diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 007b6607..e102164f 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -11,13 +11,13 @@ jobs: deploy: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 with: submodules: true # Fetch Hugo themes (true OR recursive) fetch-depth: 1 # Fetch all history for .GitInfo and .Lastmod - name: Setup Hugo - uses: peaceiris/actions-hugo@v2 + uses: peaceiris/actions-hugo@v3 with: hugo-version: "latest" extended: true @@ -26,14 +26,14 @@ jobs: run: hugo --buildFuture --minify - name: Deploy - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 if: github.ref == 'refs/heads/main' with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./public - name: Upload page build as artifact - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 if: github.ref != 'refs/heads/main' with: name: scverse.github.io diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f9393d19..ecb21d93 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,3 +6,14 @@ repos: additional_dependencies: - prettier - prettier-plugin-go-template + - repo: https://github.com/ericmjl/webp-pre-commit + rev: v0.0.12 + hooks: + # Convert only blog images + - id: convert-to-webp + files: ^static/img/blog/.*\.(png|jpe?g|gif|bmp|tiff)$ + - repo: https://github.com/shssoichiro/oxipng + rev: v10.2.0 + hooks: + - id: oxipng + args: [--strip, safe] diff --git a/assets/main.scss b/assets/main.scss index 8a3ee6e1..7bdb074c 100644 --- a/assets/main.scss +++ b/assets/main.scss @@ -95,45 +95,38 @@ $additionalInfoColor: #666666; } } -@mixin button-icon { - display: inline-block; - height: 1rem; - width: 1rem; - content: ""; - padding: 0; - margin: 0; +@each $icon in zulip, discourse, bluesky { + .i-#{$icon}::before { + display: inline-block; + height: 1rem; + width: 1rem; + content: ""; + padding: 0; + margin: 0; + background: url("/img/icons/#{$icon}.svg") no-repeat center / contain; + transition: + background 200ms ease-out, + filter 200ms ease-out; + opacity: 0.6666; // text color is #555 + .card:hover & { + opacity: 1; + } + } } -.i-zulip::before { - background: url("/img/icons/zulip.svg") no-repeat top left; - transition: background 200ms ease-out; - @include button-icon; -} -.i-discourse::before { - background: url("/img/icons/discourse.svg") no-repeat top left; - transition: background 200ms ease-out; - @include button-icon; -} .i-xcom::before { content: "𝕏"; font-weight: 900; - transition: background 200ms ease-out; -} -.i-bluesky::before { - background: center / contain no-repeat url("/img/icons/bluesky.svg"); - transition: all 200ms ease-out; - @include button-icon; + transition: + background 200ms ease-out, + filter 200ms ease-out; } .card:hover { - .i-zulip::before { - background: url("/img/icons/zulip_inv.svg") no-repeat top left; - } - .i-discourse::before { - background: url("/img/icons/discourse_inv.svg") no-repeat top left; - } + // Not discord, since it’s light-colored + .i-zulip::before, .i-bluesky::before { - filter: invert(1); + filter: invert(100%); } } @@ -143,27 +136,45 @@ $additionalInfoColor: #666666; border: none; } -#badges .btn-github:hover { +#join-content .card { + h5 { + font-weight: 700; + } + transition: all 200ms ease-in-out; + color: $navtext; + &:hover { + background: #78cbd9 !important; + transform: scale(1.02); + } +} + +#badges .btn-github:hover, +#join-content .card#github:hover { background-color: $github-black !important; color: white !important; } -#badges .btn-discourse:hover { +#badges .btn-discourse:hover, +#join-content .card#discourse:hover { background-color: $discourse-yellow !important; color: black !important; } -#badges .btn-zulip:hover { +#badges .btn-zulip:hover, +#join-content .card#zulip:hover { background-color: $zulip-blue !important; color: white !important; } -#badges .btn-twitter:hover { +#badges .btn-twitter:hover, +#join-content .card#twitter:hover { background-color: $twitter-blue !important; color: white !important; } -#badges .btn-bluesky:hover { +#badges .btn-bluesky:hover, +#join-content .card#bluesky:hover { background-color: $bluesky-blue !important; color: white !important; } -#badges .btn-youtube:hover { +#badges .btn-youtube:hover, +#join-content .card#youtube:hover { background-color: $youtube-red !important; color: white !important; } @@ -300,7 +311,7 @@ body { #scverse-logo { width: 3rem; height: 3rem; - background: url("/img/icons/scverse_bw_logo.svg") no-repeat top left; + background: url("/img/icons/scverse-bw-logo.svg") no-repeat top left; &:hover { transform: scale(1.1); } @@ -730,43 +741,6 @@ body { } } -#join-content { - .card { - h5 { - font-weight: 700; - } - transition: all 200ms ease-in-out; - color: $navtext; - &:hover { - background: #78cbd9 !important; - transform: scale(1.02); - } - &#github:hover { - color: white; - background-color: $github-black !important; - } - &#twitter:hover { - color: white; - background-color: $twitter-blue !important; - } - &#zulip:hover { - color: white; - background-color: $zulip-blue !important; - } - &#discourse:hover { - background-color: $discourse-yellow !important; - } - &#youtube:hover { - color: white; - background-color: $youtube-red !important; - } - &#bluesky:hover { - color: white; - background-color: $bluesky-blue !important; - } - } -} - #page-content { display: flex; flex-direction: column; diff --git a/content/blog/2024-conference-summary.md b/content/blog/2024-conference-summary.md index 5d1474cc..9d34f37f 100644 --- a/content/blog/2024-conference-summary.md +++ b/content/blog/2024-conference-summary.md @@ -6,7 +6,7 @@ author = "Roshan Sharma" draft = false +++ -Group photo from the scverse conference +Group photo from the scverse conference @@ -25,7 +25,7 @@ The conference had 6 keynotes from leaders of the field and founders of Scanpy/s You can learn more about what each of our speakers discussed by checking out the amazing [keynote sketches](https://lazappi.id.au/posts/2024-09-15-scverse-conference/) made by conference attendee Luke Zappia. -Keynote speakers and slides +Keynote speakers and slides ### Short talks @@ -33,7 +33,7 @@ The conference also featured several 15-minute short talks, each followed by a Q The presenters were primarily graduate students and postdoctoral researchers from various academic labs. We believe that providing opportunities for junior scientists to showcase their work and receive constructive feedback is crucial to fostering their growth. This format also allowed the audience to delve into the finer details of each method, complementing the broader discussions. Each short talk sparked extensive conversations, a testament to the effectiveness of this approach. Many attendees expressed their appreciation (some vignettes below) for the inclusion of these talks, particularly for highlighting the contributions of early-career researchers and promoting their visibility within the community. -Short talks and presenters +Short talks and presenters ### Workshops @@ -43,19 +43,19 @@ The workshops covered a wide range of topics, from live-coding demonstrations an The workshops were widely regarded as one of the conference’s major highlights, as reflected in the enthusiastic feedback from participants (see examples below). -People participating in workshops +People participating in workshops ### Poster session The conference also featured a poster session, where participants showcased their research and engaged in discussions with attendees. A total of 51 posters were presented during the two-hour session, providing ample opportunity for in-depth conversations and knowledge exchange. -Posters and discussions +Posters and discussions ### Sponsor talks The conference would not have been possible without the generous support of our sponsors. We were honored to receive sponsorships from [CZI](https://chanzuckerberg.com/) (Diamond), [Immunai](https://www.immunai.com/) (Platinum), [Altos](https://www.altoslabs.com/) (Gold), [10x Genomics](https://www.10xgenomics.com/) (Gold), [tilDB](https://tiledb.com/) (Gold), [Lamin](https://lamin.ai/) (Silver), [Latch Bio](https://latch.bio/) (Silver), [Data Intuitive](https://www.data-intuitive.com/) (Silver) and [Boehringer-Ingelheim](https://www.boehringer-ingelheim.com/de) (Silver). As part of the sponsor engagement, 10x Genomics delivered a brief presentation on their latest initiatives, CZI hosted a workshop and gave a short talk, and Immunai presented their latest research. The conference also provided an excellent opportunity for participants to network with industry leaders, fostering collaboration and knowledge exchange. -Logos of the conference sponsors +Logos of the conference sponsors ### Vignettes from participants diff --git a/content/blog/2025-07-biomni.md b/content/blog/2025-07-biomni.md index ff0e2383..b49626ba 100644 --- a/content/blog/2025-07-biomni.md +++ b/content/blog/2025-07-biomni.md @@ -6,7 +6,7 @@ author = "scverse team & Biomni team" draft = false +++ -scverse × Biomni partnership banner +scverse × Biomni partnership banner Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses. Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges. @@ -64,7 +64,7 @@ Instead of writing and debugging code across several libraries, you can now exec - [✓] Driver pathway identification (completed) - [✓] Generate comprehensive HTML report (completed) -Biomni interface +Biomni interface Biomni has successfully completed these steps in around 20 minutes. It preprocesses the data, identifies 21 distinct cell types from 17,771 high-quality cells, and maps them across spatial axes with clear anterior-posterior and dorsal-ventral organization. diff --git a/content/blog/2025-11-biocontextai.md b/content/blog/2025-11-biocontextai.md index 87b52b89..774b3180 100644 --- a/content/blog/2025-11-biocontextai.md +++ b/content/blog/2025-11-biocontextai.md @@ -13,7 +13,7 @@ BioContextAI provides a community registry for Model Context Protocol (MCP) serv These are standardized tools that allow AI systems to access specialized databases and software. This project was recently published as a [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and we are actively starting to explore and contribute scverse MCP servers. -BioContextAI overview +BioContextAI overview ## What we're building diff --git a/content/blog/2025-conference-summary.md b/content/blog/2025-conference-summary.md index 3740c73d..13aadc0e 100644 --- a/content/blog/2025-conference-summary.md +++ b/content/blog/2025-conference-summary.md @@ -7,14 +7,14 @@ draft = false +++
- Group photo from the scverse conference 2025 + Group photo from the scverse conference 2025
Attendees gather for a group photo at Stanford University
The 2nd scverse conference at Stanford University, Palo Alto, California, on November 17-19, 2025 brought together developers and scientists from academia and industry to discuss the latest advances in computational tools and experimental techniques for single cell and spatial multi omics.
- Conference in numbers infographic + Conference in numbers infographic
The conference in numbers
@@ -31,7 +31,7 @@ The conference in numbers: The conference was sold out one month in advance!
- Sponsors and travel awards + Sponsors and travel awards
Our generous sponsors and travel award recipients
@@ -43,7 +43,7 @@ Thanks to our generous sponsors, the scverse conference was also able to provide ### Keynote Speakers
- John Marioni keynote + John Marioni keynote
John Marioni, Genentech
@@ -79,11 +79,11 @@ The second day broadened the scope to RNA splicing, spatial technologies, and ec
- Short talks presenter + Short talks presenter
Short talk presentations
- Panel discussion + Panel discussion
Agentic workflows panel discussion
@@ -103,11 +103,11 @@ The discussion revolved around diverse topics, from technical discussions on [Mo
- Workshop session + Workshop session
Participants of the Biohub Workshop
- Workshop session + Workshop session
Interactive session at Biohub
@@ -127,10 +127,10 @@ The Tahoe workshop emphasized computational scalability and the emerging role of ### Poster Session
- Poster session - Poster session - Poster session - Poster session + Poster session + Poster session + Poster session + Poster session
During the two days of the conference, a total of 88 posters were presented, where participants had the chance to engage in deeper discussions about their work across the scverse ecosystem. diff --git a/content/blog/2025-core-expansion.md b/content/blog/2025-core-expansion.md index e62a8954..462509d6 100644 --- a/content/blog/2025-core-expansion.md +++ b/content/blog/2025-core-expansion.md @@ -26,7 +26,7 @@ Built in Rust with a Python front end, it handles millions of cells efficiently. The package offers preprocessing, dimensionality reduction, clustering, and visualization methods. All outputs are stored in AnnData and integrate seamlessly with scanpy and other scverse frameworks. -SnapATAC2 overview +SnapATAC2 overview ## rapids-singlecell @@ -36,7 +36,7 @@ Core steps—including PCA, neighborhood graph construction, and clustering—ar RSC integrates directly with AnnData and offers near drop-in replacements not only for scanpy, but also for selected functions from decoupler and squidpy. By preserving familiar APIs and data structures, it enables seamless GPU acceleration of existing workflows—scaling to millions of cells without the computational bottlenecks of CPU-based analysis. -RSC overview +RSC overview For more details, we refer to a recent blog post by NVIDIA: [Driving Toward Billion-Cell Analysis and Biological Breakthroughs with RAPIDS-singlecell](https://developer.nvidia.com/blog/driving-toward-billion-cell-analysis-and-biological-breakthroughs-with-rapids-singlecell) @@ -55,7 +55,7 @@ Built on AnnData and scverse libraries, pertpy fits smoothly into existing pipel It maps omics profiles to annotated biological sets, such as transcription factors, pathways, or kinases, using methods like GSEA, GSVA, and linear models. Designed for bulk, single-cell and spatial data, decoupler works directly with our scverse core data structures. -decoupler overview +decoupler overview ## What this means diff --git a/content/blog/2026-gget-joins-scverse.md b/content/blog/2026-gget-joins-scverse.md index 78ac9304..c3f1a110 100644 --- a/content/blog/2026-gget-joins-scverse.md +++ b/content/blog/2026-gget-joins-scverse.md @@ -9,7 +9,7 @@ draft = false Querying genomic reference databases is something every bioinformatician does constantly, and doing it well has historically required juggling a patchwork of APIs, file formats, and web interfaces. [gget](https://github.com/scverse/gget) was built to fix that, and is now officially part of the scverse ecosystem. -gget x scverse Overview. +gget x scverse Overview. ## What is gget? diff --git a/content/design/_index.md b/content/design/_index.md index 47ff8c73..d1ef382a 100644 --- a/content/design/_index.md +++ b/content/design/_index.md @@ -48,23 +48,23 @@ Our primary logo combines our icon with the full name. Use this version when int [[primarylogos]] name = "Icon Only" description = "Logo mark without text" - img = "../img/logo/scverse_symbol.svg" + img = "../img/logo/scverse-symbol.svg" details = "Our icon can be used independently when space is limited or when our brand is already well-established in context." [[primarylogos.links]] text = "Download SVG" - url = "../img/logo/scverse_symbol.svg" + url = "../img/logo/scverse-symbol.svg" [[primarylogos.links]] text = "Download PNG" - url = "../img/logo/scverse_symbol.png" + url = "../img/logo/scverse-symbol.png" [[trademarkedlogos]] name = "Icon (® version)" description = "Icon trademarked" - img = "../img/icons/scverse_bw_logo.svg" + img = "../img/icons/scverse-bw-logo.svg" details = "Use this version to indicate that scverse is a registered trademark in formal or legal contexts." 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