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Merge pull request #1 from concord-consortium/master
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Pull from Concord (contains Greek 5-amino-acids.json)
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birbilis authored Jul 12, 2017
2 parents 0db4a6b + cddbdbe commit 474e87b
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24 changes: 6 additions & 18 deletions .travis.yml
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@@ -1,32 +1,20 @@
dist: trusty
sudo: false
branches:
except:
- /^(wip|WIP)(-|_).*$/
notifications:
irc:
channels:
- irc.freenode.org#ccdevs
on_success: change
on_failure: always
email:
recipients:
- [email protected]
- [email protected]
- [email protected]
- [email protected]
- [email protected]
on_success: change
on_failure: always
language: ruby
language: node_js
node_js:
- "6"
cache:
bundler: true
yarn: true
directories:
- vendor
- node_modules
rvm:
- 2.0.0
bundler_args: --without development --deployment --jobs=3 --retry=3
before_script:
- travis_retry bundle install --without development --deployment --jobs=3 --retry=3
- travis_retry npm install
- make prepare-submodules
- make public
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23 changes: 15 additions & 8 deletions Dockerfile
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@@ -1,26 +1,33 @@
FROM ubuntu:trusty
FROM ubuntu:xenial

WORKDIR /srv
RUN apt-get update && apt-get upgrade -y && apt-get clean
RUN apt-get update && apt-get upgrade -y

# Install RVM
RUN apt-get install -y curl && apt-get clean
RUN apt-get install -y curl
RUN gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
RUN curl -sSL https://get.rvm.io | bash -s stable && apt-get clean
RUN curl -sSL https://get.rvm.io | bash -s stable
RUN /bin/bash -c "source /usr/local/rvm/scripts/rvm; rvm install ruby-2.0.0-p247"
RUN echo "source /usr/local/rvm/scripts/rvm" >> /root/.bashrc

# Install Node.js
RUN apt-get install -y software-properties-common && apt-get clean
RUN apt-add-repository -y ppa:chris-lea/node.js
RUN apt-get install -y nodejs npm && apt-get clean
RUN apt-get install -y nodejs npm
RUN ln -sf /usr/bin/nodejs /usr/bin/node

# Install Yarn
RUN curl -sS http://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add -
RUN echo "deb http://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list
RUN apt-get update && apt-get install -y yarn

# Setup app
RUN locale-gen en_US.UTF-8
ENV LANG en_US.UTF-8
RUN apt-get install -y git libxslt-dev libxml2-dev python-pip && apt-get clean
RUN apt-get install -y git libxslt-dev libxml2-dev python-pip
RUN pip install supervisor

# Regain some amount of diskspace
RUN apt-get clean

COPY . /srv/
RUN /bin/bash -c "source /usr/local/rvm/scripts/rvm; gem install bundle"
RUN /bin/bash -c "source /usr/local/rvm/scripts/rvm; bundle install"
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2 changes: 1 addition & 1 deletion Gemfile
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Expand Up @@ -5,7 +5,7 @@ gem "haml", "~> 4.0.0"
# Adds Hash.from_xml method used in Energy2D importer
gem 'activesupport', "~> 3"
gem 'i18n', "~> 0.6.4"
gem "s3_website", "~> 1.7.6"
gem "s3_website", "~> 3.1.0"

group :app do
gem "rack", "~> 1.5.2"
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42 changes: 20 additions & 22 deletions Gemfile.lock
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Expand Up @@ -2,9 +2,14 @@ GEM
remote: http://rubygems.org/
specs:
activesupport (3.0.0)
aws-sdk (1.39.0)
json (~> 1.4)
nokogiri (>= 1.4.4)
aws-sdk (2.8.7)
aws-sdk-resources (= 2.8.7)
aws-sdk-core (2.8.7)
aws-sigv4 (~> 1.0)
jmespath (~> 1.0)
aws-sdk-resources (2.8.7)
aws-sdk-core (= 2.8.7)
aws-sigv4 (1.0.0)
bourbon (3.1.8)
sass (>= 3.2.0)
thor
Expand All @@ -15,19 +20,19 @@ GEM
execjs
coffee-script-source (1.6.3)
colored (1.2)
configure-s3-website (1.5.5)
deep_merge (= 1.0.0)
deep_merge (1.0.0)
configure-s3-website (2.0.0)
aws-sdk (~> 2)
deep_merge (~> 1.0.0)
deep_merge (1.0.1)
dotenv (1.0.2)
em-websocket (0.5.0)
eventmachine (>= 0.12.9)
http_parser.rb (~> 0.5.3)
erubis (2.7.0)
eventmachine (1.0.3)
excon (0.23.0)
execjs (1.4.0)
multi_json (~> 1.0)
ffi (1.9.0)
filey-diff (2.0.0)
fog (1.12.1)
builder
excon (~> 0.23.0)
Expand Down Expand Up @@ -65,7 +70,7 @@ GEM
hashr (0.0.22)
http_parser.rb (0.5.3)
i18n (0.6.4)
json (1.7.7)
jmespath (1.3.1)
kramdown (1.3.0)
listen (1.3.1)
rb-fsevent (>= 0.9.3)
Expand Down Expand Up @@ -99,25 +104,18 @@ GEM
ffi (>= 0.5.0)
ruby-hmac (0.4.0)
ruby_gntp (0.3.4)
s3_website (1.7.6)
aws-sdk (~> 1)
configure-s3-website (= 1.5.5)
erubis (~> 2.7.0)
filey-diff (~> 2.0.0)
mime-types (~> 1)
simple-cloudfront-invalidator (~> 1)
thor (= 0.18.1)
zopfli (~> 0.0.3)
sass (3.2.9)
simple-cloudfront-invalidator (1.0.1)
s3_website (3.1.0)
colored (= 1.2)
configure-s3-website (= 2.0.0)
dotenv (~> 1.0)
thor (~> 0.18)
sass (3.2.9)
slop (3.4.6)
thor (0.18.1)
tilt (1.4.1)
travis-lint (1.7.0)
hashr (~> 0.0.22)
wdm (0.1.0)
zopfli (0.0.3)

PLATFORMS
ruby
Expand All @@ -144,7 +142,7 @@ DEPENDENCIES
rb-fsevent (~> 0.9.3)
rb-inotify (~> 0.9.0)
ruby_gntp (~> 0.3.4)
s3_website (~> 1.7.6)
s3_website (~> 3.1.0)
sass (~> 3.2.5)
travis-lint
wdm (~> 0.1.0)
7 changes: 2 additions & 5 deletions Makefile
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Expand Up @@ -160,11 +160,8 @@ submodule-update-tags:
#
# ------------------------------------------------

node_modules: node_modules/d3
npm install

node_modules/d3:
npm install vendor/d3
node_modules:
yarn || npm install

# ------------------------------------------------
#
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4 changes: 4 additions & 0 deletions developer-doc/setup-node.md
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Expand Up @@ -7,6 +7,8 @@

Install the latest stable version of node with installers available here: [http://nodejs.org/#download](http://nodejs.org/#download)

Install yarn using homebrew: `brew install yarn` or check other installation methods: https://yarnpkg.com/en/docs/install#mac-tab

## Linux (Ubuntu)

To install the latest stable versions of node you first need to add this PPA repositories:
Expand All @@ -22,3 +24,5 @@ For this to work as intended python software properties must also be installed.
Now install node and npm:

$ sudo apt-get install nodejs npm

2. Install Yarn: https://yarnpkg.com/en/docs/install#linux-tab
18 changes: 4 additions & 14 deletions package.json
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@@ -1,6 +1,6 @@
{
"name": "lab",
"version": "0.8.0",
"name": "lab-interactives-site",
"version": "1.0.0",
"description": "HTML5-based scientific models, visualizations, graphing, and probeware",
"keywords": [
"molecule",
Expand All @@ -11,14 +11,14 @@
"svg",
"d3"
],
"homepage": "http://lab.dev.concord.org/",
"homepage": "http://lab.concord.org/",
"author": {
"name": "Stephen Bannasch",
"url": "https://github.com/stepheneb"
},
"repository": {
"type": "git",
"url": "https://github.com/concord-consortium/lab.git"
"url": "https://github.com/concord-consortium/lab-interacties-site.git"
},
"dependencies": {
"optimist": ">=0.6.0",
Expand All @@ -44,15 +44,5 @@
"should": "3.0.1",
"sinon": ">=1.7.3",
"chai": ">=1.7.2"
},
"directories": {
"bin": "node-bin"
},
"files": [
"md-engine/2d-molecules.js",
"md-engine/2d-molecules.min.js"
],
"scripts": {
"test": "./node_modules/vows/bin/vows"
}
}
2 changes: 1 addition & 1 deletion readme.md
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Expand Up @@ -22,7 +22,7 @@ third-parties and are distributed under either BSD, MIT, or Apache 2.0 licenses.
### Prerequisites:

- [RVM, Ruby 2.0 and Bundler](developer-doc/setup-ruby.md)
- [node.js and npm](developer-doc/setup-node.md)
- [node.js, npm and yarn](developer-doc/setup-node.md)
- [additional Linux notes](developer-doc/linux-notes.md)

### Setup the local Lab repository for development
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2 changes: 1 addition & 1 deletion script/s3-deploy.sh
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Expand Up @@ -57,4 +57,4 @@ fi
# It was downloaded either by ./script/popluate-standalone.sh or this script.
rm lab.tar.gz

disable_parallel_processing=true bundle exec s3_website push --site _site --headless --config_dir config
bundle exec s3_website push --site _site --config-dir config
2 changes: 1 addition & 1 deletion script/setup.rb
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Expand Up @@ -67,7 +67,7 @@ def render_file(filename, locals)
LAB_ROOT_URL = {
:default => config_lab_root_url[:default] || "//lab-framework.concord.org/version/1.14.0/lab",
:production => config_lab_root_url[:production] || "//lab-framework.concord.org/version/1.14.0/lab",
:staging => config_lab_root_url[:staging] || "//lab-framework.concord.org/version/1.15.0-pre.1/lab",
:staging => config_lab_root_url[:staging] || "//lab-framework.concord.org/version/1.15.0-pre.4/lab",
:development => config_lab_root_url[:development] || "//lab-framework.concord.org/branch/master/lab",
:local => config_lab_root_url[:local] || "//localhost:9191/lab"
}
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