feat: allow exposure_workflow to read input config yml + refactor for compatibility with converted_util files as input #99
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…l + update func params for yml cfg
data-raw/input_config.yml
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| future_climate: "./future_climate_data_new.rds" | ||
| species: "./species_new.rds" | ||
| exposure_result_file: "exposure_result.rds" | ||
| workers: 1 |
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can you add a comment that omitting the workers parameter will result in availableCores()-1 workers being used? Or perhaps that should the default and we could just include the line commented out? E.g.
# workers: 1 # This parameter can be used to use a specific number of workers instead of the system default
docker_exposure.sh
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| @@ -2,11 +2,13 @@ | |||
| source run_container.sh | |||
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| if [ $# -lt 2 ]; then | |||
| echo "usage: $0 <data_dir> <output_dir> <extra-args>" | |||
| echo "usage: $0 <input_config_yml_file_path> <output_dir> <extra-args>" | |||
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We no longer use extra-args, right? Since they come through the yaml?
| echo "usage: $0 <input_config_yml_file_path> <output_dir> <extra-args>" | |
| echo "usage: $0 <input_config_yml_file_path> <output_dir>" |
scripts/exposure_workflow.R
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| # Load all functions from the package | ||
| log_info("Loading package functions...") | ||
| devtools::load_all() | ||
| log_info("Package functions loaded successfully.") | ||
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| # 1. Transform the distribution polygons to match the grid | ||
| log_info("Transforming distribution polygons to match the grid.") | ||
| primates_range_data <- prepare_range(primates_shp, grid) | ||
| log_info("Processed {length(primates_range_data)} species.") |
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I suggest changing the wording of these log entries to something like "loaded" vs "Processed" or "Extraction done" since we are no longer doing any processing here.
scripts/main.R
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| @@ -197,32 +217,76 @@ run_climatearray2rds <- function(args) { | |||
| } | |||
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| run_exposure <- function(args) { | |||
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| if (length(args) < 2) { | |||
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This should be taken care of by safe_parse_opts() which will provide a better error.
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updated - now as a part of check_not_null()
#88 #98
exposurecommand line to read input_config.yml. Example: Rscript scripts/main.R exposure -i input_config.ymlexposure_time_workflow()exposure_time_workflow()that is already done by converted_util functions.Execution via docker:
sh docker_exposure.sh "./data-raw/input_config.yml" "./outputs"Execution via CL locally:
Rscript scripts/main.R exposure -i data-raw/input_config.yml