diff --git a/CHANGELOG.md b/CHANGELOG.md index 068914d..31dd9ba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ # Changelog -## Unreleased + +## 0.3.0 - 27 April 2024 ### Handling gene clusters & reverse complements in resfinder - Resfinder has gene clusters which can't be passed through RGI using 'contig' mode. @@ -17,11 +18,12 @@ - A total of 10 ARO mappings changed in ARG-ANNOT ### argnorm.lib: Making argNorm more usable as a library -- A file called `lib.py` will be introduced so that users can use argNorm as a library more easily. -- Users can import the `map_to_aro` function using `from argnorm.lib import map_to_aro`. The function takes a gene name as input, maps the gene to the ARO and returns a pronto term object with the ARO mapping. +- Introduce `argnorm.lib` module +- Users can import the `map_to_aro` function from `argnorm.lib`. The function takes a gene name as input, maps the gene to the ARO and returns a pronto term object with the ARO mapping. - The `get_aro_mapping_table` function, previously within the BaseNormalizer class, has also been moved to `lib.py` to give users the ability to access the mapping tables being used for normalization. - With the introduction of `lib.py`, users will be able to access core mapping utilities through `argnorm.lib`, drug categorization through `argnorm.drug_categorization`, and the traditional normalizers through `argnorm.normalizers`. + ## 0.2.0 - 26 March 2024 #### ARO Mapping & Normalization diff --git a/docs/images/whatsnew.md b/docs/whatsnew.md similarity index 77% rename from docs/images/whatsnew.md rename to docs/whatsnew.md index 6cd7be4..d6365ab 100644 --- a/docs/images/whatsnew.md +++ b/docs/whatsnew.md @@ -1,5 +1,17 @@ ## What's New +## 0.3.0 - 27 April 2024 + +### User-facing changes +- Improved Resfinder mappings (40 gene clusters and 9 reverse complements were manually curated) +- Updated ARG-ANNOT mappings (a total of 10 mappings changed) +- argNorm is now more usable as a library +- Remove warnings + +### Internal changes +- Code has been refactored to be simpler + + ## 0.2.0 - 26 March 2024 #### ARO Mapping & Normalization diff --git a/setup.py b/setup.py index 77d69cc..06411bd 100644 --- a/setup.py +++ b/setup.py @@ -1,50 +1,42 @@ from setuptools import setup -from setuptools import find_packages -NAME = "argnorm" -AUTHOR = "See README" -EMAIL = "luispedro@big-data-biology.org" -URL = "https://github.com/BigDataBiology/argNorm" -LICENSE = "MIT" DESCRIPTION = """ -Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD). - +Normalize antibiotic resistance genes (ARGs) results by using the ARO ontology (developed by CARD). """ -if __name__ == "__main__": - setup( - name=NAME, - version="0.2.0", - author=AUTHOR, - author_email=EMAIL, - url=URL, - license=LICENSE, - description=DESCRIPTION, - packages=['argnorm', 'argnorm.data'], - include_package_data=True, - package_dir={'argnorm': 'argnorm' }, - package_data={'argnorm': ['data/*.tsv', 'data/manual_curation/*.tsv']}, - install_requires=open("./requirements.txt", "r").read().splitlines(), - long_description=open("./README.md", "r").read(), - long_description_content_type='text/markdown', - entry_points={ - "console_scripts": [ - "argnorm=argnorm.cli:main" - ] - }, - zip_safe=False, - classifiers=[ - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Development Status :: 4 - Beta", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - "Natural Language :: English" - ], - ) +setup( + name='argnorm', + version="0.3.0", + author='ArgNorm Developers', + author_email='luispedro@big-data-biology.org', + url="https://github.com/BigDataBiology/argNorm", + license='MIT', + description=DESCRIPTION, + packages=['argnorm', 'argnorm.data'], + include_package_data=True, + package_dir={'argnorm': 'argnorm' }, + package_data={'argnorm': ['data/*.tsv', 'data/manual_curation/*.tsv']}, + install_requires=open("./requirements.txt", "r").read().splitlines(), + long_description=open("./README.md", "r").read(), + long_description_content_type='text/markdown', + entry_points={ + "console_scripts": [ + "argnorm=argnorm.cli:main" + ] + }, + zip_safe=False, + classifiers=[ + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Development Status :: 4 - Beta", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Natural Language :: English" + ], +)