Merge remote-tracking branch 'template/main'

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 Reference: common-changelog.org
 
+## 1.1.6 - 2023-10-06
+
+- Use latest minor versions of Python packages in auto-cite script.
+
 ## 1.1.5 - 2023-05-19
 
 ### Changes

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.1.5
-date-released: 2023-05-19
+version: 1.1.6
+date-released: 2023-10-06
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_cite/requirements.txt

@@ -1,6 +1,7 @@
 manubot~=0.6
-PyYAML==6.0
-diskcache==5.4.0
-rich==12.6.0
-python-dotenv==0.21.0
-google-search-results==2.4.1
+PyYAML~=6.0
+diskcache~=5.6
+rich~=13.6
+python-dotenv~=0.21
+google-search-results~=2.4
+

_data/citations.yaml

@@ -0,0 +1,155 @@
+# DO NOT EDIT, GENERATED AUTOMATICALLY
+
+- id: doi:10.1093/nar/gkad289
+  title: 'MyGeneset.info: an interactive and programmatic platform for community-curated
+    and user-created collections of genes'
+  authors:
+  - Ricardo Avila
+  - Vincent Rubinetti
+  - Xinghua Zhou
+  - Dongbo Hu
+  - Zhongchao Qian
+  - Marco Alvarado Cano
+  - Everaldo Rodolpho
+  - Ginger Tsueng
+  - Casey Greene
+  - Chunlei Wu
+  publisher: Nucleic Acids Research
+  date: '2023-04-18'
+  link: https://doi.org/gr5hb5
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1101/2023.01.05.522941
+  title: Hetnet connectivity search provides rapid insights into how two biomedical
+    entities are related
+  authors:
+  - Daniel S. Himmelstein
+  - Michael Zietz
+  - Vincent Rubinetti
+  - Kyle Kloster
+  - Benjamin J. Heil
+  - Faisal Alquaddoomi
+  - Dongbo Hu
+  - David N. Nicholson
+  - Yun Hao
+  - Blair D. Sullivan
+  - Michael W. Nagle
+  - Casey S. Greene
+  publisher: Cold Spring Harbor Laboratory
+  date: '2023-01-07'
+  link: https://doi.org/grmcb9
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1093/gigascience/giad047
+  title: Hetnet connectivity search provides rapid insights into how biomedical entities
+    are related
+  authors:
+  - Daniel S Himmelstein
+  - Michael Zietz
+  - Vincent Rubinetti
+  - Kyle Kloster
+  - Benjamin J Heil
+  - Faisal Alquaddoomi
+  - Dongbo Hu
+  - David N Nicholson
+  - Yun Hao
+  - Blair D Sullivan
+  - Michael W Nagle
+  - Casey S Greene
+  publisher: GigaScience
+  date: '2022-12-28'
+  link: https://doi.org/gsd85n
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1186/s13059-020-02021-3
+  title: Compressing gene expression data using multiple latent space dimensionalities
+    learns complementary biological representations
+  authors:
+  - Gregory P. Way
+  - Michael Zietz
+  - Vincent Rubinetti
+  - Daniel S. Himmelstein
+  - Casey S. Greene
+  publisher: Genome Biology
+  date: '2020-05-11'
+  link: https://doi.org/gg2mjh
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1371/journal.pcbi.1007128
+  title: Open collaborative writing with Manubot
+  authors:
+  - Daniel S. Himmelstein
+  - Vincent Rubinetti
+  - David R. Slochower
+  - Dongbo Hu
+  - Venkat S. Malladi
+  - Casey S. Greene
+  - Anthony Gitter
+  publisher: PLOS Computational Biology
+  date: '2020-12-04'
+  link: https://doi.org/c7np
+  orcid: 0000-0002-4655-3773
+  plugin: sources.py
+  file: sources.yaml
+  type: paper
+  description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed
+    do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+  image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2
+  buttons:
+  - type: manubot
+    link: https://greenelab.github.io/meta-review/
+  - type: source
+    text: Manuscript Source
+    link: https://github.com/greenelab/meta-review
+  - type: website
+    link: http://manubot.org/
+  tags:
+  - open science
+  - collaboration
+  repo: greenelab/meta-review
+- id: doi:10.1101/573782
+  title: Sequential compression of gene expression across dimensionalities and methods
+    reveals no single best method or dimensionality
+  authors:
+  - Gregory P. Way
+  - Michael Zietz
+  - Vincent Rubinetti
+  - Daniel S. Himmelstein
+  - Casey S. Greene
+  publisher: Cold Spring Harbor Laboratory
+  date: '2019-03-11'
+  link: https://doi.org/gfxjxf
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1016/j.csbj.2020.05.017
+  title: Constructing knowledge graphs and their biomedical applications
+  authors:
+  - David N. Nicholson
+  - Casey S. Greene
+  publisher: Computational and Structural Biotechnology Journal
+  date: '2020-01-01'
+  link: https://doi.org/gg7m48
+  image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg
+  plugin: sources.py
+  file: sources.yaml
+- id: doi:10.7554/eLife.32822
+  title: Sci-Hub provides access to nearly all scholarly literature
+  authors:
+  - Daniel S Himmelstein
+  - Ariel Rodriguez Romero
+  - Jacob G Levernier
+  - Thomas Anthony Munro
+  - Stephen Reid McLaughlin
+  - Bastian Greshake Tzovaras
+  - Casey S Greene
+  publisher: eLife
+  date: '2018-03-01'
+  link: https://doi.org/ckcj
+  image: https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp
+  plugin: sources.py
+  file: sources.yaml

_members/jane-smith.md

@@ -0,0 +1,19 @@
+---
+name: Jane Smith
+image: images/photo.jpg
+role: pi
+aliases:
+  - J. Smith
+  - J Smith
+links:
+  home-page: https://janesmith.com
+  orcid: 0000-0001-8713-9213
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+Faucibus purus in massa tempor nec feugiat nisl pretium fusce.
+Elit at imperdiet dui accumsan.
+Duis tristique sollicitudin nibh sit amet commodo nulla facilisi.
+Vitae elementum curabitur vitae nunc sed velit dignissim sodales.
+Lacinia at quis risus sed vulputate odio ut.
+Magna eget est lorem ipsum.

_members/john-doe.md

@@ -0,0 +1,10 @@
+---
+name: John Doe
+image: images/photo.jpg
+role: phd
+group: alum
+links:
+  github: john-doe
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

_members/sarah-johnson.md

@@ -0,0 +1,11 @@
+---
+name: Sarah Johnson
+image: images/photo.jpg
+description: Lead Programmer
+role: programmer
+links:
+  email: [email protected]
+  twitter: sarahjohnson
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

blog/index.md

@@ -0,0 +1,21 @@
+---
+title: Blog
+nav:
+  order: 4
+  tooltip: Musings and miscellany
+---
+
+# {% include icon.html icon="fa-solid fa-feather-pointed" %}Blog
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+
+{% include section.html %}
+
+{% include search-box.html %}
+
+{% include tags.html tags=site.tags %}
+
+{% include search-info.html %}
+
+{% include list.html data="posts" component="post-excerpt" %}

contact/index.md

@@ -55,29 +55,3 @@ nav:
 {% include cols.html col1=col1 col2=col2 %}
 
 {% include section.html dark=true %}
-
-{% capture col1 %}
-<!-- 
-Lorem ipsum dolor sit amet  
-consectetur adipiscing elit  
-sed do eiusmod tempor
--->
-{% endcapture %}
-
-{% capture col2 %}
-<!-- 
-Lorem ipsum dolor sit amet  
-consectetur adipiscing elit  
-sed do eiusmod tempor
--->
-{% endcapture %}
-
-{% capture col3 %}
-<!-- 
-Lorem ipsum dolor sit amet  
-consectetur adipiscing elit  
-sed do eiusmod tempor
--->
-{% endcapture %}
-
-{% include cols.html col1=col1 col2=col2 col3=col3 %}

index.md

@@ -23,7 +23,6 @@ patients with relevant expertise and to perform genomics at scale.
 {% capture text %}
 
 
-
 {%
   include button.html
   link="research"
@@ -70,7 +69,6 @@ patients with relevant expertise and to perform genomics at scale.
 {% capture text %}
 
 
-
 {%
   include button.html
   link="team"