Merge branch 'release/v0.15.0'

Author: DilumAluthge

.codecov.yml

@@ -1 +1 @@
-comment: false
+comment: true

.gitignore

@@ -1,4 +1,4 @@
-### Directories to ignore:
+##### Directories to ignore:
 
 *.ipynb_checkpoints/
 
@@ -12,7 +12,7 @@ input/
 
 output/
 
-### Files to ignore:
+##### Files to ignore:
 
 .DS_Store
 

.travis.yml

@@ -1,18 +1,21 @@
 addons:
     apt:
         packages:
-        - gfortran
         - pdf2svg
         - pgf
         - poppler-utils
         - texlive-binaries
         - texlive-latex-base
         - texlive-latex-extra
         - texlive-pictures
-        
+
+branches:
+    except:
+        - gh-pages
+
 git:
     depth: 99999999
-    
+
 julia:
     - 0.6
     - nightly
@@ -45,10 +48,10 @@ before_install:
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi
 
 script:
-    - julia --check-bounds=yes --color=yes -e 'Pkg.clone(pwd())'
+    - julia --check-bounds=yes --color=yes -e 'Pkg.clone(pwd(), "PredictMD")'
     - julia --check-bounds=yes --color=yes -e 'Pkg.build("PredictMD")'
     - julia --check-bounds=yes --color=yes -e 'import PredictMD'
-    - julia --check-bounds=yes --color=yes -e 'Pkg.test("PredictMD", coverage=true)'
+    - julia --check-bounds=yes --color=yes -e 'Pkg.test("PredictMD"; coverage=true)'
 
 after_success:
     - julia --check-bounds=yes --color=yes -e 'cd(Pkg.dir("PredictMD")); include(joinpath("docs", "deploy_docs.jl"))'

CONTRIBUTING.md

@@ -238,11 +238,15 @@ An commit message editor will open. Type an appropriate commit message (e.g. "Bu
 git push origin release/v30.771.0
 ```
 
-**Step 10:** Wait for the Travis tests to pass. You can check on the status of the tests by going to [https://travis-ci.org/bcbi/PredictMD.jl/branches](https://travis-ci.org/bcbi/PredictMD.jl/branches) and clicking on your release branch.
+**Step 10:** Wait for all of the tests to pass. You can check on the status of the tests by going to [https://github.com/bcbi/PredictMD.jl/branches/yours](https://github.com/bcbi/PredictMD.jl/branches/yours) and scrolling down to find your release branch.
 
-**You must wait for all of the tests to pass before you can finish tagging the release.**
+* A yellow dot indicates that the tests are still running. Click on the yellow dot to see which tests are still running.
+* A red "X" indicates that one or more of the tests failed. Click on the red "X" to see which tests failed.
+* A green check mark indicates that all of the tests passed.
 
-*Sometimes, one of the build jobs will fail because a download timed out. This is especially common with the Mac builds. If this happens, just click on the job, and then click the "Restart job" button.*
+**You must wait for all of the tests to pass (green check mark) before you can finish tagging the release.**
+
+*Sometimes, one of the build jobs will fail because a download timed out. This is especially common with the Mac builds on Travis. You can usually resolve this error by restarting the failed build.*
 
 **Step 11:**  Once all of the Travis tests have passed, you can finish tagging your release using the git-flow tools:
 

README.md

@@ -1,28 +1,36 @@
-# PredictMD
+# [PredictMD](https://www.predictmd.net) - Uniform interface for machine learning in Julia
+
+## Current release: <a href="https://github.com/bcbi/PredictMD.jl/releases/latest"><img alt="Latest release" title="Latest release" src="https://img.shields.io/github/release/bcbi/PredictMD.svg"></a>
 
 <table>
     <thead>
         <tr>
-            <th>branch</th>
-            <th>travis</th>
-            <th>docs</th>
+            <th>Branch</th>
+            <th>Description</th>
+            <th>Docs</th>
+            <th>Travis</th>
+            <th>AppVeyor</th>
         </tr>
     </thead>
     <tbody>
         <tr>
             <td>master</td>
-            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Travis build status (master)" title="Travis build status (master)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=master"></a></td>
+            <td>Current release (stable)</td>
             <td><a href="https://www.predictmd.net/stable"><img alt="Documentation (stable)" title="Documentation (stable)" src="https://img.shields.io/badge/docs-stable-blue.svg"></a></td>
+            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Travis build status (master)" title="Travis build status (master)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=master"></a></td>
+            <td><a href="https://ci.appveyor.com/project/mirestrepo/predictmd-jl/history"><img alt="AppVeyor build status (master)" title="AppVeyor build status (master)" src="https://ci.appveyor.com/api/projects/status/github/bcbi/PredictMD.jl?branch=master&svg=true"></a></td>
         </tr>
         <tr>
             <td>develop</td>
-            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Travis build status (develop)" title="Travis build status (develop)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=develop"></a></td>
+            <td>Development branch (latest)</td>
             <td><a href="https://www.predictmd.net/latest"><img alt="Documentation (latest)" title="Documentation (latest)" src="https://img.shields.io/badge/docs-latest-blue.svg"></a></td>
+            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Travis build status (develop)" title="Travis build status (develop)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=develop"></a></td>
+            <td><a href="https://ci.appveyor.com/project/mirestrepo/predictmd-jl/history"><img alt="AppVeyor build status (develop)" title="AppVeyor build status (develop)" src="https://ci.appveyor.com/api/projects/status/github/bcbi/PredictMD.jl?branch=develop&svg=true"></a></td>
         </tr>
     </tbody>
 </table>
 
-PredictMD is a Julia package that provides a uniform interface for using multiple different statistics and machine learning packages. This document describes how to install and use PredictMD.
+[PredictMD](https://www.predictmd.net) is a Julia package that provides a uniform interface for using multiple different statistics and machine learning packages. This document describes how to install and use PredictMD.
 
 <table>
     <thead>
@@ -119,7 +127,7 @@ If you receive an error (e.g. "command not found"), download and install pdf2svg
 
 **Step 3:** Paste the following line into Julia and press enter:
 ```julia
-Pkg.init(); Pkg.update(); Pkg.clone("https://github.com/bcbi/PredictMD.jl.git"); Pkg.test("PredictMD");
+Pkg.init(); Pkg.update(); Pkg.clone("https://github.com/bcbi/PredictMD.jl.git"); Pkg.update(); import PredictMD; Pkg.test("PredictMD");
 ```
 You will need to wait several minutes while all of the required packages are installed and all of the tests are run.
 

REQUIRE

@@ -1,5 +1,7 @@
+##### Minimum supported version of Julia: 0.6
 julia 0.6
 
+##### Required Julia packages
 Atom
 BenchmarkTools
 CSVFiles
@@ -21,10 +23,16 @@ NBInclude
 NumericalIntegration
 PGFPlots
 PGFPlotsX
-PackageCompiler
 ProgressMeter
 RDatasets
 ROCAnalysis
 Requires
 ValueHistories
 Weave
+
+##### The following Julia packages are not required, but will be used by
+##### PredictMD if the user runs `import PACKAGENAME` or `using PACKAGENAME`
+# CUDNN
+# Clang
+# Cxx
+# LLVM

appveyor.yml

@@ -0,0 +1,58 @@
+branches:
+    except:
+        - gh-pages
+
+environment:
+    matrix:
+        - 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/x64/julia-latest-win64.exe"
+
+image: Visual Studio 2015
+
+matrix:
+    fast_finish: true # immediately finish build once one of the jobs fails
+    # allow_failures:
+        # - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+
+notifications:
+    - provider: Email
+      on_build_success: true
+      on_build_failure: true
+      on_build_status_changed: true
+
+skip_branch_with_pr: false
+
+skip_non_tags: false
+
+skip_tags: false
+
+version: '{build}'
+
+###############################################################################
+
+install:
+    - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
+    # If there's a newer build queued for the same PR, cancel this build
+    - 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." }
+    # Configure Visual Studio build environment
+    - call "C:\Program Files\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64
+    - call "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64
+    # Download the appropriate Julia Windows binary
+    - ps: (new-object net.webclient).DownloadFile(
+          $env:JULIA_URL,
+          "C:\projects\julia-binary.exe")
+    # Run Julia installer silently, output to C:\projects\julia
+    - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+
+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 --check-bounds=yes --color=yes -e "Pkg.clone(pwd(), \"PredictMD\")"
+    - C:\projects\julia\bin\julia --check-bounds=yes --color=yes -e "Pkg.build(\"PredictMD\")"
+
+test_script:
+    - C:\projects\julia\bin\julia --check-bounds=yes --color=yes -e "import PredictMD"
+    - C:\projects\julia\bin\julia --check-bounds=yes --color=yes -e "Pkg.test(\"PredictMD\")

deps/build.jl

@@ -1,7 +1,13 @@
-# Originally based on https://github.com/KristofferC/PGFPlotsX.jl/blob/master/deps/build.jl
+# Parts of this file are based on:
+# 1. https://github.com/KristofferC/PGFPlotsX.jl/blob/master/deps/build.jl
 
 import Crayons
 
+srand(999)
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )
+
 const OK =  Crayons.Box.GREEN_FG * Crayons.Box.BOLD("OK")
 const X =  Crayons.Box.RED_FG * Crayons.Box.BOLD("X")
 
@@ -56,3 +62,6 @@ const PREAMBLE_PATH = joinpath(@__DIR__, "custom_preamble.tex")
 if !isfile(PREAMBLE_PATH)
     touch(PREAMBLE_PATH)
 end
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )

docs/deploy_docs.jl

@@ -1,20 +1,37 @@
 import Documenter
 import PredictMD
 
+srand(999)
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )
+
 ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "true"
 
-Documenter.deploydocs(
-    branch = "gh-pages",
-    deps = Documenter.Deps.pip(
-        "mkdocs",
-        "pygments",
-        "python-markdown-math",
-        ),
-    julia = "0.6",
-    latest = "develop",
-    osname = "linux",
-    repo = "github.com/bcbi/PredictMD.jl.git",
-    target = "site",
-    )
+if is_windows()
+    warn(
+        string(
+            "deploy_docs is not supported on Windows, so skipping",
+            )
+        )
+else
+    Documenter.deploydocs(
+        branch = "gh-pages",
+        deps = Documenter.Deps.pip(
+            "mkdocs",
+            "pygments",
+            "python-markdown-math",
+            ),
+        julia = "0.6",
+        latest = "develop",
+        osname = "linux",
+        repo = "github.com/bcbi/PredictMD.jl.git",
+        target = "site",
+        )
+end
+
 
 ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "false"
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )

docs/make_docs.jl

@@ -2,19 +2,35 @@ import Documenter
 import Literate
 import PredictMD
 
+srand(999)
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )
+
 ENV["PREDICTMD_IS_MAKE_DOCS"] = "true"
 
-Documenter.makedocs(
-    modules = [
-        PredictMD,
-        PredictMD.Clean,
-        PredictMD.GPU,
-        ],
-    sitename = "PredictMD.jl",
-    pages = Any[
-        "index.md",
-        "library/internals.md",
-        ],
-    )
+if is_windows()
+    warn(
+        string(
+            "make_docs is not supported on Windows, so skipping",
+            )
+        )
+else
+    Documenter.makedocs(
+        modules = [
+            PredictMD,
+            PredictMD.Clean,
+            PredictMD.GPU,
+            ],
+        sitename = "PredictMD.jl",
+        pages = Any[
+            "index.md",
+            "library/internals.md",
+            ],
+        )
+end
 
 ENV["PREDICTMD_IS_MAKE_DOCS"] = "false"
+
+Base.flush( Base.STDOUT )
+Base.flush( Base.STDERR )