Monolith split#33
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Declarations in include/troll.hpp and definitions in src/troll.cpp Updated CMakeLists.txt and .gitignore accordingly Closes #7
…atized-build Add multi-platform build workflow
* Add lint/CMakeLists.txt * Add lint-style and lint-static targets (with `cpplint` and `cppcheck` respectively) * Add workflows/lint.yml * Add lint/README.md Solves #12
* create sanity folder * check script retrieves reference output from main@v4.0 * check script runs current version with reference configuration * check script compares bit by bit reference and current outputs * add cmake sanity and test target * add sanity README --------- Co-authored-by: Dimitri Fekas <dev@yare.fr>
This reverts commit 2d18e762320b29b52a00d7bd28c74e915e870485.
The global parameter registry (AssignParamFromRegistry) has been active since a previous commit. AssignValueGlobal was retained as dead code and is now deleted. Sanity check passes (all 41 output files match reference).
Context ctx is now a file-scope global in troll.cpp instead of a local in main(). RegisterParameters() takes Context& in preparation for binding parameters directly to ctx fields as globals are migrated.
Moves iterperyear, nbiter, iter, nbout, freqout, nbdays, nbsteps_varday, inv_nbsteps_varday, nbhours_covered, timestep from file-scope globals into ctx.time (Context::TimeState). - Adds timestep field to TimeState in context.hpp (was missing) - Removes the ten globals from troll.hpp - Updates all call sites in troll.cpp to use ctx.time.* - Binds nbiter and nbout in RegisterParameters() to ctx.time fields and removes their extern declarations from param_registry.cpp - Preserves output column header string literals unchanged
Moves sites, cols, rows, nbspp, HEIGHT, SBORD, length_dcell, linear_nb_dcells, sites_per_dcell, nbdcells, site_DCELL, i_sites_per_dcell, NV, NH, LV, LH, RMAX, dbhmaxincm, leafdem_resolution from global scope into Context::Grid. - Adds NV, NH, LV, LH, RMAX, dbhmaxincm, leafdem_resolution fields to Grid struct in context.hpp - Removes global definitions from troll.hpp - Removes corresponding extern declarations from param_registry.cpp and rebinds cols, rows, HEIGHT, length_dcell, NV, NH, leafdem_resolution to ctx.grid fields in RegisterParameters() - Fixes one string literal "Number of sites"
Moves all 16 model flag/option globals (_NONRANDOM, _GPPcrown, _BASICTREEFALL, _SEEDTRADEOFF, _NDD, _CROWN_MM, _OUTPUT_extended, _OUTPUT_inventory, _FromInventory, _sapwood, _seedsadditional, _LL_parameterization, _LA_regulation, _OUTPUT_pointcloud, _SOIL_LAYER_WEIGHT, _WATER_RETENTION_CURVE) from global scope into Context::ModelOptions. - Adds _OUTPUT_extended and _OUTPUT_inventory fields missing from the struct in context.hpp - Removes global definitions from troll.hpp - Removes 8 extern declarations from param_registry.cpp and rebinds 11 registry-registered options to ctx.opt fields
Extracts AssignSpeciesParam, AssignValuePointcloud, ReadInputGeneral, ReadInputSpecies, ReadInputDailyvar, ReadInputClimate, ReadInputSoil (and BuildSpeciesRegistry static helper) — 837 lines — from troll.cpp into src/input.cpp. Adds forward declarations to troll.hpp; input.cpp also needs params/param_registry.hpp for AssignParamFromRegistry.
Extracted InitialiseOutputStreams, Initialise, InitialiseABC, ReadInputPointcloud, ReadInputInventory, AllocMem, FreeMem from troll.cpp into src/memory.cpp (-1178 lines). All forward declarations were already present in troll.hpp.
Extract Average, OutputField, OutputSnapshot, OutputVisual, OutputCHM, OutputLAI, TrackingData_andOutput, all OutputABC*/UpdateABC* helpers, MPI_Share* stubs, and CloseOutputs (~3187 lines) from troll.cpp.
Extracted Evolution, UpdateSeeds, UpdateField, FillSeed, RecruitTree, TriggerTreefall, TriggerTreefallSecondary from troll.cpp (337–1073) into src/simulation.cpp. troll.cpp now contains only main() (~338 lines).
Replace int placeholder fields in OutputConfig with real std::fstream objects; add missing conditional streams (MIP_Lichstein, Output_ABC, WATER, TRACK_INDIVIDUALS). Remove extern fstream declarations from troll.hpp and global definitions from troll.cpp. Update all call sites in troll.cpp, output.cpp, memory.cpp, crown.cpp, and tree.cpp to use ctx.out.*. Move OutputConfig to end of Context to keep hot fields at low struct offsets.
- Species::Init() → Species::Init(Context &ctx) - crown.cpp: GetRadiusSlope, UpdateLAI3D, OutputCrownSliced, GetPPFDabove, GetCanopyEnvironment, AddCrownVolumeLayer all take ctx - Templates: CircleAreaUpdateCrownStatistic_template and LoopLayerUpdateCrownStatistic_template take Context &ctx; GetRadiusLayer promoted to template type param G (enables lambdas) - lookup_tables.cpp: InitialiseIntraspecific, InitialiseLookUpLAImax, InitialiseLookUpTables take ctx - Update all call sites (memory.cpp, tree.cpp, output.cpp, input.cpp) with lambdas where callbacks are involved
- AssignValuePointcloud, ReadInputSpecies, ReadInputDailyvar (×2), ReadInputClimate (×2), ReadInputSoil in src/input.cpp - ReadInputPointcloud, ReadInputInventory in src/memory.cpp - Updated declarations in include/troll.hpp - Updated all call sites in src/memory.cpp and src/troll.cpp
UpdateSeeds, UpdateField, FillSeed (skipped—called from tree.cpp), RecruitTree, TriggerTreefall, TriggerTreefallSecondary, GetTimeofyear. Updated declarations in troll.hpp and all call sites.
Remove extern Context ctx from headers and file-scope definition from
troll.cpp. Declare as local Context ctx{} in main() — value-init
zero-initializes all POD members identically to the old global.
Bug fixed along the way: CloseOutputs() only closed output[0..9],
leaving output[11,21-24,28-33] unclosed. When ctx was global, exit(0)
triggered static destructor cleanup which flushed all fstream buffers
automatically. With ctx as a local variable, exit(0) bypasses local
destructors, so those buffers were silently lost. Fixed by extending
the close loop to cover all 40 slots.
- Create include/species.hpp and include/tree.hpp with class declarations (previously inlined in troll.hpp); move leafFluxes struct to tree.hpp - context.hpp includes species.hpp + tree.hpp and gains vector<Species> S and vector<Tree> T fields in Context - troll.hpp reduced to includes, globals, free-function declarations - Remove file-scope vector<Species> S and vector<Tree> T from troll.cpp - Replace all bare S[]/T[] and S./T. vector-method call sites with ctx.S[]/ctx.T[] across tree.cpp, output.cpp, simulation.cpp, memory.cpp, lookup_tables.cpp, input.cpp
All six functions in the #ifdef Output_ABC block that accessed ctx.* without having ctx in scope now take Context &ctx as their first parameter: OutputABC, OutputABCConservationTraits, OutputABC_ground, OutputABC_species, OutputABC_CHM, OutputABC_transmittance Also fixes a latent bug in OutputABCConservationTraits where gslrng (undefined) was used instead of ctx.rng.gslrand. OutputABCWriteHeaders unchanged — it only writes to the passed fstreams. Call site in troll.cpp updated: OutputABC() → OutputABC(ctx).
Correct typos and improve clarity in REFACTORING.md.
Discuss potential removal of MPI globals
Closed
philippeverley
approved these changes
Jul 3, 2026
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Hello, since we'd left things half-way back in November with @philippeverley , it bugged me and I continued on on this whenever I found some time.
Yesterday I solved a bug that delayed me quite a bit, and the monolith is broken 🎉 ! So it's time for a PR to the dev branch perhaps.
Please read the REFACTORING.md file. I made some splitting/architectural decisions on judjement, but - since I'm an outsider - perhaps some of those are to be revised. Even if so, from now on the codebase should be easier to manage/refactor. There are still some things to do, but I am quite confident I haven't broken anything. See the Confidence section in REFACTORING.md