clean: update docs, add targets prune command

Author: dshemetov

Makefile

@@ -19,13 +19,13 @@ prod-flu:
 
 prod: prod-covid prod-flu update-site netlify
 
-prod-backtest-covid:
+prod-covid-backtest:
 	export BACKTEST_MODE=TRUE; export TAR_RUN_PROJECT=covid_hosp_prod; Rscript scripts/run.R
 
-prod-backtest-flu:
+prod-flu-backtest:
 	export BACKTEST_MODE=TRUE; export TAR_RUN_PROJECT=flu_hosp_prod; Rscript scripts/run.R
 
-prod-backtest: prod-backtest-covid prod-backtest-flu
+prod-backtest: prod-covid-backtest prod-flu-backtest
 
 explore-covid:
 	export TAR_RUN_PROJECT=covid_hosp_explore; Rscript scripts/run.R
@@ -35,6 +35,20 @@ explore-flu:
 
 explore: explore-covid explore-flu update-site netlify
 
+prune: prune-covid-prod prune-flu-prod prune-covid-explore prune-flu-explore
+
+prune-covid-prod:
+	export TAR_PROJECT=covid_hosp_prod; export BACKTEST_MODE=TRUE; Rscript -e "targets::tar_prune()"
+
+prune-flu-prod:
+	export TAR_PROJECT=flu_hosp_prod; export BACKTEST_MODE=TRUE; Rscript -e "targets::tar_prune()"
+
+prune-covid-explore:
+	export TAR_PROJECT=covid_hosp_explore; Rscript -e "targets::tar_prune()"
+
+prune-flu-explore:
+	export TAR_PROJECT=flu_hosp_explore; Rscript -e "targets::tar_prune()"
+
 commit-covid:
 	cd ../covid19-forecast-hub; \
 	git pull --rebase --autostash origin main; \
@@ -115,9 +129,11 @@ upload: push
 dashboard:
 	Rscript scripts/dashboard.R
 
-update-site:
+sync-reports:
 	aws s3 sync s3://forecasting-team-data/2024/reports/ reports/; \
-	aws s3 sync reports/ s3://forecasting-team-data/2024/reports/; \
+	aws s3 sync reports/ s3://forecasting-team-data/2024/reports/
+
+update-site: sync-reports
 	Rscript -e "suppressPackageStartupMessages(source(here::here('R', 'load_all.R'))); update_site()" > cache/update_site_log.txt
 
 netlify:

README.md

@@ -37,7 +37,9 @@ Run the pipeline using:
 # Install renv and R dependencies
 make install
 
-# Pull various data used by the forecasters from the AWS bucket
+# Sync data and forecasts from the AWS bucket
+# - downloads the aux_data/ folder which contains non-public data used by some forecasters
+# - downloads previously generated forecasts, to save recomputing them
 # Requires the AWS CLI to be installed and configured
 # Reference: https://awscli.amazonaws.com/v2/documentation/api/latest/reference/s3/index.html
 # Installation instructions: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html
@@ -61,7 +63,7 @@ make update_site && make netlify
 make submit-flu
 make submit-covid
 
-# Push the data to the AWS bucket (requires AWS CLI)
+# Push your forecasts to the AWS bucket (requires AWS CLI)
 make push
 ```