Prepare development for v6.0.2 #238
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- SOILWAT2 has gained a comprehensive structure that controls almost all other structs in the program (mainly dealing with simulation values) - SOILWAT2 also has other structs dealing with files (LOG_INFO), paths (PATH_INFO), etc. * `SW_R_lib.c/h` gain these variables as globals (SW_ALL, PATH_INFO, LOG_INFO, SW_OUTPUT_POINTERS) - `SW_R_lib.c` also gains "EchoInits" and "QuietMode" as globals since on the SOILWAT2 side, they have been converted from a global to a local variable in `main()` - See DrylandEcology/SOILWAT2#349 for more information
- Previously, SW_SITE contained a variable called "lyr" which held a dynamic amount of informations for up to a MAX_LAYERS amount of layers * This has been removed in the newest development of SOILWAT2 to control less dynamically allocated memory and all variables have been moved to SW_SITE * Removed any instance of "lyr" being used and replaced with direct access through SW_SITE
- On the SOILWAT2 side, variable type LOG_INFO holds information pertaining to a log file - Also on the SOILWAT2 side, `LogError()` was updated to no longer use a log file pointer directly, but now takes in LOG_INFO as an argument
- A lot of SOILWAT2 functions had their interfaces updated as a part of the program becoming threadsafe * This commit directly updates function calls that were not included in previous commits dealing with individual types (SW_WEATHER, SW_MODEL, etc.)
- Previously, "EchoInits" was made local to "SW_R_lib.c" but is needed in more than one file * `SW_R_lib.h` gains "EchoInits" as an externed global
- The function `SW_F_name()` was removed as a result of functions gaining access to LOG_INFO * Instead of calling a function only to return a string, it was more direct and explanatory to use "InFiles" within PATH_INFO
- SOILWAT2 completely removed the global "errstr", so any function in need of it, gains a local version of it
SW_R_lib.c - Mainly, functions in need of LOG_INFO now have the global instance sent in - Corrected "InFiles" when being sent in to `sw_init_args()` rSW_*.c - Calls to `Str_Dup()` are now sent in the global instance of LOG_INFO - Update any other calls to SOILWAT2 functions that have had their interfaces changed - Update use of macro `ForEachSoilLayer()` in rSW_SoilWater.c to take in SW_SITE's "n_layers
- SOILWAT2 removed "_Sep" as a global, so the function `onSet_SW_OUT()` can no longer access it - `onGet_SW_OUT()` gains it as a local variable set to a tab (\t)
- Previous commit: 12ac215 - Fully convert SW_GEN_OUT in rSW_Output.c * Functions gain pointer to global SW_GEN_OUT (within SW_ALL) to simplify/reduce the accessing of the variables
- Finish the conversions started in the previous commit: 148260a
- In the previous commit (5a02f5a), calls to `interpolate_monthlyValues()` and `calcSiteClimate()` used "SW_Model" which wasn't committed
- SOILWAT2, like `SW_F_name()`, removed `SW_WeatherPrefix()` because it was found calling another function was superfluous
- Remove "// externs ..." comments - Include SW_Site.h for enums "N_SWRCs" and "N_PTFs" and the functions `swrc2str()` and `ptf2str()` - Correct capitalization of "LogInfo"
# Conflicts: # DESCRIPTION # NEWS.md
- SOILWAT2 moved all instances of LOG_INFO in function prototypes to the last position aside from `LogError()`
- This function was updated on the SOILWAT2 side because of the lack of necessity for the type PATH_INFO
- lintr v3.1.0 https://github.com/r-lib/lintr/releases/tag/v3.1.0 - applied lints * [sort_linter] sort(years, na.last = TRUE) is better than years[order(years)] * [matrix_apply_linter] Use rowSums(...) rather than apply(..., MARGIN = 1, FUN = sum) * [boolean_arithmetic_linter] Use any() to express logical aggregations. For example, replace length(which(x == y)) == 0 with !any(x == y). * unnecessary_nested_if_linter] Don't use nested `if` statements, where a single `if` with the combined conditional expression will do. For example, instead of `if (x) { if (y) { ... }}`, use `if (x && y) { ... }` * [unnecessary_lambda_linter] Pass pdf directly as a symbol to lapply() instead of wrapping it in an unnecessary anonymous function. For example, prefer lapply(DF, sum) to lapply(DF, function(x) sum(x)). * [implicit_assignment_linter] Avoid implicit assignments in function calls. For example, instead of `if (x <- 1L) { ... }`, write `x <- 1L; if (x) { ... }`. --> however, I believe that those in tests are false positives for those tests that test assignments via a replacement method, etc. --> silence `implicit_assignment_linter` - newly silenced linters * indentation_linter * implicit_assignment_linter (because of perceived false positives in test code)
- It's possible for a SOILWAT2 to crash when being called from an R function - When that happens, memory could not be properly deallocated and thus cause a memory leak - Using a local variable, sw_exec, sw_inputDataFromFiles, dbW_generateWeather, and sw_outputData detect if C quit early and frees all model memory
Codecov Report
@@ Coverage Diff @@
## main #238 +/- ##
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+ Coverage 58.61% 58.69% +0.08%
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Files 42 42
Lines 8058 8074 +16
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+ Hits 4723 4739 +16
Misses 3335 3335
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- This method of memory freeing does not work, so it has been undone
* Updates to match SOILWAT2's reentrancy and threadsafety preparations
* Add SOILWAT2's new main types - SW_ALL, SW_OUTPUT_POINTERS, LOG_INFO, and PATH_INFO - as globals
* SOILWAT2 pull request: DrylandEcology/SOILWAT2#349
N1ckP3rsl3y
approved these changes
Aug 4, 2023
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Accommodate SOILWAT2 v7.1.0 developments (DrylandEcology/SOILWAT2#351)
Updating rSOILWAT2 to be compatible with SOILWAT2 v7.1.0 (thread-safety and reentrancy) will not affect the user interface and is expected to produce identical simulation output
previously, this was targeted for v6.0.1 (PR Development towards v6.0.1 #235)