Doctests for Julia 0.7/1.0

Author: diegozea

Diff for: .travis.yml

@@ -5,6 +5,8 @@ os:
 julia:
   - 0.7
   - 1.0
+  - nightly
+
 notifications:
   email: false
 
@@ -16,4 +18,4 @@ after_success:
   - julia -e 'using Pkg; using PairwiseListMatrices; cd(dirname(pathof(PairwiseListMatrices))); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
   - julia -e 'using Pkg; Pkg.add("Documenter")'
   - julia -e 'using Pkg; Pkg.add("Plots"); Pkg.add("GR")' # Plots
-  - julia -e 'cd(dirname(pathof(PairwiseListMatrices))); include(joinpath("docs", "make.jl"))'
+  - julia -e 'cd(dirname(pathof(PairwiseListMatrices))); include(joinpath("..", "docs", "make.jl"))'

Diff for: NEWS.md

@@ -7,6 +7,9 @@ PairwiseListMatrices v0.6 was the last version with Julia 0.6 support.
 
 * `writecsv` changed to `writedlm` using `delim=','`.   
 
+* A type parameter to indicate the wrapped matrix type was added to
+`NamedResidueMatrix`, which is now `NamedResidueMatrix{Array{Residue,2}}`.  
+
 ### Changes from v0.5 to v0.6
 
 PairwiseListMatrices v0.6 requires Julia v0.6.

Diff for: REQUIRE

@@ -1,3 +1,3 @@
-julia 0.7 1.0
+julia 0.7
 NamedArrays
 RecipesBase

Diff for: appveyor.yml

@@ -2,6 +2,7 @@ environment:
   matrix:
   - julia_version: 0.7
   - julia_version: 1.0
+  - julia_version: latest
 
 platform:
   - x86 # 32-bit

Diff for: docs/make.jl

@@ -1,6 +1,7 @@
 using Documenter, PairwiseListMatrices
 
 makedocs(
+    doctest = true,
     format = :html,
     sitename = "PairwiseListMatrices",
     modules = [PairwiseListMatrices],
@@ -13,7 +14,6 @@ makedocs(
 deploydocs(
     repo   = "github.com/diegozea/PairwiseListMatrices.jl.git",
     target = "build",
-    julia  = "0.6",
     deps   = nothing,
     make   = nothing
 )

Diff for: src/PairwiseListMatrices.jl

@@ -1,6 +1,12 @@
 __precompile__()
 
+"""
+This package allows you to use a pairwise list as a symmetric matrix.
 
+```julia
+using PairwiseListMatrices
+```
+"""
 module PairwiseListMatrices
 
 # standard libraries
@@ -28,18 +34,10 @@ export  @iterateupper,
         from_table, to_table,
         to_dict,
         join,
-        to_dataframe, from_dataframe
+        writedlm
 
 include("macros.jl")
 include("pairwiselistmatrix.jl")
 include("plotrecipes.jl")
 
-function to_dataframe(args...)
-    throw(ErrorException("Deprecated function, use DataFrame(to_dict(args...)) instead."))
-end
-
-function from_dataframe(args...)
-    throw(ErrorException("Deprecated function, use from_table(args...) instead."))
-end
-
 end

Diff for: src/macros.jl

@@ -6,9 +6,11 @@ In the body `list` will be the list field of the `PairwiseListMatrix` and `k` th
 over that list. Other variables should be interpolated in a quote. You must not modify the
 value of `k`.
 
-```julia
+```jldoctest
+julia> using PairwiseListMatrices
+
 julia> PLM = PairwiseListMatrix([1,2,3], false)
-3×3 PairwiseListMatrices.PairwiseListMatrix{Int64,false,Array{Int64,1}}:
+3×3 PairwiseListMatrix{Int64,false,Array{Int64,1}}:
  0  1  2
  1  0  3
  2  3  0
@@ -37,17 +39,19 @@ second is the body of the loop. In the body `diag` will be the diag field of the
 `PairwiseListMatrix` and `k` the index over that vector.
 Other variables should be interpolated in a quote. You must not modify the value of `k`.
 
-```julia
+```jldoctest
+julia> using PairwiseListMatrices
+
 julia> PLM = PairwiseListMatrix([1,2,3], false)
-3×3 PairwiseListMatrices.PairwiseListMatrix{Int64,false,Array{Int64,1}}:
+3×3 PairwiseListMatrix{Int64,false,Array{Int64,1}}:
  0  1  2
  1  0  3
  2  3  0
 
 julia> @iteratediag PLM diag[k] += 10k
 
 julia> PLM
-3×3 PairwiseListMatrices.PairwiseListMatrix{Int64,false,Array{Int64,1}}:
+3×3 PairwiseListMatrix{Int64,false,Array{Int64,1}}:
  10   1   2
   1  20   3
   2   3  30
@@ -75,9 +79,11 @@ You can also use the respective `i` and `j` indexes for that position `k` in the
 triangular part of the matrix. Other variables should be interpolated in a quote.
 You must not modify the values of `i`, `j` or `k`.
 
-```julia
+```jldoctest
+julia> using PairwiseListMatrices
+
 julia> PLM = PairwiseListMatrix([1,2,3], true)
-2×2 PairwiseListMatrices.PairwiseListMatrix{Int64,true,Array{Int64,1}}:
+2×2 PairwiseListMatrix{Int64,true,Array{Int64,1}}:
  1  2
  2  3
 
@@ -86,7 +92,9 @@ julia> mat = zeros(Int, 2, 2)
  0  0
  0  0
 
-julia> @iterateupper PLM true :(\$mat)[i,j] = list[k]
+julia> let mat = mat # To avoid using global
+           @iterateupper PLM true :(\$mat)[i,j] = list[k]
+       end
 
 julia> mat
 2×2 Array{Int64,2}: