Dev (#21)

* plot update (ldict)

* plotting

* docs pkg

* docs, minor fix

* docs

* show ds

* show res ds

* save plots

* version bump

* update

.github/workflows/Documenter.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-22.04
     timeout-minutes: 40
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Update
         run: sudo apt-get update
       - name: Install Pandoc

.github/workflows/Tier1.yml

@@ -36,15 +36,26 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.version == '1' && matrix.arch == 'x64' }}
         with:
-          files: lcov.info
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.10"
+version = "0.5.11"
 
 
 

docs/src/details.md

@@ -10,6 +10,9 @@ ll = LimitRule(;lloq = 0.1, btmax = 0.0, atmax = NaN, nan = NaN, rm = true)
 It means that all values below `lloq` will be replaced by `btmax` before Tmax and replaced by `atmax` after Tmax; `NaN` values will be replaced by `nan`. If `rm` is `true`, all `NaN` values will be deleted. 
 
 
+See also: [`applylimitrule!`](@ref).
+
+
 ## Calculation steps for PK NCA
 
 ### Step 1

src/MetidaNCA.jl

@@ -22,13 +22,21 @@ uniqueidlist,
 indsdict!,
 subset
 
+using MetidaBase.Requires
+
 export pkimport, upkimport, pdimport, nca!, nca, DoseTime, ElimRange, LimitRule, NoPageSort,
 auc_sparse,
 setdosetime!, setkelauto!, setkelrange!, applylimitrule!, setbl!, setth!,
 pkplot,
 getkeldata, getkelauto, getkelrange, getdosetime, getbl, getth, subset
 metida_table
 
+function __init__()
+    @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
+        import Plots:savefig
+    end
+end
+
 const LOG2 = log(2)
 
     include("types.jl")

src/plots.jl

@@ -375,6 +375,9 @@ end
     pagesort::Union{Nothing, Symbol, AbstractVector{Symbol}, NoPageSort} = nothing,
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
+    ldict = nothing,
+    savepath::Union{Nothing, AbstractString} = nothing,
+    namepref::Union{Nothing, AbstractString} = nothing,
     kwargs...) where T <: AbstractSubject
 
 PK plot for subject set.
@@ -383,7 +386,9 @@ PK plot for subject set.
 * `pagesort` - different pages by this id key;
 * `filter` - use only subjects if filter ⊆ subject id;
 * `uylims` - same ylims for all dataset;
-* `ldict` - Dict with labels for replace.
+* `ldict` - Dict with labels for replace;
+* `savepath` - path for plot saving;
+* `namepref` - name prefix for saving files.
 
 Use `pagesort = MetidaNCA.NoPageSort()` to prevent page plotting.
 """
@@ -393,7 +398,9 @@ function pkplot(data::DataSet{T};
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
     ldict = nothing,
-    savepng = nothing,
+    savepath::Union{Nothing, AbstractString} = nothing,
+    namepref::Union{Nothing, AbstractString} = nothing,
+
     kwargs...) where T <: AbstractSubject
 
     kwargs = Dict{Symbol, Any}(kwargs)
@@ -424,9 +431,8 @@ function pkplot(data::DataSet{T};
             kwargs[:legend] = false
         end
     end
-
+    p = []
     if isnothing(typesort) && isnothing(pagesort)
-        p = []
         printtitle = false
         if !(:title in k)
             printtitle = true
@@ -440,20 +446,38 @@ function pkplot(data::DataSet{T};
             end
             push!(p, pkplot(subj; kwargs...))
         end
-        return p
     elseif !isnothing(pagesort) && !isa(pagesort, NoPageSort)  
         if isa(pagesort, Symbol) pagesort = [pagesort] end
-        p = []
         pagelist = uniqueidlist(data, pagesort)
         for id in pagelist
             push!(p, pageplot(data, id, typelist; ldict, kwargs...))
         end
-        return p
     else
         if !(:title in k) && !isnothing(filter)
             kwargs[:title] = plotlabel(filter)
         end
-        return pageplot(data, nothing, typelist; ldict, kwargs...)
+        push!(p,pageplot(data, nothing, typelist; ldict, kwargs...))
+    end
+
+    if !isnothing(savepath)
+        if @isdefined savefig
+            if isfile(savepath)
+                error("File found on this path...")
+            elseif !isdir(savepath)
+                mkpath(savepath)
+            end
+            if isnothing(namepref) namepref = "plot" end
+            for i = 1: length(p) 
+                savefig(p[i], joinpath(savepath, namepref*"_$(i).png"))
+            end
+        else
+            @warn "savefig not defined, install Plots.jl for plot writing... plots NOT saved..."
+        end
+    end
+    if length(p) > 1
+        return p
+    else
+        return p[1]
     end
 end
 

src/show.jl

@@ -71,7 +71,8 @@ end
 function Base.show(io::IO, obj::DataSet{ST}) where ST <: AbstractSubject
     println(io, "DataSet: $(subject_type_str(ST))")
     println(io, "Length: $(length(obj))")
-    for i = 1:length(obj)
+    lo = min(length(obj), 20)
+    for i = 1:lo
         print(io, "Subject $(i): ")
         if length(obj[i].id) > 0
             for (k, v) in obj[i].id
@@ -82,6 +83,9 @@ function Base.show(io::IO, obj::DataSet{ST}) where ST <: AbstractSubject
             println(io, "-")
         end
     end
+    if lo < length(obj) 
+        printstyled(io, "$(length(obj) - lo) subjects omitted... \n"; color = :blue)
+    end
 end
 
 function Base.show(io::IO, obj::T) where T <: NCAResult
@@ -92,7 +96,8 @@ end
 function Base.show(io::IO, obj::DataSet{Res}) where Res <: NCAResult
     println(io, "DataSet: PK/PD NCA result")
     println(io, "Length: $(length(obj))")
-    for i = 1:length(obj)
+    lo = min(length(obj), 20)
+    for i = 1:lo
         print(io, "Subject $(i): ")
         if length(obj[i].data.id) > 0
             for (k, v) in obj[i].data.id
@@ -103,4 +108,7 @@ function Base.show(io::IO, obj::DataSet{Res}) where Res <: NCAResult
             println(io, "-")
         end
     end
+    if lo < length(obj) 
+        printstyled(io, "$(length(obj) - lo) subjects omitted... \n"; color = :blue)
+    end
 end