diff --git a/Project.toml b/Project.toml new file mode 100644 index 0000000..1eab795 --- /dev/null +++ b/Project.toml @@ -0,0 +1,52 @@ +name = "FlashWeave" +uuid = "2be3f83a-7913-5748-9f20-7d448995b934" +keywords = ["metagenomics", "microbiome", "probabilistic-graphical-models", "high-performance-computing", "compositional-data", "metadata", "ecological-network", "co-occurence", "julia", "bioinformatics"] +license = "GPL-3.0" +desc = "Inference of microbial interaction networks from large-scale heterogeneous abundance data" +version = "0.15.0" +authors = ["Janko Tackmann "] + +[deps] +Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" +DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" +DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" +Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" +LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383" +SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622" +SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" + +[compat] +Combinatorics = "1" +DataStructures = "0.17"#[0.12.0]" +Distributions = "0.21"#"0.16, 0.21, 0.22" +FileIO = "1" +HDF5 = "0.12"#"≥ 0.10.0" +JLD2 = "0.1"#"≥ 0.1.0" +JSON = "0.21"#"≥ 0.19.0" +LightGraphs = "1" +SimpleWeightedGraphs = "1" +StatsBase = "0.32"#"[0.25.0, 0.32]" +julia = "1" + +[extras] +DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" +Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" +Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[targets] +test = ["Statistics", "DelimitedFiles", "Test", "SparseArrays", "Random", "Logging", "Distributed"] diff --git a/REQUIRE b/REQUIRE deleted file mode 100644 index e206fdb..0000000 --- a/REQUIRE +++ /dev/null @@ -1,12 +0,0 @@ -julia 1.0 - -Combinatorics 0.7.0 -Distributions 0.16.0 -DataStructures 0.11.0 -FileIO 1.0.0 -HDF5 0.10.0 -JLD2 0.1.0 -JSON 0.19.0 -LightGraphs 1.0.0 -StatsBase 0.25.0 -SimpleWeightedGraphs 1.0.0 diff --git a/test/tests.jl b/test/tests.jl index 7d81988..e0ec9a0 100644 --- a/test/tests.jl +++ b/test/tests.jl @@ -1,6 +1,5 @@ using FlashWeave using FlashWeave: TestResult -#using FileIO using Test using DelimitedFiles @@ -10,8 +9,6 @@ data_clr_nz, mask = FlashWeave.preprocess_data_default(data, "fz_nz", verbose=fa data_bin, mask = FlashWeave.preprocess_data_default(data, "mi", verbose=false, prec=64) data_mi_nz, mask = FlashWeave.preprocess_data_default(data, "mi_nz", verbose=false, prec=64) -#exp_dict = load(joinpath("data", "tests_expected.jld2"))["exp_dict"] - function compare_test_results(r1::FlashWeave.TestResult, r2::FlashWeave.TestResult) isapprox(r1.stat, r2.stat, rtol=1e-2) && isapprox(r1.pval, r2.pval, rtol=1e-2) && r1.df == r2.df && r1.suff_power == r2.suff_power end