Merge pull request #10 from OpenMendel/Julia-0.7

upgrade to Julia 0.7+

Author: Hua-Zhou

.travis.yml

@@ -4,24 +4,34 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 matrix:
   allow_failures:
     - julia: nightly
 addons:
     apt_packages:
         - gfortran
-# uncomment the following lines to override the default test script
-script:
-  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-  - julia --check-bounds=yes --depwarn=no -e 'Pkg.clone(pwd()); Pkg.build("VarianceComponentModels"); Pkg.test("VarianceComponentModels"; coverage=true)'
-after_success:
-  - julia -e 'Pkg.add("Coverage"); cd(Pkg.dir("VarianceComponentModels")); using Coverage; Coveralls.submit(Coveralls.process_folder()); Codecov.submit(process_folder())'
-  - julia -e 'Pkg.add("Documenter"); cd(Pkg.dir("VarianceComponentModels")); include(joinpath("docs", "make.jl"))'
 notifications:
-  email:
-    on_success: change
-    on_failure: always
-  recipients:
-    - huazhou@ucla.edu
+  email: false
+git:
+  depth: 99999999
+
+# before_script: # install dependent unregistered packages
+#   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+#   - julia -e 'using Pkg; Pkg.add([PackageSpec(url="https://github.com/OpenMendel/VarianceComponentModels.jl.git", rev="juliav0.7"), PackageSpec(url="https://github.com/OpenMendel/VarianceComponentModels.jl.git", rev="master")]);'
+after_script:  # TODO: change to after_success once https://github.com/JuliaLang/julia/issues/28306 is fixed
+  # push coverage results to Codecov and Coveralls
+  - julia -e 'using Pkg, VarianceComponentModels; cd(joinpath(dirname(pathof(VarianceComponentModels)), "..")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder()); Coveralls.submit(process_folder())'
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.0
+      os: osx
+      script:
+        - julia -e 'using Pkg; Pkg.add("Documenter")'
+        - julia -e 'using VarianceComponentModels; include(joinpath(dirname(pathof(VarianceComponentModels)), "..", "docs", "make.jl"))'
+      after_script: skip
+      after_success: skip

Project.toml

@@ -0,0 +1,20 @@
+name = "VarianceComponentModels"
+uuid = "813005db-34b4-5f71-be9e-1bbf0a1d8f1c"
+keywords = ["variance components model", "GWAS"]
+author = ["Hua Zhou <huazhou@ucla.edu>", "OpenMendel Team"]
+version = "0.1.0"
+
+[deps]
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+MathProgBase = "fdba3010-5040-5b88-9595-932c9decdf73"
+Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[targets]
+test = ["Test", "Random"]

README.md

@@ -8,15 +8,20 @@ This [Julia](http://julialang.org/) package provides computational routines for
 
 ## Installation
 
-Within Julia, use the package manager to install VarianceComponentModels:
+This package requires Julia v0.7.0 or later, which can be obtained from
+https://julialang.org/downloads/ or by building Julia from the sources in the
+https://github.com/JuliaLang/julia repository.
 
-    Pkg.clone("https://github.com/OpenMendel/VarianceComponentModels.jl.git")
-
-This package supports Julia v0.5 and v0.6.
+The package has not yet been registered and must be installed using the repository location.
+Start julia and use the `]` key to switch to the package manager REPL
+```julia
+(v0.7) pkg> add https://github.com/OpenMendel/VarianceComponentModels.jl.git#Julia-0.7
+```
+Use the backspace key to return to the Julia REPL.
 
 ## Citation
 
-If you use this analysis package in your research, please cite the following reference in the resulting publications:
+If you use [OpenMendel](https://openmendel.github.io) analysis packages in your research, please cite the following reference in the resulting publications:
 
 *Lange K, Papp JC, Sinsheimer JS, Sripracha R, Zhou H, Sobel EM (2013) Mendel: The Swiss army knife of genetic analysis programs. Bioinformatics 29:1568-1570.*
 

REQUIRE

@@ -1,39 +1,37 @@
 environment:
   matrix:
-  - JULIAVERSION: "julialang/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIAVERSION: "julialang/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1
+  - julia_version: nightly
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
 
 branches:
   only:
     - master
     - /release-.*/
 
-matrix:
-  allow_failures:
-    - JULIAVERSION: "julianightlies/bin/winnt/x86/julia-latest-win32.exe"
-    - JULIAVERSION: "julianightlies/bin/winnt/x64/julia-latest-win64.exe"
-
 notifications:
   - provider: Email
     on_build_success: false
     on_build_failure: false
     on_build_status_changed: false
 
 install:
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $("http://s3.amazonaws.com/"+$env:JULIAVERSION),
-        "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(), \"VarianceComponentModels\"); Pkg.build(\"VarianceComponentModels\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia --check-bounds=yes -e "Pkg.test(\"VarianceComponentModels\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"