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The lock refresh in 4c2d59d floated flake8 7.1 -> 7.3 (pyflakes 3.2 -> 3.4), which added F824. These declarations were for names only read, never assigned, in the inner scope, so removing them does not change behavior. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…extension, typed lookups, single Excel open - Scan, rewrite, and append only within the reader's logical rows (before the first empty row). - Extend an existing ProtectedDonor sheet's headers for copied fields, or reject unsafe shapes before mutating. - Resolve non-token references (UUID/accession) as ProtectedDonors via workbook identifiers or typed portal lookup. - Report permission/outage lookup failures distinctly from definitive absence. - Open the Excel workbook once in StructuredDataSet so the progress counting pass cannot pre-create the staged output.
pytest.ini (re-added in fb05879 with only the `last` marker) takes precedence over [tool.pytest.ini_options] in pyproject.toml, silently disabling basetemp, redis_exec, markers, and filterwarnings. On macOS the missing --basetemp=/tmp/pytest makes pytest-redis' unix socket path exceed 104 chars (UnixSocketTooLong), and unregistered markers produce ~150 PytestUnknownMarkWarnings. Move the `last` marker into pyproject.toml and update filterwarnings for current third-party deprecation warnings (pkg_resources is now a UserWarning in setuptools 81; declare_namespace, cgi via WebOb, prettytable constants via pip-licenses). Drop the obsolete Python 3.7 boto3 filter. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Developers commonly export IDENTITY locally (conftest needs it to load env config), which conflicts with the identity the ini builder sets and causes a RuntimeError. Clear it for the duration of the test. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
CPython 3.12.15 made urllib's HTTPPasswordMgr scheme-aware, changing the internal passwd dict key from ((authority, path),) to ((scheme, authority, path),). The test indexed that private dict directly and broke with KeyError on the 3.12 CI leg. Use find_user_password(), which works across Python versions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Coverage Report for CI Build 38934819545Coverage increased (+0.9%) to 75.501%Details
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Coverage Regressions3 previously-covered lines in 3 files lost coverage.
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