Merge branch 'JuliaDynamics:main' into Issue-#399

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 2.16.0
+
+ - Add `load_function` keyword argument to `collect_results` to customize how data is loaded from file before being converted to a dataframe by `collect_results`
+
 # 2.15.0
 
  - Add `wload_kwargs` to `produce_or_load` to allow passing kwargs to `wload`

Project.toml

@@ -1,7 +1,7 @@
 name = "DrWatson"
 uuid = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
 repo = "https://github.com/JuliaDynamics/DrWatson.jl.git"
-version = "2.15.0"
+version = "2.16.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

src/result_collection.jl

@@ -52,6 +52,7 @@ See also [`collect_results`](@ref).
 * `black_list = [:gitcommit, :gitpatch, :script]`: List of keys not to include from result-file.
 * `special_list = []`: List of additional (derived) key-value pairs
   to put in `df` as explained below.
+*  `load_function = wload`: Load function. Defaults to `wload`. You may want to specify a custom load function for example if you store results as a struct and you want the fields of the struct to form the columns of the dataframe. The struct is saved to file as a one-element dictionary so the dataframe will only have a single column. To work around this you could convert it to a dictionary by specifying `load_function = (filename) -> struct2dict(wload(filename)["mykey"])`. This way `collect_results` will receive a `Dict` whose keys are the fields of the struct.
 
 `special_list` is a `Vector` where each entry
 is a derived quantity to be included in `df`. There are two types of entries.
@@ -92,6 +93,7 @@ function collect_results!(filename, folder;
     newfile = false, # keyword only for defining collect_results without !
     rinclude = [r""],
     rexclude = [r"^\b$"],
+    load_function = wload,
     kwargs...)
 
     @assert all(eltype(r) <: Regex for r in (rinclude, rexclude)) "Elements of `rinclude` and `rexclude` must be Regex expressions."
@@ -102,7 +104,7 @@ function collect_results!(filename, folder;
         mtimes = Dict{String,Float64}()
     else
         verbose && @info "Loading existing result collection..."
-        data = wload(filename)
+        data = load_function(filename)
         df = data["df"]
         # Check if we have pre-recorded mtimes (if not this could be because of an old results database).
         if "mtime" ∈ keys(data)
@@ -172,7 +174,7 @@ function collect_results!(filename, folder;
         mtimes[file] = mtime_file
 
         fpath = rpath === nothing ? file : joinpath(rpath, file)
-        df_new = to_data_row(FileIO.query(fpath); kwargs...)
+        df_new = to_data_row(FileIO.query(fpath); load_function=load_function, kwargs...)
         #add filename
         df_new[!, :path] .= file
         if replace_entry
@@ -233,18 +235,17 @@ is_valid_file(file, valid_filetypes) =
     any(endswith(file, v) for v in valid_filetypes)
 
 # Use wload per default when nothing else is available
-function to_data_row(file::File; kwargs...)
+function to_data_row(file::File; load_function=wload, kwargs...)
     fpath = filename(file)
     @debug "Opening $(filename(file)) with fallback wload."
-    return to_data_row(wload(fpath), fpath; kwargs...)
+    return to_data_row(load_function(fpath), fpath; kwargs...)
 end
 # Specialize for JLD2 files, can do much faster mmapped access
-function to_data_row(file::File{format"JLD2"}; kwargs...)
+function to_data_row(file::File{format"JLD2"}; load_function=(filename) -> JLD2.jldopen(filename, "r"), kwargs...)
     fpath = filename(file)
     @debug "Opening $(filename(file)) with jldopen."
-    JLD2.jldopen(filename(file), "r") do data
-        return to_data_row(data, fpath; kwargs...)
-    end
+    data = load_function(fpath)
+    return to_data_row(data, fpath; kwargs...)
 end
 function to_data_row(data, file;
         white_list = collect(keys(data)),

test/update_results_tests.jl

@@ -64,6 +64,22 @@ cres_relpath = collect_results!(relpathname, folder;
     rpath = projectdir())
 @info all(startswith.(cres[!,"path"], "data"))
 
+struct dummy
+    a::Float64
+    b::Int64
+    c::Matrix{Float64}
+end
+_dummy_matrix = rand(3,3)
+_dummy = dummy(1.0, 1, _dummy_matrix)
+wsave(datadir("dummy.jld2"), "dummy", _dummy)
+
+actual_dataframe = collect_results(datadir(), rinclude=[r"dummy.jld2"], load_function=(filename) -> struct2dict(wload(filename)["dummy"]))
+_dataframe_vector = Vector{Union{Missing, Matrix{Float64}}}(undef, 1)
+_dataframe_vector[1] = _dummy_matrix
+expected_dataframe = DataFrame(a = 1.0, b = 1, c = _dataframe_vector, path = datadir("dummy.jld2"))
+
+@test actual_dataframe == expected_dataframe
+
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