V1.2 science updates and bug fixes#27

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hhughes92 wants to merge 94 commits intocirevo/initial-improvementsfrom

hh-modeller-improvements

Commits on Aug 20, 2025

chore: move constants to one file and import when needed, to avoid errors in duplication
hhughes92
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chore: rename dens as wood_dens
hhughes92
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Tidy up constants.py and pull through changes to other files
hhughes92
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Rename "N_TREES" to "N_COHORTS" and add to command line arguments. "N_TREES" could be confused with stand density, but here means number of species or cohorts.
hhughes92
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Clarify list length function
hhughes92
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Add source information to emission factors. Fix bug in emit.py
hhughes92
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Update crop IPCC defaults to 2019 values. Where crop names have changed and are not available in IPCC 2019, the values were not changed.
hhughes92
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Clarifications on generalised soil model functions/classes
hhughes92
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Commits on Sep 1, 2025

Commits on Sep 2, 2025

Remove implied limit of 3 cohorts of trees. Note: the input data template has not yet been updated with instructions on how to add more cohorts.
hhughes92
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Commits on Sep 5, 2025

fix: key typo in GWP
hhughes92
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Commits on Sep 10, 2025

Commits on Sep 11, 2025

Commits on Oct 16, 2025

Commits on Nov 6, 2025

Fix formula issue in template
hhughes92
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Commits on Nov 10, 2025

Commits on Nov 11, 2025

Fix permissions on data template
hhughes92
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Commits on Nov 12, 2025

Commits on Dec 1, 2025

Correct chave_wet (coefficients from Table 4 of source paper) as agreed with TRP reviewer
hhughes92
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Commits on Dec 17, 2025

Commits on Dec 20, 2025

Commits on Dec 22, 2025

Update names for clarity
hhughes92
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Commits on Jan 5, 2026

Commits on Jan 6, 2026

Apply validation 0-1 to turnover of tree biomass pools
hhughes92
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Commits on Jan 7, 2026

Consistently use math.log (not np.log): math.log works for single numbers, np.log works for arrays and is slower than math.log for single numbers.
hhughes92
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Commits on Jan 13, 2026

Commits on Jan 14, 2026

Bug fix: crop residues removed double-accounted for proportion left. Was (AG residues left) * (1- proportion left), fixed to be based on (total AG residues) * (1- proportion left)
hhughes92
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Commits on Jan 15, 2026

fix: incorrect equation introduced recently. corrected.
hhughes92
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Commits on Jan 19, 2026

Update flux: use a function that calculates flux in order (thinning, mortality, turnover) so that proportions are applied to remaining biomass after each flux. This allows all proportions 0-1 to be…
hhughes92
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Commits on Jan 22, 2026

Commits on Jan 29, 2026

Bug fix: add burn_off information to crop_emissions. Default for burn_off_base and burn_off_project is True (conservative), but input data should be used where available.
hhughes92
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