revert deleted files

Author: josephmje

dmriprep/__init__.py

@@ -2,8 +2,8 @@
 
 """Top-level package for dmriprep."""
 
-__author__ = """Michael Joseph"""
-__email__ = "[email protected]"
+__author__ = """Anisha Keshavan"""
+__email__ = "[email protected]"
 __version__ = "0.1.0"
 
 import errno
@@ -22,7 +22,7 @@
 
 # get the log level from environment variable
 if "DMIRPREP_LOGLEVEL" in os.environ:
-    loglevel = os.environ["dmriprep_LOGLEVEL"]
+    loglevel = os.environ["DMRIPREP_LOGLEVEL"]
     module_logger.setLevel(getattr(logging, loglevel.upper()))
 else:
     module_logger.setLevel(logging.WARNING)
@@ -45,15 +45,14 @@
 handler.setLevel(logging.DEBUG)
 
 # create a logging format
-formatter = logging.Formatter(
-    "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-)
+formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
 handler.setFormatter(formatter)
 
 # add the handlers to the logger
 module_logger.addHandler(handler)
 module_logger.info("Started new dmriprep session")
 
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions

dmriprepViewer/.babelrc

@@ -0,0 +1,18 @@
+{
+  "presets": [
+    ["env", {
+      "modules": false,
+      "targets": {
+        "browsers": ["> 1%", "last 2 versions", "not ie <= 8"]
+      }
+    }],
+    "stage-2"
+  ],
+  "plugins": ["transform-vue-jsx", "transform-runtime"],
+  "env": {
+    "test": {
+      "presets": ["env", "stage-2"],
+      "plugins": ["transform-vue-jsx", "transform-es2015-modules-commonjs", "dynamic-import-node"]
+    }
+  }
+}

dmriprepViewer/README.md

@@ -0,0 +1,30 @@
+# dmriprep-viewer
+
+> Viewer for dmriprep reports
+
+## Build Setup
+
+``` bash
+# install dependencies
+npm install
+
+# serve with hot reload at localhost:8080
+npm run dev
+
+# build for production with minification
+npm run build
+
+# build for production and view the bundle analyzer report
+npm run build --report
+
+# run unit tests
+npm run unit
+
+# run e2e tests
+npm run e2e
+
+# run all tests
+npm test
+```
+
+For a detailed explanation on how things work, check out the [guide](http://vuejs-templates.github.io/webpack/) and [docs for vue-loader](http://vuejs.github.io/vue-loader).

dmriprepViewer/config/dev.env.js

@@ -0,0 +1,7 @@
+'use strict'
+const merge = require('webpack-merge')
+const prodEnv = require('./prod.env')
+
+module.exports = merge(prodEnv, {
+  NODE_ENV: '"development"'
+})

dmriprepViewer/config/index.js

@@ -0,0 +1,76 @@
+'use strict'
+// Template version: 1.3.1
+// see http://vuejs-templates.github.io/webpack for documentation.
+
+const path = require('path')
+
+module.exports = {
+  dev: {
+
+    // Paths
+    assetsSubDirectory: 'static',
+    assetsPublicPath: '/',
+    proxyTable: {},
+
+    // Various Dev Server settings
+    host: 'localhost', // can be overwritten by process.env.HOST
+    port: 8080, // can be overwritten by process.env.PORT, if port is in use, a free one will be determined
+    autoOpenBrowser: false,
+    errorOverlay: true,
+    notifyOnErrors: true,
+    poll: false, // https://webpack.js.org/configuration/dev-server/#devserver-watchoptions-
+
+    // Use Eslint Loader?
+    // If true, your code will be linted during bundling and
+    // linting errors and warnings will be shown in the console.
+    useEslint: true,
+    // If true, eslint errors and warnings will also be shown in the error overlay
+    // in the browser.
+    showEslintErrorsInOverlay: false,
+
+    /**
+     * Source Maps
+     */
+
+    // https://webpack.js.org/configuration/devtool/#development
+    devtool: 'cheap-module-eval-source-map',
+
+    // If you have problems debugging vue-files in devtools,
+    // set this to false - it *may* help
+    // https://vue-loader.vuejs.org/en/options.html#cachebusting
+    cacheBusting: true,
+
+    cssSourceMap: true
+  },
+
+  build: {
+    // Template for index.html
+    index: path.resolve(__dirname, '../dist/index.html'),
+
+    // Paths
+    assetsRoot: path.resolve(__dirname, '../dist'),
+    assetsSubDirectory: 'static',
+    assetsPublicPath: '/dmriprep/',
+
+    /**
+     * Source Maps
+     */
+
+    productionSourceMap: true,
+    // https://webpack.js.org/configuration/devtool/#production
+    devtool: '#source-map',
+
+    // Gzip off by default as many popular static hosts such as
+    // Surge or Netlify already gzip all static assets for you.
+    // Before setting to `true`, make sure to:
+    // npm install --save-dev compression-webpack-plugin
+    productionGzip: false,
+    productionGzipExtensions: ['js', 'css'],
+
+    // Run the build command with an extra argument to
+    // View the bundle analyzer report after build finishes:
+    // `npm run build --report`
+    // Set to `true` or `false` to always turn it on or off
+    bundleAnalyzerReport: process.env.npm_config_report
+  }
+}

dmriprepViewer/config/prod.env.js

@@ -0,0 +1,4 @@
+'use strict'
+module.exports = {
+  NODE_ENV: '"production"'
+}

dmriprepViewer/config/test.env.js

@@ -0,0 +1,7 @@
+'use strict'
+const merge = require('webpack-merge')
+const devEnv = require('./dev.env')
+
+module.exports = merge(devEnv, {
+  NODE_ENV: '"testing"'
+})

dmriprepViewer/deploy.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+set -e # exit with nonzero exit code if anything fails
+
+if [[ $TRAVIS_BRANCH == "master" && $TRAVIS_PULL_REQUEST == "false" ]]; then
+
+echo "Starting to update gh-pages\n"
+
+#copy data we're interested in to other place
+cp -R dist $HOME/dist
+
+#go to home and setup git
+cd $HOME
+git config --global user.email "[email protected]"
+git config --global user.name "Travis"
+
+#using token clone gh-pages branch
+git clone --quiet --branch=gh-pages https://${GH_TOKEN}@github.com/${GH_USER}/${GH_REPO}.git gh-pages > /dev/null
+
+#go into directory and copy data we're interested in to that directory
+cd gh-pages
+cp -Rf $HOME/dist/* .
+
+echo "Allow files with underscore https://help.github.com/articles/files-that-start-with-an-underscore-are-missing/" > .nojekyll
+echo "[View live](https://${GH_USER}.github.io/${GH_REPO}/)" > README.md
+
+#add, commit and push files
+git add -f .
+git commit -m "Travis build $TRAVIS_BUILD_NUMBER"
+git push -fq origin gh-pages > /dev/null
+
+echo "Done updating gh-pages\n"
+
+else
+ echo "Skipped updating gh-pages, because build is not triggered from the master branch."
+fi;

dmriprepViewer/index.html

@@ -0,0 +1,12 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width,initial-scale=1.0">
+    <title>dmriprep-viewer</title>
+  </head>
+  <body>
+    <div id="app"></div>
+    <!-- built files will be auto injected -->
+  </body>
+</html>

dmriprepViewer/src/App.vue

@@ -0,0 +1,30 @@
+<template>
+  <div id="app">
+    <router-view/>
+  </div>
+</template>
+
+<script>
+import Vue from 'vue';
+import BootstrapVue from 'bootstrap-vue';
+// eslint-disable-next-line
+import 'bootstrap/dist/css/bootstrap.css';
+import 'bootstrap-vue/dist/bootstrap-vue.css';
+
+Vue.use(BootstrapVue);
+
+export default {
+  name: 'App',
+};
+</script>
+
+<style>
+#app {
+  font-family: 'Avenir', Helvetica, Arial, sans-serif;
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
+  text-align: center;
+  color: #2c3e50;
+  margin-top: 60px;
+}
+</style>