Math-related fixes

README.md

@@ -2,9 +2,9 @@
 
 **Lens** provides a novel way of looking at content on the web. It is designed to make life easier for researchers, reviewers, authors and readers.
 
-- **Read the [announcement](http://elifesciences.org/elife-news/lens)**
-- **Watch the [introduction video](http://vimeo.com/67254579).**
-- **See Lens in [action](http://lens.elifesciences.org/00778)**
+- **Read the [announcement](https://elifesciences.org/elife-news/lens)**
+- **Watch the [introduction video](https://vimeo.com/67254579).**
+- **See Lens in [action](https://lens.elifesciences.org/00778)**
 
 ## Using Lens
 
@@ -29,33 +29,45 @@ However, now let's look into developing our own extensions.
 
 ### Prerequisites
 
-For Lens development, you need to have Node.js >=0.10.x installed.
+For Lens development, you need to have Node.js >=10.x installed.
 
 You need to repeat that install step whenever you updated the screwdriver repo.
 
 ### Setup
 
 1. Clone the `lens-starter` repository
 
-  ```bash
-  $ git clone https://github.com/elifesciences/lens-starter.git
-  ```
+```bash
+  git clone https://github.com/elifesciences/lens-starter.git
+  cd lens-starter
+```
+
+2. Configure System
 
-2. Fetch dependencies
+As stated above, you'll need version 10.x of Node installed, and you'll also need version 2.7.x of Python available. You can use [nvm](https://github.com/nvm-sh/nvm) to manage which version of node to use on a per-project basis, and [PyEnv](https://github.com/pyenv/pyenv) to do the same for Python. With both of these tools setup, you can...
 
-  ```bash
-  $ cd lens-starter
-  $ npm install
-  ```
+```bash
+echo "lts/dubnium" > .nvmrc
+nvm install
+nvm use
+echo "2.7.17" > .python-version
+pyenv install
+pvenv local
+```
 
-3. Run the server
+3. Fetch dependencies
 
-  ```bash
-  ~/projects/lens-starter $ node server
-  Lens running on port 4001
-  http://127.0.0.1:4001/
-  ```
+```bash
+npm install
+```
+
+4. Run the server
+
+```bash
+npm start
+```
 
+Then navigate to http://127.0.0.1:4001/ in your web browser.
 
 ### Converter
 
@@ -94,7 +106,7 @@ ElifeConverter.Prototype = function() {
       return [baseURL, node.url].join('');
     } else {
       node.url = [
-        "http://cdn.elifesciences.org/elife-articles/",
+        "https://cdn.elifesciences.org/elife-articles/",
         state.doc.id,
         "/suppl/",
         node.url
@@ -203,7 +215,7 @@ Lens can easily be extended with a customized panel. It can be used to show addi
 - Pull in metrics (click count, number of articles citing that article etc.)
 - Retrieve related articles dynamically (e.g. important ones that reference the existing one)
 
-For demonstration we will look at the implementation of a simple Altmetrics panel. It will pull data asynchronously from the Altmetrics API (http://api.altmetric.com/v1/doi/10.7554/eLife.00005) and render the information in Lens.
+For demonstration we will look at the implementation of a simple Altmetrics panel. It will pull data asynchronously from the Altmetrics API (https://api.altmetric.com/v1/doi/10.7554/eLife.00005) and render the information in Lens.
 
 #### Panel Definition
 
@@ -241,7 +253,7 @@ AltmetricsController.Prototype = function() {
     var doi = this.document.get('publication_info').doi;
 
     $.ajax({
-      url: "http://api.altmetric.com/v1/doi/"+doi,
+      url: "https://api.altmetric.com/v1/doi/"+doi,
       dataType: "json",
     }).done(function(res) {
       cb(null, res);
@@ -335,9 +347,9 @@ Mobile support has been removed with Lens 2.0 to reduce technical debt and itera
 
 ## Credits
 
-Lens was developed in collaboration between [UC Berkeley](http://bioegrad.berkeley.edu/) graduate student [Ivan Grubisic](http://www.linkedin.com/pub/ivan-grubisic/26/353/739) and [eLife](http://elifesciences.org). The team of [Substance](http://substance.io) is helping with the technical execution.
+Lens was developed in collaboration between [UC Berkeley](http://bioegrad.berkeley.edu/) graduate student [Ivan Grubisic](https://www.linkedin.com/pub/ivan-grubisic/26/353/739) and [eLife](https://elifesciences.org). The team of [Substance](http://substance.io) is helping with the technical execution.
 
-Substantial contributions were made by [HighWire](highwire.org), which launched Lens for a number of science journals in fall 2014 (The Journal of Biological Chemistry, The Plant Cell, Journal of Lipid Research, mBio®, and more). [The American Mathematical Society (AMS)](http://ams.org/) made Lens ready for advanced rendering of math articles.
+Substantial contributions were made by [HighWire](http://highwire.org), which launched Lens for a number of science journals in fall 2014 (The Journal of Biological Chemistry, The Plant Cell, Journal of Lipid Research, mBio®, and more). [The American Mathematical Society (AMS)](http://ams.org/) made Lens ready for advanced rendering of math articles.
 
 Thanks go to the following people, who made Lens possible:
 

article/README.md

@@ -1,12 +1,12 @@
 Lens Article
 =====
 
-The Lens Article Format is an implementation the [Substance Document Model](http://github.com/substance/document) dedicated to scientific content. It features basic content types such as paragraphs, headings, and various figure types such as images, tables and videos complete with captions and cross-references.
+The Lens Article Format is an implementation the [Substance Document Model](https://github.com/substance/document) dedicated to scientific content. It features basic content types such as paragraphs, headings, and various figure types such as images, tables and videos complete with captions and cross-references.
 
 The document defintions can be extended easily, so you can either create your own flavour or contribute to the Lens Article Format directly.
 
 ## Why creating another spec for scientific documents?
 
 - XML-based formats such as NML are hard to consume by webclients
 - Strict separation of content and style. Existing formats target print, and thus contain style information, which makes them hard to process by computer programs
-- The greatest advantage of Lens Articles is that any of them can be viewed in [Lens](http://github.com/elifesciences/lens), a modern web-based interface for consuming science content.
+- The greatest advantage of Lens Articles is that any of them can be viewed in [Lens](https://github.com/elifesciences/lens), a modern web-based interface for consuming science content.

article/article_util.js

@@ -19,9 +19,9 @@ util.formatDate = function (pubDate) {
   var parts = pubDate.split("-");
   if (parts.length >= 3) {
     // new Date(year, month [, day [, hours[, minutes[, seconds[, ms]]]]])
-    // Note: months are 0-based
+    // Note: months are 0-based, which are stripped using a regexp
     var localDate = new Date(parts[0], parts[1]-1, parts[2]);
-    return localDate.toUTCString().slice(0, 16);
+    return localDate.toDateString().slice(4, 16).replace(/\b0+/g, '')
   } else if (parts.length === 2) {
     var month = parts[1].replace(/^0/, "");
     var year = parts[0];

article/nodes/_affiliation/affiliation.js

@@ -15,7 +15,8 @@ Affiliation.type = {
     "country": "string",
     "department": "string",
     "institution": "string",
-    "label": "string"
+    "label": "string",
+    "specific_use": "string"
   }
 };
 

article/nodes/citation/citation.js

@@ -90,7 +90,7 @@ Citation.example = {
   "citation_urls": [
     {
       "name": "PubMed",
-      "url": "http://www.ncbi.nlm.nih.gov/pubmed/19606141"
+      "url": "https://www.ncbi.nlm.nih.gov/pubmed/19606141"
     }
   ]
 };

article/nodes/composite/composite_view.js

@@ -16,10 +16,6 @@ CompositeView.Prototype = function() {
   // =============================
   //
 
-  // Render Markup
-  // --------
-  //
-
   this.render = function() {
     NodeView.prototype.render.call(this);
 

article/nodes/contributor/contributor.css

@@ -1,5 +1,5 @@
 /*
-Contributor 
+Contributor
 --------------------------------------- */
 
 .lens-article .resources .content-node.contributor .resource-header .name {
@@ -9,16 +9,16 @@ Contributor
 }
 
 .lens-article .content-node.contributor .content {
-  
+
 }
 
 .lens-article .content-node.contributor .affiliation {
-  margin-top: 10px;
-  font-size: 14px;
+  margin-top: 12px;
+  margin-bottom: 12px;
 }
 
 .lens-article .content-node.contributor .contributor-bio {
-  padding-top: 30px;  
+  padding-top: 30px;
 }
 
 .lens-article .content-node.contributor .contributor-bio .bio {
@@ -44,8 +44,10 @@ Contributor
   margin-bottom: 20px;
 }
 
-.lens-article .content-node.contributor .label {
-  font-size: 14px;
-  margin-top: 20px;
-  color: #999;
-}
+.lens-article .content-node.contributor .contrib-label {
+  font-weight: 600;
+}
+
+.lens-article .content-node.contributor .contrib-data {
+  margin-bottom: 12px;
+}