clean up after name changel

EcoJulia · Sep 28, 2016 · 95cc813 · 95cc813
1 parent 5f0ac60
commit 95cc813
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Showing 11 changed files with 549 additions and 2,458 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,4 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
-*.DS_Store
-.DS_Store
-.DS_Store
-
 .DS_Store
diff --git a/.travis.yml b/.travis.yml
@@ -11,4 +11,4 @@ notifications:
 # uncomment the following lines to override the default test script
 #script:
 #  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-#  - julia -e 'Pkg.clone(pwd()); Pkg.build("MacroEcology"); Pkg.test("MacroEcology"; coverage=true)'
+#  - julia -e 'Pkg.clone(pwd()); Pkg.build("SpatialEcology"); Pkg.test("SpatialEcology"; coverage=true)'
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,4 +1,4 @@
-The MacroEcology.jl package is licensed under the MIT "Expat" License:
+The SpatialEcology.jl package is licensed under the MIT "Expat" License:
 
 > Copyright (c) 2016: Michael K. Borregaard.
 >

diff --git a/REQUIRE b/REQUIRE
@@ -4,4 +4,5 @@ RecipesBase
 NamedArrays
 Shapefile
 DataFrames
-Bio
+Reexport
+#Bio
diff --git a/appveyor.yml b/appveyor.yml
@@ -28,7 +28,7 @@ build_script:
 # Need to convert from shallow to complete for Pkg.clone to work
   - IF EXIST .git\shallow (git fetch --unshallow)
   - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"MacroEcology\"); Pkg.build(\"MacroEcology\")"
+      Pkg.clone(pwd(), \"SpatialEcology\"); Pkg.build(\"SpatialEcology\")"
 
 test_script:
-  - C:\projects\julia\bin\julia --check-bounds=yes -e "Pkg.test(\"MacroEcology\")"
+  - C:\projects\julia\bin\julia --check-bounds=yes -e "Pkg.test(\"SpatialEcology\")"
diff --git a/doc/.ipynb_checkpoints/Testing SpatialEcology plotting-checkpoint.ipynb b/doc/.ipynb_checkpoints/Testing SpatialEcology plotting-checkpoint.ipynb
diff --git a/doc/Testing SpatialEcology plotting.ipynb b/doc/Testing SpatialEcology plotting.ipynb
diff --git a/mamob.jld b/mamob.jld
diff --git a/scratch.jl b/scratch.jl
@@ -11,7 +11,7 @@ mama = Assemblage(mam)
 using JLD
 
 jldopen("mamobj.jld", "w") do file
-   addrequire(file, MacroEcology)
+   addrequire(file, SpatialEcology)
    write(file, "mam", mama)
 end
 

diff --git a/src/SpatialEcology.jl b/src/SpatialEcology.jl
@@ -1,17 +1,20 @@
 __precompile__()
 module SpatialEcology
 
-using DataFrames
-import Bio.Phylo
-using NamedArrays
+using Reexport
+@reexport using DataFrames
+@reexport using NamedArrays
+
+#import Bio.Phylo
+import RecipesBase
 import Shapefile
 import Base: getindex, setindex!, size, show, summary
 
 include("DataTypes.jl")
 include("Constructor_helperfunctions.jl")
 include("Constructors.jl")
 include("Commatrix_functions.jl")
-include("Gettersandsetters.jl")
+include("GetandSetdata.jl")
 include("Gridfunctions.jl")
 include("Subsetting.jl")
 #include("PlotRecipes.jl")
@@ -21,6 +24,5 @@ export nspecies, nsites, occupancy, richness, records, sitenames, specnames
 export setindex!, getindex, size, show, summary
 export coords, subset!, subset, addshape!, deleteshape!
 export xcells, ycells, cells, xmin, xmax, ymin, ymax, xrange, yrange, xcellsize, ycellsize, cellsize, boundingbox #it is possible that I will export none of these
-#export DataFrames, NamedArrays
 
 end # module
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,4 +1,4 @@
-using MacroEcology
+using SpatialEcology
 using Base.Test
 
 # write your own tests here
@@ -8,5 +8,3 @@ using Base.Test
 function tes{T <: Union{Int, Bool}}(x::AbstractMatrix{T})
     println("success")
 end
-
-tst = OccMatrix(zeros(Int, 2, 2))