Update dependencies, clean debug statement

Project.toml

@@ -37,8 +37,15 @@ JSON = "0.21"
 Graphs = "1, 1.6"
 SimpleWeightedGraphs = "1, 1.1, 1.2"
 StatsBase = "0.32, 0.33"
-julia = "1.6"
 StableRNGs = "1"
+julia = "1.6"
+DelimitedFiles = "1.6"
+Distributed = "1.6"
+Logging = "1.6"
+Random = "1.6"
+SparseArrays = "1.6"
+Statistics = "1.6"
+Test = "1.6"
 
 [extras]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"

README.md

@@ -133,7 +133,7 @@ BIOM 2.0 ([description](http://biom-format.org/documentation/format_versions/bio
 
 ### Meta data tables ###
 
-Meta data should generally be provided as delimited format (see for instance [example1](https://github.com/meringlab/FlashWeave.jl/blob/master/test/data/HMP_SRA_gut/HMP_SRA_gut_tiny_meta.tsv) or [example2](https://github.com/meringlab/FlashWeave.jl/blob/master/test/data/HMP_SRA_gut/HMP_SRA_gut_tiny_meta_oneHotTest.tsv)), separately from the OTU table. Notably, this implies that FlashWeave does not yet support reading meta data directly from BIOM files, but requires a separate delimited meta data file (support will be added in an upcoming version).
+Meta data should generally be provided as delimited format (see for instance [example1](https://github.com/meringlab/FlashWeave.jl/blob/master/test/data/HMP_SRA_gut/HMP_SRA_gut_tiny_meta.tsv) or [example2](https://github.com/meringlab/FlashWeave.jl/blob/master/test/data/HMP_SRA_gut/HMP_SRA_gut_tiny_meta_oneHotTest.tsv)), separately from the OTU table. Notably, this implies that FlashWeave does not yet support reading meta data directly from BIOM files, but requires a separate delimited meta data file (support will be added in an upcoming version). **NOTE: OTU table and metadata table must be aligned such that each row corresponds to the same sample in both files (i.e. sample 1 data is found in row 1 in both files, etc.).**
 
 For JLD2, however, you can already provide HDF5 keys linked to meta data tables (and optionally headers):
 

src/learning.jl

@@ -13,7 +13,7 @@ function prepare_lgl(data::AbstractMatrix{ElType}, test_name::String, time_limit
 
 
     if time_limit == -1.0
-        if parallel == "multi_il"
+        if parallel == "multi_il" && max_k > 0
             time_limit = round(log2(size(data, 2)))
             verbose && println("Setting 'time_limit' to $time_limit s.")
         else

src/tests.jl

@@ -61,14 +61,7 @@ function test(X::Int, Y::Int, data::AbstractMatrix{<:Integer}, test_obj::Abstrac
             pval = 1.0
             suff_power = false
         else
-            try
-                mi_stat = mutual_information(sub_ctab, levels_x, levels_y, test_obj.marg_i, test_obj.marg_j)
-            catch DomainError
-                display(test_obj.ctab)
-                display(sub_ctab)
-                @show X Y test_obj.marg_i test_obj.marg_j levels_x levels_y n_obs
-                error("debug")
-            end
+            mi_stat = mutual_information(sub_ctab, levels_x, levels_y, test_obj.marg_i, test_obj.marg_j)
 
             df = adjust_df(test_obj.marg_i, test_obj.marg_j, levels_x, levels_y)
             pval = mi_pval(abs(mi_stat), df, n_obs)