Fix microbes remove #218
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Fix microbes remove #218
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Co-authored-by: David LeBauer <dlebauer@gmail.com>
Co-authored-by: David LeBauer <dlebauer@gmail.com>
Co-authored-by: David LeBauer <dlebauer@gmail.com>
Co-authored-by: David LeBauer <dlebauer@gmail.com>
Co-authored-by: David LeBauer <dlebauer@gmail.com>
Co-authored-by: Mike Longfritz <Mike.Longfritz@gmail.com>
Co-authored-by: Mike Longfritz <Mike.Longfritz@gmail.com>
ayushman1210
requested review from
Alomir,
dlebauer,
infotroph,
mdietze and
mswilburn
as code owners
- Remove MICROBES metadata from context initialization - Remove microbes field from struct Context - Remove --microbes CLI flag and all related options - Remove microbe-specific parameter initializations (efficiency, maxIngestionRate, etc.) - Remove calcMicrobeFluxes() function and always use calcSoilMaintRespiration() - Simplify updatePoolsForSoil() to remove microbe pool updates - Remove microbe initialization from setupModel() - Always set microbePulseEff = 0 (direct exudation to soil) - Fix NULL pointer check in frontend.c (clang-tidy warning) - Update documentation to remove MICROBES option references - Run clang-format, clang-tidy, and prettier on modified files BREAKING CHANGE: MICROBES option is no longer supported or recognized. The model now always uses the non-microbes pathway for soil respiration.
Remove all microbe-specific parameters from smoke test parameter files since MICROBES feature has been deprecated and removed from the codebase. This allows smoke tests to run without 'unknown parameter' warnings.
- Remove MICROBES configuration line from sipnet.in files - Remove MICROBES entries from sipnet.config reference files - These changes reflect the complete removal of the MICROBES feature
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Change: Added a fail-fast check in validateContext() that logs an error and exits when ctx.microbes is true.
fixes:#207