Merge branch 'master' of github.com:akeshavan/preAFQ

Author: Adam Richie-Halford

.travis.yml

@@ -1,15 +1,25 @@
-# Config file for automatic testing at travis-ci.org
-
-language: python
-python:
-  - 3.6
-  - 3.5
-  - 3.4
-
-# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox-travis
-
-# Command to run tests, e.g. python setup.py test
-script: tox
-
-
+sudo: false
+language: node_js
+node_js:
+- '6.0'
+cache:
+  directories:
+  - preafqViewer/node_modules
+branches:
+  only:
+  - master
+notifications:
+  email: false
+before_script:
+- cd preafqViewer
+- npm prune
+script:
+- npm run build
+- npm test
+after_success:
+- bash ./deploy.sh
+env:
+  global:
+  - GH_USER: akeshavan
+  - GH_REPO: preAFQ
+  - secure: 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

docker/Dockerfile

@@ -85,17 +85,24 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     && conda config --system --prepend channels conda-forge \
     && conda config --system --set auto_update_conda false \
     && conda config --system --set show_channel_urls true \
-    && sync && conda clean -tipsy && sync \
-    && conda create -y -q --name preafq
-
-RUN conda install -y -q --name preafq \
-           -c \
-           conda-forge \
-           python=3.6 \
-           nipype \
-           dipy \
-           boto3 \
-    && sync && conda clean -tipsy && sync
+    && sync && conda clean -tipsy && sync 
+#    && conda create -y -q --name preafq
+
+# RUN conda install -y -q --name preafq \
+#            -c \
+#            conda-forge \
+#            python=3.6 \
+#            nipype \
+#            dipy \
+#            boto3 \
+#     && sync && conda clean -tipsy && sync
+
+ADD environment.yml environment.yml
+RUN apt-get update && apt-get install -y git gcc
+RUN conda env create -f environment.yml 
+
+#&& sync && conda clean -tipsy && sync
+
 
 RUN sed -i '$isource activate preafq' $ND_ENTRYPOINT 
 

preafqViewer/build/build.js

@@ -0,0 +1,41 @@
+'use strict'
+require('./check-versions')()
+
+process.env.NODE_ENV = 'production'
+
+const ora = require('ora')
+const rm = require('rimraf')
+const path = require('path')
+const chalk = require('chalk')
+const webpack = require('webpack')
+const config = require('../config')
+const webpackConfig = require('./webpack.prod.conf')
+
+const spinner = ora('building for production...')
+spinner.start()
+
+rm(path.join(config.build.assetsRoot, config.build.assetsSubDirectory), err => {
+  if (err) throw err
+  webpack(webpackConfig, (err, stats) => {
+    spinner.stop()
+    if (err) throw err
+    process.stdout.write(stats.toString({
+      colors: true,
+      modules: false,
+      children: false, // If you are using ts-loader, setting this to true will make TypeScript errors show up during build.
+      chunks: false,
+      chunkModules: false
+    }) + '\n\n')
+
+    if (stats.hasErrors()) {
+      console.log(chalk.red('  Build failed with errors.\n'))
+      process.exit(1)
+    }
+
+    console.log(chalk.cyan('  Build complete.\n'))
+    console.log(chalk.yellow(
+      '  Tip: built files are meant to be served over an HTTP server.\n' +
+      '  Opening index.html over file:// won\'t work.\n'
+    ))
+  })
+})

preafqViewer/build/check-versions.js

@@ -0,0 +1,54 @@
+'use strict'
+const chalk = require('chalk')
+const semver = require('semver')
+const packageConfig = require('../package.json')
+const shell = require('shelljs')
+
+function exec (cmd) {
+  return require('child_process').execSync(cmd).toString().trim()
+}
+
+const versionRequirements = [
+  {
+    name: 'node',
+    currentVersion: semver.clean(process.version),
+    versionRequirement: packageConfig.engines.node
+  }
+]
+
+if (shell.which('npm')) {
+  versionRequirements.push({
+    name: 'npm',
+    currentVersion: exec('npm --version'),
+    versionRequirement: packageConfig.engines.npm
+  })
+}
+
+module.exports = function () {
+  const warnings = []
+
+  for (let i = 0; i < versionRequirements.length; i++) {
+    const mod = versionRequirements[i]
+
+    if (!semver.satisfies(mod.currentVersion, mod.versionRequirement)) {
+      warnings.push(mod.name + ': ' +
+        chalk.red(mod.currentVersion) + ' should be ' +
+        chalk.green(mod.versionRequirement)
+      )
+    }
+  }
+
+  if (warnings.length) {
+    console.log('')
+    console.log(chalk.yellow('To use this template, you must update following to modules:'))
+    console.log()
+
+    for (let i = 0; i < warnings.length; i++) {
+      const warning = warnings[i]
+      console.log('  ' + warning)
+    }
+
+    console.log()
+    process.exit(1)
+  }
+}

preafqViewer/build/logo.png

@@ -0,0 +1,101 @@
+'use strict'
+const path = require('path')
+const config = require('../config')
+const ExtractTextPlugin = require('extract-text-webpack-plugin')
+const packageConfig = require('../package.json')
+
+exports.assetsPath = function (_path) {
+  const assetsSubDirectory = process.env.NODE_ENV === 'production'
+    ? config.build.assetsSubDirectory
+    : config.dev.assetsSubDirectory
+
+  return path.posix.join(assetsSubDirectory, _path)
+}
+
+exports.cssLoaders = function (options) {
+  options = options || {}
+
+  const cssLoader = {
+    loader: 'css-loader',
+    options: {
+      sourceMap: options.sourceMap
+    }
+  }
+
+  const postcssLoader = {
+    loader: 'postcss-loader',
+    options: {
+      sourceMap: options.sourceMap
+    }
+  }
+
+  // generate loader string to be used with extract text plugin
+  function generateLoaders (loader, loaderOptions) {
+    const loaders = options.usePostCSS ? [cssLoader, postcssLoader] : [cssLoader]
+
+    if (loader) {
+      loaders.push({
+        loader: loader + '-loader',
+        options: Object.assign({}, loaderOptions, {
+          sourceMap: options.sourceMap
+        })
+      })
+    }
+
+    // Extract CSS when that option is specified
+    // (which is the case during production build)
+    if (options.extract) {
+      return ExtractTextPlugin.extract({
+        use: loaders,
+        fallback: 'vue-style-loader'
+      })
+    } else {
+      return ['vue-style-loader'].concat(loaders)
+    }
+  }
+
+  // https://vue-loader.vuejs.org/en/configurations/extract-css.html
+  return {
+    css: generateLoaders(),
+    postcss: generateLoaders(),
+    less: generateLoaders('less'),
+    sass: generateLoaders('sass', { indentedSyntax: true }),
+    scss: generateLoaders('sass'),
+    stylus: generateLoaders('stylus'),
+    styl: generateLoaders('stylus')
+  }
+}
+
+// Generate loaders for standalone style files (outside of .vue)
+exports.styleLoaders = function (options) {
+  const output = []
+  const loaders = exports.cssLoaders(options)
+
+  for (const extension in loaders) {
+    const loader = loaders[extension]
+    output.push({
+      test: new RegExp('\\.' + extension + '$'),
+      use: loader
+    })
+  }
+
+  return output
+}
+
+exports.createNotifierCallback = () => {
+  const notifier = require('node-notifier')
+
+  return (severity, errors) => {
+    if (severity !== 'error') return
+
+    const error = errors[0]
+    const filename = error.file && error.file.split('!').pop()
+
+    notifier.notify({
+      title: packageConfig.name,
+      message: severity + ': ' + error.name,
+      subtitle: filename || '',
+      icon: path.join(__dirname, 'logo.png')
+    })
+  }
+}

preafqViewer/build/utils.js

@@ -0,0 +1,22 @@
+'use strict'
+const utils = require('./utils')
+const config = require('../config')
+const isProduction = process.env.NODE_ENV === 'production'
+const sourceMapEnabled = isProduction
+  ? config.build.productionSourceMap
+  : config.dev.cssSourceMap
+
+module.exports = {
+  loaders: utils.cssLoaders({
+    sourceMap: sourceMapEnabled,
+    extract: isProduction
+  }),
+  cssSourceMap: sourceMapEnabled,
+  cacheBusting: config.dev.cacheBusting,
+  transformToRequire: {
+    video: ['src', 'poster'],
+    source: 'src',
+    img: 'src',
+    image: 'xlink:href'
+  }
+}

preafqViewer/build/vue-loader.conf.js

@@ -0,0 +1,92 @@
+'use strict'
+const path = require('path')
+const utils = require('./utils')
+const config = require('../config')
+const vueLoaderConfig = require('./vue-loader.conf')
+
+function resolve (dir) {
+  return path.join(__dirname, '..', dir)
+}
+
+const createLintingRule = () => ({
+  test: /\.(js|vue)$/,
+  loader: 'eslint-loader',
+  enforce: 'pre',
+  include: [resolve('src'), resolve('test')],
+  options: {
+    formatter: require('eslint-friendly-formatter'),
+    emitWarning: !config.dev.showEslintErrorsInOverlay
+  }
+})
+
+module.exports = {
+  context: path.resolve(__dirname, '../'),
+  entry: {
+    app: './src/main.js'
+  },
+  output: {
+    path: config.build.assetsRoot,
+    filename: '[name].js',
+    publicPath: process.env.NODE_ENV === 'production'
+      ? config.build.assetsPublicPath
+      : config.dev.assetsPublicPath
+  },
+  resolve: {
+    extensions: ['.js', '.vue', '.json'],
+    alias: {
+      'vue$': 'vue/dist/vue.esm.js',
+      '@': resolve('src'),
+    }
+  },
+  module: {
+    rules: [
+      ...(config.dev.useEslint ? [createLintingRule()] : []),
+      {
+        test: /\.vue$/,
+        loader: 'vue-loader',
+        options: vueLoaderConfig
+      },
+      {
+        test: /\.js$/,
+        loader: 'babel-loader',
+        include: [resolve('src'), resolve('test'), resolve('node_modules/webpack-dev-server/client')]
+      },
+      {
+        test: /\.(png|jpe?g|gif|svg)(\?.*)?$/,
+        loader: 'url-loader',
+        options: {
+          limit: 10000,
+          name: utils.assetsPath('img/[name].[hash:7].[ext]')
+        }
+      },
+      {
+        test: /\.(mp4|webm|ogg|mp3|wav|flac|aac)(\?.*)?$/,
+        loader: 'url-loader',
+        options: {
+          limit: 10000,
+          name: utils.assetsPath('media/[name].[hash:7].[ext]')
+        }
+      },
+      {
+        test: /\.(woff2?|eot|ttf|otf)(\?.*)?$/,
+        loader: 'url-loader',
+        options: {
+          limit: 10000,
+          name: utils.assetsPath('fonts/[name].[hash:7].[ext]')
+        }
+      }
+    ]
+  },
+  node: {
+    // prevent webpack from injecting useless setImmediate polyfill because Vue
+    // source contains it (although only uses it if it's native).
+    setImmediate: false,
+    // prevent webpack from injecting mocks to Node native modules
+    // that does not make sense for the client
+    dgram: 'empty',
+    fs: 'empty',
+    net: 'empty',
+    tls: 'empty',
+    child_process: 'empty'
+  }
+}