Julia 1.0 support

Get tests passing on 1.0 plus some extras

.travis.yml

@@ -3,21 +3,18 @@ language: julia
 os:
   - linux
   - osx
-  - windows
 julia:
+  - 1.0
   - 0.7
   - nightly
 notifications:
   email: false
-git:
-  depth: 99999999
-
+#
 # uncomment the following lines to allow failures on nightly julia
 # (tests will run but not make your overall status red)
 matrix:
  allow_failures:
  - julia: nightly
- - os: windows
 
 ## uncomment and modify the following lines to manually install system packages
 #addons:
@@ -31,10 +28,5 @@ matrix:
 # script:
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("Microbiome"); Pkg.test("Microbiome"; coverage=true)'
 after_success:
-  # push coverage results to Coveralls
-  - julia -e 'cd(Pkg.dir("Microbiome")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
-  # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("Microbiome")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  # build docs
-  - julia -e 'Pkg.add("Documenter")'
-  - julia -e 'cd(Pkg.dir("Microbiome")); include(joinpath("docs", "make.jl"))'
+  - 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())'

README.md

@@ -1,16 +1,18 @@
 ![Microbiome.jl logo](logo.png)
 
-# Microbiome.jl <small>For analysis of microbiome and microbial community data</small>
+## For analysis of microbiome and microbial community data
+
+**Latest Release:**
 
 [![Latest Release](https://img.shields.io/github/release/BioJulia/Microbiome.jl.svg)](https://github.com/BioJulia/Microbiome.jl/releases/latest)
-[![Microbiome](http://pkg.julialang.org/badges/Microbiome_0.6.svg)](http://pkg.julialang.org/?pkg=Microbiome)
-[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/Microbiome.jl/blob/master/LICENSE)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/Microbiome.jl/stable)
-[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/Microbiome.jl/latest)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/Microbiome.jl/blob/master/LICENSE)
 ![BioJulia maintainer: kescobo](https://img.shields.io/badge/BioJulia%20Maintainer-kescobo-blue.svg)
 
-**Development builds:**
+**Development Status**
+
 [![Build Status](https://travis-ci.org/BioJulia/Microbiome.jl.svg?branch=master)](https://travis-ci.org/BioJulia/Microbiome.jl)
+[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/Microbiome.jl/latest)
 
 ## Description
 
@@ -22,13 +24,35 @@ and are imported here.
 
 Install Microbiome from the Julia REPL:
 
+```
+pkg> add Microbiome
+```
+or
+
 ```julia
+julia> using Pkg
 julia> Pkg.add("Microbiome")
 ```
 
 If you are interested in the cutting edge of the development, please check out
 the master branch to try new features before release.
 
+```
+pkg> add Microbiome#master
+```
+
+or
+
 ```julia
-julia> Pkg.checkout("Microbiome")
+julia> using Pkg
+julia> Pkg.add("Microbiome#master")
 ```
+
+## Companion Packages
+
+You might also be interested in some functionality provided by
+[MicrobiomePlots.jl](https://github.com/BioJulia/MicrobiomePlots)
+and [BiobakeryUtils.jl](https://github.com/BioJulia/BiobakeryUtils).
+
+Microbiome.jl uses [EcoBase](https://github.com/EcoJulia/EcoBase.jl) under the hood
+for many of its types and methods.  

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.7-alpha
+julia 0.7
 SpatialEcology 0.4
 StatsBase
 Reexport

appveyor.yml

@@ -1,16 +1,18 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1.0
+  - julia_version: latest
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
 
 ## uncomment the following lines to allow failures on nightly julia
 ## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+matrix:
+  allow_failures:
+  - julia_version: latest
 
 branches:
   only:
@@ -24,24 +26,12 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 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(), \"Microbiome\"); Pkg.build(\"Microbiome\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"Microbiome\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"