greene website

Author: kingston-aditya

404.md

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+---
+title: 404
+permalink: /404.html
+---
+
+{:.center}
+Page not found :(
+
+{:.center}
+The page you're looking for may have moved.
+Try [searching the whole site](https://www.google.com/search?q=site%3A{{ "" | absolute_url }}) for the content you want.

CNAME

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+greenelab.com

Gemfile

@@ -1,3 +1,17 @@
-source 'https://rubygems.org'
+source "https://rubygems.org"
 
-gem 'jekyll'
+gem "jekyll"
+group :jekyll_plugins do
+  gem "jekyll-feed"
+  gem "jekyll-redirect-from"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", "~> 1.2"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]

Gemfile.lock

@@ -1,63 +1,82 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.5.2)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     colorator (1.1.0)
-    concurrent-ruby (1.1.3)
-    em-websocket (0.5.1)
+    concurrent-ruby (1.1.7)
+    em-websocket (0.5.2)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
-    eventmachine (1.2.7)
-    ffi (1.9.25)
+    eventmachine (1.2.7-x64-mingw32)
+    ffi (1.13.1-x64-mingw32)
     forwardable-extended (2.6.0)
     http_parser.rb (0.6.0)
-    i18n (0.9.5)
+    i18n (1.8.5)
       concurrent-ruby (~> 1.0)
-    jekyll (3.8.5)
+    jekyll (4.1.1)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (~> 0.7)
-      jekyll-sass-converter (~> 1.0)
+      i18n (~> 1.0)
+      jekyll-sass-converter (~> 2.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 1.14)
+      kramdown (~> 2.1)
+      kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
-      mercenary (~> 0.3.3)
+      mercenary (~> 0.4.0)
       pathutil (~> 0.9)
-      rouge (>= 1.7, < 4)
+      rouge (~> 3.0)
       safe_yaml (~> 1.0)
-    jekyll-sass-converter (1.5.2)
-      sass (~> 3.4)
-    jekyll-watch (2.1.2)
+      terminal-table (~> 1.8)
+    jekyll-feed (0.15.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-sass-converter (2.1.0)
+      sassc (> 2.0.1, < 3.0)
+    jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (1.17.0)
-    liquid (4.0.1)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
-    mercenary (0.3.6)
+    kramdown (2.3.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.3)
+    listen (3.3.1)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.4.0)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (3.0.3)
-    rb-fsevent (0.10.3)
-    rb-inotify (0.9.10)
-      ffi (>= 0.5.0, < 2)
-    rouge (3.3.0)
-    ruby_dep (1.5.0)
-    safe_yaml (1.0.4)
-    sass (3.7.2)
-      sass-listen (~> 4.0.0)
-    sass-listen (4.0.0)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
+    public_suffix (4.0.6)
+    rb-fsevent (0.10.4)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    rexml (3.2.4)
+    rouge (3.25.0)
+    safe_yaml (1.0.5)
+    sassc (2.4.0-x64-mingw32)
+      ffi (~> 1.9)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    thread_safe (0.3.6)
+    tzinfo (1.2.8)
+      thread_safe (~> 0.1)
+    tzinfo-data (1.2020.4)
+      tzinfo (>= 1.0.0)
+    unicode-display_width (1.7.0)
+    wdm (0.1.1)
 
 PLATFORMS
-  ruby
+  x64-mingw32
 
 DEPENDENCIES
   jekyll
+  jekyll-feed
+  jekyll-redirect-from
+  tzinfo (~> 1.2)
+  tzinfo-data
+  wdm (~> 0.1.1)
 
 BUNDLED WITH
-   1.16.2
+   2.1.4

README.md

@@ -1,3 +1,5 @@
-# Mangul Lab
+<h1 align="center">Greene Lab Website</h1>
+<p align="center"><img height="200" src="https://raw.githubusercontent.com/greenelab/brand/master/text/for-light-bg.png?raw=true" alt="Lab Website Template"></p>
 
-University of Southern California
+This website was generated from the Greene Lab's own [`lab-website-template`](https://github.com/greenelab/lab-website-template).
+See its readme for documentation on how to work with this site.

_config.yml

@@ -1,40 +1,55 @@
-# Welcome to Jekyll!
-#
-# This config file is meant for settings that affect your whole blog, values
-# which you are expected to set up once and rarely need to edit after that.
-# For technical reasons, this file is *NOT* reloaded automatically when you use
-# 'jekyll serve'. If you change this file, please restart the server process.
+# https://jekyllrb.com/docs/configuration/
 
-# Site settings
-title: The Sanders Lab
-email: [email protected]
-description: 
+# site-wide variables
+title: The Greene Lab # title of site, used in tab name and elsewhere
+email: [email protected] # default email
+google: Casey Greene # default name to search on Google Scholar
+github: greenelab # default GitHub user/org, without the @
+twitter: GreeneScientist # default Twitter handle, without the @
+instagram: greenelab # default Instagram handle, without the @
+youtube: "" # default YouTube channel handle
+
+# base directory where site is hosted
+# set to "" if hosting at a custom domain, eg yoursite.com
 baseurl: ""
-url: ""
 
-include:
-  - .htaccess
-  - _pages
+# default front matter parameters for markdown files
+# defaults can be overridden on a particular page, eg:
+# ---
+# description: Description unique to this page
+# background: images/different-bg-for-this-page.jpg
+# ---
+defaults:
+  # all markdown files
+  - scope:
+      path: ""
+    values:
+      description: Where data and biology # description that will show under search engine results
+      background: images/backgrounds/laptop-paper.jpg # background image in header and footer
+      layout: default
+  # markdown files in /_members
+  - scope:
+      type: "members"
+    values:
+      layout: member
+  # markdown files in /_posts
+  - scope:
+      type: "posts"
+    values:
+      layout: post
+
+collections:
+  members:
+    output: true
 
+# sass settings
 sass:
-  sass_dir: _sass
+  sass_dir: css
 
-# Conversion
-markdown: kramdown
+# syntax highlighting
 highlighter: rouge
-lsi: false
-excerpt_separator: "\n\n"
-incremental: false
-
-# Markdown Processing
-kramdown:
-  input: GFM
-  hard_wrap: false
-  auto_ids: true
-  footnote_nr: 1
-  entity_output: as_char
-  toc_levels: 1..6
-  smart_quotes: lsquo,rsquo,ldquo,rdquo
-  enable_coderay: false
-  parse_block_html: true # default for kramdown is false. This will enable using Markdown links
 
+# build settings
+plugins:
+  - jekyll-feed
+  - jekyll-redirect-from

_data/.DS_Store

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+# a script to automatically generate citations for papers the research list component
+
+# before running:
+# install python                    https://www.python.org/downloads/
+# install pip                       https://pip.pypa.io/en/stable/installing/
+# install manubot                   https://github.com/manubot/manubot#installation
+
+import sys
+import os
+import json
+import yaml
+import subprocess
+from datetime import datetime
+
+# input and output files
+current_dir = os.path.dirname(os.path.realpath(__file__))
+input_file = os.path.join(current_dir, "research-input.yml")
+output_file = os.path.join(current_dir, "research-output.yml")
+
+# load input papers as yaml
+try:
+    with open(input_file, encoding="utf8") as file:
+        input_papers = yaml.load(file, Loader=yaml.FullLoader)
+except Exception:
+    print("Problem with input file.")
+    sys.exit(1)
+
+# load existing output papers as yaml
+try:
+    with open(output_file, encoding="utf8") as file:
+        output_papers = yaml.load(file, Loader=yaml.FullLoader)
+except Exception:
+    output_papers = []
+
+# get citation metadata for each paper
+new_papers = []
+for index, input_paper in enumerate(input_papers, start=1):
+    # show progress
+    print("\n------------------------------")
+    print(f"Paper {index} of {len(input_papers)}")
+    print("------------------------------\n")
+
+    # if input paper already exists in output, use that citation info to save time
+    matches = [p for p in output_papers if p.get("id", "") == input_paper.get("id", "")]
+    if len(matches) > 0:
+        print("Paper already in output. Using existing citation.")
+        new_papers.append(matches[0])
+
+    # otherwise, run manubot to get new citation metadata
+    else:
+        print("Paper not in output. Running Manubot to generate citation.\n")
+        commands = ["manubot", "cite", input_paper["id"], "--log-level", "DEBUG"]
+        output = subprocess.Popen(commands, stdout=subprocess.PIPE)
+        citation = json.loads(output.communicate()[0])[0]
+
+        # take only the needed info from the citation
+        new_paper = {}
+        # output_ title
+        new_paper["title"] = citation.get("title", "")
+        # output_ authors
+        new_paper["authors"] = []
+        for author in citation.get("author", []):
+            new_author = author.get("given", "") + " " + author.get("family", "")
+            new_paper["authors"].append(new_author)
+        # output_ publisher
+        new_paper["publisher"] = citation.get("container-title", citation.get("publisher", citation.get("collection-title", "")))
+        # output_ date
+        date_parts = citation.get("issued").get("date-parts")[0]
+        date_parts += (3 - len(date_parts)) * [1] # default month and day to 1
+        new_paper["date"] = "-".join([str(part) for part in date_parts])
+        # output_ link
+        new_paper["link"] = citation.get("URL", "")
+        # add to list
+        new_papers.append(new_paper)
+
+# merge any extra properties specified in the input papers into the final output
+print("\nCopying additional metadata from input to output.")
+for index, new_paper in enumerate(new_papers):
+    new_paper.update(input_papers[index])
+    # ensure date in proper format (w/ leading 0's) for correct date sorting
+    new_paper["date"] = datetime.strptime(new_paper["date"], "%Y-%m-%d").strftime("%Y-%m-%d")
+
+# write new list of papers to output file
+with open(output_file, mode="w") as file:
+    yaml.dump(new_papers, file, default_flow_style=False, sort_keys=False)