Merge pull request #214 from DrylandEcology/release/devel_v6.0.0

Release rSOILWAT2 v6.0.0

Updating with SOILWAT2 v7.0.0 https://github.com/DrylandEcology/SOILWAT2/releases/tag/v7.0.0

see https://github.com/DrylandEcology/rSOILWAT2/milestone/9

- Update github actions to use r-lib actions v2 (#205)
- Upgrade tests to use testthat edition 3 (#191)
- Integrate with SOILWAT2's new read_all_weather() (#204)
- Integrate SOILWAT2's new calc_SiteClimate() (#205)
- Integrate SOILWAT2's new vegetation cover estimation (#206)
- Implement multiple soil water retention curves (#207)
- Accomodate SOILWAT2's file re-organization (#208)
- Integrate SOILWAT2's soil density descriptor (#209)
- Daily variables for atmospheric demand (#229)

.Rbuildignore

@@ -2,6 +2,7 @@
 ^CODE_OF_CONDUCT\.md$
 ^Meta$
 ^doc$
+^backup$
 ^data-raw$
 \.git*
 ^\.travis\.yml$
@@ -15,20 +16,23 @@
 ^\.Rproj\.user$
 ^cran-comments\.md$
 ^NEWS\.md$
+tests/rSOILWAT_IntegrationTestOutput
 src/SOILWAT2/\.git
+src/SOILWAT2/\.github
 src/SOILWAT2/doc
-src/SOILWAT2/googletest
-src/SOILWAT2/test
-src/SOILWAT2/testing
+src/SOILWAT2/build
+src/SOILWAT2/external/googletest
+src/SOILWAT2/tests
 src/SOILWAT2/\.travis\.yml
 src/SOILWAT2/appveyor\.yml
 src/SOILWAT2/codecov\.yml
 src/SOILWAT2/Doxyfile
 src/SOILWAT2/README\.md
-src/SOILWAT2/run_gcov\.sh
+src/SOILWAT2/NEWS\.md
+src/SOILWAT2/tools
 src/SOILWAT2/\.LSAN_suppr\.txt
-src/SOILWAT2/SW_Main\.c
-src/SOILWAT2/SW_Output_mock\.c
+src/SOILWAT2/src/SW_Main\.c
+src/SOILWAT2/src/SW_Output_mock\.c
 src/*\.o
 src/*\.so
 src/*\.dll

.gitignore

@@ -36,6 +36,7 @@ Thumbs.db
 rSOILWAT2.Rcheck
 rSOILWAT_IntegrationTestOutput/
 tests/spelling.Rout.save
+backup/
 
 # Package build files
 *tar.gz
@@ -49,3 +50,4 @@ doc
 # Locally knitted vignettes
 vignettes/*.pdf
 vignettes/*.html
+vignettes/*.log

.lintr

@@ -12,6 +12,7 @@ linters: lintr::linters_with_tags(
   todo_comment_linter = NULL,
   nonportable_path_linter = NULL,
   expect_identical_linter = NULL,
+  function_argument_linter = NULL,
   yoda_test_linter = NULL)
 exclusions: list(
   "R/RcppExports.R",

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rSOILWAT2
-Version: 5.4.1
+Version: 6.0.0
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
-Description: Access to the C-based SOILWAT2 v6.7.0 and functionality for
+Description: Access to the C-based SOILWAT2 v7.0.0 and functionality for
   SQLite-database of weather data.
 Authors@R: c(
   person(
@@ -35,16 +35,18 @@ Suggests:
   rSW2exter (>= 0.1.0),
   soilDB,
   spelling (>= 2.1.0),
-  testthat
+  testthat (>= 3.0.0)
 Remotes:
     github::DrylandEcology/rSW2utils,
     github::DrylandEcology/rSW2data,
     github::DrylandEcology/rSW2exter
 NeedsCompilation: yes
+SystemRequirements: GNU make
 License: GPL-3
 URL: https://github.com/DrylandEcology/rSOILWAT2
 BugReports: https://github.com/DrylandEcology/rSOILWAT2/issues
 Encoding: UTF-8
+Config/testthat/edition: 3
 RoxygenNote: 7.2.3
 LazyData: true
 Language: en-US

NAMESPACE

@@ -16,7 +16,11 @@ export(calc_RRs_Chambers2014)
 export(calc_RRs_Maestas2016)
 export(calc_SMTRs)
 export(calc_SiteClimate)
+export(calc_dailyInputFlags)
+export(check_SWRC_vs_PTF)
 export(check_TranspirationRegions)
+export(check_ptf_availability)
+export(check_swrcp)
 export(check_updatedDB)
 export(check_version)
 export(compare_weather)
@@ -61,6 +65,7 @@ export(dbW_upgrade_v2to3)
 export(dbW_upgrade_v31to32)
 export(dbW_upgrade_v3to31)
 export(dbW_version)
+export(dbW_weatherData_round)
 export(dbW_weatherData_to_blob)
 export(dbW_weatherData_to_dataframe)
 export(dbW_weatherData_to_monthly)
@@ -72,23 +77,30 @@ export(format_timestamp)
 export(getStartYear)
 export(getWeatherData_folders)
 export(get_evaporation)
+export(get_soilmoisture)
 export(get_soiltemp)
 export(get_timestamp)
 export(get_transpiration)
 export(get_version)
 export(get_years_from_weatherDF)
 export(get_years_from_weatherData)
 export(has_soilTemp_failed)
+export(is_missing_weather)
+export(list_matched_swrcs_ptfs)
 export(lookup_annual_CO2a)
+export(nrow_output)
 export(prepare_TranspirationRegions)
 export(print_mkv_files)
+export(ptf_estimate)
+export(ptf_names)
 export(set_Markov)
 export(set_WeatherHistory)
 export(set_missing_weather)
 export(set_requested_flags)
 export(set_swCarbon)
 export(set_swCloud)
 export(set_swFiles)
+export(set_swMarkov)
 export(set_swOUT)
 export(set_swProd)
 export(set_swSWC)
@@ -99,16 +111,48 @@ export(set_swWeatherData)
 export(set_swYears)
 export(setup_time_simulation_run)
 export(simTiming_ForEachUsedTimeUnit)
+export(swCarbon)
+export(swCloud)
+export(swEstab)
+export(swEstabSpecies)
+export(swFiles)
+export(swInputData)
+export(swLog)
+export(swMarkov)
+export(swMonthlyScalingParams)
+export(swOUT)
 export(swOUT_TimeStepsForEveryKey)
+export(swOUT_key)
+export(swOutput)
+export(swOutput_KEY)
+export(swProd)
+export(swSWC)
+export(swSWC_hist)
+export(swSite)
+export(swSoils)
+export(swWeather)
+export(swWeatherData)
+export(swYears)
 export(sw_Cheatgrass_ClimVar)
 export(sw_dailyC4_TempVar)
 export(sw_exec)
 export(sw_inputData)
 export(sw_inputDataFromFiles)
 export(sw_out_flags)
 export(sw_outputData)
+export(sw_verbosity)
+export(swrc_conversion)
+export(swrc_names)
+export(swrc_swp_to_vwc)
+export(swrc_vwc_to_swp)
+export(time_columns)
 export(update_biomass)
 export(update_requested_years)
+export(upgrade_weatherHistory)
+export(weatherGenerator_dataColumns)
+export(weatherHistory)
+export(weather_dataAggFun)
+export(weather_dataColumns)
 exportClasses(swCarbon)
 exportClasses(swCloud)
 exportClasses(swEstab)
@@ -138,6 +182,7 @@ exportMethods("set_WeatherHistory<-")
 exportMethods("set_swCarbon<-")
 exportMethods("set_swCloud<-")
 exportMethods("set_swFiles<-")
+exportMethods("set_swMarkov<-")
 exportMethods("set_swOUT<-")
 exportMethods("set_swProd<-")
 exportMethods("set_swSWC<-")
@@ -168,6 +213,7 @@ exportMethods("swFiles_OutputPrefix<-")
 exportMethods("swFiles_Prod<-")
 exportMethods("swFiles_ProjDir<-")
 exportMethods("swFiles_SWCsetup<-")
+exportMethods("swFiles_SWRCp<-")
 exportMethods("swFiles_SiteParams<-")
 exportMethods("swFiles_Soils<-")
 exportMethods("swFiles_WeatherPrefix<-")
@@ -210,12 +256,16 @@ exportMethods("swSite_IntrinsicSiteParams<-")
 exportMethods("swSite_ModelCoefficients<-")
 exportMethods("swSite_ModelFlags<-")
 exportMethods("swSite_SWClimits<-")
+exportMethods("swSite_SWRCflags<-")
 exportMethods("swSite_SnowSimulationParams<-")
+exportMethods("swSite_SoilDensityInputType<-")
 exportMethods("swSite_SoilTemperatureConsts<-")
 exportMethods("swSite_SoilTemperatureFlag<-")
 exportMethods("swSite_TranspCoefficients<-")
 exportMethods("swSite_TranspirationRegions<-")
+exportMethods("swSite_hasSWRCp<-")
 exportMethods("swSoils_Layers<-")
+exportMethods("swSoils_SWRCp<-")
 exportMethods("swWeather_DaysRunningAverage<-")
 exportMethods("swWeather_FirstYearHistorical<-")
 exportMethods("swWeather_MonScalingParams<-")
@@ -233,7 +283,9 @@ exportMethods(get_Markov)
 exportMethods(get_WeatherHistory)
 exportMethods(get_swCarbon)
 exportMethods(get_swCloud)
+exportMethods(get_swEstab)
 exportMethods(get_swFiles)
+exportMethods(get_swMarkov)
 exportMethods(get_swOUT)
 exportMethods(get_swProd)
 exportMethods(get_swSWC)
@@ -242,7 +294,6 @@ exportMethods(get_swSoils)
 exportMethods(get_swWeather)
 exportMethods(get_swWeatherData)
 exportMethods(get_swYears)
-exportMethods(initialize)
 exportMethods(swCarbon_CO2ppm)
 exportMethods(swCarbon_DeltaYear)
 exportMethods(swCarbon_Scenario)
@@ -265,6 +316,7 @@ exportMethods(swFiles_OutputPrefix)
 exportMethods(swFiles_Prod)
 exportMethods(swFiles_ProjDir)
 exportMethods(swFiles_SWCsetup)
+exportMethods(swFiles_SWRCp)
 exportMethods(swFiles_SiteParams)
 exportMethods(swFiles_Soils)
 exportMethods(swFiles_WeatherPrefix)
@@ -306,12 +358,16 @@ exportMethods(swSite_IntrinsicSiteParams)
 exportMethods(swSite_ModelCoefficients)
 exportMethods(swSite_ModelFlags)
 exportMethods(swSite_SWClimits)
+exportMethods(swSite_SWRCflags)
 exportMethods(swSite_SnowSimulationParams)
+exportMethods(swSite_SoilDensityInputType)
 exportMethods(swSite_SoilTemperatureConsts)
 exportMethods(swSite_SoilTemperatureFlag)
 exportMethods(swSite_TranspCoefficients)
 exportMethods(swSite_TranspirationRegions)
+exportMethods(swSite_hasSWRCp)
 exportMethods(swSoils_Layers)
+exportMethods(swSoils_SWRCp)
 exportMethods(swWeather_DaysRunningAverage)
 exportMethods(swWeather_FirstYearHistorical)
 exportMethods(swWeather_MonScalingParams)
@@ -325,13 +381,13 @@ exportMethods(swYears_EndYear)
 exportMethods(swYears_FDOFY)
 exportMethods(swYears_StartYear)
 exportMethods(swYears_isNorth)
+exportMethods(sw_upgrade)
 importFrom(methods,"as<-")
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,getSlots)
 importFrom(methods,inheritedSlotNames)
-importFrom(methods,initialize)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(methods,slotNames)