Merge pull request #49 from ResearchLuxembourg/develop

develop→master merge for 2.0.1

Author: exaexa

Project.toml

@@ -7,3 +7,12 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 PlotUtils = "995b91a9-d308-5afd-9ec6-746e21dbc043"
 RollingFunctions = "b0e4dd01-7b14-53d8-9b45-175a3e362653"
 XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
+
+[compat]
+CSV = "0.10"
+CairoMakie = "0.8"
+DataFrames = "1.3"
+Distributions = "0.25"
+PlotUtils = "1.3"
+RollingFunctions = "0.6"
+XLSX = "0.8"

components/lib/common.jl

@@ -12,7 +12,7 @@ function read_one_sheet_xlsx(fn)
 
     length(sheets) == 1 || @throw DomainError length(sheets) "unexpected number of sheets"
 
-    return DataFrame(XLSX.gettable(xls[sheets[1]])...)
+    return DataFrame(XLSX.gettable(xls[sheets[1]]))
 end
 
 normalize!(x; sum_args...) = x ./= sum(x; sum_args...)

run_pipeline.sh

@@ -15,18 +15,18 @@ log () {
 
 echo "found $FILE" | log find_input
 
-IMAGE=researchluxembourg/restimator
+IMAGE=ghcr.io/researchluxembourg/restimator
 MOUNT="-v $PWD/input:/tool/input -v $PWD/output:/tool/output -v $PWD/logs:/tool/logs "
 DOCKER="docker run --rm $MOUNT $IMAGE julia --project "
 
 mkdir -p output logs
 export RESTIMATOR_OUTDIR=output
 
-if $DOCKER components/check_input.jl "$FILE" | log check
+if $DOCKER components/check_input.jl "$FILE"
 then
-	$DOCKER components/estimate_r_t.jl "$FILE" | log rt
-	$DOCKER components/estimate_r_eff.jl "$FILE" | log reff
+	$DOCKER components/estimate_r_t.jl "$FILE" 2>&1 | log rt
+	$DOCKER components/estimate_r_eff.jl "$FILE" 2>&1 | log reff
 else
 	echo $0: check failed >&2
 	exit 1
-fi
+fi 2>&1 | log check