pin biopython<1.80; i dont have time to fix all of these nuances

Author: Jon Palmer

Dockerfile

@@ -7,7 +7,7 @@ RUN mamba install -n base --yes conda-pack
 # Install funannotate deps from bioconda
 # here specifying specific versions to be able to set ENV below
 RUN mamba create -c conda-forge -c bioconda -c defaults \
-    -n funannotate --yes "python>=3.6,<3.9" biopython xlrd==1.2.0 \
+    -n funannotate --yes "python>=3.6,<3.9" "biopython<1.80" xlrd==1.2.0 \
     "trinity==2.8.5" "evidencemodeler==1.1.1" "pasa==2.4.1" "codingquarry==2.0" \
     "proteinortho==6.0.16" goatools matplotlib-base natsort numpy pigz \
     pandas psutil requests "scikit-learn<1.0.0" scipy seaborn "blast=2.2.31" \

setup.py

@@ -12,22 +12,28 @@
 from setuptools import find_packages, setup, Command
 
 # Package meta-data.
-NAME = 'funannotate'
-DESCRIPTION = 'funannotate: eukaryotic genome annotation pipeline'
-URL = 'https://github.com/nextgenusfs/funannotate'
-EMAIL = '[email protected]'
-AUTHOR = 'Jon Palmer'
-REQUIRES_PYTHON = '>=3.6.0, <3.10'
+NAME = "funannotate"
+DESCRIPTION = "funannotate: eukaryotic genome annotation pipeline"
+URL = "https://github.com/nextgenusfs/funannotate"
+EMAIL = "[email protected]"
+AUTHOR = "Jon Palmer"
+REQUIRES_PYTHON = ">=3.6.0, <3.10"
 VERSION = None
 
 # What packages are required for this module to be executed?
 REQUIRED = [
-    'biopython', 'goatools',
-    'seaborn','psutil',
-    'pandas','matplotlib',
-    'natsort', 'numpy',
-    'requests', 'scikit-learn',
-    'scipy', 'distro'
+    "biopython<1.80",
+    "goatools",
+    "seaborn",
+    "psutil",
+    "pandas",
+    "matplotlib",
+    "natsort",
+    "numpy",
+    "requests",
+    "scikit-learn",
+    "scipy",
+    "distro",
 ]
 
 # What packages are optional?
@@ -45,30 +51,30 @@
 # Import the README and use it as the long-description.
 # Note: this will only work if 'README.md' is present in your MANIFEST.in file!
 try:
-    with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
-        long_description = '\n' + f.read()
+    with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
+        long_description = "\n" + f.read()
 except FileNotFoundError:
     long_description = DESCRIPTION
 
 # Load the package's __version__.py module as a dictionary.
 about = {}
 if not VERSION:
-    with open(os.path.join(here, NAME, '__version__.py')) as f:
+    with open(os.path.join(here, NAME, "__version__.py")) as f:
         exec(f.read(), about)
 else:
-    about['__version__'] = VERSION
+    about["__version__"] = VERSION
 
 
 class UploadCommand(Command):
     """Support setup.py upload."""
 
-    description = 'Build and publish the package.'
+    description = "Build and publish the package."
     user_options = []
 
     @staticmethod
     def status(s):
         """Prints things in bold."""
-        print(('\033[1m{0}\033[0m'.format(s)))
+        print(("\033[1m{0}\033[0m".format(s)))
 
     def initialize_options(self):
         pass
@@ -78,56 +84,55 @@ def finalize_options(self):
 
     def run(self):
         try:
-            self.status('Removing previous builds…')
-            rmtree(os.path.join(here, 'dist'))
+            self.status("Removing previous builds…")
+            rmtree(os.path.join(here, "dist"))
         except OSError:
             pass
 
-        self.status('Building Source and Wheel (universal) distribution…')
-        os.system('{0} setup.py sdist bdist_wheel --universal'.format(sys.executable))
+        self.status("Building Source and Wheel (universal) distribution…")
+        os.system("{0} setup.py sdist bdist_wheel --universal".format(sys.executable))
 
-        self.status('Uploading the package to PyPI via Twine…')
-        os.system('twine upload dist/*')
+        self.status("Uploading the package to PyPI via Twine…")
+        os.system("twine upload dist/*")
 
-        self.status('Pushing git tags…')
-        os.system('git tag v{0}'.format(about['__version__']))
-        os.system('git push --tags')
+        self.status("Pushing git tags…")
+        os.system("git tag v{0}".format(about["__version__"]))
+        os.system("git push --tags")
 
         sys.exit()
 
 
 # Where the magic happens:
 setup(
     name=NAME,
-    version=about['__version__'],
+    version=about["__version__"],
     description=DESCRIPTION,
     long_description=long_description,
-    long_description_content_type='text/markdown',
+    long_description_content_type="text/markdown",
     author=AUTHOR,
     author_email=EMAIL,
     python_requires=REQUIRES_PYTHON,
     url=URL,
-    packages=find_packages(exclude=('tests',)),
+    packages=find_packages(exclude=("tests",)),
     entry_points={
-        'console_scripts':
-            ['funannotate=funannotate.funannotate:main'],
+        "console_scripts": ["funannotate=funannotate.funannotate:main"],
     },
     install_requires=REQUIRED,
     extras_require=EXTRAS,
     include_package_data=True,
-    license='BSD-2',
-    #scripts=['scripts/funannotate'],
+    license="BSD-2",
+    # scripts=['scripts/funannotate'],
     classifiers=[
         # Trove classifiers
         # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-        'Development Status :: 4 - Beta',
-        'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python',
-        'Operating System :: Unix',
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Bio-Informatics'
-        ],
+        "Development Status :: 4 - Beta",
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python",
+        "Operating System :: Unix",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
     cmdclass={
-        'upload': UploadCommand,
+        "upload": UploadCommand,
     },
 )