From ed59208edb7ec75438962334c7c801dbe6ab4aae Mon Sep 17 00:00:00 2001
From: jonascremer <44954750+jonascremer@users.noreply.github.com>
Date: Sun, 31 Dec 2023 19:00:36 -0800
Subject: [PATCH] update publication, show github and paper websites
---
.bundle/config | 2 +
Gemfile | 15 +-
Gemfile.lock | 263 ++++++++++++++++++++++++++++++---
Gemfileold | 9 ++
_data/publications.yml | 5 +-
_pages/publications.md | 5 +-
_posts/2018-06-30-demo-post.md | 105 -------------
7 files changed, 268 insertions(+), 136 deletions(-)
create mode 100644 .bundle/config
create mode 100644 Gemfileold
delete mode 100644 _posts/2018-06-30-demo-post.md
diff --git a/.bundle/config b/.bundle/config
new file mode 100644
index 0000000..10c4c8f
--- /dev/null
+++ b/.bundle/config
@@ -0,0 +1,2 @@
+---
+BUNDLE_CLEAN: "true"
diff --git a/Gemfile b/Gemfile
index 644e340..aa5eb8d 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,8 +1,13 @@
source 'https://rubygems.org'
-gem 'jekyll', '3.8.5'
+gem 'github-pages'
-group :jekyll_plugins do
- gem 'jekyll-paginate'
- gem 'jekyll-sitemap'
-end
\ No newline at end of file
+#gem 'jekyll', '3.8.5'
+
+#group :jekyll_plugins do
+# gem 'jekyll-paginate'
+# gem 'jekyll-sitemap'
+#end
+
+
+gem "webrick", "~> 1.8"
diff --git a/Gemfile.lock b/Gemfile.lock
index 7dbe559..96a5539 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,66 +1,287 @@
GEM
remote: https://rubygems.org/
specs:
- addressable (2.7.0)
- public_suffix (>= 2.0.2, < 5.0)
+ activesupport (7.1.2)
+ base64
+ bigdecimal
+ concurrent-ruby (~> 1.0, >= 1.0.2)
+ connection_pool (>= 2.2.5)
+ drb
+ i18n (>= 1.6, < 2)
+ minitest (>= 5.1)
+ mutex_m
+ tzinfo (~> 2.0)
+ addressable (2.8.6)
+ public_suffix (>= 2.0.2, < 6.0)
+ base64 (0.2.0)
+ bigdecimal (3.1.5)
+ coffee-script (2.4.1)
+ coffee-script-source
+ execjs
+ coffee-script-source (1.11.1)
colorator (1.1.0)
- concurrent-ruby (1.1.8)
- em-websocket (0.5.2)
+ commonmarker (0.23.10)
+ concurrent-ruby (1.2.2)
+ connection_pool (2.4.1)
+ dnsruby (1.70.0)
+ simpleidn (~> 0.2.1)
+ drb (2.2.0)
+ ruby2_keywords
+ em-websocket (0.5.3)
eventmachine (>= 0.12.9)
- http_parser.rb (~> 0.6.0)
+ http_parser.rb (~> 0)
+ ethon (0.16.0)
+ ffi (>= 1.15.0)
eventmachine (1.2.7)
- ffi (1.13.1)
+ execjs (2.9.1)
+ faraday (2.8.1)
+ base64
+ faraday-net_http (>= 2.0, < 3.1)
+ ruby2_keywords (>= 0.0.4)
+ faraday-net_http (3.0.2)
+ ffi (1.16.3)
forwardable-extended (2.6.0)
- http_parser.rb (0.6.0)
- i18n (0.9.5)
+ gemoji (3.0.1)
+ github-pages (228)
+ github-pages-health-check (= 1.17.9)
+ jekyll (= 3.9.3)
+ jekyll-avatar (= 0.7.0)
+ jekyll-coffeescript (= 1.1.1)
+ jekyll-commonmark-ghpages (= 0.4.0)
+ jekyll-default-layout (= 0.1.4)
+ jekyll-feed (= 0.15.1)
+ jekyll-gist (= 1.5.0)
+ jekyll-github-metadata (= 2.13.0)
+ jekyll-include-cache (= 0.2.1)
+ jekyll-mentions (= 1.6.0)
+ jekyll-optional-front-matter (= 0.3.2)
+ jekyll-paginate (= 1.1.0)
+ jekyll-readme-index (= 0.3.0)
+ jekyll-redirect-from (= 0.16.0)
+ jekyll-relative-links (= 0.6.1)
+ jekyll-remote-theme (= 0.4.3)
+ jekyll-sass-converter (= 1.5.2)
+ jekyll-seo-tag (= 2.8.0)
+ jekyll-sitemap (= 1.4.0)
+ jekyll-swiss (= 1.0.0)
+ jekyll-theme-architect (= 0.2.0)
+ jekyll-theme-cayman (= 0.2.0)
+ jekyll-theme-dinky (= 0.2.0)
+ jekyll-theme-hacker (= 0.2.0)
+ jekyll-theme-leap-day (= 0.2.0)
+ jekyll-theme-merlot (= 0.2.0)
+ jekyll-theme-midnight (= 0.2.0)
+ jekyll-theme-minimal (= 0.2.0)
+ jekyll-theme-modernist (= 0.2.0)
+ jekyll-theme-primer (= 0.6.0)
+ jekyll-theme-slate (= 0.2.0)
+ jekyll-theme-tactile (= 0.2.0)
+ jekyll-theme-time-machine (= 0.2.0)
+ jekyll-titles-from-headings (= 0.5.3)
+ jemoji (= 0.12.0)
+ kramdown (= 2.3.2)
+ kramdown-parser-gfm (= 1.1.0)
+ liquid (= 4.0.4)
+ mercenary (~> 0.3)
+ minima (= 2.5.1)
+ nokogiri (>= 1.13.6, < 2.0)
+ rouge (= 3.26.0)
+ terminal-table (~> 1.4)
+ github-pages-health-check (1.17.9)
+ addressable (~> 2.3)
+ dnsruby (~> 1.60)
+ octokit (~> 4.0)
+ public_suffix (>= 3.0, < 5.0)
+ typhoeus (~> 1.3)
+ html-pipeline (2.14.3)
+ activesupport (>= 2)
+ nokogiri (>= 1.4)
+ http_parser.rb (0.8.0)
+ i18n (1.14.1)
concurrent-ruby (~> 1.0)
- jekyll (3.8.5)
+ jekyll (3.9.3)
addressable (~> 2.4)
colorator (~> 1.0)
em-websocket (~> 0.5)
- i18n (~> 0.7)
+ i18n (>= 0.7, < 2)
jekyll-sass-converter (~> 1.0)
jekyll-watch (~> 2.0)
- kramdown (~> 1.14)
+ kramdown (>= 1.17, < 3)
liquid (~> 4.0)
mercenary (~> 0.3.3)
pathutil (~> 0.9)
rouge (>= 1.7, < 4)
safe_yaml (~> 1.0)
+ jekyll-avatar (0.7.0)
+ jekyll (>= 3.0, < 5.0)
+ jekyll-coffeescript (1.1.1)
+ coffee-script (~> 2.2)
+ coffee-script-source (~> 1.11.1)
+ jekyll-commonmark (1.4.0)
+ commonmarker (~> 0.22)
+ jekyll-commonmark-ghpages (0.4.0)
+ commonmarker (~> 0.23.7)
+ jekyll (~> 3.9.0)
+ jekyll-commonmark (~> 1.4.0)
+ rouge (>= 2.0, < 5.0)
+ jekyll-default-layout (0.1.4)
+ jekyll (~> 3.0)
+ jekyll-feed (0.15.1)
+ jekyll (>= 3.7, < 5.0)
+ jekyll-gist (1.5.0)
+ octokit (~> 4.2)
+ jekyll-github-metadata (2.13.0)
+ jekyll (>= 3.4, < 5.0)
+ octokit (~> 4.0, != 4.4.0)
+ jekyll-include-cache (0.2.1)
+ jekyll (>= 3.7, < 5.0)
+ jekyll-mentions (1.6.0)
+ html-pipeline (~> 2.3)
+ jekyll (>= 3.7, < 5.0)
+ jekyll-optional-front-matter (0.3.2)
+ jekyll (>= 3.0, < 5.0)
jekyll-paginate (1.1.0)
+ jekyll-readme-index (0.3.0)
+ jekyll (>= 3.0, < 5.0)
+ jekyll-redirect-from (0.16.0)
+ jekyll (>= 3.3, < 5.0)
+ jekyll-relative-links (0.6.1)
+ jekyll (>= 3.3, < 5.0)
+ jekyll-remote-theme (0.4.3)
+ addressable (~> 2.0)
+ jekyll (>= 3.5, < 5.0)
+ jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+ rubyzip (>= 1.3.0, < 3.0)
jekyll-sass-converter (1.5.2)
sass (~> 3.4)
+ jekyll-seo-tag (2.8.0)
+ jekyll (>= 3.8, < 5.0)
jekyll-sitemap (1.4.0)
jekyll (>= 3.7, < 5.0)
+ jekyll-swiss (1.0.0)
+ jekyll-theme-architect (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-cayman (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-dinky (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-hacker (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-leap-day (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-merlot (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-midnight (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-minimal (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-modernist (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-primer (0.6.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-github-metadata (~> 2.9)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-slate (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-tactile (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-theme-time-machine (0.2.0)
+ jekyll (> 3.5, < 5.0)
+ jekyll-seo-tag (~> 2.0)
+ jekyll-titles-from-headings (0.5.3)
+ jekyll (>= 3.3, < 5.0)
jekyll-watch (2.2.1)
listen (~> 3.0)
- kramdown (1.17.0)
- liquid (4.0.3)
- listen (3.4.0)
+ jemoji (0.12.0)
+ gemoji (~> 3.0)
+ html-pipeline (~> 2.2)
+ jekyll (>= 3.0, < 5.0)
+ kramdown (2.3.2)
+ rexml
+ kramdown-parser-gfm (1.1.0)
+ kramdown (~> 2.0)
+ liquid (4.0.4)
+ listen (3.8.0)
rb-fsevent (~> 0.10, >= 0.10.3)
rb-inotify (~> 0.9, >= 0.9.10)
mercenary (0.3.6)
+ minima (2.5.1)
+ jekyll (>= 3.5, < 5.0)
+ jekyll-feed (~> 0.9)
+ jekyll-seo-tag (~> 2.1)
+ minitest (5.20.0)
+ mutex_m (0.2.0)
+ nokogiri (1.16.0-aarch64-linux)
+ racc (~> 1.4)
+ nokogiri (1.16.0-arm-linux)
+ racc (~> 1.4)
+ nokogiri (1.16.0-arm64-darwin)
+ racc (~> 1.4)
+ nokogiri (1.16.0-x86-linux)
+ racc (~> 1.4)
+ nokogiri (1.16.0-x86_64-darwin)
+ racc (~> 1.4)
+ nokogiri (1.16.0-x86_64-linux)
+ racc (~> 1.4)
+ octokit (4.25.1)
+ faraday (>= 1, < 3)
+ sawyer (~> 0.9)
pathutil (0.16.2)
forwardable-extended (~> 2.6)
- public_suffix (4.0.6)
- rb-fsevent (0.10.4)
+ public_suffix (4.0.7)
+ racc (1.7.3)
+ rb-fsevent (0.11.2)
rb-inotify (0.10.1)
ffi (~> 1.0)
+ rexml (3.2.6)
rouge (3.26.0)
+ ruby2_keywords (0.0.5)
+ rubyzip (2.3.2)
safe_yaml (1.0.5)
sass (3.7.4)
sass-listen (~> 4.0.0)
sass-listen (4.0.0)
rb-fsevent (~> 0.9, >= 0.9.4)
rb-inotify (~> 0.9, >= 0.9.7)
+ sawyer (0.9.2)
+ addressable (>= 2.3.5)
+ faraday (>= 0.17.3, < 3)
+ simpleidn (0.2.1)
+ unf (~> 0.1.4)
+ terminal-table (1.8.0)
+ unicode-display_width (~> 1.1, >= 1.1.1)
+ typhoeus (1.4.1)
+ ethon (>= 0.9.0)
+ tzinfo (2.0.6)
+ concurrent-ruby (~> 1.0)
+ unf (0.1.4)
+ unf_ext
+ unf_ext (0.0.9.1)
+ unicode-display_width (1.8.0)
+ webrick (1.8.1)
PLATFORMS
- universal-darwin-21
+ aarch64-linux
+ arm-linux
+ arm64-darwin
+ x86-linux
+ x86_64-darwin
+ x86_64-linux
DEPENDENCIES
- jekyll (= 3.8.5)
- jekyll-paginate
- jekyll-sitemap
+ github-pages
+ webrick (~> 1.8)
BUNDLED WITH
- 2.2.4
+ 2.5.3
diff --git a/Gemfileold b/Gemfileold
new file mode 100644
index 0000000..d472bfc
--- /dev/null
+++ b/Gemfileold
@@ -0,0 +1,9 @@
+source 'https://rubygems.org'
+
+gem 'jekyll', '3.8.5'
+
+group :jekyll_plugins do
+ gem 'jekyll-paginate'
+ gem 'jekyll-sitemap'
+end
+
diff --git a/_data/publications.yml b/_data/publications.yml
index 62f76f8..ddd648c 100644
--- a/_data/publications.yml
+++ b/_data/publications.yml
@@ -15,12 +15,14 @@
The differing prevalences of propionate and butyrate-producing bacteria in the human gut microbiota
authors: Rebecca Christensen, Yu Han Daisy Wang, Markus Arnoldini, and Jonas Cremer
journal: bioRxiv
+ github: https://github.com/rchristensen26/Butyrate_Propionate_Comparative_Analysis
doi: 10.1101/2023.11.27.568948
- title: >
hplc-py: A Python Package For Rapid Peak Quantification in Complex Chromatograms
authors: Griffin Chure and Jonas Cremer
journal: chemRxiv
doi: 10.26434/chemrxiv-2023-m2n4r
+ paper_website: https://cremerlab.github.io/hplc-py/
github: https://github.com/cremerlab/hplc-py
- title: >
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
@@ -38,7 +40,7 @@
doi: 10.7554/eLife.84878
github: https://github.com/cremerlab/flux_parity
paper_website: https://cremerlab.github.io/flux_parity/
- notes: "Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal: Matching metabolic supply to demand optimizes microbial growth. Trends in Microbiology, 2023."
+ notes: 'Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal: Matching metabolic supply to demand optimizes microbial growth. Trends in Microbiology, 2023 '
2022:
- title: >
@@ -48,6 +50,7 @@
journal: PRL
volume: 129
doi: 10.1103/PhysRevLett.129.138101
+ notes: 'Editor suggestion and featured in Physics'
- title: >
Coordination of gene expression with cell size enables Escherichia coli
to efficiently maintain motility across conditions
diff --git a/_pages/publications.md b/_pages/publications.md
index 3fcae50..66710cd 100644
--- a/_pages/publications.md
+++ b/_pages/publications.md
@@ -16,10 +16,7 @@ featured_image: /images/blackboard.jpg
{% for paper in year[1] %}
{{paper.title}}
{{paper.authors}}
-{{paper.journal}} {{paper.volume}}{{paper.issue}} ({{year[0]}}) doi: `{{paper.doi}}`
-{% if paper.github != "" %}
-GitHub Repository
-{% endif %}
+{{paper.journal}} {{paper.volume}}{{paper.issue}} ({{year[0]}}) doi: `{{paper.doi}}`
{% if paper.github|default() %} GitHub Repository{% endif %}{% if paper.paper_website|default() %} Paper Website {% endif %}{% if paper.notes|default() %}{{paper.notes}} {% endif %}
{% endfor %}
{% endfor %}
diff --git a/_posts/2018-06-30-demo-post.md b/_posts/2018-06-30-demo-post.md
deleted file mode 100644
index d9e75c0..0000000
--- a/_posts/2018-06-30-demo-post.md
+++ /dev/null
@@ -1,105 +0,0 @@
----
-title: 'Demo Post'
-date: 2018-06-30 00:00:00
-description: This page is a demo that shows everything you can do inside portfolio and blog posts.
-featured_image: '/images/demo/demo-square.jpg'
----
-
-
-
-## Demo content
-
-This page is a demo that shows everything you can do inside portfolio and blog posts.
-
-We've included everything you need to create engaging posts about your work, and show off your case studies in a beautiful way.
-
-**Obviously,** we’ve styled up *all the basic* text formatting options [available in markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet).
-
-You can create lists:
-
-* Simple bulleted lists
-* Like this one
-* Are cool
-
-And:
-
-1. Numbered lists
-2. Like this other one
-3. Are great too
-
-You can also add blockquotes, which are shown at a larger width to help break up the layout and draw attention to key parts of your content:
-
-> “Simple can be harder than complex: You have to work hard to get your thinking clean to make it simple. But it’s worth it in the end because once you get there, you can move mountains.”
-
-The theme also supports markdown tables:
-
-| Item | Author | Supports tables? | Price |
-|----------------------|---------------|------------------|-------|
-| Duet Jekyll Theme | Jekyll Themes | Yes | $49 |
-| Index Jekyll Theme | Jekyll Themes | Yes | $49 |
-| Journal Jekyll Theme | Jekyll Themes | Yes | $49 |
-
-And footnotes[^1], which link to explanations[^2] at the bottom of the page[^3].
-
-[^1]: Beautiful modern, minimal theme design.
-[^2]: Powerful features to show off your work.
-[^3]: Maintained and supported by the theme developer.
-
-You can throw in some horizontal rules too:
-
----
-
-### Image galleries
-
-Here's a really neat custom feature we added – galleries:
-
-
-
-Inspired by the Galleries feature from WordPress, we've made it easy to create grid layouts for your images. Just use a bit of simple HTML in your post to create a masonry grid image layout:
-
-```html
-
-```
-
-*See what we did there? Code and syntax highlighting is built-in too!*
-
-Change the number inside the 'columns' setting to create different types of gallery for all kinds of purposes. You can even click on each image to seamlessly enlarge it on the page.
-
----
-
-### Image carousels
-
-Here's another gallery with only one column, which creates a carousel slide-show instead.
-
-A nice little feature: the carousel only advances when it is in view, so your visitors won't scroll down to find it half way through your images.
-
-
-
-
-
- 
-