Merge pull request #11 from KrishnaswamyLab/dev

Add Travis CI testing and update README

.Rbuildignore

@@ -11,9 +11,11 @@
 ^data/desktop\.ini$ # Windows detritus
 ^\.git$             # git repository
 ^desktop\.ini$
-^phater\.Rproj$
+^phateR\.Rproj$
 ^README\.Rmd$
 ^data/desktop\.ini$
 ^\.git$
 ^\.git/*$
 ^\.travis\.yml$
+^travis_setup\.sh$
+^miniconda\.sh$

.travis.yml

@@ -1,5 +1,34 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-language: R
-sudo: false
+language: r
+sudo: required
 cache: packages
+
+os:
+  - linux
+  - osx
+
+r:
+  - oldrel
+  - release
+  - devel
+
+env:
+  global:
+    - PATH="$HOME/miniconda/bin:$PATH"
+    - RETICULATE_PYTHON="$HOME/miniconda/bin/python"
+
+before_install:
+  - chmod +x travis_setup.sh
+  - ./travis_setup.sh
+  - pip install --user phate
+
+r_packages:
+  - Matrix
+  - ggplot2
+  - reticulate
+  - devtools
+  - gridGraphics
+  - cowplot
+
+warnings_are_errors: true

DESCRIPTION

@@ -15,16 +15,15 @@ Encoding: UTF-8
 LazyData: true
 Depends:
     R (>= 3.3),
-    Matrix (>= 1.2-12)
+    Matrix (>= 1.2-0)
 Imports:
     methods,
     stats,
     graphics,
-    reticulate (>= 1.7),
+    reticulate (>= 1.4),
     ggplot2
 Suggests:
     gridGraphics,
-    cowplot,
-    tidyverse
+    cowplot
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 6.0.1

README.Rmd

@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 
 [![Latest PyPI version](https://img.shields.io/pypi/v/phate.svg)](https://pypi.org/project/phate/)
 [![Latest CRAN version](https://img.shields.io/cran/v/phateR.svg)](https://cran.r-project.org/package=phateR)
+[![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/phateR.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/phateR)
 [![Read the Docs](https://img.shields.io/readthedocs/phate.svg)](https://phate.readthedocs.io/)
 [![bioRxiv Preprint](https://zenodo.org/badge/DOI/10.1101/120378.svg)](https://www.biorxiv.org/content/early/2017/12/01/120378)
 [![Twitter](https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow)](https://twitter.com/KrishnaswamyLab)
@@ -28,6 +29,15 @@ For a thorough overview of the PHATE visualization method, please see the [bioRx
 
 For our Python and Matlab implementations, please see [KrishnaswamyLab/PHATE](https://github.com/KrishnaswamyLab/PHATE).
 
+## Table of Contents
+
+  * [Installation](#installation)
+    * [Installation from CRAN and PyPi](#installation-from-cran-and-pypi)
+    * [Installation with devtools and <code>reticulate</code>](#installation-with-devtools-and-reticulate)
+    * [Installation from source](#installation-from-source)
+  * [Tutorial](#tutorial)
+  * [Issues](#issues)
+
 ## Installation
 
 In order to use PHATE in R, you must also install the Python package.

README.md

@@ -5,6 +5,7 @@ phateR v0.2.6
 
 [![Latest PyPI version](https://img.shields.io/pypi/v/phate.svg)](https://pypi.org/project/phate/)
 [![Latest CRAN version](https://img.shields.io/cran/v/phateR.svg)](https://cran.r-project.org/package=phateR)
+[![Travis CI Build](https://api.travis-ci.com/KrishnaswamyLab/phateR.svg?branch=master)](https://travis-ci.com/KrishnaswamyLab/phateR)
 [![Read the Docs](https://img.shields.io/readthedocs/phate.svg)](https://phate.readthedocs.io/)
 [![bioRxiv Preprint](https://zenodo.org/badge/DOI/10.1101/120378.svg)](https://www.biorxiv.org/content/early/2017/12/01/120378)
 [![Twitter](https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow)](https://twitter.com/KrishnaswamyLab)
@@ -21,6 +22,15 @@ preprint](https://www.biorxiv.org/content/early/2017/12/01/120378)
 For our Python and Matlab implementations, please see
 [KrishnaswamyLab/PHATE](https://github.com/KrishnaswamyLab/PHATE).
 
+## Table of Contents
+
+  * [Installation](#installation)
+    * [Installation from CRAN and PyPi](#installation-from-cran-and-pypi)
+    * [Installation with devtools and <code>reticulate</code>](#installation-with-devtools-and-reticulate)
+    * [Installation from source](#installation-from-source)
+  * [Tutorial](#tutorial)
+  * [Issues](#issues)
+
 ## Installation
 
 In order to use PHATE in R, you must also install the Python package.

travis_setup.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# install python
+if [[ $TRAVIS_OS_NAME == "linux" ]]; then
+    wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
+elif [[ $TRAVIS_OS_NAME == "osx" ]]; then
+    wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh
+fi
+
+bash miniconda.sh -b -p $HOME/miniconda
+hash -r
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+conda info -a
+pip install --upgrade pip