diff --git a/_cite/.cache/05/58/d24fe9872ce5648b095dd0e0be5e.val b/_cite/.cache/04/cb/3787b3ce6bbc27bd9803c3372599.val similarity index 99% rename from _cite/.cache/05/58/d24fe9872ce5648b095dd0e0be5e.val rename to _cite/.cache/04/cb/3787b3ce6bbc27bd9803c3372599.val index 5aacc033..cc5fae7f 100644 Binary files a/_cite/.cache/05/58/d24fe9872ce5648b095dd0e0be5e.val and b/_cite/.cache/04/cb/3787b3ce6bbc27bd9803c3372599.val differ diff --git a/_cite/.cache/81/25/01cece46c35745539dce92a4aad2.val b/_cite/.cache/7b/67/3c4f5364e7697a4a2b878562a46b.val similarity index 100% rename from _cite/.cache/81/25/01cece46c35745539dce92a4aad2.val rename to _cite/.cache/7b/67/3c4f5364e7697a4a2b878562a46b.val diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 23ad85ec..90832d39 100644 Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ diff --git a/_data/citations.yaml b/_data/citations.yaml index 835c1027..52609041 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -1340,14 +1340,13 @@ orcid: 0000-0002-0005-0441 plugin: orcid.py file: orcid.yaml -- id: doi:10.5281/ZENODO.18745493 +- id: doi:10.5281/ZENODO.18745492 title: DynamicalSystemFramework authors: - Gregorio Berselli - - Simone Balducci publisher: Zenodo - date: '2026-02-23' - link: https://doi.org/hbqgxc + date: '2026-03-12' + link: https://doi.org/hbszpq orcid: 0009-0004-7797-9138 plugin: orcid.py file: orcid.yaml diff --git a/_includes/meta.html b/_includes/meta.html index 2bcb5775..4838b85d 100644 --- a/_includes/meta.html +++ b/_includes/meta.html @@ -32,9 +32,11 @@ {% assign description = description | xml_escape %} +{% assign svg = "images/icon.svg" | file_exists %} +{% assign logo_svg = "images/logo.svg" | file_exists %} {% assign png = "images/logo.png" | file_exists %} {% assign jpg = "images/icon.jpg" | file_exists %} -{% assign icon = png | default: jpg | relative_url %} +{% assign icon = svg | default: logo_svg | default: png | default: jpg | relative_url %} {% assign jpg = "images/share.jpg" | file_exists %} {% assign png = "images/share.png" | file_exists %} diff --git a/_styles/header.scss b/_styles/header.scss index b2802be4..7664a2c0 100644 --- a/_styles/header.scss +++ b/_styles/header.scss @@ -47,6 +47,25 @@ header a { height: 100%; } +.logo svg { + overflow: visible; +} + +.logo svg path, +.logo svg rect, +.logo svg circle, +.logo svg ellipse, +.logo svg polygon, +.logo svg polyline, +.logo svg line { + stroke: #fff; + stroke-width: 3; + stroke-linecap: round; + stroke-linejoin: round; + paint-order: stroke fill; + vector-effect: non-scaling-stroke; +} + .title-text { display: flex; justify-content: flex-start; @@ -165,4 +184,4 @@ header[data-big] { .subtitle { font-size: var(--large); } -} +} \ No newline at end of file diff --git a/images/icon.png b/images/icon.png deleted file mode 100644 index 0017a6a1..00000000 Binary files a/images/icon.png and /dev/null differ diff --git a/images/icon.svg b/images/icon.svg new file mode 100644 index 00000000..bb79b5d0 --- /dev/null +++ b/images/icon.svg @@ -0,0 +1,285 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/images/logo.png b/images/logo.png deleted file mode 100644 index 0017a6a1..00000000 Binary files a/images/logo.png and /dev/null differ diff --git a/images/logo.svg b/images/logo.svg new file mode 100644 index 00000000..bc2a51ce --- /dev/null +++ b/images/logo.svg @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/testbed.md b/testbed.md deleted file mode 100644 index 1877abfe..00000000 --- a/testbed.md +++ /dev/null @@ -1,444 +0,0 @@ ---- -title: Testbed -header: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -footer: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -header-dark: false -footer-dark: false ---- - -# Testbed - -{% include section.html %} - -# Basic formatting - -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. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. - -[External link](https://some-website.org/) - -[Internal link](team) - -_italic text_ - -**bold text** - -~~strike-through text~~ - -
-
-Text with extra blank lines above and below -
-
- -- list item a -- list item b -- list item c - -1. ordered list item 1 -1. ordered list item 2 -1. ordered list item 3 - - - -1. top level list item - - nested list item - 1. even deeper nested list item - -Plain image: - -![plain image](/images/photo.jpg) - -# Heading 1 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -## Heading 2 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -### Heading 3 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -#### Heading 4 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -##### Heading 5 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -###### Heading 6 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - ---- - -| TABLE | Game 1 | Game 2 | Game 3 | Total | -| :---- | :----: | :----: | :----: | ----: | -| Anna | 144 | 123 | 218 | 485 | -| Bill | 90 | 175 | 120 | 385 | -| Cara | 102 | 214 | 233 | 549 | - -> It was the best of times it was the worst of times. -> It was the age of wisdom, it was the age of foolishness. -> It was the spring of hope, it was the winter of despair. - -```javascript -// some code with syntax highlighting -const popup = document.querySelector("#popup"); -popup.style.width = "100%"; -popup.innerText = - "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua."; -``` - -This sentence has `inline code`, useful for making references to variables, packages, versions, etc. within a sentence. - -Lorem ipsum dolor sit amet. -{:.left} -Consectetur adipiscing elit. -{:.center} -Sed do eiusmod tempor incididunt. -{:.right} - -
-Hidden content - -**Lorem** _ipsum_ [dolor sit amet](), consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -
- -{% include section.html %} - -# Jekyll Spaceship - -| Stage | Direct Products | ATP Yields | -| -----------------: | --------------: | ---------: | -| Glycolysis | 2 ATP | | -| ^^ | 2 NADH | 3--5 ATP | -| Pyruvaye oxidation | 2 NADH | 5 ATP | -| Citric acid cycle | 2 ATP | | -| ^^ | 6 NADH | 15 ATP | -| ^^ | 2 FADH | 3 ATP | -| 30--32 ATP | | | - -$ a \* b = c ^ b $ - -$ 2^{\frac{n-1}{3}} $ - -$ \int_a^b f(x)\,dx. $ - -```mermaid! -pie title Pets adopted by volunteers - "Dogs" : 386 - "Cats" : 85 - "Rats" : 35 -``` - -{% include section.html %} - -# Components - -## Section - -{% include section.html background="images/background.jpg" %} - -Section, `background` - -{% include section.html dark=true %} - -Section, `dark=true` - -{% include section.html background="images/background.jpg" dark=true %} - -Section, `background` `dark=true` - -{% include section.html size="wide" %} - -Section, `size=wide` - -{% include section.html size="full" %} - -Section, `size=full` w/ figure - -{% include figure.html image="https://images.rawpixel.com/image_1000/cHJpdmF0ZS9sci9pbWFnZXMvd2Vic2l0ZS8yMDIyLTA1L2ZsMjYyODgwODcyMjYtaW1hZ2VfMS1rb3k1Zzkxay5qcGc.jpg" link="team" width="100%" %} - -{% include section.html %} - -## Figure - -{% include figure.html image="images/icon.png" %} -{% include figure.html image="images/icon.png" caption="_Lorem_ **ipsum**." %} -{% include figure.html image="images/icon.png" caption="_Lorem_ **ipsum**. `px` width" width="400px" %} -{% include figure.html image="images/icon.png" caption="_Lorem_ **ipsum**. `%` width" link="team" width="50%" %} -{% include figure.html image="images/icon.png" caption="_Lorem_ **ipsum**. `px` height" link="team" height="200px" %} -{% include figure.html image="images/fallback.svg" caption="_Lorem_ **ipsum**. `px` width, svg" link="team" width="400px" %} -{% include figure.html image="images/fallback.svg" caption="_Lorem_ **ipsum**. `%` width, svg" link="team" width="50%" %} -{% include figure.html image="images/fallback.svg" caption="_Lorem_ **ipsum**. `px` height, svg" link="team" height="200px" %} - -{% include section.html %} - -## Button - -{% include button.html type="github" %} -{% include button.html type="github" style="bare" %} -{% include button.html type="github" icon="fa-brands fa-youtube" text="Override Text" tooltip="Override tooltip" %} -{% include button.html type="github" text="" style="bare" %} -{% include button.html type="github" text="" link="github-handle" %} - -{% include section.html %} - -## Icon - -{% include icon.html icon="fa-solid fa-bacteria" %} -{% include icon.html icon="fa-solid fa-virus" %} -{% include icon.html icon="fa-solid fa-flask" %} -{% include icon.html icon="manubot.svg" %} - -{% include icon.html icon="fa-brands fa-github" %} Lorem -{% include icon.html icon="fa-solid fa-microscope" %} Ipsum -{% include icon.html icon="manubot.svg" %} Dolor - -{% include section.html %} - -## Feature - -{% capture text %} -_Lorem_ **ipsum** dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture%} -{% include feature.html image="images/icon.png" link="team" title="Title" text=text %} -{% include feature.html image="images/icon.png" title="Title" text=text flip=true %} -{% include feature.html link="team" %} - -{% include section.html %} - -## List - -### List citations - -{% include list.html data="citations" component="citation" %} - ---- - -### List projects - -{% include list.html data="projects" component="card" %} - ---- - -### List team members - -{% include list.html data="members" component="portrait" %} - ---- - -### List blog posts - -{% include list.html data="posts" component="post-excerpt" %} - -{% include section.html %} - -## Citation - -{% include citation.html lookup="doi:10.1016/j.csbj.2020.05.017" %} -{% include citation.html lookup="Open collaborative writing" style="rich" %} -{% include citation.html title="Manual title" authors="Manual authors" %} - -{% include section.html %} - -## Card - -{% include card.html image="images/icon.png" link="https://nasa.gov/" title="A Large Card" subtitle="A cool card" description="A cool description" tooltip="A cool tooltip" tags="manual tag" repo="greenelab/lab-website-template" %} -{% include card.html image="images/icon.png" title="A Small Card" subtitle="A cool card" description="_Lorem_ **ipsum**" tooltip="A cool tooltip" tags="manual tag" repo="greenelab/lab-website-template" style="small" %} - -{% include section.html %} - -## Portrait - -{% include portrait.html lookup="jane-smith" %} -{% include portrait.html lookup="john-doe" style="small" %} -{% include portrait.html name="Manual name" style="small" %} -{% include portrait.html style="small" %} - -{% include section.html %} - -## Post Excerpt - -{% include post-excerpt.html lookup="example-post-1" %} -{% include post-excerpt.html title="Manual title" author="Manual author" date="2020-02-20" last_modified_at="" %} - -{% include section.html %} - -## Alert - -{% capture lorem %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture %} -{% capture content %}**Tip** {{ lorem }}{% endcapture %} -{% include alert.html type="tip" content=content %} -{% capture content %}**Help** {{ lorem }}{% endcapture %} -{% include alert.html type="help" content=content %} -{% capture content %}**Info** {{ lorem }}{% endcapture %} -{% include alert.html type="info" content=content %} -{% capture content %}**Success** {{ lorem }}{% endcapture %} -{% include alert.html type="success" content=content %} -{% capture content %}**Warning** {{ lorem }}{% endcapture %} -{% include alert.html type="warning" content=content %} -{% capture content %}**Error** {{ lorem }}{% endcapture %} -{% include alert.html type="error" content=content %} - -{% include section.html %} - -## Tags - -{% include tags.html tags="ovarian cancer, dataset, gene expression" repo="greenelab/lab-website-template" link="blog" %} - -{% include section.html %} - -## Float - -### Figures - -{% capture content %} -{% include figure.html image="images/icon.png" caption="Caption" width="200px" %} -{% endcapture %} -{% include float.html content=content %} -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. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. -{% include float.html clear=true %} - -### Code - -{% capture content %} - -```javascript -const test = "Lorem ipsum dolor sit amet, consectetur adipiscing elit."; -``` - -{% endcapture %} -{% include float.html content=content flip=true %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. Tristique magna sit amet purus gravida quis blandit turpis cursus. Ultrices eros in cursus turpis massa tincidunt dui ut ornare. A cras semper auctor neque vitae tempus quam pellentesque nec. At tellus at urna condimentum mattis pellentesque. Ipsum consequat nisl vel pretium. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget gravida. Integer vitae justo eget magna fermentum iaculis eu non diam. Mus mauris vitae ultricies leo integer malesuada nunc vel. Leo integer malesuada nunc vel risus. Ornare arcu odio ut sem nulla pharetra. Purus semper eget duis at tellus at urna condimentum. Enim neque volutpat ac tincidunt vitae semper quis lectus. - -{% include section.html %} - -## Grid - -### Regular - -With Markdown images - -{% capture content %} -![image](https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2) - -![image](https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg) - -![image](https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp) - -![image]({{ "/images/icon.png" | relative_url }}) - -![image]({{ "/images/icon.png" | relative_url }}) - -![image]({{ "/images/icon.png" | relative_url }}) -{% endcapture %} -{% include grid.html content=content %} - -### Square - -With figure components - -{% capture content %} -{% include figure.html image="https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2" %} -{% include figure.html image="https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg" %} -{% include figure.html image="https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp" %} -{% include figure.html image="images/icon.png" %} -{% include figure.html image="images/icon.png" %} -{% include figure.html image="images/icon.png" %} -{% endcapture %} -{% include grid.html style="square" content=content %} - -### Grid of citations - -{% capture content %} -{% include list.html data="citations" component="citation" style="rich" %} -{% endcapture %} -{% include grid.html content=content %} - -### Grid of blog posts - -{% capture content %} -{% include list.html data="posts" component="post-excerpt" %} -{% endcapture %} -{% include grid.html content=content %} - -{% include section.html %} - -## Cols - -### Text - -{% capture col1 %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture %} -{% capture col2 %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. -{% endcapture %} -{% capture col3 %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. Tristique magna sit amet purus gravida quis blandit turpis cursus. Ultrices eros in cursus turpis massa tincidunt dui ut ornare. A cras semper auctor neque vitae tempus quam pellentesque nec. At tellus at urna condimentum mattis pellentesque. Ipsum consequat nisl vel pretium. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget gravida. Integer vitae justo eget magna fermentum iaculis eu non diam. Mus mauris vitae ultricies leo integer malesuada nunc vel. Leo integer malesuada nunc vel risus. Ornare arcu odio ut sem nulla pharetra. Purus semper eget duis at tellus at urna condimentum. Enim neque volutpat ac tincidunt vitae semper quis lectus. -{% endcapture %} -{% include cols.html col1=col1 col2=col2 col3=col3 %} - -### Images - -{% capture col1 %} -{% include figure.html image="images/icon.png" caption="Fig. 1a" %} -Lorem _ipsum_ dolor **sit** amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture %} -{% capture col2 %} -{% include figure.html image="images/icon.png" caption="Fig. 1b" %} -Lorem _ipsum_ dolor **sit** amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture %} -{% capture col3 %} -{% include figure.html image="images/icon.png" caption="Fig. 1c" %} -Lorem _ipsum_ dolor **sit** amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -{% endcapture %} -{% include cols.html col1=col1 col2=col2 col3=col3 %} - -### Code - -{% capture col1 %} - -```javascript -const test = "Lorem ipsum dolor sit amet"; -``` - -{% endcapture %} -{% capture col2 %} - -```javascript -const test = "Lorem ipsum dolor sit amet"; -``` - -{% endcapture %} -{% capture col3 %} - -```javascript -const test = "Lorem ipsum dolor sit amet"; -``` - -{% endcapture %} -{% include cols.html col1=col1 col2=col2 col3=col3 %} - -{% include section.html %} - -## Search - -{% include search-box.html %} -{% include search-info.html %} - -{% include section.html %} - -## Site Search - -{% include site-search.html %}