From 174f7db06427a266e0e4535127cf69e732e5e7e3 Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Fri, 19 Oct 2018 11:12:56 -0400
Subject: [PATCH 1/5] Update for Pkg3

---
 .travis.yml           | 17 ++++++++++++++---
 Project.toml          | 24 ++++++++++++++++++++++++
 coverage/Project.toml |  2 ++
 coverage/coverage.jl  |  3 +++
 docs/Project.toml     |  5 +++++
 docs/make.jl          |  2 +-
 6 files changed, 49 insertions(+), 4 deletions(-)
 create mode 100644 Project.toml
 create mode 100644 coverage/Project.toml
 create mode 100644 coverage/coverage.jl
 create mode 100644 docs/Project.toml

diff --git a/.travis.yml b/.travis.yml
index 907fed8..d2ed833 100644
--- a/.travis.yml
+++ b/.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
diff --git a/Project.toml b/Project.toml
new file mode 100644
index 0000000..5822b6e
--- /dev/null
+++ b/Project.toml
@@ -0,0 +1,24 @@
+authors = ["kescobo <kevbonham@gmail.com"]
+desc = "Functions for working with microbial community data"
+keywords = ["microbiology", "microbiome", "biology"]
+license = "MIT"
+name = "Microbiome"
+version = ""
+uuid = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c"
+
+[compat]
+julia = "0.7, 1.0"
+SpatialEcology = "^0.4"
+
+[deps]
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/coverage/Project.toml b/coverage/Project.toml
new file mode 100644
index 0000000..4fbdc47
--- /dev/null
+++ b/coverage/Project.toml
@@ -0,0 +1,2 @@
+[deps]
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
diff --git a/coverage/coverage.jl b/coverage/coverage.jl
new file mode 100644
index 0000000..7277147
--- /dev/null
+++ b/coverage/coverage.jl
@@ -0,0 +1,3 @@
+using Coverage
+ cd(joinpath(@__DIR__, "..")) do
+    Codecov.submit(Codecov.process_folder())
diff --git a/docs/Project.toml b/docs/Project.toml
new file mode 100644
index 0000000..53bc6f8
--- /dev/null
+++ b/docs/Project.toml
@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "~0.19"
diff --git a/docs/make.jl b/docs/make.jl
index 0a57289..ce5f688 100644
--- a/docs/make.jl
+++ b/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,

From b9dc4d8920dc8c9d64456a3707fd56c1f0c43e7c Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Fri, 19 Oct 2018 11:22:07 -0400
Subject: [PATCH 2/5] Add version number

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 5822b6e..f52b797 100644
--- a/Project.toml
+++ b/Project.toml
@@ -3,7 +3,7 @@ desc = "Functions for working with microbial community data"
 keywords = ["microbiology", "microbiome", "biology"]
 license = "MIT"
 name = "Microbiome"
-version = ""
+version = "0.4.0"
 uuid = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c"
 
 [compat]

From fc7bca360e8e8a87e77947f9b78da0876278c708 Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Fri, 19 Oct 2018 11:33:26 -0400
Subject: [PATCH 3/5] Add SpatialEcology to deps

---
 Project.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Project.toml b/Project.toml
index f52b797..776a5ec 100644
--- a/Project.toml
+++ b/Project.toml
@@ -11,6 +11,7 @@ julia = "0.7, 1.0"
 SpatialEcology = "^0.4"
 
 [deps]
+SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"

From a115a72204a5043cb4e7acbc25d79c12d04d1c72 Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Fri, 19 Oct 2018 11:49:37 -0400
Subject: [PATCH 4/5] Add stdlib packages to deps

---
 Project.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Project.toml b/Project.toml
index 776a5ec..99eb085 100644
--- a/Project.toml
+++ b/Project.toml
@@ -11,6 +11,8 @@ julia = "0.7, 1.0"
 SpatialEcology = "^0.4"
 
 [deps]
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Statistics = "1c261c3c-9a38-5c8c-b229-00278e4435fb"
 SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"

From c241d4f62e0d4e2f1729a0a20f269b12f49fbde6 Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Fri, 19 Oct 2018 12:28:24 -0400
Subject: [PATCH 5/5] Fix Project.toml

---
 .gitignore   |  1 +
 Project.toml | 12 +++++++-----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 9385135..59a1109 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ scratch*
 *.jl.mem
 docs/build/
 docs/site/
+Manifest.toml
diff --git a/Project.toml b/Project.toml
index 99eb085..5ee806b 100644
--- a/Project.toml
+++ b/Project.toml
@@ -11,17 +11,19 @@ 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"
-Statistics = "1c261c3c-9a38-5c8c-b229-00278e4435fb"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
 
 [targets]
 test = ["Test"]
+coverage = ["Coverage"]