Update dependencies for click and requests packages

.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

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

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='[email protected], [email protected], [email protected], [email protected]',
-    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="[email protected], [email protected], [email protected], [email protected]",
+    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",
     ],
 )