I am planning on submitting cellphonedb to the bioconda-recipes repository. I am using conda's skeleton command to pull information from the PyPI repository and automatically build the recipe. However, I am encountering this error:
$ conda skeleton pypi --version 2.1.5 --python-version 3.7 cellphonedb
Using url https://files.pythonhosted.org/packages/fc/8e/d1a7289367e8299218a4a1b3c0e6df2390d56f34c2c3b5b5def70630d517/CellPhoneDB-2.1.5.tar.gz (12.0 MB) for cellphonedb.
Downloading cellphonedb
PyPI URL: https://files.pythonhosted.org/packages/fc/8e/d1a7289367e8299218a4a1b3c0e6df2390d56f34c2c3b5b5def70630d517/CellPhoneDB-2.1.5.tar.gz
Using cached download
Unpacking cellphonedb...
done
working in /var/folders/5r/s597hc5j3w93_x8_tn57w3g80000gn/T/tmp15ru0injconda_skeleton_CellPhoneDB-2.1.5.tar.gz
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/miniconda3/conda-bld/skeleton_1613724919243/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold
The following NEW packages will be INSTALLED:
ca-certificates: 2020.12.5-h033912b_0 conda-forge
certifi: 2020.12.5-py37hf985489_1 conda-forge
libcxx: 11.0.1-habf9029_0 conda-forge
libffi: 3.3-h046ec9c_2 conda-forge
ncurses: 6.2-h2e338ed_4 conda-forge
openssl: 1.1.1j-hbcf498f_0 conda-forge
patch: 2.7.6-hbcf498f_1002 conda-forge
pip: 21.0.1-pyhd8ed1ab_0 conda-forge
python: 3.7.9-h7728216_100_cpython conda-forge
python_abi: 3.7-1_cp37m conda-forge
pyyaml: 5.4.1-py37hf967b71_0 conda-forge
readline: 8.0-h0678c8f_2 conda-forge
setuptools: 49.6.0-py37hf985489_3 conda-forge
sqlite: 3.34.0-h17101e1_0 conda-forge
tk: 8.6.10-h0419947_1 conda-forge
wheel: 0.36.2-pyhd3deb0d_0 conda-forge
xz: 5.2.5-haf1e3a3_1 conda-forge
yaml: 0.2.5-haf1e3a3_0 conda-forge
zlib: 1.2.11-h7795811_1010 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Applying patch: /var/folders/5r/s597hc5j3w93_x8_tn57w3g80000gn/T/tmp15ru0injconda_skeleton_CellPhoneDB-2.1.5.tar.gz/pypi-distutils.patch
Applying patch: /var/folders/5r/s597hc5j3w93_x8_tn57w3g80000gn/T/tmp15ru0injconda_skeleton_CellPhoneDB-2.1.5.tar.gz/pypi-distutils.patch with args:
['-Np0', '-i', '/var/folders/5r/s597hc5j3w93_x8_tn57w3g80000gn/T/tmpljmli50r/pypi-distutils.patch.native', '--binary']
patching file core.py
Hunk #1 succeeded at 168 with fuzz 2 (offset 1 line).
patching file core.py
Hunk #1 succeeded at 168 with fuzz 2 (offset 1 line).
Leaving build/test directories:
Work:
/opt/miniconda3/conda-bld/skeleton_1613724919243/work
Test:
/opt/miniconda3/conda-bld/skeleton_1613724919243/test_tmp
Leaving build/test environments:
Test:
source activate /opt/miniconda3/conda-bld/skeleton_1613724919243/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
Build:
source activate /opt/miniconda3/conda-bld/skeleton_1613724919243/_build_env
Traceback (most recent call last):
File "/opt/miniconda3/bin/conda-skeleton", line 11, in <module>
sys.exit(main())
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/cli/main_skeleton.py", line 65, in main
return execute(sys.argv[1:])
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/cli/main_skeleton.py", line 60, in execute
api.skeletonize(args.packages, args.repo, output_dir=args.output_dir, recursive=args.recursive,
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/api.py", line 276, in skeletonize
skeleton_return = module.skeletonize(packages, output_dir=output_dir, version=version,
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/skeletons/pypi.py", line 317, in skeletonize
get_package_metadata(package, d, data, output_dir, python_version,
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/skeletons/pypi.py", line 755, in get_package_metadata
metadata["summary"] = get_summary(pkginfo)
File "/opt/miniconda3/lib/python3.8/site-packages/conda_build/skeletons/pypi.py", line 904, in get_summary
return pkginfo.get("summary", "Summary of the package").replace('"', r'\"')
AttributeError: 'NoneType' object has no attribute 'replace'
From what I can see, the error is caused by the empty summary section of the PyPI repository. Would it possible for someone on the team to flesh out the PyPI repository?
I am planning on submitting cellphonedb to the bioconda-recipes repository. I am using conda's skeleton command to pull information from the PyPI repository and automatically build the recipe. However, I am encountering this error:
From what I can see, the error is caused by the empty summary section of the PyPI repository. Would it possible for someone on the team to flesh out the PyPI repository?