Merge pull request #26 from kescobo/pkg3

Update for Pkg3

.gitignore

@@ -5,3 +5,4 @@ scratch*
 *.jl.mem
 docs/build/
 docs/site/
+Manifest.toml

.travis.yml

@@ -4,8 +4,8 @@ os:
   - linux
   - osx
 julia:
-  - 1.0
   - 0.7
+  - 1.0
   - nightly
 notifications:
   email: false
@@ -28,5 +28,16 @@ matrix:
 # script:
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("Microbiome"); Pkg.test("Microbiome"; coverage=true)'
 after_success:
-  - julia --project -e 'import Pkg; Pkg.add("Documenter"); include("docs/make.jl")'
-  - julia --project -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia --project=coverage/ -e 'using Pkg; Pkg.instantiate()'
+  - julia --project=coverage/ coverage/coverage.jl
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.0
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();
+                                    Pkg.develop(PackageSpec(path=pwd()))'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip

Project.toml

@@ -0,0 +1,29 @@
+authors = ["kescobo <[email protected]"]
+desc = "Functions for working with microbial community data"
+keywords = ["microbiology", "microbiome", "biology"]
+license = "MIT"
+name = "Microbiome"
+version = "0.4.0"
+uuid = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c"
+
+[compat]
+julia = "0.7, 1.0"
+SpatialEcology = "^0.4"
+
+[deps]
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
+
+[targets]
+test = ["Test"]
+coverage = ["Coverage"]

coverage/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"

coverage/coverage.jl

@@ -0,0 +1,3 @@
+using Coverage
+ cd(joinpath(@__DIR__, "..")) do
+    Codecov.submit(Codecov.process_folder())

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "~0.19"

docs/make.jl

@@ -14,7 +14,7 @@ makedocs(
 
 deploydocs(
     repo = "github.com/BioJulia/Microbiome.jl.git",
-    julia = "0.6",
+    julia = "1.0",
     osname = "linux",
     target = "build",
     deps = nothing,