Tests not working because quilt / botocore / urllib3 issue

donovanr commented 4 years ago

Traceback (most recent call last):
  File "scripts/download_test_data.py", line 10, in <module>
    from quilt3 import Package
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/quilt3/__init__.py", line 12, in <module>
    from . import admin
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/quilt3/admin.py", line 2, in <module>
    from .session import get_registry_url, get_session
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/quilt3/session.py", line 13, in <module>
    import botocore.session
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/session.py", line 30, in <module>
    import botocore.credentials
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/credentials.py", line 34, in <module>
    from botocore.config import Config
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/config.py", line 16, in <module>
    from botocore.endpoint import DEFAULT_TIMEOUT, MAX_POOL_CONNECTIONS
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/endpoint.py", line 22, in <module>
    from botocore.awsrequest import create_request_object
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/awsrequest.py", line 25, in <module>
    import botocore.utils
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/botocore/utils.py", line 30, in <module>
    from urllib3.util.url import IPV6_ADDRZ_RE
ImportError: cannot import name 'IPV6_ADDRZ_RE' from 'urllib3.util.url' (/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/urllib3/util/url.py)

donovanr commented 4 years ago

further output from the github CI logs

ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 PyMCubes-0.1.2 PyWavelets-1.1.1 PyYAML-5.3.1 Send2Trash-1.5.0 Werkzeug-1.0.1 actk-0.2.0 aics-dask-utils-0.2.0 aicsfeature-0.2.1 aicsimageio-3.3.1 aicsimageprocessing-0.7.4 aicspylibczi-2.6.0 appdirs-1.4.4 argon2-cffi-20.1.0 async-generator-1.10 attrs-20.2.0 aws-requests-auth-0.4.3 backcall-0.2.0 black-20.8b1 bleach-3.2.1 bokeh-2.2.2 boto3-1.16.0 botocore-1.19.0 certifi-2020.6.20 cffi-1.14.3 chardet-3.0.4 click-7.1.2 cloudpickle-1.6.0 codecov-2.1.10 coverage-5.3 croniter-0.3.35 cycler-0.10.0 dask-2.30.0 dask-jobqueue-0.7.1 datastep-0.1.8 decorator-4.4.2 defusedxml-0.6.0 distributed-2.30.0 dnspython-2.0.0 docker-4.3.1 docutils-0.15.2 entrypoints-0.3 fire-0.3.1 flake8-3.8.4 flake8-debugger-3.2.1 flask-1.1.2 flask-cors-3.0.9 flask-json-0.3.4 fsspec-0.8.4 gitdb-4.0.5 gitpython-3.1.9 h5py-2.10.0 heapdict-1.0.1 idna-2.10 imagecodecs-2020.5.30 imageio-2.9.0 importlib-resources-3.0.0 iniconfig-1.1.1 ipykernel-5.3.4 ipython-7.18.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 itsdangerous-1.1.0 jedi-0.17.2 jmespath-0.10.0 joblib-0.17.0 jsonlines-1.2.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.7 jupyter-console-6.2.0 jupyter-core-4.6.3 jupyterlab-pygments-0.1.2 kiwisolver-1.2.0 locket-0.2.0 lxml-4.6.1 mahotas-1.4.11 marshmallow-3.8.0 marshmallow-oneofschema-2.1.0 matplotlib-3.3.2 mccabe-0.6.1 mistune-0.8.4 msgpack-1.0.0 mypy-extensions-0.4.3 natsort-7.0.1 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nest-asyncio-1.4.1 networkx-2.5 notebook-6.1.4 packaging-20.4 pandas-1.1.3 pandocfilters-1.4.2 parso-0.7.1 partd-1.1.0 pathspec-0.8.0 pendulum-2.1.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.0.0 pluggy-0.13.1 prefect-0.13.12 prometheus-client-0.8.0 prompt-toolkit-3.0.8 psutil-5.7.2 ptyprocess-0.6.0 py-1.9.0 pyarrow-2.0.0 pycodestyle-2.6.0 pycparser-2.20 pyflakes-2.2.0 pygments-2.7.1 pyparsing-2.4.7 pyrsistent-0.17.3 pytest-6.1.1 pytest-cov-2.10.1 pytest-raises-0.11 python-box-5.1.1 python-dateutil-2.8.0 python-slugify-4.0.1 pytz-2020.1 pytzdata-2020.1 pyzmq-19.0.2 qtconsole-4.7.7 qtpy-1.9.0 quilt3-3.2.1 readlif-0.2.1 regex-2020.10.15 requests-2.24.0 requests-futures-1.0.0 s3transfer-0.3.3 scikit-fmm-2019.1.30 scikit-image-0.17.2 scikit-learn-0.23.2 scipy-1.5.3 six-1.15.0 smmap-3.0.4 sortedcontainers-2.2.2 tabulate-0.8.7 tblib-1.7.0 tenacity-6.2.0 termcolor-1.1.0 terminado-0.9.1 testpath-0.4.4 text-unidecode-1.3 threadpoolctl-2.1.0 tifffile-2020.10.1 toml-0.10.1 toolz-0.11.1 tornado-6.0.4 tqdm-4.50.2 traitlets-5.0.5 typed-ast-1.4.1 typing-extensions-3.7.4.3 urllib3-1.24.3 vtk-9.0.1 wcwidth-0.2.5 webencodings-0.5.1 websocket-client-0.57.0 widgetsnbextension-3.5.1 zict-2.0.0

We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

botocore 1.19.0 requires urllib3<1.26,>=1.25.4; python_version != "3.4", but you'll have urllib3 1.24.3 which is incompatible.

evamaxfield commented 4 years ago

Please don't assign me, I don't work on this project anymore :upside_down_face:

ritvikvasan commented 4 years ago

I think changing urllib3<1.25 to urllib3>1.25 in the datastep repo dependency list might resolve this. All of the tests for that repo pass when I made this change, even though it says "# quilt conflict" next to it https://github.com/AllenCellModeling/datastep/blob/5ec173e3ec3ba1fbb4c73f054b84e539ec5eb9f4/setup.py#L52

heeler commented 4 years ago

I'll have a look later today. Only just saw that this was in my queue.

AllenCell / cvapipe

Tests not working because quilt / botocore / urllib3 issue #29