Remove microbes

[ayushman1210]

Added a deprecation check in [context.c]in the [validateContext()] function that:

1. Detects when MICROBES is enabled (ctx.microbes = 1)
2. Throws a clear error with educational rationale
3. Prevents the program from running (exit code with failure)

Location: [context.c] lines 192-201

• Timing: Validation occurs after config file is read but before main model run
• Exit Status: Uses existing EXIT_CODE_BAD_PARAMETER_VALUE exit code
• Error thrown when ctx.microbes = 1

Fixes

#207

[Alomir]

@ayushman1210 - Thanks for your work on this so far! See my other comments for some more changes that should be done - but, for sipnet.c, there's still a lot more to do. We would like to see all of the code handling microbes removed. As a start, look for checks on ctx.microbes for areas that need to be trimmed and cleaned up.

[Copilot]

Pull request overview

This pull request aims to deprecate and remove the MICROBES feature from SIPNET, as described in issue #207. The microbes feature was confusing, unverified, and not scientifically justified (per Zobitz et al. 2008). The PR removes microbes-related code, parameters, CLI options, and updates documentation across the codebase.

Changes:

• Removed microbes context flag and associated CLI options
• Removed all microbe-related parameters and state variables from the model
• Simplified soil respiration calculations by removing microbe-specific code paths
• Updated test files and documentation to reflect microbes removal

Reviewed changes

Copilot reviewed 31 out of 36 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
80	Spurious file - appears to be accidentally added code snippet
src/common/context.c	Removed microbes from context initialization and validation (but missing deprecation check)
src/common/context.h	Removed microbes field from Context struct
src/sipnet/cli.c	Removed --microbes CLI flag and related usage documentation
src/sipnet/cli.h	Updated NUM_FLAG_OPTIONS count from 15 to 14
src/sipnet/sipnet.c	Removed microbes logic from model calculations, simplified soil respiration, code formatting improvements
src/sipnet/state.h	Removed microbe-related parameters and state variables, updated comments
tests/smoke/russell_*/sipnet.param	Removed microbe-related parameters from test parameter files
tests/smoke/russell_*/sipnet.config	Removed MICROBES from generated config files
tests/smoke/russell_4/sipnet.in	Changed MICROBES from 1 to 0 with deprecation comment
tests/sipnet/test_sipnet_infrastructure/*	Removed microbe parameters from test files and added NULL check
tests/sipnet/test_modeling/events.out	New test output file
tests/sipnet/test_events_*/events.out	New test output files
docs/user-guide/*.md	Removed microbes documentation and use cases
docs/parameters.md	Formatting and clarification improvements to parameter documentation

Comments suppressed due to low confidence (3)

src/common/context.c:199

• The PR description states that a deprecation check was added in validateContext() at lines 192-201 that detects when MICROBES is enabled and throws an error. However, no such validation code exists in this function. Currently, if a user sets MICROBES = 1 in their input file, it will only produce a warning ("ignoring input file parameter MICROBES") and the program will continue running. This does not meet the minimum requirement stated in issue #207 to "throw error when ctx.microbes = 1". The deprecation check needs to be implemented to fail fast with a clear error message when MICROBES is set to 1.

void validateContext(void) {
  int hasError = 0;

  if (ctx.soilPhenol && ctx.gdd) {
    logError("soil-phenol and gdd may not both be turned on\n");
    hasError = 1;
  }

  if (ctx.nitrogenCycle && !ctx.litterPool) {
    logError("nitrogen-cycle requires litter-pool to be turned on\n");
    hasError = 1;
  }

  if (hasError) {
    exit(EXIT_CODE_BAD_PARAMETER_VALUE);
  }
}

src/sipnet/sipnet.c:465

• The documentation in docs/user-guide/model-outputs.md states that microbeC should be present in the output as column 8 (always 0). However, the output code has been modified to completely remove microbeC from the output. This creates a breaking change where:

1. The column numbers in the documentation no longer match the actual output
2. Any user scripts that parse the output file by column number will break
3. The promise of backward compatibility implied by the documentation is not fulfilled

Either the output should retain microbeC as column 8 (outputting 0 for backward compatibility), or the documentation should be updated to reflect its complete removal and all column numbers should be adjusted accordingly.

void outputState(FILE *out, int year, int day, double time) {

  fprintf(out, "%4d %3d %5.2f %10.2f %10.2f %12.2f ", year, day, time,
          envi.plantWoodC, envi.plantLeafC, trackers.woodCreation);
  fprintf(out, "%8.2f ", envi.soilC);
  fprintf(out, "%11.2f %9.2f", envi.coarseRootC, envi.fineRootC);
  fprintf(out, " %8.2f %9.2f %15.3f %8.2f ", envi.litterC, envi.soilWater,
          trackers.soilWetnessFrac, envi.snow);
  fprintf(
      out,
      "%8.2f %8.2f %8.2f %8.2f %12.3f %8.3f %8.3f %8.3f %8.3f %8.3f %18.8f ",
      trackers.npp, trackers.nee, trackers.totNee, trackers.gpp,
      trackers.rAboveground, trackers.rSoil, trackers.rRoot, trackers.ra,
      trackers.rh, trackers.rtot, trackers.evapotranspiration);
  fprintf(out, "%19.4f %8.3f %9.4f %10.4f %9.6f %10.4f\n", fluxes.transpiration,
          envi.minN, envi.soilOrgN, envi.litterN, fluxes.nVolatilization,
          fluxes.nLeaching);

src/sipnet/sipnet.c:1245

• The calcRootAndWoodFluxes function still returns a double value (the sum of fine and coarse root exudates), but this return value is no longer used anywhere in the codebase after the removal of the microbes feature. The function signature should be changed to void to reflect that it no longer returns a meaningful value. The comment on line 1199 should also be updated to remove the outdated return value description.

double calcRootAndWoodFluxes(void) {
  double coarseExudate, fineExudate;  // exudates in and out of soil
  double npp, gppSoil;  // running means of our tracker variables

  npp = getMeanTrackerMean(meanNPP);
  gppSoil = getMeanTrackerMean(meanGPP);
  if (npp > 0) {
    // :: from [3], root model description and eq (3)
    fluxes.coarseRootCreation = params.coarseRootAllocation * npp;
    fluxes.fineRootCreation = params.fineRootAllocation * npp;
    fluxes.woodCreation = params.woodAllocation * npp;
  } else {
    fluxes.coarseRootCreation = 0;
    fluxes.fineRootCreation = 0;
    fluxes.woodCreation = 0;
  }

  if ((gppSoil > 0) && (envi.fineRootC > 0)) {
    // :: from [3], eq (5)
    coarseExudate = params.coarseRootExudation * gppSoil;
    fineExudate = params.fineRootExudation * gppSoil;
  } else {
    fineExudate = 0;
    coarseExudate = 0;
  }

  // :: from [3], roots model descriptions
  // All root exudates contribute to root loss (microbes no longer modeled)
  fluxes.coarseRootLoss =
      coarseExudate + params.coarseRootTurnoverRate * envi.coarseRootC;
  fluxes.fineRootLoss =
      fineExudate + params.fineRootTurnoverRate * envi.fineRootC;

  // Wood litter, in g C * m^-2 ground area * day^-1
  // turnover rate is fraction lost per day
  fluxes.woodLitter = envi.plantWoodC * params.woodTurnoverRate;

  // :: from [3], root model description
  calcRootResp(&fluxes.rCoarseRoot, params.coarseRootQ10,
               params.baseCoarseRootResp, envi.coarseRootC);
  calcRootResp(&fluxes.rFineRoot, params.fineRootQ10, params.baseFineRootResp,
               envi.fineRootC);

  return fineExudate + coarseExudate;
}

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