diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index db033e9..7e11e7c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9', '3.10'] + python-version: ['3.10', '3.11'] steps: - name: Checkout reposistory uses: actions/checkout@v3 diff --git a/CHANGELOG.md b/CHANGELOG.md index 214a669..580766a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,10 +8,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/). ## [Unreleased] +## [1.5.0] - 2023-12-05 ### Changed - Upgrade libraries: `numpy`, `lxml`, `scikitlearn`, `scipy`, `medcat`. - Added `scispacy` dependency. +### Added +- Support for Python 3.11. + +### Removed +- Support for Python 3.9. + ## [1.4.1] - 2023-09-08 ### Changed @@ -114,7 +121,8 @@ Downstream moderate risk update release. -[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.4.1...HEAD +[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.5.0...HEAD +[1.5.0]: https://github.com/Paul Landes/mednlp/compare/v1.4.1...v1.5.0 [1.4.1]: https://github.com/Paul Landes/mednlp/compare/v1.4.0...v1.4.1 [1.4.0]: https://github.com/Paul Landes/mednlp/compare/v1.3.2...v1.4.0 [1.3.2]: https://github.com/Paul Landes/mednlp/compare/v1.3.1...v1.3.2 diff --git a/LICENSE.md b/LICENSE.md index acf447a..ca5a3bf 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2021 Paul Landes +Copyright (c) 2021 - 2023 Paul Landes Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in diff --git a/README.md b/README.md index c74b48c..3e4a9ad 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # Medical natural language parsing and utility library [![PyPI][pypi-badge]][pypi-link] -[![Python 3.9][python39-badge]][python39-link] [![Python 3.10][python310-badge]][python310-link] +[![Python 3.11][python311-badge]][python311-link] [![Build Status][build-badge]][build-link] A natural language medical domain parsing library. This library: @@ -85,18 +85,29 @@ This API utilizes the following frameworks: ## Citation If you use this project in your research please use the following BibTeX entry: + ```bibtex -@article{Landes_DiEugenio_Caragea_2021, - title={DeepZensols: Deep Natural Language Processing Framework}, - url={http://arxiv.org/abs/2109.03383}, - note={arXiv: 2109.03383}, - journal={arXiv:2109.03383 [cs]}, - author={Landes, Paul and Di Eugenio, Barbara and Caragea, Cornelia}, - year={2021}, - month={Sep} +@inproceedings{landes-etal-2023-deepzensols, + title = "{D}eep{Z}ensols: A Deep Learning Natural Language Processing Framework for Experimentation and Reproducibility", + author = "Landes, Paul and + Di Eugenio, Barbara and + Caragea, Cornelia", + editor = "Tan, Liling and + Milajevs, Dmitrijs and + Chauhan, Geeticka and + Gwinnup, Jeremy and + Rippeth, Elijah", + booktitle = "Proceedings of the 3rd Workshop for Natural Language Processing Open Source Software (NLP-OSS 2023)", + month = dec, + year = "2023", + address = "Singapore, Singapore", + publisher = "Empirical Methods in Natural Language Processing", + url = "https://aclanthology.org/2023.nlposs-1.16", + pages = "141--146" } ``` + ## Community Please star the project and let me know how and where you use this API. @@ -119,10 +130,10 @@ Copyright (c) 2021 - 2023 Paul Landes [pypi]: https://pypi.org/project/zensols.mednlp/ [pypi-link]: https://pypi.python.org/pypi/zensols.mednlp [pypi-badge]: https://img.shields.io/pypi/v/zensols.mednlp.svg -[python39-badge]: https://img.shields.io/badge/python-3.9-blue.svg -[python39-link]: https://www.python.org/downloads/release/python-390 [python310-badge]: https://img.shields.io/badge/python-3.10-blue.svg [python310-link]: https://www.python.org/downloads/release/python-3100 +[python311-badge]: https://img.shields.io/badge/python-3.11-blue.svg +[python311-link]: https://www.python.org/downloads/release/python-3110 [build-badge]: https://github.com/plandes/mednlp/workflows/CI/badge.svg [build-link]: https://github.com/plandes/mednlp/actions diff --git a/src/python/requirements.txt b/src/python/requirements.txt index d34045a..d9a6038 100644 --- a/src/python/requirements.txt +++ b/src/python/requirements.txt @@ -1,11 +1,11 @@ # base -numpy>=1.25.2 lxml~=4.9.3 +numpy~=1.25.2 scikit-learn~=1.3.2 # medcat -pandas~=2.1.3 blis~=0.7.11 +pandas~=2.1.3 scipy~=1.9.3 scispacy~=0.5.3 medcat~=1.9.3 @@ -14,5 +14,5 @@ medcat~=1.9.3 ctakes-parser~=0.1.0 # zensols -zensols.install~=1.0.0 -zensols.nlp~=1.8.0 +zensols.install~=1.1.0 +zensols.nlp~=1.9.0 diff --git a/zenbuild b/zenbuild index 33fb638..b94e8df 160000 --- a/zenbuild +++ b/zenbuild @@ -1 +1 @@ -Subproject commit 33fb6386fdbc5907b87de3cd4cc3fb6d4768ceac +Subproject commit b94e8df21d092fa23eeea59babf84b9c9ed69fe0