Comments compomics

.github/workflows/test-build.yml

@@ -0,0 +1,23 @@
+name: Test Quarto Build
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches-ignore: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render site
+        run: quarto render --no-execute

TODO.md

@@ -16,9 +16,14 @@
 - [x] Website deployment issue to have a python environment (Arthur)
 - [x] Unify the overall view of each separate part of the website. 
 
+
 ## Deploy to www.compomics.com (after site checked)
 - [] Add root `CNAME` file containing `www.compomics.com` + list it under project resources in `_quarto.yml`
 - [] Set `site-url: https://www.compomics.com` in `_quarto.yml`
 - [] GitHub repo Settings → Pages: set custom domain `www.compomics.com`, then enable Enforce HTTPS
 - [] DNS at registrar: `www` CNAME → `compomics.github.io`; apex `compomics.com` → GitHub Pages A records (185.199.108-111.153)
-- [] Flip DNS last (cuts over from old site, no fast rollback)
+- [] Flip DNS last (cuts over from old site, no fast rollback)
+
+## Todo after deployment
+
+- [] Modernise the classic "Bioinformatics for Proteomics" tutorial (`tutorials/posts/2026-06-01-bioinformatics-for-proteomics.qmd`). Ported as-is with 2014-era materials linked from Google Drive; deprecation warning kept in place until done. TODO: replace deprecated PRIDE XML with mzIdentML/mzTab (needs editing the module 3 slide decks, not just the page text); refresh slides/screenshots to current tool UIs; rehost slides + exercise resources off Google Drive; decide combined page vs per-module split; optionally write the missing MS1 (4.3) and targeted (4.4) quantification sections; update the functional-analysis module (module 2 pins no tools). Tool versions already bumped (PeptideShaker 3.0.11, SearchGUI 4.3.15). (Arthur)

_quarto.yml

@@ -1,6 +1,10 @@
 project:
   type: website
   output-dir: _site
+  # Guard: fail the build loudly if the team page's inline memberData has a JS
+  # syntax error or a card with no data entry (both silently break card clicks).
+  pre-render:
+    - scripts/check-team-data.js
   render:
     - "**/*.qmd"
     - "**/*.md"
@@ -40,8 +44,6 @@ website:
         href: publications/index.qmd
       - text: "Tutorials"
         href: tutorials/index.qmd
-      - text: "News"
-        href: news/index.qmd
       - icon: github
         href: https://github.com/compomics
         aria-label: GitHub

assets/compomics.scss

@@ -6,7 +6,7 @@ $font-family-heading:    "Bricolage Grotesque", system-ui, sans-serif;
 $font-family-monospace:  "JetBrains Mono", monospace;
 $headings-font-family:   $font-family-heading;
 $headings-font-weight:   700;
-$font-size-root: 13px;
+$font-size-root: 14px;
 
 // Colour tokens ($ink, $cream, $line, $primary, $surface-hover, $icon-bg …)
 // are defined per-theme in compomics-light.scss / compomics-dark.scss
@@ -331,293 +331,9 @@ blockquote {
 // Tools page styles live in tools/tools.scss (loaded site-wide via _quarto.yml,
 // same pattern as team/teams.scss).
 
-// ── Team grid ────────────────────────────────────────────────────────────────
-.team-grid {
-  display: grid;
-  grid-template-columns: repeat(auto-fill, minmax(150px, 1fr));
-  gap: 2.2rem 1.4rem;
-  margin: 2.5rem 0;
-}
-
-.team-card-wrap {
-  display: contents;
-}
-
-.team-grid-selectors {
-  margin-bottom: 1.75rem;
-}
-
-.team-card {
-  display: flex;
-  flex-direction: column;
-  align-items: center;
-  text-align: center;
-  text-decoration: none;
-  color: inherit;
-  transition: transform 0.18s ease;
-
-  appearance: none;
-  border: none;
-  background: transparent;
-  padding: 0;
-  cursor: pointer;
-
-  &:hover {
-    transform: translateY(-5px);
-    text-decoration: none;
-    color: inherit;
-
-    .team-photo {
-      filter: grayscale(0%);
-      border-color: $primary;
-      box-shadow: 0 8px 24px rgba(0, 0, 0, 0.18), 0 0 0 3px rgba(31, 95, 143, 0.12);
-    }
-    .team-name { color: $primary; }
-  }
-
-  &.is-selected {
-    .team-photo {
-      filter: grayscale(0%);
-      border-color: $primary;
-      box-shadow: 0 0 0 4px rgba(31, 95, 143, 0.08);
-    }
-
-    .team-name { color: $primary; }
-  }
-}
-
-.team-photo {
-  width: 150px;
-  height: 150px;
-  border-radius: 50%;
-  object-fit: cover;
-  object-position: center top;
-  border: 1px solid $line;
-  box-shadow: none;
-  margin-bottom: 0.75rem;
-  display: block;
-  transition: filter 0.2s ease, box-shadow 0.2s ease, border-color 0.2s ease;
-  filter: grayscale(12%);
-
-  &:hover { filter: grayscale(0%); }
-}
-
-.team-name {
-  font-family: $font-family-heading;
-  font-size: 1.02rem;
-  font-weight: 700;
-  color: $ink;
-  margin-bottom: 0.1rem;
-  line-height: 1.3;
-  height: calc(1.02rem * 1.3 * 2);
-  display: flex;
-  align-items: center;
-  justify-content: center;
-}
-
-.team-role {
-  font-family: $font-family-sans-serif;
-  font-size: 0.74rem;
-  text-transform: uppercase;
-  letter-spacing: 0.06em;
-  color: $muted;
-  line-height: 1.35;
-}
-
-.team-section-title {
-  font-family: $font-family-sans-serif;
-  font-size: 0.78rem;
-  font-weight: 700;
-  text-transform: uppercase;
-  letter-spacing: 0.1em;
-  color: $muted;
-  margin: 3rem 0 0.5rem;
-  padding-bottom: 0.5rem;
-  border-bottom: 1px solid $line;
-}
-
-.team-shell-intro {
-  max-width: none;
-  margin-bottom: 1rem;
-
-  p {
-    margin: 0.35rem 0 0;
-    color: $muted;
-    font-size: 0.94rem;
-    line-height: 1.7;
-  }
-}
-
-.team-detail-panel,
-.team-profile-expander {
-  position: relative;
-  margin-top: 2rem;
-  padding: clamp(1.6rem, 3.5vw, 2.8rem);
-  border-radius: 1rem;
-  overflow: hidden;
-  border: 1px solid rgba(90, 167, 218, 0.20);
-  background: linear-gradient(135deg, #0d1f38, #142d50);
-  box-shadow: 0 24px 70px rgba(0, 0, 0, 0.32), 0 0 0 1px rgba(90, 167, 218, 0.08);
-
-  &[hidden] { display: none; }
-
-  &::before {
-    content: "";
-    position: absolute;
-    inset: 0;
-    background:
-      radial-gradient(circle at top right, rgba(90, 167, 218, 0.22), rgba(90, 167, 218, 0) 42%),
-      linear-gradient(135deg, rgba(10, 20, 40, 0.20), rgba(10, 20, 40, 0.55));
-    pointer-events: none;
-  }
-}
-
-.team-profile-expander {
-  grid-column: 1 / -1;
-  margin-top: 0.5rem;
-  margin-bottom: 1rem;
-  display: grid;
-  gap: 1.15rem;
-  color: #f6f2ea;
-
-  max-height: 0;
-  opacity: 0;
-  transition: max-height 0.45s cubic-bezier(0.4, 0, 0.2, 1), opacity 0.3s ease;
-
-  &::after {
-    content: "";
-    position: absolute;
-    top: -8px;
-    left: var(--notch-x, 50%);
-    transform: translateX(-50%);
-    width: 0;
-    height: 0;
-    border-left: 8px solid transparent;
-    border-right: 8px solid transparent;
-    border-bottom: 8px solid #0d1f38;
-    pointer-events: none;
-    z-index: 2;
-  }
-}
-
-.team-detail-copy {
-  position: relative;
-  z-index: 1;
-  display: grid;
-  gap: 1.15rem;
-  color: #f6f2ea;
-}
-
-.team-detail-header {
-  display: grid;
-  gap: 0.35rem;
-  max-width: 72ch;
-}
-
-.team-detail-eyebrow {
-  font-family: $font-family-sans-serif;
-  font-size: 0.72rem;
-  font-weight: 700;
-  letter-spacing: 0.14em;
-  text-transform: uppercase;
-  color: rgba(255, 255, 255, 0.72);
-}
-
-.team-detail-header h3 {
-  margin: 0;
-  font-size: clamp(2rem, 4vw, 2.8rem);
-  color: #fff;
-  line-height: 1.08;
-}
-
-.team-detail-role {
-  margin: 0;
-  color: rgba(255, 255, 255, 0.8);
-  font-size: 0.92rem;
-  letter-spacing: 0.03em;
-}
-
-.team-detail-section {
-  max-width: 78ch;
-  padding-top: 0.35rem;
-
-  h4 {
-    margin: 0 0 0.35rem;
-    color: rgba(255, 255, 255, 0.88);
-    font-family: $font-family-heading;
-    font-size: 0.9rem;
-    text-transform: none;
-    letter-spacing: -0.01em;
-  }
-
-  p {
-    margin: 0;
-    color: rgba(255, 255, 255, 0.9);
-    line-height: 1.8;
-    font-size: 0.98rem;
-  }
-}
-
-.team-pub-list {
-  display: flex;
-  flex-direction: column;
-  gap: 0.45rem;
-}
-
-.team-pub-item {
-  display: inline-flex;
-  flex-wrap: wrap;
-  align-items: baseline;
-  gap: 0.25rem 0.6rem;
-  padding: 0.45rem 0.8rem 0.45rem 0.8rem;
-  border: 1px solid rgba(90, 167, 218, 0.28);
-  border-radius: 0.4rem;
-  background: rgba(255, 255, 255, 0.04);
-  max-width: fit-content;
-  text-decoration: none;
-  cursor: pointer;
-  transition: border-color 0.15s ease, background 0.15s ease, box-shadow 0.15s ease;
-
-  &::after {
-    content: "↗";
-    font-size: 0.7rem;
-    color: rgba(90, 167, 218, 0.55);
-    align-self: center;
-    margin-left: 0.15rem;
-    transition: color 0.15s ease, transform 0.15s ease;
-    display: inline-block;
-  }
-
-  &:hover {
-    border-color: rgba(90, 167, 218, 0.65);
-    background: rgba(90, 167, 218, 0.12);
-    box-shadow: 0 0 12px rgba(90, 167, 218, 0.18);
-    text-decoration: none;
-
-    &::after {
-      color: rgba(90, 167, 218, 0.95);
-      transform: translate(1px, -1px);
-    }
-  }
-}
-
-.team-pub-title {
-  font-family: $font-family-heading;
-  font-size: 0.88rem;
-  font-weight: 600;
-  color: rgba(255, 255, 255, 0.95);
-  line-height: 1.3;
-}
-
-.team-pub-venue {
-  font-family: $font-family-sans-serif;
-  font-size: 0.72rem;
-  font-weight: 600;
-  text-transform: uppercase;
-  letter-spacing: 0.08em;
-  color: rgba(90, 167, 218, 0.85);
-  white-space: nowrap;
-}
+// ── Team page styles live in team/teams.scss ────────────────────────────────
+// (grid, cards, and the profile expander were consolidated there so the two
+//  files no longer both style the team page)
 
 // ── Location section — single elegant panel, address + map ───────────────────
 .location-section {