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Merge branch 'release/v0.17.0'
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‎.travis.yml

Lines changed: 35 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -35,26 +35,45 @@ os:
3535
- linux
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- osx
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38-
###############################################################################
38+
############################################################################
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4040
before_install:
41-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
42-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install basictex; fi
43-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Library/TeX/texbin:"$PATH"; fi
44-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self; fi
45-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install luatex85; fi
46-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install pgfplots; fi
47-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install standalone; fi
48-
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi
41+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
42+
then brew update; fi
43+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
44+
then brew cask install basictex; fi
45+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
46+
then export PATH=/Library/TeX/texbin:"$PATH"; fi
47+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
48+
then sudo tlmgr update --self; fi
49+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
50+
then sudo tlmgr install luatex85; fi
51+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
52+
then sudo tlmgr install pgfplots; fi
53+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
54+
then sudo tlmgr install standalone; fi
55+
- if [[ "$TRAVIS_OS_NAME" == "osx" ]];
56+
then brew install pdf2svg; fi
4957

5058
script:
51-
- julia --check-bounds=yes --color=yes -e 'Pkg.clone(pwd(), "PredictMD")'
52-
- julia --check-bounds=yes --color=yes -e 'Pkg.build("PredictMD")'
53-
- julia --check-bounds=yes --color=yes -e 'import PredictMD'
54-
- julia --check-bounds=yes --color=yes -e 'Pkg.test("PredictMD"; coverage=true)'
59+
- julia --check-bounds=yes --color=yes -e '
60+
Pkg.clone(pwd(), "PredictMD")'
61+
- julia --check-bounds=yes --color=yes -e '
62+
Pkg.build("PredictMD")'
63+
- julia --check-bounds=yes --color=yes -e '
64+
import PredictMD'
65+
- julia --check-bounds=yes --color=yes -e '
66+
Pkg.test("PredictMD"; coverage=true)'
5567

5668
after_success:
5769
- julia --check-bounds=yes --color=yes -e 'Pkg.add("Coverage");'
58-
- julia --check-bounds=yes --color=yes -e 'cd(Pkg.dir("PredictMD")); using Coverage; Codecov.submit(Codecov.process_folder());'
59-
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then julia --check-bounds=yes --color=yes -e 'cd(Pkg.dir("PredictMD")); using Coverage; Coveralls.submit(Coveralls.process_folder());'; fi
60-
- julia --check-bounds=yes --color=yes -e 'cd(Pkg.dir("PredictMD")); include(joinpath("docs", "deploy_docs.jl"))'
70+
- julia --check-bounds=yes --color=yes -e 'cd(Pkg.dir("PredictMD"));
71+
using Coverage; Codecov.submit(Codecov.process_folder());'
72+
- if [[ "$TRAVIS_OS_NAME" == "linux" ]];
73+
then julia --check-bounds=yes --color=yes -e '
74+
cd(Pkg.dir("PredictMD"));
75+
using Coverage;
76+
Coveralls.submit(Coveralls.process_folder());'; fi
77+
- julia --check-bounds=yes --color=yes -e '
78+
cd(Pkg.dir("PredictMD"));
79+
include(joinpath("docs", "deploy_docs.jl"))'

‎CONTRIBUTING.md

Lines changed: 179 additions & 61 deletions
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‎README.md

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,9 @@
11
# PredictMD - Uniform interface for machine learning in Julia
22

3-
<a href="https://github.com/bcbi/PredictMD.jl/releases/latest"><img alt="Current release" title="Current release" src="https://img.shields.io/github/release/bcbi/PredictMD.svg"></a>
3+
<a href="https://github.com/bcbi/PredictMD.jl/releases/latest"><img alt="Current release" title="Current release" src="https://img.shields.io/github/release/bcbi/PredictMD.svg" /> </a> <a href="https://zenodo.org/badge/latestdoi/109460252"> <img alt="DOI for current release" title="DOI for current release" src="https://zenodo.org/badge/109460252.svg"/></a>
44

5-
[PredictMD](https://www.predictmd.net) is a Julia package that provides a uniform interface for using multiple different statistics and machine learning packages.
5+
[PredictMD](https://www.predictmd.net) is a Julia package that provides a
6+
uniform interface for using multiple different machine learning packages.
67

78
### Table of Contents
89
- [Installation](#installation)
@@ -11,20 +12,25 @@
1112

1213
## Installation
1314

14-
To install PredictMD, open Julia (e.g. open a terminal, type `julia`, and press enter) and run the following command:
15+
To install PredictMD, open Julia
16+
(e.g. open a terminal, type `julia`, and press enter)
17+
and run the following command:
1518
```julia
1619
Pkg.clone("https://github.com/bcbi/PredictMD.jl")
1720
```
1821

19-
After you install PredictMD, you should run the test suite to make sure that everything is working. You can run the test suite with the following Julia command:
22+
After you install PredictMD, you should run the test suite to make sure that
23+
everything is working. You can run the test suite with the following
24+
Julia command:
2025
```julia
2126
Pkg.test("PredictMD")
2227
```
2328

2429
## Documentation
2530

26-
The [PredictMD documentation](https://www.predictmd.net/stable) contains useful
27-
information, including instructions for use, example code, and a description of
31+
The [PredictMD documentation](https://www.predictmd.net/stable) contains
32+
useful information, including instructions for use, example code, and a
33+
description of
2834
PredictMD's internals.
2935

3036
## CI/CD
@@ -40,28 +46,79 @@ PredictMD's internals.
4046
<tbody>
4147
<tr>
4248
<td>Travis CI</td>
43-
<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>
44-
<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>
49+
<td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches">
50+
<img alt="Travis build status (master)"
51+
title="Travis build status (master)"
52+
src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=master"
53+
/></a></td>
54+
<td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches">
55+
<img alt="Travis build status (develop)"
56+
title="Travis build status (develop)"
57+
src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=develop"
58+
/></a></td>
4559
</tr>
4660
<tr>
4761
<td>AppVeyor CI</td>
48-
<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>
49-
<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>
62+
<td>
63+
<a
64+
href="https://ci.appveyor.com/project/mirestrepo/predictmd-jl/history">
65+
<img alt="AppVeyor build status (master)"
66+
title="AppVeyor build status (master)" src="https://ci.appveyor.com/api/projects/status/github/bcbi/PredictMD.jl?branch=master&svg=true"
67+
/>
68+
</a></td>
69+
<td><a href="https://ci.appveyor.com/project/mirestrepo/predictmd-jl/history">
70+
<img alt="AppVeyor build status (develop)"
71+
title="AppVeyor build status (develop)" src="https://ci.appveyor.com/api/projects/status/github/bcbi/PredictMD.jl?branch=develop&svg=true"
72+
/>
73+
</a></td>
5074
</tr>
5175
<tr>
5276
<td>CodeCov</td>
53-
<td><a href="https://codecov.io/gh/bcbi/PredictMD.jl/branch/master"><img alt="CodeCov (master)" title="CodeCov (master)" src="https://codecov.io/gh/bcbi/PredictMD.jl/branch/master/graph/badge.svg" /></a></td>
54-
<td><a href="https://codecov.io/gh/bcbi/PredictMD.jl/branch/develop"><img alt="CodeCov (develop)" title="CodeCov (develop)" src="https://codecov.io/gh/bcbi/PredictMD.jl/branch/develop/graph/badge.svg" /></a></td>
77+
<td>
78+
<a
79+
href="https://codecov.io/gh/bcbi/PredictMD.jl/branch/master">
80+
<img alt="CodeCov (master)" title="CodeCov (master)"
81+
src="https://codecov.io/gh/bcbi/PredictMD.jl/branch/master/graph/badge.svg"
82+
/></a></td>
83+
<td>
84+
<a
85+
href="https://codecov.io/gh/bcbi/PredictMD.jl/branch/develop">
86+
<img alt="CodeCov (develop)" title="CodeCov (develop)" src="https://codecov.io/gh/bcbi/PredictMD.jl/branch/develop/graph/badge.svg"
87+
/></a></td>
5588
</tr>
5689
<tr>
5790
<td>Coveralls</td>
58-
<td><a href="https://coveralls.io/github/bcbi/PredictMD.jl?branch=master"><img alt="Coverage status (master)" title="Coverage status (master)" src="https://coveralls.io/repos/github/bcbi/PredictMD.jl/badge.svg?branch=master" /></a></td>
59-
<td><a href="https://coveralls.io/github/bcbi/PredictMD.jl?branch=develop"><img alt="Coverage status (develop)" title="Coverage status (develop)" src="https://coveralls.io/repos/github/bcbi/PredictMD.jl/badge.svg?branch=develop" /></a></td>
91+
<td>
92+
<a
93+
href="https://coveralls.io/github/bcbi/PredictMD.jl?branch=master">
94+
<img alt="Coverage status (master)"
95+
title="Coverage status (master)"
96+
src="https://coveralls.io/repos/github/bcbi/PredictMD.jl/badge.svg?branch=master"
97+
/></a></td>
98+
<td>
99+
<a
100+
href="https://coveralls.io/github/bcbi/PredictMD.jl?branch=develop">
101+
<img alt="Coverage status (develop)" title="Coverage status (develop)" src="https://coveralls.io/repos/github/bcbi/PredictMD.jl/badge.svg?branch=develop"
102+
/></a></td>
60103
</tr>
61104
<tr>
62105
<td>docs</td>
63-
<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>
64-
<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>
106+
<td><a href="https://www.predictmd.net/stable">
107+
<img
108+
alt="Documentation (stable)"
109+
title="Documentation (stable)"
110+
src="https://img.shields.io/badge/docs-stable-blue.svg" />
111+
</a>
112+
</td>
113+
<td>
114+
<a
115+
href="https://www.predictmd.net/latest">
116+
<img
117+
alt="Documentation (latest)"
118+
title="Documentation (latest)"
119+
src="https://img.shields.io/badge/docs-latest-blue.svg" />
120+
</a>
121+
</td>
65122
</tr>
66123
</tbody>
67124
</table>

‎appveyor.yml

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,9 @@ branches:
44

55
environment:
66
matrix:
7-
- JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
7+
- JULIA_URL:
8+
"https://julialang-s3.julialang.org/bin/winnt/\
9+
x64/0.6/julia-0.6-latest-win64.exe"
810

911
image: Visual Studio 2015
1012

@@ -25,7 +27,7 @@ skip_tags: false
2527

2628
version: '{build}'
2729

28-
###############################################################################
30+
############################################################################
2931

3032
install:
3133
- ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"

‎deps/build.jl

Lines changed: 34 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -25,17 +25,30 @@ if have_lualatex
2525
elseif have_pdflatex
2626
default_engine = "PDFLATEX"
2727
else
28-
warn(string("No LaTeX installation found, figures will not be generated. ",
29-
"Make sure either pdflatex or lualatex are installed and that ",
30-
"the correct paths are set then run Pkg.build(\"PredictMD\")"))
28+
warn(
29+
string(
30+
"No LaTeX installation found, ",
31+
"figures will not be generated. ",
32+
"Make sure either pdflatex or lualatex are installed ",
33+
"and that the correct paths are set ",
34+
"then run Pkg.build(\"PredictMD\")",
35+
)
36+
)
3137
end
3238

3339
print(STDERR, "Looking for pdftoppm...")
3440
have_pdftoppm = try success(`pdftoppm -v`); catch; false; end
3541
println(STDERR, " ", have_pdftoppm ? OK : X)
3642
if !have_pdftoppm
37-
warn(string("Did not find `pdftoppm`, png output will be disabled. Install `pdftoppm` ",
38-
"and run Pkg.build(\"PredictMD\") to enable"))
43+
warn(
44+
string(
45+
"Did not find `pdftoppm`, ",
46+
"png output will be disabled. ",
47+
"Install `pdftoppm` and run ",
48+
"Pkg.build(\"PredictMD\") ",
49+
"to enable.",
50+
)
51+
)
3952
end
4053

4154
print(STDERR, "Looking for pdf2svg...")
@@ -44,12 +57,25 @@ svgpath = joinpath(@__DIR__, "pdf2svg.svg")
4457
have_pdf2svg = try success(`pdf2svg $pdfpath $svgpath`); catch; false; end
4558
println(STDERR, " ", have_pdf2svg ? OK : X)
4659
if !have_pdf2svg
47-
warn(string("Did not find `pdf2svg`, svg output will be disabled. Install `pdf2svg` ",
48-
"and run Pkg.build(\"PredictMD\") to enable"))
60+
warn(
61+
string(
62+
"Did not find `pdf2svg`, ",
63+
"svg output will be disabled. ",
64+
"Install `pdf2svg` and run ",
65+
"Pkg.build(\"PredictMD\")",
66+
"to enable.",
67+
)
68+
)
4969
end
5070

5171
if !have_pdf2svg && !have_pdftoppm
52-
warn(string("Found neither pdf2svg or pdftoppm, figures will not be viewable in Jupyter or Juno"))
72+
warn(
73+
string(
74+
"Found neither pdf2svg or pdftoppm, ",
75+
"figures will not be viewable in ",
76+
"IJulia/Jupyter notebooks.",
77+
)
78+
)
5379
end
5480

5581
open(joinpath(@__DIR__, "deps.jl"), "w") do f

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