diff --git a/.github/workflows/test-cde.yml b/.github/workflows/test-cde.yml index 9a836721..c3112c53 100644 --- a/.github/workflows/test-cde.yml +++ b/.github/workflows/test-cde.yml @@ -24,6 +24,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + pip install wheel setuptools pip install nbsphinx==0.3.5 nbsphinx-link m2r ipython ipykernel sphinx-rtd-theme pip install future==0.17.1 pip install unittest2==1.1.0 diff --git a/requirements/production.txt b/requirements/production.txt index ee9b6618..3b0aa5bc 100644 --- a/requirements/production.txt +++ b/requirements/production.txt @@ -1,6 +1,6 @@ appdirs>=1.4.0 beautifulsoup4>=4.5.3 -click==6.7 +click>=7.0.0 cssselect>=1.0.1 DAWG-Patched tabledataextractor @@ -10,13 +10,15 @@ pdfminer.six>=20160614 python-crfsuite>=0.9.1 python-dateutil>=2.6.0 PyYAML>=3.12 -requests>=2.12.5 +requests>=2.28.1 six>=1.10.0 selenium>=3.14.1 protobuf==3.* scipy numpy deprecation +wheel +setuptools yaspin tokenizers scikit-learn==0.22.1 diff --git a/setup.py b/setup.py index 89ba79f8..81c5456e 100644 --- a/setup.py +++ b/setup.py @@ -5,71 +5,73 @@ from setuptools import setup, find_packages -if os.path.exists('README.md'): - long_description = open('README.md').read() +if os.path.exists("README.md"): + long_description = open("README.md").read() else: - long_description = '''A toolkit for extracting chemical information from the scientific literature.''' + long_description = """A toolkit for extracting chemical information from the scientific literature.""" setup( - name='chemdataextractor2', - version='2.1.2', - author='Matt Swain, Callum Court, Juraj Mavracic, Taketomo Isazawa, and contributors', - author_email='m.swain@me.com, cc889@cam.ac.uk, jm2111@cam.ac.uk, ti250@cam.ac.uk', - license='MIT', - url='https://github.com/CambridgeMolecularEngineering/ChemDataExtractor2', + name="chemdataextractor2", + version="2.1.2", + author="Matt Swain, Callum Court, Juraj Mavracic, Taketomo Isazawa, and contributors", + author_email="m.swain@me.com, cc889@cam.ac.uk, jm2111@cam.ac.uk, ti250@cam.ac.uk", + license="MIT", + url="https://github.com/CambridgeMolecularEngineering/ChemDataExtractor2", packages=find_packages(), - description='A toolkit for extracting chemical information from the scientific literature.', + description="A toolkit for extracting chemical information from the scientific literature.", long_description=long_description, - long_description_content_type='text/markdown', - keywords='text-mining mining chemistry cheminformatics nlp html xml science scientific', + long_description_content_type="text/markdown", + keywords="text-mining mining chemistry cheminformatics nlp html xml science scientific", zip_safe=False, - entry_points={'console_scripts': ['cde = chemdataextractor.cli:cli']}, - tests_require=['pytest'], + entry_points={"console_scripts": ["cde = chemdataextractor.cli:cli"]}, + tests_require=["pytest"], install_requires=[ - 'appdirs', - 'beautifulsoup4', - 'click==6.7', - 'cssselect', - 'lxml', - 'nltk', - 'pdfminer.six', - 'python-dateutil', - 'requests==2.21.0', - 'six', - 'python-crfsuite', - 'tabledataextractor', + "appdirs", + "beautifulsoup4", + "click>=7.0.0", + "cssselect", + "lxml", + "nltk", + "pdfminer.six", + "python-dateutil", + "requests>=2.28.1", + "six", + "python-crfsuite", + "tabledataextractor", 'DAWG-Patched; python_version >= "3.7.0"', 'DAWG; python_version < "3.7.0"', - 'PyYAML', - 'selenium==3.141.0', - 'numpy', + "PyYAML", + "selenium==3.141.0", + "numpy", 'numpy==1.16; python_version < "3.7.0"', 'numpy<1.20; python_version >= "3.7.0"', - 'protobuf==3.*', + "protobuf==3.*", # 'scipy', - 'yaspin', - 'deprecation', - 'allennlp==0.9.0', - 'tokenizers', - 'scikit-learn==0.22.1', - 'overrides==3.1.0', - 'boto3==1.15.18', - 'unittest2', - 'playsound' + "yaspin", + "deprecation", + "allennlp==0.9.0", + "tokenizers", + "scikit-learn==0.22.1", + "overrides==3.1.0", + "boto3==1.15.18", + "unittest2", + "wheel", + "setuptools", + "playsound", ], classifiers=[ - 'Intended Audience :: Developers', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: MIT License', - 'Operating System :: OS Independent', - 'Programming Language :: Python :: 2', - 'Programming Language :: Python :: 2.7', - 'Topic :: Internet :: WWW/HTTP :: Indexing/Search', - 'Topic :: Scientific/Engineering', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Topic :: Scientific/Engineering :: Chemistry', - 'Topic :: Text Processing', - 'Topic :: Text Processing :: Linguistic', - 'Topic :: Text Processing :: Markup :: HTML', + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.7", + "Topic :: Internet :: WWW/HTTP :: Indexing/Search", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Text Processing", + "Topic :: Text Processing :: Linguistic", + "Topic :: Text Processing :: Markup :: HTML", ], )