up TargetedEstimation dep

Manifest.toml

@@ -2379,8 +2379,8 @@ version = "1.10.0"
 
 [[deps.TargetedEstimation]]
 deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "HDF5", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "MultipleTesting", "Optim", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"]
-git-tree-sha1 = "98ae29ef85f5bbeb088b1003c58ced0e0e6104d3"
-repo-rev = "acc1de14e05517b6b5e1fe441526f097edb8eb19"
+git-tree-sha1 = "9cf3987b177a22ca374b9b11ab7a89de5bdd56b3"
+repo-rev = "f4620ef1565f71019fa539e746ff109727e6671c"
 repo-url = "https://github.com/TARGENE/TargetedEstimation.jl"
 uuid = "2573d147-4098-46ba-9db2-8608d210ccac"
 version = "0.9.0"

src/cli.jl

@@ -109,8 +109,8 @@ function cli_settings()
     end
 
     @add_arg_table s["summary-plots"] begin
-        "results-prefix"
-            help = "Prefix to result files."
+        "results-file"
+            help = "Path to the results file."
             required = true
 
         "--outprefix"
@@ -201,7 +201,7 @@ function julia_main()::Cint
         )
     elseif cmd == "summary-plots"
         summary_plots(
-            cmd_settings["results-prefix"],
+            cmd_settings["results-file"],
             outprefix=cmd_settings["outprefix"],
             verbosity=cmd_settings["verbosity"],
         )

src/inputs_from_config.jl

@@ -121,16 +121,20 @@ function estimands_from_flat_list(estimands_configs, dataset, variants, outcomes
     return estimands
 end
 
+function treatments_from_variant(variant::Symbol, dataset)
+    variant_levels = sort(levels(dataset[!, variant], skipmissing=true))
+    return NamedTuple{(variant,)}([variant_levels])
+end
+
 function gwas_estimands(dataset, variants, outcomes, confounders; 
     outcome_extra_covariates=[],
     positivity_constraint=0.,
     verbosity=0,
     )
     estimands = []
     verbosity > 0 && @info(string("Generating GWAS estimands."))
-    for v in variants
-        variant_levels = sort(levels(dataset[!, v], skipmissing=true))
-        treatments = NamedTuple{(Symbol(v),)}([variant_levels])
+    for variant in Symbol.(variants)
+        treatments = treatments_from_variant(variant, dataset)
         try_append_new_estimands!(
             estimands, 
             dataset, 

src/plots.jl

@@ -5,22 +5,9 @@ log10_uniform_quantiles(n) = -log10.(collect(LinRange(0., 1., n + 1))[2:end])
 
 log10_beta_quantiles(n, alpha) = -log10.([quantile(Beta(k, n + 1 − k), alpha) for k in 1:n])
 
-function read_results_file(file)
-    jldopen(file) do io
-        return reduce(vcat, (io[key] for key in keys(io)))
-    end
-end
-
-function read_results_files(prefix)
-    directory_, prefix_ = splitdir(prefix)
-    directory = directory_ == "" ? "." : directory_
-    matching_files = [joinpath(directory_, file) for file in readdir(directory) if startswith(file, prefix_)]
-    reduce(vcat, (read_results_file(file) for file in matching_files))
-end
-
-function load_results(file_or_prefix; verbosity=0)
+function load_results(resultsfile; verbosity=0)
     verbosity > 0 && @info "Loading results."
-    results = isfile(file_or_prefix) ? read_results_file(file_or_prefix) : read_results_files(file_or_prefix)
+    results = jldopen(io -> io["results"], resultsfile)
     estimators = collect(key for key ∈ keys(first(results)) if key !== :SAMPLE_IDS)
     results_df = DataFrame([[r[id] for r in results] for id in 1:length(estimators)], estimators)
     for estimator in estimators
@@ -57,10 +44,10 @@ function qqplot(results, outprefix)
     return fig
 end
 
-function summary_plots(results_prefix;
+function summary_plots(results_file;
     outprefix="final",
     verbosity=0
     )
-    results = load_results(results_prefix; verbosity=verbosity)
+    results = load_results(results_file; verbosity=verbosity)
     qqplot(results, outprefix)
 end

test/inputs_from_gwas_config.jl

@@ -104,4 +104,5 @@ end
 end
 
 end
+
 true

test/runtests.jl

@@ -2,11 +2,12 @@ using TargeneCore
 using Test
 
 TESTDIR = joinpath(pkgdir(TargeneCore), "test")
-
-@test include(joinpath(TESTDIR, "utils.jl"))
-@test include(joinpath(TESTDIR, "dataset.jl"))
-@test include(joinpath(TESTDIR, "plots.jl"))
-@test include(joinpath(TESTDIR, "confounders.jl"))
-@test include(joinpath(TESTDIR, "inputs_from_estimands.jl"))
-@test include(joinpath(TESTDIR, "inputs_from_config.jl"))
-@test include(joinpath(TESTDIR, "inputs_from_gwas_config.jl"))
+@testset "Test TargeneCore" begin
+    @test include(joinpath(TESTDIR, "utils.jl"))
+    @test include(joinpath(TESTDIR, "dataset.jl"))
+    @test include(joinpath(TESTDIR, "plots.jl"))
+    @test include(joinpath(TESTDIR, "confounders.jl"))
+    @test include(joinpath(TESTDIR, "inputs_from_estimands.jl"))
+    @test include(joinpath(TESTDIR, "inputs_from_config.jl"))
+    @test include(joinpath(TESTDIR, "inputs_from_gwas_config.jl"))
+end

test/testutils.jl

@@ -109,36 +109,16 @@ end
 
 function save(estimates; prefix="tmle_output")
     outputs = TargetedEstimation.Outputs(
-        json=TargetedEstimation.JSONOutput(filename=prefix*".json"),
-        jls=TargetedEstimation.JLSOutput(filename=prefix*".jls"),
-        hdf5=TargetedEstimation.HDF5Output(filename=prefix*".hdf5")
+        json=prefix*".json",
+        jls=prefix*".jls",
+        hdf5=prefix*".hdf5"
     )
-    TargetedEstimation.initialize(outputs)
-    batches = collect(Iterators.partition(estimates, 2))
-    nbatches = length(batches)
-    for (batchid, batch) in enumerate(batches)
-        # Append JSON Output
-        TargetedEstimation.update_file(outputs.json, batch; finalize=nbatches==batchid)
-        # Append JLS Output
-        TargetedEstimation.update_file(outputs.jls, batch)
-        # Append HDF5 Output
-        TargetedEstimation.update_file(outputs.hdf5, batch)
-    end
+    TargetedEstimation.write(outputs, estimates)
 end
 
 make_fake_outputs(estimates_generator=make_estimates; prefix="tmle_output") = 
     save(estimates_generator(); prefix=prefix)
 
-function clean(;prefix="tmle_output")
-    dir_, prefix_ = splitdir(prefix)
-    dir = dir_ == "" ? "." : dir_
-    for filename in readdir(dir)
-        if startswith(filename, prefix_)
-            rm(joinpath(dir_, filename))
-        end
-    end
-end
-
 ### Fixtures for inputs_from_estimands
 
 function make_estimands_configuration()