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Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Superseded by #60 pathwaycommons HTTPError test coverage. |
Understood. Acknowledging that this work is superseded and stopping work on this task. |
Drop distutils for Python 3.12 compatibility (closes #58)
Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the
optional in-process engine is discoverable via `pip install bionetgen[bngsim]`,
while keeping bngsim out of install_requires (never a hard dependency). The
extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge.
Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the
method-independent gdat/scan output schema (bngsim #58) the parity differ
normalizes against; 0.9.10 is the current validated release. Refresh the
floor-rationale comment, which still cited the stale 0.6.0/#40 reason.
Update the version-guard test's minimum-version case to 0.9.10.
With bngsim absent the bridge soft-imports to the legacy subprocess path
unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped,
0 errors with bngsim genuinely uninstalled).
🎯 What: The testing gap addressed
The
name2uniprotfunction inbionetgen/atomizer/utils/pathwaycommons.pywas missing test coverage. Because it makes HTTP requests to UniProt to fetch IDs, it needed to be tested using mocked calls to ensure deterministic and safe testing.📊 Coverage: What scenarios are now tested
name2uniprotwith a valid organism correctly passes the parameter to UniProt and parses the response.name2uniprotwithout an organism makes the HTTP request correctly without the organism query parameter.✨ Result: The improvement in test coverage
The
name2uniprotfunction now has 100% path coverage for its active implementation. Since the development sandbox has complex import dependencies (likecementandsympy), the tests useimportliband scopedsys.modulespatching via a custom pytest fixture to ensure complete test isolation and zero global state pollution for the rest of the test suite.PR created automatically by Jules for task 15794140290505221084 started by @akutuva21