diff --git a/CHANGELOG.md b/CHANGELOG.md index 29fc0fc..4b25f89 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/CITATION.cff b/CITATION.cff index 6891d10..22d406c 100644 --- a/CITATION.cff +++ b/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" diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index bfe0778..4bbcc12 100644 Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ diff --git a/_cite/requirements.txt b/_cite/requirements.txt index ebfb855..9808e76 100644 --- a/_cite/requirements.txt +++ b/_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 + diff --git a/_data/citations.yaml b/_data/citations.yaml new file mode 100644 index 0000000..0cc985a --- /dev/null +++ b/_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 diff --git a/_members/jane-smith.md b/_members/jane-smith.md new file mode 100644 index 0000000..f4cae89 --- /dev/null +++ b/_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. diff --git a/_members/john-doe.md b/_members/john-doe.md new file mode 100644 index 0000000..0e441c6 --- /dev/null +++ b/_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. diff --git a/_members/sarah-johnson.md b/_members/sarah-johnson.md new file mode 100644 index 0000000..b0d97b4 --- /dev/null +++ b/_members/sarah-johnson.md @@ -0,0 +1,11 @@ +--- +name: Sarah Johnson +image: images/photo.jpg +description: Lead Programmer +role: programmer +links: + email: sarah.johnson@gmail.com + twitter: sarahjohnson +--- + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/blog/index.md b/blog/index.md new file mode 100644 index 0000000..b86f359 --- /dev/null +++ b/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" %} diff --git a/contact/index.md b/contact/index.md index 60dddf5..34323a3 100644 --- a/contact/index.md +++ b/contact/index.md @@ -55,29 +55,3 @@ nav: {% include cols.html col1=col1 col2=col2 %} {% include section.html dark=true %} - -{% capture col1 %} - -{% endcapture %} - -{% capture col2 %} - -{% endcapture %} - -{% capture col3 %} - -{% endcapture %} - -{% include cols.html col1=col1 col2=col2 col3=col3 %} diff --git a/index.md b/index.md index 8e91d46..fe1c62f 100644 --- a/index.md +++ b/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"