Merge pull request #27 from PALEOtoolkit/logging_tidyup

Tidy up logging

src/Forcings/COPSEForcings.jl

@@ -321,32 +321,36 @@ function setup_force_spreadsheet(m::PB.ReactionMethod, pars, (), cellrange::PB.A
     attribute_name == :setup || return nothing
 
     forcingfile = joinpath(pars.datafolder[], pars.datafile[])
-    @info "setup_force_spreadsheet ReactionForce_spreadsheet $(PB.fullname(rj)): "*
-        "loading $(pars.forcename[]) forcing from 'datafolder/datafile'='$(forcingfile)'"
-    rj.forcing_data = _read_xlsx(forcingfile, sheetname=pars.sheetname[])
+
+    io = IOBuffer()
+    println(io, "setup_force_spreadsheet ReactionForce_spreadsheet $(PB.fullname(rj)): ")
+    println(io, "    loading $(pars.forcename[]) forcing from 'datafolder/datafile'='$(forcingfile)'")
+    rj.forcing_data = _read_xlsx(io, forcingfile, sheetname=pars.sheetname[])
 
     sp_times = pars.timemultiplier[]*rj.forcing_data[:, pars.timecolumn[]]
-    @info "    'tforce' from $(pars.timemultiplier[]) * column $(pars.timecolumn[]) ($(names(rj.forcing_data)[pars.timecolumn[]]))"
+    println(io, "    'tforce' from $(pars.timemultiplier[]) * column $(pars.timecolumn[]) ($(names(rj.forcing_data)[pars.timecolumn[]]))")
 
     sp_values = Float64.(rj.forcing_data[:, pars.datacolumn[]])
-    @info "    '$(pars.forcename[])' from column $(pars.datacolumn[]) ($(names(rj.forcing_data)[pars.datacolumn[]]))"
+    println(io, "    '$(pars.forcename[])' from column $(pars.datacolumn[]) ($(names(rj.forcing_data)[pars.datacolumn[]]))")
 
     # sort in ascending time order
     sp_perm = sortperm(sp_times)
     rj.force_times = sp_times[sp_perm]
     rj.force_values = sp_values[sp_perm]
 
     extrap_past = isnan(pars.extrap_value_past[]) ? "earlist value in spreadsheet = $(first(rj.force_values))" : "'extrap_value_past' = $(pars.extrap_value_past[])"
-    @info "    extrapolating out-of-range tforce < $(first(rj.force_times)) (yr) to $extrap_past"
+    println(io, "    extrapolating out-of-range tforce < $(first(rj.force_times)) (yr) to $extrap_past")
     extrap_future = isnan(pars.extrap_value_future[]) ? "latest value in spreadsheet = $(last(rj.force_values))" : "'extrap_value_future' = $(pars.extrap_value_future[])"
-    @info "    extrapolating out-of-range tforce > $(last(rj.force_times)) (yr) to $extrap_future"
+    println(io, "    extrapolating out-of-range tforce > $(last(rj.force_times)) (yr) to $extrap_future")
 
     # create interpolation object
     rj.interp_FORCE = Interpolations.LinearInterpolation(
         rj.force_times, rj.force_values, 
         extrapolation_bc = Interpolations.Flat() # only used for extrap_value_past, future == NaN
     )
 
+    @info String(take!(io))
+
     return nothing
 end
 
@@ -367,16 +371,16 @@ function do_force_spreadsheet(m::PB.ReactionMethod, pars, (var_tforce, var_FORCE
     return nothing
 end
 
-function _read_xlsx(forcingfile; sheetname="Sheet1")
+function _read_xlsx(io, forcingfile; sheetname="Sheet1")
 
-    @info "    read_xlsx: spreadsheet $(forcingfile) sheet $(sheetname)"
+    println(io, "    read_xlsx: spreadsheet $(forcingfile) sheet $(sheetname)")
 
     xf = XLSX.readxlsx(forcingfile)
 
     # Read using built-in iterator - assumes single header row, automatic type conversion
     df = XLSX.eachtablerow(xf[sheetname]) |> DataFrames.DataFrame
 
-    @info "    read_xlsx read $(DataFrames.describe(df))"
+    println(io, "    read_xlsx read $(DataFrames.describe(df))")
 
     return df
 end

src/Forcings/LipForcing.jl

@@ -82,19 +82,19 @@ end
 #####################################################
 
 """
-    read_lips_xlsx(lipfile)  -> LIPdata::NamedTuple
+    read_lips_xlsx(io, lipfile)  -> LIPdata::NamedTuple
 
 read LIP data from spreadsheet
 """
-function read_lips_xlsx(lipfile)
+function read_lips_xlsx(io, lipfile)
 
-    @info "    read_lips_xlsx: spreadsheet $(lipfile)"
+    println(io, "    read_lips_xlsx: spreadsheet $(lipfile)")
 
     xf = XLSX.readxlsx(lipfile)
     sh = xf["Sheet1"]
 
     column_names = sh["A1:I1"]
-    @info "    read_lips_xlsx: column_names: $(column_names)"
+    println(io, "    read_lips_xlsx: column_names: $(column_names)")
     expected_column_names = ["Age" "Name" "Type" "Continental areas" "All volumes" "CO2 release (min)" "CO2 release (max)" "Degassing duration" "Present day area"]
     column_names == expected_column_names || error("spreadsheet column names don't match expected_column_names=", expected_column_names)
 
@@ -296,24 +296,28 @@ function setup_force_LIPs(m::PB.ReactionMethod, pars, (), cellrange::PB.Abstract
 
     attribute_name == :setup || return nothing
 
+    io = IOBuffer()
+
     lipfile = joinpath(pars.datafolder[], pars.datafile[])
-    @info "setup_force_LIPs! ReactionForce_LIPs: $(PB.fullname(rj)) loading LIP forcing from 'datafolder/datafile'='$(lipfile)'"
+    println(io, "setup_force_LIPs! ReactionForce_LIPs: $(PB.fullname(rj)) loading LIP forcing from 'datafolder/datafile'='$(lipfile)'")
 
-    rj.LIP_data = read_lips_xlsx(lipfile)
+    rj.LIP_data = read_lips_xlsx(io, lipfile)
 
     lipkwargs = (smoothempl=pars.smoothempl[], )
 
     rj.default_lambda = find_default_lambda(pars.present_day_CFB_area[], rj.LIP_data, lipkwargs )
 
-    @info "    found default_lambda=$(rj.default_lambda) "*
-        "to match present_day_CFB_area = $(pars.present_day_CFB_area[]) km^2"
+    println(io, "    found default_lambda=$(rj.default_lambda) "*
+        "to match present_day_CFB_area = $(pars.present_day_CFB_area[]) km^2")
 
     co2releasefield = Symbol(pars.co2releasefield[])
-    @info "    add LIP CO2 release from $(pars.co2releasefield[]) field"
+    println(io, "    add LIP CO2 release from $(pars.co2releasefield[]) field")
 
     empty!(rj.LIPs)
     rj.LIPs = create_LIPs(rj.LIP_data, co2releasefield, rj.default_lambda; lipkwargs...)
-
+
+    @info String(take!(io))
+
     return nothing
 end