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v2.0.0 SIPNET Overhaul

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@Alomir Alomir released this 17 Sep 22:00
· 27 commits to master since this release
v2.0.0
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Learn about vigilant mode.

DOI

Added

  • Irrigation events (#26)
  • Changelog (#33)
  • Model structure and parameter documentation (#42)
  • Build docs and push to gh-pages (#41)
  • Add documentation website (pecanproject.github.io/sipnet) with automated builds (#53)
  • Handle planting & harvest events(#55)
  • events.out file for agronomic event handling (#57)
  • Utility tools/trim_first_chars.sh to trim the first n characters from every row in a file, useful for updating old input files to remove location column
  • Expanded smoke test cases to better cover SIPNET modeling options (#109, #114)
  • Converted all compile-time switches not removed or hard-coded to be on into switches to run-time options (#114)
  • Added extensive documentation in code listing the source(s) that the code implements (#135)
  • Added python tool for comparing smoke test results with expected values (#142)

Fixed

  • Fixed OOM issue when reading bad data (#38, #45)
  • Event order checks no longer only compare to first record (#74, #77)
  • Fixed long-standing bug wherein microbePulseEff was not set to 0 when MICROBES was off (#114)
  • Fixed long-standing bug with missing rSoil flux calc when LITTER_POOL is on (#139)
  • Fixed long-standing bug with missing frozen soil check in soilBreakdown when LITTER_POOL is on (#140)

Changed

  • Reorganized codebase (#34, #37)
  • Document & combine calclighteff functions (#35)
  • Deprecated: "RUNTYPE" is obsolete. Will be silently ignored if set to 'standard' or error if set to anything else. Runs in 'standard' mode by default.
  • Deprecated: "LOCATION" is obsolete. Will be ignored with warning. (#92)
  • Deprecated: All columns in *.param except for name and value. Will be ignored with warning. (#92)
  • Deprecated: location and soilWetness columns in input climate files. If both are present, will be ignored with warning. (#92, #127)
  • Changed: sipnet.out columns will be zero when relevant modes are off (e.g., litter, microbes) (#143)
  • Changed: reorganized code in sipnet to better model fluxes-then-pool-updates flow (#154)
  • Changed: sipnet.out format; it no longer has loc, litterWater or fPAR columns (#155)

Removed

  • Removed many experimental sites, data, and executable code as part of reorg (#34, #37)
  • Removed obsolete run types senstest and montecarlo and associated code (#69, #76)
  • Removed obsolete estimate program and associated code (#70, #82)
  • Removed multi-site support; in particular, output files no longer have a location column (#92)
  • Removed or hard-codes 'on' many compile time switches (#114)
  • Removed SOIL_QUALITY mode (#125)
  • Removed soilWetness mode (#127)
  • Removed obsolete model params; sipnet now warns on unknown params in the params file (#124)

Full Changelog: v1.3.0...v2.0.0

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