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nextstrain / cli

The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
https://docs.nextstrain.org/projects/cli/
MIT License
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CI tests failing since 28 Nov #408

Open tsibley opened 13 hours ago

tsibley commented 13 hours ago

Error is:

AttributeError: module 'lib' has no attribute 'X509_V_FLAG_NOTIFY_POLICY' ``` Traceback (most recent call last): File "/home/runner/miniconda3/envs/test/bin/nextstrain", line 5, in from nextstrain.cli.__main__ import main File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/__init__.py", line 21, in from .command import all_commands, version File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/command/__init__.py", line 1, in from . import ( File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/command/build.py", line 23, in from .. import runner File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/runner/__init__.py", line 7, in from . import ( File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/runner/aws_batch/__init__.py", line 95, in from . import jobs, s3 File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/runner/aws_batch/jobs.py", line 10, in from ... import aws File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/nextstrain/cli/aws/__init__.py", line 5, in import boto3 File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/boto3/__init__.py", line 17, in from boto3.session import Session File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/boto3/session.py", line 17, in import botocore.session File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/session.py", line 26, in import botocore.client File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/client.py", line 15, in from botocore import waiter, xform_name File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/waiter.py", line 18, in from botocore.docs.docstring import WaiterDocstring File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/docs/__init__.py", line 15, in from botocore.docs.service import ServiceDocumenter File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/docs/service.py", line 14, in from botocore.docs.client import ( File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/docs/client.py", line 18, in from botocore.docs.example import ResponseExampleDocumenter File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/docs/example.py", line 13, in from botocore.docs.shape import ShapeDocumenter File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/docs/shape.py", line 19, in from botocore.utils import is_json_value_header File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/utils.py", line 39, in import botocore.httpsession File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/botocore/httpsession.py", line 45, in from urllib3.contrib.pyopenssl import ( File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/urllib3/contrib/pyopenssl.py", line 50, in import OpenSSL.crypto File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/OpenSSL/__init__.py", line 8, in from OpenSSL import crypto, SSL File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/OpenSSL/crypto.py", line 1579, in class X509StoreFlags(object): File "/home/runner/miniconda3/envs/test/lib/python3.9/site-packages/OpenSSL/crypto.py", line 1598, in X509StoreFlags NOTIFY_POLICY = _lib.X509_V_FLAG_NOTIFY_POLICY AttributeError: module 'lib' has no attribute 'X509_V_FLAG_NOTIFY_POLICY' ```

Example of last good run and first bad run.

tsibley commented 13 hours ago

GitHub Actions runner image version remains the same across both (ubuntu-20.04 20241124.1.0), which was my first thought here. But I realized that didn't make sense as the issue is within the ambient runtime set up by our CI tests using Conda, which means it uses its own OpenSSL library instead of the system's.

pyOpenSSL is implicated in the error message, so I checked its release history, and sure enough, 24.3.0 was released (after our normal daily CI run) and tests broke the next morning. I highly suspect that's not spurious correlation. Need to verify though.

tsibley commented 13 hours ago

May be deeper: