Pytorch-ie

* Initial datasets setup (155) ChristophAlt
* Reworked TaskModule and Pipeline (149) ChristophAlt
* Make readme examples work in interactive interpreter (145) ChristophAlt
* Update main dependencies to latest version (141) ChristophAlt
* Drop python 3.8 support (143) ChristophAlt
* Prototype annotations, documents, and dataset (130) ArneBinder

* implement Model.test_step (133) ArneBinder

* Refactor datamodule (121) ArneBinder
* refactor conll2003 (122) ArneBinder
* fix 124 (125) GabrielKP
* add train test for transformer_token_classification (115) ArneBinder

:beetle: Fixes

* exclude spans that are out of valid window (128) ArneBinder

:beetle: Fixes

* Fix missing pass of is_training to encode_input (108) ArneBinder

* add prepare_documents (102) ArneBinder
* revert using the commit hash as prerelease identifier (106) ArneBinder
* use commit hash instead of date for pre-release identifier (104) ArneBinder

:hammer: Refactoring

* Refactor/document typed (95) ArneBinder

* control if statistics are collected and shown (85) ArneBinder
* make it optional to include ill formed spans when predicting (79) ArneBinder
* Windowing for token classification (72) ArneBinder
* simplify transformer_token_classification_taskmodule (71) ArneBinder
* tests for TransformerTokenClassificationTaskModule (67) ArneBinder
* implement 63 (65) ArneBinder
* annotation getters default to None (64) (70) ChristophAlt
* implement windowing for text classification based rel (47) ArneBinder
* add tests for TransformerRETextClassificationTaskModule (58) ArneBinder
* create tests from the examples that check the actual pipeline output (59) ArneBinder
* pipeline: cleanup argument handling (57) ArneBinder
* Fix issue 51 (55) ChristophAlt
* show pipeline progress (48) ArneBinder
* implement serialize_brat() and add test for that and load_brat() (31) ArneBinder
* Unittests for TransformerSpanClassificationModel (38) ChristophAlt
* partitioning for TransformerRETextClassificationTaskModule (43) ArneBinder
* Fix remaining mypy errors (39) ChristophAlt
* fix stupid bug in TransformerTokenClassificationTaskModule introduced… (37) ArneBinder
* fix a lot of typing in mdules/ and taskmodules/ (33) ArneBinder
* fix TaskEncodingDataset: use correct base type (35) ArneBinder
* fix typing for data/ and core/ (32) ArneBinder
* Unittests for Taskmodule (34) ChristophAlt
* [WIP] Add transformer seq2seq model and taskmodule (28) ChristophAlt
* add and improve type annotations to taskmodules (27) ArneBinder
* fix encode_target for self.single_sentence=True (26) ArneBinder
* fix signature of TransformerSpanClassificationTaskModule.encode_target (24) ArneBinder
* add general DataModule and brat dataset (19) ArneBinder
* use consistent function names in taskmodule and pipeline (22) ArneBinder
* remove inplace doc modification (16) ArneBinder

:beetle: Fixes

* fix brat equivalence_relations (84) ArneBinder
* fix warnings for unaligened span (82) ArneBinder
* fix checks for required span annotations (81) ArneBinder
* fix decode (66) ArneBinder
* Fix brat serialization with newlines (61) ArneBinder
* fix label id creation for single_sentence=False in encode_input (45) ArneBinder
* fix issue 49 (50) ArneBinder

:construction_worker: Continuous Integration

* Properly configure coverage.py (90) ChristophAlt
* Add labeler and release-drafter to github workflow (88) ChristophAlt
* Prepare CI / CD pipeline for initial release (76) ChristophAlt

:books: Documentation

* Readme refactoring (96) ChristophAlt

:hammer: Refactoring

* refactor example test documents (89) ArneBinder
* move utility functions into own package (80) ArneBinder

:package: Dependencies

* Switch to src layout (92) ChristophAlt