Merge pull request #12 from PharmCat/dev

fix df export
PharmCat · Aug 23, 2023 · cd2d8fc · cd2d8fc · PharmCat · Aug 23, 2023
2 parents dfb82a5 + bc5f87e
commit cd2d8fc
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diff --git a/.github/workflows/Tier1.yml b/.github/workflows/Tier1.yml
@@ -8,8 +8,7 @@ on:
       - 'README.md'
       - '.github/**'
       - 'docs/**'
-      - 'validation/**'
-      - 'test/validation**'
+      - 'img/**'
       - 'change.log'
       - '.gitignore'
   pull_request:
@@ -19,24 +18,32 @@ on:
       - 'LICENSE.md'
       - 'README.md'
 jobs:
-  ci:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.6, 1.8, 1]
-        julia-arch: [x64]
-        os: [ubuntu-latest, macOS-latest, windows-latest]
+        version:
+          - '1.6'
+          - '1.8'
+          - '1'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
-      - uses: julia-actions/julia-buildpkg@master
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.julia-version == '1.8' && matrix.arch == 'x64' }}
-      - uses: codecov/codecov-action@v1
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.julia-version == '1.8' && matrix.arch == 'x64' }}
+      - uses: codecov/codecov-action@v3
         with:
-          file: lcov.info
+          files: lcov.info
 
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "MetidaStats"
 uuid = "75cdad26-409a-4e43-8ad7-d54b4fa665a0"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 

diff --git a/src/MetidaStats.jl b/src/MetidaStats.jl
@@ -8,6 +8,7 @@ module MetidaStats
     Tables,
     indsdict!,
     metida_table,
+    metida_table_,
     getid,
     MetidaTable,
     sortbyvec!,

diff --git a/src/descriptive.jl b/src/descriptive.jl
@@ -29,94 +29,6 @@ const STATLIST = [:n,
 :sek, 
 :sum]
 
-#=
-function sortbyvec!(a, vec)
-    sort!(a, by = x -> findfirst(y -> x == y, vec))
-end
-=#
-#=
-ispositive(::Missing) = false
-ispositive(x::AbstractFloat) = isnan(x) ? false : x > zero(x)
-ispositive(x) = x > zero(x)
-################################################################################
-struct SkipNonPositive{T}
-    x::T
-end
-skipnonpositive(itr) = SkipNonPositive(itr)
-
-Base.IteratorEltype(::Type{SkipNonPositive{T}}) where {T} = Base.IteratorEltype(T)
-#Base.eltype(::Type{SkipNonPositive{T}}) where {T} = nonmissingtype(eltype(T))
-function Base.iterate(itr::SkipNonPositive, state...)
-    y = iterate(itr.x, state...)
-    y === nothing && return nothing
-    item, state = y
-    while !ispositive(item)
-        y = iterate(itr.x, state)
-        y === nothing && return nothing
-        item, state = y
-    end
-    item, state
-end
-Base.IndexStyle(::Type{<:SkipNonPositive{T}}) where {T} = IndexStyle(T)
-Base.eachindex(itr::SkipNonPositive) =
-    Iterators.filter(i -> ispositive(@inbounds(itr.x[i])), eachindex(itr.x))
-Base.keys(itr::SkipNonPositive) =
-    Iterators.filter(i -> ispositive(@inbounds(itr.x[i])), keys(itr.x))
-Base.@propagate_inbounds function getindex(itr::SkipNonPositive, I...)
-    v = itr.x[I...]
-    !ispositive(v) && throw(ErrorException("the value at index $I is non positive"))
-    v
-end
-function Base.length(itr::SkipNonPositive)
-    n = 0
-    for i in itr n+=1 end
-    n
-end
-################################################################################
-struct SkipNaNorMissing{T}
-    x::T
-end
-skipnanormissing(itr) = SkipNaNorMissing(itr)
-
-Base.IteratorEltype(::Type{SkipNaNorMissing{T}}) where {T} = Base.IteratorEltype(T)
-#Base.eltype(::Type{SkipNaNorMissing{T}}) where {T} = nonmissingtype(eltype(T))
-function Base.iterate(itr::SkipNaNorMissing, state...)
-    y = iterate(itr.x, state...)
-    y === nothing && return nothing
-    item, state = y
-    while isnanormissing(item)
-        y = iterate(itr.x, state)
-        y === nothing && return nothing
-        item, state = y
-    end
-    item, state
-end
-Base.IndexStyle(::Type{<:SkipNaNorMissing{T}}) where {T} = IndexStyle(T)
-Base.eachindex(itr::SkipNaNorMissing) =
-    Iterators.filter(i -> isnanormissing(@inbounds(itr.x[i])), eachindex(itr.x))
-Base.keys(itr::SkipNaNorMissing) =
-    Iterators.filter(i -> isnanormissing(@inbounds(itr.x[i])), keys(itr.x))
-Base.@propagate_inbounds function getindex(itr::SkipNaNorMissing, I...)
-    v = itr.x[I...]
-    !isnanormissing(v) && throw(ErrorException("The value at index $I is NaN or missing!"))
-    v
-end
-function Base.length(itr::SkipNaNorMissing)
-    n = 0
-    for i in itr n+=1 end
-    n
-end
-=#
-################################################################################
-#=
-length2(x) = length(x)
-function length2(itr::Base.SkipMissing)
-    n = 0
-    for i in itr n+=1 end
-    n
-end
-=#
-################################################################################
 """
     dataimport(data; vars, sort = nothing)
 
@@ -477,7 +389,7 @@ end
 #
 ################################################################################
 
-function MetidaBase.metida_table(obj::DataSet{DS}; sort = nothing, stats = nothing, id = nothing) where DS <: Descriptives
+function MetidaBase.metida_table_(obj::DataSet{DS}; sort = nothing, stats = nothing, id = nothing) where DS <: Descriptives
     idset  = Set(keys(first(obj).data.id))
     resset = Set(keys(first(obj).result))
     if length(obj) > 1
@@ -509,7 +421,7 @@ function MetidaBase.metida_table(obj::DataSet{DS}; sort = nothing, stats = nothi
     end
     mt1 = metida_table((getid(obj, :, c) for c in idset)...; names = idset)
     mt2 = metida_table((obj[:, c] for c in ressetl)...; names = ressetl)
-    MetidaTable(merge(mt1.table, mt2.table))
+    merge(mt1.table, mt2.table)
 end
 
 ################################################################################

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,5 +1,6 @@
 using MetidaStats
 using MetidaBase
+import MetidaBase: metida_table
 using StatsBase
 using Test
 using DataFrames, CSV
@@ -15,15 +16,18 @@ io       = IOBuffer();
 
     di  = MetidaStats.dataimport(ds, vars = [:var1, :var2])
 
-    mt  = MetidaStats.metida_table(des; stats = [:mean, :geom])
+    mt  = metida_table(des; stats = [:mean, :geom])
 
-    mt  = MetidaStats.metida_table(des; stats = [:mean, :geom], id = [:Variable,:row])
+    mt  = MetidaBase.metida_table(des; stats = [:mean, :geom], id = [:Variable,:row])
 
     des2 = MetidaStats.descriptives(ds, [:var1, :var2], [:col, :row]; skipmissing = true, skipnonpositive = true, stats = MetidaStats.STATLIST)
 
+    @test_nowarn DataFrame(des2)
+
     @test des[:, :mean] == des2[:, :mean]
 
-    show(io, des)
+    @test_nowarn show(io, des)
+    @test_nowarn show(io, di)
 
     sort!(des2, [:col, :row, :Variable])
 
@@ -111,7 +115,6 @@ io       = IOBuffer();
     di  = MetidaStats.dataimport(ds, vars = [:var1, :var2], sort = [:col, :row])
     sort!(di, [:col, :row, :Variable])
 
-
     des2[1, :skew] ≈ skewness(di[1].obs)
 
     des2[1, :kurt] ≈ kurtosis(di[1].obs)
@@ -121,6 +124,7 @@ io       = IOBuffer();
     sort!(des3, [:col, :row, :Variable])
     @test des3[2, :mean] ≈ des2[2, :mean]
     @test des3[2, :geom] === NaN
+
     des4 = MetidaStats.descriptives(ds, [:var1], [:col, :row]; skipmissing = false, skipnonpositive = false, stats = MetidaStats.STATLIST)
     sort!(des4, [:col, :row, :Variable])
     @test des4[1, :mean] ≈ des2[1, :mean]