the full frequency distribution of the
span lengths when --verbose is passed. To make things simpler, I
rewrote some of the formatter functions so that I can call them
whenever.
Another notable change is that instead of showing percentages as
Integers, I showed them as floats (max 2-decimal places). I did this
because it looks weird when it displays (0%).
* Update logic on how total is computed
The way the 90% thresholding is computed now is that we keep
adding the percentages until we reach >= 90%. I also updated the wording
and used the term "At least" to denote that >= 90% of your spans have
these distributions.
* Fix display when showing the threshold percentage
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add better phrasing for span information
* Update spacy/cli/debug_data.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add minor edits for whitespaces etc.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add glossary entry for root
There was already one but it was lower case, maybe that should be
removed?
* remove lowercase root
On reflection, that was probably just a mistake.
* Add lowercase root back
It's harmless to leave it there.
