Cnlp-transformers

What's Changed
* Updated dependencies to fix huggingface hub issue in Docker builds

What's Changed
* Training a single model can be done with multiple datasets and tasks, providing task names selects columns from datasets to train on.
* Move versioning into cnlpt.__version__ by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/139
* Update CONTRIBUTING.md and GitHub Actions to reflect new dev branch naming convention by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/140
* merge docs and github actions changes into dev-v0.6.0 by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/144
* Realign baseline models with new task flow by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/150
* Improved Sphinx docs by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/154
* Move type strings into annotations
* Setup autodoc type hints
* Add support for loading local encoders for fine-tuning by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/152
* Drop support for Python 3.7 by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/161
* Add functionality to get chunk attentions from hierarchical model forward() so that we can visualize hierarchical attention. by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/162
* Add requirements for transform_prot by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/153
* Save config.json in training for CNN models; load best model before prediction (for all models) by spencerthomas1722 in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/164
* extract chemprot requirements from main setup.cfg (PyPI disallows direct dependency links) by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/168

New Contributors
* spencerthomas1722 made their first contribution in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/164

**Full Changelog**: https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/compare/v0.5.0...v0.6.0

What's Changed
* Dockerization by dogversioning in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/108
* 103 add examples to readme for e2e relations and tagging using publicly available datasets by etgld in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/109
* Clarify build and release process in CONTRIBUTING.md by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/110
* Merge changes in main into v0.5.0 by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/113
* add early return with zero statuses by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/112
* Preloading models for docker servers by dogversioning in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/115
* Sync v0.5.0 with main by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/119
* Integrate changes to json format reading by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/117
* Move examples into subdirectory to clean up README by vanh17 in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/129
* Issue 130 - separate out hierarchical model to not inherit by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/131
* Update doctimerel rest to use current helper methods in cnlp_rest. by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/135
* Move hierarchical encoder head config into CnlpConfig by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/125

New Contributors
* dogversioning made their first contribution in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/108

**Full Changelog**: https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/compare/v0.4.0...v0.5.0

What's Changed
The biggest change in this release is to the way datasets are managed. We now use Huggingface Datasets as a backend and so we have removed much of the dataset processing code. Fine-tuning on a new task no longer involves writing code, but it does require dataset to be in one of a few standard formats.

* v0.3.2: remove usage of deprecated ALL_PRETRAINED_CONFIG_ARCHIVE_MAP by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/98
* using new datasets library (motivated by mimic los task) by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/99
* V0.4.0 by tmills in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/104


**Full Changelog**: https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/compare/v0.3.2...v0.4.0

What's Changed
* v0.3.2: remove usage of deprecated ALL_PRETRAINED_CONFIG_ARCHIVE_MAP by angus-lherrou in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/94

**Full Changelog**: https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/compare/v0.3.1...v0.3.2

What's Changed
* Add GitHub Actions for building and testing new versions in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/87
* Add basic testing capabilities in https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/pull/89
* Bugfixes for 85, 88, and 91 in 93


**Full Changelog**: https://github.com/Machine-Learning-for-Medical-Language/cnlp_transformers/compare/v0.3.0...v0.3.1