Merge pull request #1 from alanderos91/develop

Minor fixes

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.gitignore

@@ -3,3 +3,4 @@
 *.jl.mem
 docs/build/
 docs/site/
+.ipynb_checkpoints

.travis.yml

@@ -2,14 +2,22 @@ language: julia
 
 os:
   - linux
+  - osx
 
 julia:
   - 0.5
 
 notifications:
   email: false
 
+script:
+#  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+  - julia -e 'Pkg.clone(pwd())'
+  - julia -e 'Pkg.test("BioSimulator", coverage=true)'
+
 after_success:
+  - julia -e 'cd(Pkg.dir("BioSimulator")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+  - julia -e 'cd(Pkg.dir("BioSimulator")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
   - julia -e 'ENV["PYTHON"]=""; Pkg.add("PyPlot"); using PyPlot'
   - julia -e 'Pkg.add("Documenter"); Pkg.add("JSON")'
   - julia -e 'cd(Pkg.dir("BioSimulator")); include(joinpath("docs", "make.jl"))'

README.md

@@ -2,9 +2,9 @@
 
 *A stochastic simulation framework in Julia.*
 
-| **Documentation**                                                               | **Build Status**                                                                                |
-|:-------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------:|
-| [![][docs-stable-img]][docs-stable-url] [![][docs-latest-img]][docs-latest-url] | [![][travis-img]][travis-url] <!---[![][appveyor-img]][appveyor-url]---> <!---[![][codecov-img]][codecov-url]---> |
+| **Documentation**                                                                           | **Build Status**                                                              | **Code Coverage**                                                                            |
+|---------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------|
+| [![Stable][docs-stable-img]][docs-stable-url] [![Latest][docs-latest-img]][docs-latest-url] | [![Travis][travis-img]][travis-url] [![Appveyor][appveyor-img]][appveyor-url] | [![Coverage Status][coveralls-img]][coveralls-url] [![codecov.io][codecov-img]][codecov-url] |
 
 ## Installation
 
@@ -25,8 +25,6 @@ This package is tested against Julia `0.5` on Linux, OS X, and Windows.
 
 ## Contributing
 
-TODO
-
 [docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
 [docs-latest-url]: https://alanderos91.github.io/BioSimulator.jl/latest/
 
@@ -36,12 +34,13 @@ TODO
 [travis-img]: https://travis-ci.org/alanderos91/BioSimulator.jl.svg?branch=master
 [travis-url]: https://travis-ci.org/alanderos91/BioSimulator.jl
 
-[//]: # (setup appveyor)
-[appveyor-img]: https://ci.appveyor.com/api/projects/status/xe0ghtyas12wv555/branch/master?svg=true
-[appveyor-url]: https://ci.appveyor.com/project/alanderos91/biosimulator-jl/branch/master
+[appveyor-img]: https://ci.appveyor.com/api/projects/status/xnug0ey8xpx8we48?svg=true
+[appveyor-url]: https://ci.appveyor.com/project/alanderos91/biosimulator-jl
 
 [issues-url]: https://github.com/alanderos91/BioSimulator.jl/issues
 
-[//]: # (setup codecov)
-[codecov-img]: https://codecov.io/gh/alaneros91/BioSimulator.jl/branch/master/graph/badge.svg
+[coveralls-img]: https://coveralls.io/repos/github/alanderos91/BioSimulator.jl/badge.svg?branch=master
+[coveralls-url]: https://coveralls.io/github/alanderos91/BioSimulator.jl?branch=master
+
+[codecov-img]: https://codecov.io/gh/alanderos91/BioSimulator.jl/branch/master/graph/badge.svg
 [codecov-url]: https://codecov.io/gh/alanderos91/BioSimulator.jl

appveyor.yml

@@ -1,10 +1,13 @@
 environment:
   matrix:
-  - JULIAVERSION: "julialang/bin/winnt/x86/0.3/julia-0.3-latest-win32.exe"
-  - JULIAVERSION: "julialang/bin/winnt/x64/0.3/julia-0.3-latest-win64.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x64/julia-latest-win64.exe"
-
+    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.5/julia-0.5-latest-win32.exe"
+    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.5/julia-0.5-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"
+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"
 branches:
   only:
     - master
@@ -17,10 +20,12 @@ notifications:
     on_build_status_changed: false
 
 install:
+  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
 # Download most recent Julia Windows binary
   - ps: (new-object net.webclient).DownloadFile(
-        $("http://s3.amazonaws.com/"+$env:JULIAVERSION),
+        $env:JULIA_URL,
         "C:\projects\julia-binary.exe")
+  - set PATH=C:\Miniconda3;C:\Miniconda3\Scripts;%PATH%
 # Run installer silently, output to C:\projects\julia
   - C:\projects\julia-binary.exe /S /D=C:\projects\julia