Workflow and Configuration file update (#216)

* udpate changelog

* update changelog

* replace parameters with config in functions.

* update description and readme

* add config.yaml example

* update config tests to use new test config file

* remove redundant functions for new workflow.

* change pops_lite and pops_multirun to a single function called pops_simulate that does what pops_lite did.

* remove functions

* update documentation

* update configuration function to handle new config_yaml with new variable names.

* remove now unused lists

* update tests and add test config yaml files

* add config.yaml and test structure

* update configuration to more easily handle tests.

* update create summary stats to use new variable names

* general updates more to come as tests are converted over to using the config file workflow.

* update pops model to only take in config. This simplifies future updates.

* update pops simulate to use the new pops_model api.

* update pops testing function

* update some tests

* update files

* update pops test

* add data and configs for tests

* udpate some tests and add associated yamls

* update remaining pops single run tests and add configs.

* updates to pops and config based on new yaml and testing

* update pops_model

* lint

* add files and update calibrate and tests

* add import from yaml

* lint

* update data

* update config yamls

* update tests

* update data

* update configuration function

* update calculate all stats

* update validate function

* update other functions

* update

* update tests and lint

* remove rds files from git so that they don't affect tests

* update output path in yamls

* update calibrate test path

* add folder

* update test coverage yaml

Author: ChrisJones687

.github/workflows/test-coverage.yaml

@@ -16,15 +16,16 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      
       - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
 
+      - name: Install macOS system dependencies
+        if: runner.os == 'macOS'
+        run: brew install gdal proj
       # - uses: r-lib/actions/setup-r-dependencies@v2
       #   with:
       #     extra-packages: any::covr

.gitignore

@@ -7,3 +7,4 @@ rpops.Rproj
 docs
 inst/doc
 *env
+*.rds

CHANGELOG.md

@@ -40,6 +40,8 @@ this repository.
 
 - In PoPS Core we are more explicit with types and round to the nearest int for model aspects that require it (@wenzeslaus, #203, #204, #205, #206, and #210 and @ChrisJones687, #208 and #209).
 
+- The workflow for PoPS has changed for version 3.0.0 and newer. We have moved to using a config file (.ymal or .csv). We then create a configuration variable in R and write out an .rds file that can be used in all other functions, see workflow documentation for more information (@ChrisJones687 #)
+
 ### Fixed
 
 - Fixed MCC calculations that returned NaN with very large datasets (@ChrisJones687, #161).
@@ -64,7 +66,7 @@ this repository.
 - `validate`, `calibrate`, `pops_multirun`,  and `pops` now take use_survival_rates, survival_rate_month, 
   survival_rate_day, and survival_rates_file (@ChrisJones687, #147).
 
- - `validate`, `calibrate`, `pops_multirun`,  and `pops` now take network_movement as a parameter. This 
+- `validate`, `calibrate`, `pops_multirun`,  and `pops` now take network_movement as a parameter. This 
     parameter controls how dispersal occurs along the network (@ChrisJones687, #147).
 
 ### Changed

DESCRIPTION

@@ -32,7 +32,8 @@ Imports:
     aws.s3,
     Metrics,
     methods,
-    truncnorm
+    truncnorm,
+    yaml
 License: GPL-3 | file LICENSE
 BugReports: https://github.com/ncsu-landscape-dynamics/rpops/issues
 URL: http://www.github.com/ncsu-landscape-dynamics/rpops
@@ -53,5 +54,5 @@ Suggests:
     pkgdown
 LinkingTo: 
     Rcpp
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr

NAMESPACE

@@ -2,14 +2,11 @@
 
 export(calibrate)
 export(configuration)
-export(configuration_qad_lite)
 export(create_summary_stats_and_stacks)
 export(pops)
-export(pops_lite)
 export(pops_model)
-export(pops_multirun)
+export(pops_simulate)
 export(quantity_allocation_disagreement)
-export(quantity_allocation_disagreement_lite)
 export(validate)
 importFrom(MASS,mvrnorm)
 importFrom(Metrics,rmse)
@@ -18,10 +15,8 @@ importFrom(Rcpp,sourceCpp)
 importFrom(aws.s3,head_object)
 importFrom(aws.s3,save_object)
 importFrom(doParallel,registerDoParallel)
-importFrom(foreach,"%:%")
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
-importFrom(foreach,foreach)
 importFrom(foreach,registerDoSEQ)
 importFrom(landscapemetrics,lsm_c_enn_mn)
 importFrom(landscapemetrics,lsm_c_lpi)
@@ -65,4 +60,5 @@ importFrom(terra,yres)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,write.csv)
+importFrom(yaml,yaml.load_file)
 useDynLib(PoPS, .registration = TRUE)

R/calibrate.R

@@ -218,7 +218,7 @@ time_checks <- function(end_date, start_date, time_step, output_frequency, outpu
     duration <- lubridate::interval(start_date, end_date)
 
     if (time_step == "week") {
-      number_of_time_steps <- ceiling(lubridate::time_length(duration, "week"))
+      number_of_time_steps <- floor(lubridate::time_length(duration, "week"))
     } else if (time_step == "month") {
       number_of_time_steps <- ceiling(lubridate::time_length(duration, "month"))
     } else if (time_step == "day") {