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…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Superseded by #89 nbopen stdout/stderr handling. |
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).
This replaces the usage of
run_commandinbionetgen/core/main.py:236with a directsubprocess.Popencall. This allows passing the pre-configuredstdoutandstderrconfiguration streams dynamically resolved from theapp.config, captures the output utilizingprocess.communicate(), and logs the output through the application's built-inapp.log.infoandapp.log.errorlogger.PR created automatically by Jules for task 337248941238460958 started by @akutuva21