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Rewrite for spaCy v3 #173

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wants to merge 279 commits into from
Closed

Rewrite for spaCy v3 #173

wants to merge 279 commits into from
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Commits on Apr 24, 2020

  1. Fix flake errors

    @honnibal
    honnibal committed Apr 24, 2020
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  2. Clean up annotation_setters module

    @honnibal
    honnibal committed Apr 24, 2020
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  3. Update

    @honnibal
    honnibal committed Apr 24, 2020
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  4. Format

    @honnibal
    honnibal committed Apr 24, 2020
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  5. Fix flake errors

    @honnibal
    honnibal committed Apr 24, 2020
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Commits on Apr 25, 2020

  1. Add extension implementations

    @honnibal
    honnibal committed Apr 25, 2020
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  2. Tidy and fix

    @honnibal
    honnibal committed Apr 25, 2020
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  3. Format

    @honnibal
    honnibal committed Apr 25, 2020
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  4. Fix model wrapper

    @honnibal
    honnibal committed Apr 25, 2020
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  5. Fix component

    @honnibal
    honnibal committed Apr 25, 2020
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  6. Add imports

    @honnibal
    honnibal committed Apr 25, 2020
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  7. Fix bug

    @honnibal
    honnibal committed Apr 25, 2020
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  8. Work on dummy tokenizer

    @honnibal
    honnibal committed Apr 25, 2020
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Commits on Apr 26, 2020

  1. Add test util

    @honnibal
    honnibal committed Apr 26, 2020
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  2. Move dummy test thing to tests module

    @honnibal
    honnibal committed Apr 26, 2020
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  3. Fix dummy model

    @honnibal
    honnibal committed Apr 26, 2020
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  4. Fix model wrapper

    @honnibal
    honnibal committed Apr 26, 2020
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  5. Add test for pipeline component

    @honnibal
    honnibal committed Apr 26, 2020
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  6. Fix test

    @honnibal
    honnibal committed Apr 26, 2020
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  7. Fix alignment

    @honnibal
    honnibal committed Apr 26, 2020
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  8. Test set_annotations

    @honnibal
    honnibal committed Apr 26, 2020
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  9. Fix TransformerOutput.empty method

    @honnibal
    honnibal committed Apr 26, 2020
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  10. Remove print statement

    @honnibal
    honnibal committed Apr 26, 2020
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  11. Try to set nO dimension

    @honnibal
    honnibal committed Apr 26, 2020
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  12. Fix listener

    @honnibal
    honnibal committed Apr 26, 2020
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  13. Add test for pipeline component

    @honnibal
    honnibal committed Apr 26, 2020
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  14. Move add_extensions to util.py

    @honnibal
    honnibal committed Apr 26, 2020
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  15. Add layers

    @honnibal
    honnibal committed Apr 26, 2020
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  16. Rethink extensions

    @honnibal
    honnibal committed Apr 26, 2020
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  17. Reorg

    @honnibal
    honnibal committed Apr 26, 2020
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  18. Add docs property to TransformerOutput

    @honnibal
    honnibal committed Apr 26, 2020
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  19. Remove print statement

    @honnibal
    honnibal committed Apr 26, 2020
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  20. Reorg

    @honnibal
    honnibal committed Apr 26, 2020
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  21. Reorg

    @honnibal
    honnibal committed Apr 26, 2020
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  22. Reorg

    @honnibal
    honnibal committed Apr 26, 2020
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  23. Reorg

    @honnibal
    honnibal committed Apr 26, 2020
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  24. Get tests passing after refactor

    @honnibal
    honnibal committed Apr 26, 2020
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Commits on Apr 27, 2020

  1. Starting to train

    @honnibal
    honnibal committed Apr 27, 2020
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  2. Update util

    @honnibal
    honnibal committed Apr 27, 2020
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  3. Temporarily add train-from-config script

    @honnibal
    honnibal committed Apr 27, 2020
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  4. Fix training

    @honnibal
    honnibal committed Apr 27, 2020
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  5. Dont pad by default

    @honnibal
    honnibal committed Apr 27, 2020
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  6. Add pos cfg

    @honnibal
    honnibal committed Apr 27, 2020
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  7. Update cfg

    @honnibal
    honnibal committed Apr 27, 2020
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Commits on Apr 28, 2020

  1. Update tok2vec

    @honnibal
    honnibal committed Apr 28, 2020
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  2. Update examples

    @honnibal
    honnibal committed Apr 28, 2020
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  3. Refactor

    @honnibal
    honnibal committed Apr 28, 2020
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  4. Refactor

    @honnibal
    honnibal committed Apr 28, 2020
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  5. Add BatchEncoding

    @honnibal
    honnibal committed Apr 28, 2020
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  6. Fix flake8 errors

    @honnibal
    honnibal committed Apr 28, 2020
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  7. Format

    @honnibal
    honnibal committed Apr 28, 2020
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  8. Get test_pipeline_component passing

    @honnibal
    honnibal committed Apr 28, 2020
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  9. Get test_model_wrapper passing

    @honnibal
    honnibal committed Apr 28, 2020
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  10. Fix tok2vec

    @honnibal
    honnibal committed Apr 28, 2020
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  11. Fix alignment

    @honnibal
    honnibal committed Apr 28, 2020
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  12. Improve example script

    @honnibal
    honnibal committed Apr 28, 2020
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  13. Fixes

    @honnibal
    honnibal committed Apr 28, 2020
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  14. Fix train-from-config script

    @honnibal
    honnibal committed Apr 28, 2020
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Commits on Apr 29, 2020

  1. Add dep config

    @honnibal
    honnibal committed Apr 29, 2020
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Commits on Apr 30, 2020

  1. Set nO for transformer

    @honnibal
    honnibal committed Apr 30, 2020
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  2. Update example configs

    @honnibal
    honnibal committed Apr 30, 2020
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  3. Update example scripts

    @honnibal
    honnibal committed Apr 30, 2020
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  4. Fix lr rate in config

    @honnibal
    honnibal committed Apr 30, 2020
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Commits on May 4, 2020

  1. update srsly requirement

    @svlandeg
    svlandeg committed May 4, 2020
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  2. also update package requirements in setup.cfg

    @svlandeg
    svlandeg committed May 4, 2020
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Commits on May 5, 2020

  1. Hack in a function for strided spans

    @honnibal
    honnibal committed May 5, 2020
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  2. Update wrapper: average tokens instead of last

    @honnibal
    honnibal committed May 5, 2020
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  3. Update train_from_config script

    @honnibal
    honnibal committed May 5, 2020
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  4. Fix tok2vec wrapper

    @honnibal
    honnibal committed May 5, 2020
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  5. Merge branch 'feature/spacy-v3' of https://github.com/explosion/spacy… 

    …-transformers into feature/spacy-v3
    @honnibal
    honnibal committed May 5, 2020
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Commits on May 6, 2020

  1. Update DummyTransformer test util

    @honnibal
    honnibal committed May 6, 2020
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  2. Fix width property of TransformerData

    @honnibal
    honnibal committed May 6, 2020
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  3. Add find_last_hidden util

    @honnibal
    honnibal committed May 6, 2020
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  4. Add linear layer in transformer tok2vec

    @honnibal
    honnibal committed May 6, 2020
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  5. Add linear layer for transformers

    @honnibal
    honnibal committed May 6, 2020
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Commits on May 8, 2020

  1. Remove print statements

    @honnibal
    honnibal committed May 8, 2020
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  2. Cleanup

    @honnibal
    honnibal committed May 8, 2020
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  3. Allow max_batch_size in transformer component

    @honnibal
    honnibal committed May 8, 2020
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  4. Fix alignment

    @honnibal
    honnibal committed May 8, 2020
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  5. Fix tok2vec gradient

    @honnibal
    honnibal committed May 8, 2020
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  6. Clean up wrapper a bit

    @honnibal
    honnibal committed May 8, 2020
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  7. Register span functions

    @honnibal
    honnibal committed May 8, 2020
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  8. Update configs

    @honnibal
    honnibal committed May 8, 2020
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  9. Clean up wrapper

    @honnibal
    honnibal committed May 8, 2020
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Commits on May 10, 2020

  1. Refactor alignment

    @honnibal
    honnibal committed May 10, 2020
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  2. Move types

    @honnibal
    honnibal committed May 10, 2020
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  3. Update requirements

    @honnibal
    honnibal committed May 10, 2020
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  4. Update alignment

    @honnibal
    honnibal committed May 10, 2020
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  5. Use Ragged for alignment

    @honnibal
    honnibal committed May 10, 2020
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  6. Use configurable alignment pooling

    @honnibal
    honnibal committed May 10, 2020
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  7. Update alignment

    @honnibal
    honnibal committed May 10, 2020
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  8. Start testing alignment

    @honnibal
    honnibal committed May 10, 2020
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  9. Remove unused code

    @honnibal
    honnibal committed May 10, 2020
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  10. WIP on refactor

    @honnibal
    honnibal committed May 10, 2020
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  11. WIP on new alignment

    @honnibal
    honnibal committed May 10, 2020
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  12. Tmp

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    honnibal committed May 10, 2020
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  13. Configure mypy

    @honnibal
    honnibal committed May 10, 2020
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  14. Fix test util

    @honnibal
    honnibal committed May 10, 2020
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  15. Update alignment

    @honnibal
    honnibal committed May 10, 2020
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  16. Hack types

    @honnibal
    honnibal committed May 10, 2020
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  17. Update tok2vec

    @honnibal
    honnibal committed May 10, 2020
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  18. Format

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    honnibal committed May 10, 2020
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  19. Remove unused imports

    @honnibal
    honnibal committed May 10, 2020
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  20. Work on updating tests

    @honnibal
    honnibal committed May 10, 2020
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  21. Work on updating tests

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    honnibal committed May 10, 2020
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Commits on May 11, 2020

  1. Use thinc 8.0.0a6

    @honnibal
    honnibal committed May 11, 2020
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  2. Fix wrapper

    @honnibal
    honnibal committed May 11, 2020
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  3. Fix dummy tokenizer

    @honnibal
    honnibal committed May 11, 2020
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  4. Fix test

    @honnibal
    honnibal committed May 11, 2020
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  5. Update alignment test

    @honnibal
    honnibal committed May 11, 2020
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  6. Fix test

    @honnibal
    honnibal committed May 11, 2020
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  7. New alignment mostly working, apart from strided

    @honnibal
    honnibal committed May 11, 2020
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Commits on May 12, 2020

  1. Mostly working -- need to fix overlapping spans

    @honnibal
    honnibal committed May 12, 2020
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  2. WIP on span alignment

    @honnibal
    honnibal committed May 12, 2020
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  3. Update alignment to use spans

    @honnibal
    honnibal committed May 12, 2020
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  4. Update wrapper

    @honnibal
    honnibal committed May 12, 2020
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Commits on May 13, 2020

  1. fix config files

    @svlandeg
    svlandeg committed May 13, 2020
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  2. Fix alignment

    @honnibal
    honnibal committed May 13, 2020
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  3. Kludge type errors

    @honnibal
    honnibal committed May 13, 2020
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  4. Tweak alignment code

    @honnibal
    honnibal committed May 13, 2020
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Commits on May 14, 2020

  1. Fix span stride

    @honnibal
    honnibal committed May 14, 2020
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  2. Fix strided alignment

    @honnibal
    honnibal committed May 14, 2020
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  3. Fix strided alignment

    @honnibal
    honnibal committed May 14, 2020
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  4. Flake8

    @honnibal
    honnibal committed May 14, 2020
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  5. Format

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  6. Fix doc stride

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  7. Merge remote-tracking branch 'upstream/feature/spacy-v3' into feature… 

    …/v3-io
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  8. Document joint-core-bert config file

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  9. set doc extension when creating pipeline component, force to True

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  10. testing a TransformerFromFile IO solution (WIP)

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  11. shift IO responsibility to pipeline component

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  12. add newline

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  13. tidying

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Commits on May 16, 2020

  1. Add comment on get_alignment

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Commits on May 17, 2020

  1. Update configs for simple vs tb NER

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  2. Set accumulate_gradient = 2

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  3. Set accumulate_gradient = 2

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  4. Fallback to rule-based sentencizer if no SBD in get_sent_spans spanner

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  5. Update joint-core-bert config

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  6. Add config for joint-dep-pos-bert

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  7. Tmp

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  8. Remove distilbert config

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Commits on May 18, 2020

  1. Add nan check

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  2. Update joint-core-bert config. Getting pretty great onto5 results

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  3. Update joint-dep-pos-bert config

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  4. More explicitly clear gradient in case called multiple times

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  5. Update joint-core-bert.cfg

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  6. merge upstream spacy-v3 branch

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  7. Merge pull request #178 from svlandeg/feature/v3-io 

    IO for transformer component
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  8. Call cuda on transformer if necessary

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  9. Add todo

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  10. Merge branch 'feature/spacy-v3' of https://github.com/explosion/spacy… 

    …-transformers into feature/spacy-v3
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Commits on May 19, 2020

  1. Document and test apply_alignment function

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  2. Clean up unused stuff

    @honnibal
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  3. Add length assertion

    @honnibal
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  4. Fix alignment if tokens excluded from spans

    @honnibal
    honnibal committed May 19, 2020
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  5. Improve strided span

    @honnibal
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  6. Add test for strided spans

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  7. Pin spacy and thinc versions

    @honnibal
    honnibal committed May 19, 2020
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  8. Fix merge conflicts

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Commits on May 20, 2020

  1. Handle case where no tokens align

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  2. Update backprop

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  3. Merge branch 'feature/spacy-v3' of https://github.com/explosion/spacy… 

    …-transformers into feature/spacy-v3
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  4. Update joint-core-bert example

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  5. Update readme

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  6. Merge branch 'feature/spacy-v3' of https://github.com/explosion/spacy… 

    …-transformers into feature/spacy-v3
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Commits on May 21, 2020

  1. Start refactor

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  2. Refactor

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  3. Update pipeline component

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  4. Refactor

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  5. Try to untangle serialization

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  6. Refactor

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  7. Refactor layers

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  8. Refactor

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  9. Update init

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  10. Refactor

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  11. Refactor

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  12. Refactor

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  13. Refactor

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  14. Add arch

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  15. Refactor

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  16. Update

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  17. Fix flake8

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    honnibal committed May 21, 2020
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  18. Fix flake8

    @honnibal
    honnibal committed May 21, 2020
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  19. Format

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  20. Refactor

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  21. Clean up assert

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    honnibal committed May 21, 2020
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  22. Fix init

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    honnibal committed May 21, 2020
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  23. Fix imports

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    honnibal committed May 21, 2020
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  24. Fix bugs

    @honnibal
    honnibal committed May 21, 2020
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  25. Format

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  26. Refactor

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  27. Update test

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    honnibal committed May 21, 2020
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  28. Update

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    honnibal committed May 21, 2020
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  29. Get tests passing

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  30. Register TransformerModel architecture

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    honnibal committed May 21, 2020
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  31. Update config

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  32. Remove width arg

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  33. Remove width

    @honnibal
    honnibal committed May 21, 2020
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  34. Remove width arg

    @honnibal
    honnibal committed May 21, 2020
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  35. Remove old example tasks

    @honnibal
    honnibal committed May 21, 2020
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  36. Update component

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    honnibal committed May 21, 2020
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  37. Fix type annotation

    @honnibal
    honnibal committed May 21, 2020
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  38. Remove old examples

    @honnibal
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  39. Move configs

    @honnibal
    honnibal committed May 21, 2020
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  40. Trim redundant configs

    @honnibal
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  41. Update readme

    @honnibal
    honnibal committed May 21, 2020
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  42. Rename config

    @honnibal
    honnibal committed May 21, 2020
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  43. Update albert config

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  44. Update spacy_transformers/tests/test_alignment.py 

    Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
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  45. Merge branch 'feature/spacy-v3' of https://github.com/explosion/spacy… 

    …-transformers into feature/spacy-v3
    @honnibal
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  46. Fix span_getters

    @honnibal
    honnibal committed May 21, 2020
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  47. Fix catalogue

    @honnibal
    honnibal committed May 21, 2020
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  48. Improve shape inference

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  49. Fix max batch size

    @honnibal
    honnibal committed May 21, 2020
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  50. Update train-from-config

    @honnibal
    honnibal committed May 21, 2020
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  51. Update bert config

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  52. Update config

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  53. Update spacy_transformers/pipeline_component.py 

    Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
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    honnibal and svlandeg committed May 21, 2020
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Commits on May 22, 2020

  1. Try to register spaCy entry-points

    @honnibal
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  2. Simplify get_token_positions

    @honnibal
    honnibal committed May 22, 2020
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  3. Preserve doc structure in span getters

    @honnibal
    honnibal committed May 22, 2020
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  4. Fix entry points

    @honnibal
    honnibal committed May 22, 2020
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  5. Fix import

    @honnibal
    honnibal committed May 22, 2020
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  6. Increment version

    @honnibal
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  7. Specify use_pytorch_for_gpu_memory

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Commits on May 23, 2020

  1. Align via offset mapping if possible

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  2. Align via offset mapping if possible

    @honnibal
    honnibal committed May 23, 2020
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  3. Update config

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Commits on May 24, 2020

  1. Update config

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Commits on May 26, 2020

  1. Merge master into v3 branch (#185)

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  2. Merge branch 'master' into feature/spacy-v3

    @svlandeg
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  3. Delete language.py

    @svlandeg
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Commits on May 27, 2020

  1. fix align indices in split_by_doc

    @svlandeg
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  2. remove duplicate pytokenizations requirement

    @svlandeg
    svlandeg committed May 27, 2020
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  3. width argument in Listener was removed

    @svlandeg
    svlandeg committed May 27, 2020
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  4. small edits in the readme documentation

    @svlandeg
    svlandeg committed May 27, 2020
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  5. typing fixes

    @svlandeg
    svlandeg committed May 27, 2020
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  6. remove unused imports

    @svlandeg
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  7. update Azure pipelines

    @svlandeg
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  8. Update Azure pipelines

    @svlandeg
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  9. update Azure pipelines

    @svlandeg
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  10. Fix requirement

    @honnibal
    honnibal committed May 27, 2020
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  11. Fix pipeline

    @honnibal
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  12. Fix CI

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  13. Fix CI

    @honnibal
    honnibal committed May 27, 2020
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  14. Fix test

    @honnibal
    honnibal committed May 27, 2020
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  15. Format

    @honnibal
    honnibal committed May 27, 2020
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  16. Merge pull request #188 from svlandeg/fixes/varia 

    Various small fixes
    @honnibal
    honnibal committed May 27, 2020
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  17. Merge pull request #186 from svlandeg/bugfix/split-by-doc 

    fix align indices in split_by_doc
    @honnibal
    honnibal committed May 27, 2020
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