Development for v6.1.0 #245
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…up capabilities currently and to prepare for potential domain integration later
…ion from SOILWAT2 to rSOILWAT2 (namely the spinup functionality)
- More details about DayMet: noleap calendar; no wind data - Code examples illustrate now lack of wind data and obtaining atmospheric CO2 values
* renamed rSW_Model to rSW_Domain * added new file M_swSpinup.R to handle new spinup variables * incorporated new spinup variable with the existing years variables in the new domain file
* Something is still causing errors in terms of when files are read or not
- update to commit 3d349b9f7bf8db981df8b13f551f17210746e5e0 on branch release/devel_v8.0.0 ** now includes merged feature_nc_output ** submodule pcg changed remote origin
- Package-level updates:
* NEWS
* Submodule SOILWAT2 now at commit 6467716e415b42a13170d2b14452019b46f099fe (includes a few minor bug fixes)
* SOILWAT2 test example input files
* rSOILWAT2 test objects
* rSOILWAT2 tests for spinup functionality
* Vignette with spinup demonstration
* Export and document new methods to interact with spinup functionality: set_swSpinup(), get_sw_Spinup(), swSpinup_SpinupActive(), swSpinup_SpinupDuration(), swSpinup_SpinupMode(), swSpinup_SpinupScope(), swSpinup_SpinupSeed()
- Class upgrade functionality
* sw_upgrade() now adds (i) new slot "spinup" for objects of class "swInputData" and (ii) adds additional input files for objects of class "swFiles"
- Class "swSpinup"
* Added missing generic method "swSpinup_SpinupActive<-"
* Added missing spinup methods: get_swSpinup(), set_swSpinup(), swSpinup_SpinupActive()
* Validity tests now agree with C implementation
* Renamed spinup code file from R/M_swSpinup.R to R/B_swSpinup.R -- package building/installation requires that "swSpinup" is available before "swInputData" is processed
- Class "swInputData"
* Added new slot "spinup"
* Implemented upgrade functionality for new slot "spinup" in sw_upgrade() method of "swInputData"
* Implemented "spinup"-methods for class "swInputData"
Updates to interface to C code of SOILWAT2 (v8.0.0-devel)
- New "spinup" functionality
* `sw_start()` now calls `SW_CTL_run_spinup()` to run the spinup
- New struct "SW_Domain"
* SW_R_lib gains new global "SoilWatDomain" (rSOILWAT2 does not represent a domain to the R user -- it is fixed internally at size 1 reproducing previous behavior)
* New call to `SW_DOM_soilProfile()` (see SOILWAT2's `main()`) by functions that set up SOILWAT2 inputs, i.e., `sw_start()` and `onGetInputDataFromFiles()`
* rSW2_readAllWeatherFromDisk() gains argument "sw_template" which hold default rSOILWAT2 inputs that serve as template (now required by `setupSOILWAT2()`)
* New `onSet_SW_DOM()` and `onGet_SW_DOM()` to pass values via memory between rSOILWAT2 and SOILWAT2 structures/classes
** Note that `onSet_SW_DOM()` currently hard-codes a domain size of 1
* New `rSW_CTL_setup_domain()` (equivalent to SOILWAT2's `SW_CTL_setup_domain()`): obtain inputs for "files" and "domain" (from disk or via memory); construct and set up the domain
- Order of obtaining inputs ("files" and new "domain" are now called earlier by `SW_CTL_setup_domain()` and not longer later by `SW_CTL_obtain_inputs()` as previously):
* `setupSOILWAT2()` now sets up the domain and thus obtains inputs (from disk or via memory): new arguments "from_files" and "InputData" -- only `onGetInputDataFromFiles()` is reading inputs from disk, all other functionality passes inputs via memory (from the R user to the SOILWAT2 C code)
* Move call to `onSet_SW_F()` from `rSW_CTL_obtain_inputs()` to `rSW_CTL_setup_domain()` -- matching SOILWAT2's new `SW_CTL_setup_domain()`
- (De)allocating memory (new dedicated functions for finer control):
* De-allocation of SOILWAT2 memory now requires a separate call to `SW_DOM_deconstruct()`
* `onSet_MKV()` gains call to new `allocateMKV()`
* `onSet_SW_VES()` gains calls to `SW_VES_construct()` and new `SW_VES_alloc_outptrs()` as well as `SW_VegEstab_alloc_outptrs()`
* `sw_start()` gains call to `SW_CTL_alloc_outptrs()`
- `cInF` of sw_consts() again contains the correct (newly increased number of) input file names --> this should be fixing "undefined behavior" in `SET_STRING_ELT(cnames, i, mkChar(cInF[i]));` --> this should be fixing "segfault" in `.Call(C_sw_consts)`
- tests and example code was failing when external data sources were offline or changed their delivery format - now failures are captured correctly
- compare_weather() now creates boxplots of correlation of each variables with precipitation (in addition to the already implemented mean and standard variation of each variable) - compare_weather() now creates a new figure that shows the long-term (across years) daily, weekly, and monthly means of each variable (plus a time series of annual values)
- compare_weather() accepts weather sets from different years; thus, the new added plot that compares time-series across years (commit ab6cd73) failed if years differed -> now create time-series comparisons only if comparable data are available - also fix test expectations: now five (instead of four) figures are produced
- update to commit 36cb14ec060b841f0be3679387f0168ae27d6ffd - includes "Fix sw_fail_on_error() for rSOILWAT2"
* SOILWAT2 updated to v8.0.0-devel which now includes a simulation domain; however, this has no impact on rSOILWAT2. * New spin-up functionality (@niteflyunicorns, @dschlaep). A user-requested sequence of (random) years is simulated (without output) before the actual simulation run to provide better starting values (e.g., soil moisture, soil temperature).
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #245 +/- ##
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+ Coverage 58.93% 58.95% +0.02%
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Files 43 44 +1
Lines 8593 8863 +270
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+ Hits 5064 5225 +161
- Misses 3529 3638 +109 ☔ View full report in Codecov by Sentry. |
- update SOILWAT2 to commit 8670d8767123a129976a1861178b104e10784bbe ** feature_format: formatted code, include header directives, and adjusted macros ** feature_compile_lib: improved compilation as library
- declare C11 as system requirement because * R v4.3.0 now requires C11 or later to satisfy "R_ext/Complex.h:77:5: warning: anonymous structs are a C11 extension" * C11 is apparently required to find externed SOILWAT2 variables in flat namespace Update 'makevars' - removed "-I.." because SOILWAT2 files no longer include rSOILWAT2 header files - removed "sw_sources" because SOILWAT2 now automatically includes correct source files
- Use fmin/fmax instead of macros min/max (now MIN/MAX) when used with types float or double - Renamed swprintf to sw_printf
- SOILWAT2 has two new structs - SW_OUT_DOM & SW_OUT_RUN * SW_OUT_DOM - Holds output information that is constant between simulation runs * SW_OUT_RUN - Holds output information that will change during simulation runs - SOILWAT2 removed SW_OUTPUT_POINTERS - SOILWAT2 functions `SW_CTL_setup_model()` & `SW_OUT_construct()` gain new parameter * Parameter determines if SW_OUT_RUN should be zeroed out - Remove instances of SW_OUTPUT_POINTERS - Rename SW_ALL to SW_RUN and `SoilWatAll` to `SoilWatRun` - Update call to `SW_CTL_setup_model()` to provide the flag input - Update `inst/extdata/example1/Input/outsetup.in` to turn on the ESTABL with a sumtype of AVG
… example inputs - SOILWAT2 example inputs: ESTABL output method is now "AVG" by default (and no longer "OFF") - however, rSOILWAT2 turns off ESTABL output for its own "example1"
N1ckP3rsl3y
approved these changes
Jul 11, 2024
- update NEWS - update SOILWAT2 submodule to v8.0.0
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