From 6802f3479051a42934ab4a5d824796824551677f Mon Sep 17 00:00:00 2001 From: Jan N Rose Date: Sun, 7 Jun 2026 15:32:10 +0200 Subject: [PATCH 1/2] Clean up dev setup --- .gitignore | 1 - .vscode/settings.json | 9 ++++++ README.md | 3 +- _config.yml | 1 + scripts/pages-serve | 70 +++++++++++++++++++++---------------------- 5 files changed, 46 insertions(+), 38 deletions(-) create mode 100644 .vscode/settings.json diff --git a/.gitignore b/.gitignore index badbc02..ca35be0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1 @@ _site -.sass-cache diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..7e02342 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,9 @@ +{ + "files.exclude": { + "_site": true + }, + "explorer.fileNesting.enabled": true, + "explorer.fileNesting.patterns": { + "*": "${capture}.lock" + } +} \ No newline at end of file diff --git a/README.md b/README.md index 8031dbe..4b21683 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,8 @@ make build make serve ``` -This will rebuild the site, then serves `_site` at `http://localhost:4000`. +This will start Jekyll in watch mode and serve the site at +`http://localhost:4000`. Content changes are rebuilt automatically. Useful overrides: diff --git a/_config.yml b/_config.yml index 8bef2b3..0c257a0 100644 --- a/_config.yml +++ b/_config.yml @@ -18,6 +18,7 @@ url: https://cmrcs.org markdown: kramdown theme: minima +# Files to not copy to _site/ (dotfiles are excluded by default) exclude: - Gemfile - Gemfile.lock diff --git a/scripts/pages-serve b/scripts/pages-serve index 63c861f..68ecdd2 100755 --- a/scripts/pages-serve +++ b/scripts/pages-serve @@ -16,55 +16,53 @@ if ! command -v docker >/dev/null 2>&1; then fi rm -rf "${repo_root}/${destination_dir#./}" -config_path="${repo_root}/${source_dir#./}/_config.yml" -config_backup="$(mktemp)" -if [ ! -f "${config_path}" ]; then - echo "Cannot find Jekyll config at ${config_path}" >&2 +if [ ! -f "${repo_root}/${source_dir#./}/_config.yml" ]; then + echo "Cannot find Jekyll config at ${repo_root}/${source_dir#./}/_config.yml" >&2 exit 1 fi -cp "${config_path}" "${config_backup}" - -cleanup() { - cp "${config_backup}" "${config_path}" - rm -f "${config_backup}" -} - -trap cleanup EXIT - -{ - echo - printf 'baseurl: "%s"\n' "${local_baseurl}" -} >> "${config_path}" - docker run --rm \ --platform "${platform}" \ + --publish "${port}:${port}" \ --volume "${repo_root}:/github/workspace" \ --workdir /github/workspace \ --env GITHUB_WORKSPACE=/github/workspace \ --env GITHUB_REPOSITORY="${GITHUB_REPOSITORY:-CMRCS/cmrcs.github.io}" \ --env GITHUB_API_URL="${GITHUB_API_URL:-https://api.github.com}" \ - --env INPUT_SOURCE="${source_dir}" \ - --env INPUT_DESTINATION="${destination_dir}" \ - --env INPUT_FUTURE="${PAGES_FUTURE:-false}" \ - --env INPUT_BUILD_REVISION="${build_revision}" \ - --env INPUT_VERBOSE="${PAGES_VERBOSE:-true}" \ - --env INPUT_TOKEN="${GITHUB_TOKEN:-}" \ + --env JEKYLL_GITHUB_TOKEN="${GITHUB_TOKEN:-}" \ + --env JEKYLL_BUILD_REVISION="${build_revision}" \ + --env PAGES_REPO_NWO="${GITHUB_REPOSITORY:-CMRCS/cmrcs.github.io}" \ + --env PAGES_API_URL="${GITHUB_API_URL:-https://api.github.com}" \ + --env PAGES_PORT="${port}" \ + --env PAGES_SOURCE="${source_dir}" \ + --env PAGES_DESTINATION="${destination_dir}" \ + --env PAGES_LOCAL_BASEURL="${local_baseurl}" \ + --env PAGES_FUTURE="${PAGES_FUTURE:-false}" \ + --env PAGES_VERBOSE="${PAGES_VERBOSE:-true}" \ + --env JEKYLL_ENV=development \ --entrypoint bash \ "${image}" \ -lc ' - /entrypoint.sh - ' + set -euo pipefail -cleanup -trap - EXIT + cd /usr/local/bundle -docker run --rm \ - --platform "${platform}" \ - --publish "${port}:${port}" \ - --volume "${repo_root}:/github/workspace" \ - --workdir /github/workspace \ - --entrypoint ruby \ - "${image}" \ - -run -e httpd "${destination_dir#./}" -p "${port}" -b 0.0.0.0 + args=() + if [ "${PAGES_VERBOSE:-true}" = "true" ]; then + args+=(--verbose) + fi + if [ "${PAGES_FUTURE:-false}" = "true" ]; then + args+=(--future) + fi + + bundle exec jekyll serve \ + "${args[@]}" \ + --host 0.0.0.0 \ + --port "${PAGES_PORT:-4000}" \ + --source "${GITHUB_WORKSPACE}/${PAGES_SOURCE:-./}" \ + --destination "${GITHUB_WORKSPACE}/${PAGES_DESTINATION:-./_site}" \ + --baseurl "${PAGES_LOCAL_BASEURL:-}" \ + --watch \ + --force_polling + ' From e5cb524d26c308434cb7f60624bf3c58830003a6 Mon Sep 17 00:00:00 2001 From: Jan N Rose Date: Sun, 7 Jun 2026 16:24:19 +0200 Subject: [PATCH 2/2] Add people and publications --- _data/people.yml | 27 ++ _data/publications.yml | 11 + _layouts/people_index.html | 24 ++ _layouts/person.html | 64 +++++ _layouts/publication.html | 36 +++ _layouts/publications_index.html | 32 +++ _layouts/site.html | 1 + assets/css/pages.css | 262 ++++++++++++++++++ people/andrew-scott.md | 6 + people/denis-doorly.md | 6 + people/index.md | 4 + people/jan-rose.md | 10 + publications/index.md | 4 + ...-insights-dt-cmr-virtual-microstructure.md | 12 + 14 files changed, 499 insertions(+) create mode 100644 _data/people.yml create mode 100644 _data/publications.yml create mode 100644 _layouts/people_index.html create mode 100644 _layouts/person.html create mode 100644 _layouts/publication.html create mode 100644 _layouts/publications_index.html create mode 100644 assets/css/pages.css create mode 100644 people/andrew-scott.md create mode 100644 people/denis-doorly.md create mode 100644 people/index.md create mode 100644 people/jan-rose.md create mode 100644 publications/index.md create mode 100644 publications/novel-insights-dt-cmr-virtual-microstructure.md diff --git a/_data/people.yml b/_data/people.yml new file mode 100644 index 0000000..74e6ac9 --- /dev/null +++ b/_data/people.yml @@ -0,0 +1,27 @@ +- id: andrew-scott + name: Andrew D. Scott + image: + summary: + role: + focus: + orcid: 0000-0001-7656-3123 + linkedin: scottandrewd + webpage: https://profiles.imperial.ac.uk/andrew.scott +- id: denis-doorly + name: Denis J. Doorly + image: + summary: + role: + focus: + orcid: Orcid identifier0000-0002-5372-4702 + linkedin: + webpage: https://profiles.imperial.ac.uk/d.doorly +- id: jan-rose + name: Jan N. Rose + image: + summary: Completed his PhD in 2021, working on realistic histology-based DT-CMR simulation using Monte Carlo methods. + role: Alumn + focus: Cardiac microstructure, Monte Carlo modelling + orcid: 0000-0002-2273-7439 + linkedin: janniklasrose + github: janniklasrose diff --git a/_data/publications.yml b/_data/publications.yml new file mode 100644 index 0000000..7bc7e97 --- /dev/null +++ b/_data/publications.yml @@ -0,0 +1,11 @@ +- id: novel-insights-dt-cmr-virtual-microstructure + year: 2019 + title: Novel insights into in-vivo diffusion tensor cardiovascular magnetic resonance using computational modeling and a histology-based virtual microstructure + doi: 10.1002/mrm.27561 + authors: + - person: jan-rose + - name: Sonia Nielles-Vallespin + - name: Pedro F. Ferreira + - name: David N. Firmin + - person: andrew-scott + - person: denis-doorly diff --git a/_layouts/people_index.html b/_layouts/people_index.html new file mode 100644 index 0000000..0f87ac7 --- /dev/null +++ b/_layouts/people_index.html @@ -0,0 +1,24 @@ +--- +layout: site +--- + +
+
+

{{ page.title }}

+
{{ content }}
+
+ +
+ {% for person in site.data.people %} +
+ Profile image for {{ person.name }} +
+

{{ person.role }}

+

{{ person.name }}

+

{{ person.summary }}

+ View profile +
+
+ {% endfor %} +
+
diff --git a/_layouts/person.html b/_layouts/person.html new file mode 100644 index 0000000..24eb9a8 --- /dev/null +++ b/_layouts/person.html @@ -0,0 +1,64 @@ +--- +layout: site +--- +{% assign person = site.data.people | where: "id", page.person_id | first %} + +
+
+

{{ person.name }}

+
+
+ +
+ {{ content }} +

Publications

+ {% assign authored_publications = "" | split: "" %} + {% for publication in site.data.publications %} + {% for author in publication.authors %} + {% if author.person == person.id %} + {% assign authored_publications = authored_publications | push: publication %} + {% endif %} + {% endfor %} + {% endfor %} + {% if authored_publications.size > 0 %} +
    + {% for publication in authored_publications %} +
  • + {{ publication.title }} + {{ publication.year }} +
    • + {% endfor %} +
+ {% else %} +

No publications listed yet.

+ {% endif %} +
+
+
diff --git a/_layouts/publication.html b/_layouts/publication.html new file mode 100644 index 0000000..d81e80e --- /dev/null +++ b/_layouts/publication.html @@ -0,0 +1,36 @@ +--- +layout: site +--- +{% assign publication = site.data.publications | where: "id", page.publication_id | first %} + +
+
+

{{ publication.title }}

+
+
+ +
+ {{ content }} +
+
+
diff --git a/_layouts/publications_index.html b/_layouts/publications_index.html new file mode 100644 index 0000000..b4434b3 --- /dev/null +++ b/_layouts/publications_index.html @@ -0,0 +1,32 @@ +--- +layout: site +--- + +
+
+

{{ page.title }}

+
{{ content }}
+
+ +
+ {% for publication in site.data.publications %} +
+
+

{{ publication.title }}

+

+ {% for author in publication.authors %} + {% if author.person %} + {% assign person = site.data.people | where: "id", author.person | first %} + {{ person.name }}{% unless forloop.last %}, {% endunless %} + {% else %} + {{ author.name }}{% unless forloop.last %}, {% endunless %} + {% endif %} + {% endfor %} +

+ Read publication page +
+
{{ publication.year }}
+
+ {% endfor %} +
+
diff --git a/_layouts/site.html b/_layouts/site.html index 330957a..b42e2e3 100644 --- a/_layouts/site.html +++ b/_layouts/site.html @@ -6,6 +6,7 @@ {{ page.title }} | {{ site.title }} +
diff --git a/assets/css/pages.css b/assets/css/pages.css new file mode 100644 index 0000000..744dfc4 --- /dev/null +++ b/assets/css/pages.css @@ -0,0 +1,262 @@ +.people-grid { + display: grid; + gap: 18px; + grid-template-columns: repeat(auto-fit, minmax(240px, 1fr)); +} + +.person-card, +.publication-item, +.detail-panel, +.project-card { + background: var(--panel); + border: 1px solid var(--line); +} + +.person-card { + display: grid; + grid-template-rows: auto 1fr; + min-height: 100%; + overflow: hidden; +} + +.person-card img { + display: block; + height: 240px; + object-fit: cover; + width: 100%; +} + +.person-card-body { + padding: 24px; +} + +.person-card h2, +.publication-item h2 { + font-size: 1.12rem; + margin: 0 0 14px; +} + +.person-card p, +.publication-item p, +.detail-panel p, +.project-card p { + color: var(--muted); + margin: 0; +} + +.role { + color: var(--teal); + font-size: 0.8rem; + font-weight: 800; + letter-spacing: 0.1em; + margin: 0 0 12px; + text-transform: uppercase; +} + +.text-link { + color: var(--ink); + display: inline-block; + font-weight: 800; + margin-top: 18px; + text-decoration: none; +} + +.text-link:hover { + color: var(--teal); +} + +.publication-list, +.project-grid { + display: grid; + gap: 16px; +} + +.project-grid { + gap: 18px; +} + +.publication-item { + display: grid; + gap: 22px; + grid-template-columns: minmax(0, 1fr) 150px; + padding: 26px; +} + +.publication-heading { + grid-template-columns: 1fr; +} + +.publication-heading .page-title { + max-width: none; +} + +.project-card { + display: grid; + gap: 22px; + grid-template-columns: minmax(0, 0.9fr) minmax(280px, 0.8fr); + padding: 28px; +} + +.project-card h2 { + font-size: clamp(1.45rem, 2.2vw, 2rem); + line-height: 1.12; + margin: 0; +} + +.project-main { + align-content: start; + display: grid; + gap: 14px; +} + +.project-meta { + border-left: 1px solid var(--line); + padding-left: 22px; +} + +.project-meta + .project-meta { + margin-top: 24px; +} + +.project-meta h3 { + font-size: 0.82rem; + letter-spacing: 0.08em; + margin: 0 0 10px; + text-transform: uppercase; +} + +.authors, +.meta { + color: var(--muted); + font-size: 0.95rem; + margin: 0 0 12px; +} + +.authors a, +.detail-panel a, +.linked-list a, +.project-meta a { + color: var(--ink); + font-weight: 750; + text-decoration-color: rgba(0, 125, 138, 0.4); + text-decoration-thickness: 2px; + text-underline-offset: 3px; +} + +.authors a:hover, +.detail-panel a:hover, +.linked-list a:hover, +.project-meta a:hover { + color: var(--teal); +} + +.summary { + margin-top: 12px; +} + +.year { + align-self: start; + border-left: 4px solid var(--gold); + color: var(--ink); + font-size: 1.5rem; + font-weight: 850; + padding-left: 18px; +} + +.detail-grid { + display: grid; + gap: 28px; + grid-template-columns: 320px minmax(0, 1fr); +} + +.detail-panel { + padding: 26px; +} + +.detail-panel img { + display: block; + margin-bottom: 22px; + width: 100%; +} + +.detail-panel dl { + display: grid; + gap: 12px; + margin: 0; +} + +.detail-panel dt { + color: var(--muted); + font-size: 0.82rem; + font-weight: 800; + letter-spacing: 0.08em; + text-transform: uppercase; +} + +.detail-panel dd { + margin: 0; +} + +.linked-list { + display: grid; + gap: 14px; + list-style: none; + margin: 18px 0 0; + padding: 0; +} + +.linked-list li { + border-top: 1px solid var(--line); + display: grid; + gap: 10px; + grid-template-columns: minmax(0, 1fr) auto; + padding-top: 14px; +} + +.linked-list span { + color: var(--muted); + font-weight: 750; +} + +.linked-list.compact { + gap: 10px; + margin-top: 0; +} + +.linked-list.compact li { + gap: 8px; + grid-template-columns: 1fr; + padding-top: 10px; +} + +.profile-links { + display: flex; + flex-wrap: wrap; + gap: 10px 14px; + list-style: none; + margin: 0; + padding: 0; +} + +.prose .person-publications-heading { + margin-top: 64px; +} + +@media (max-width: 850px) { + .detail-grid, + .publication-item, + .project-card { + grid-template-columns: 1fr; + } + + .project-card { + padding: 24px; + } + + .project-meta { + border-left: 0; + border-top: 1px solid var(--line); + padding-left: 0; + padding-top: 18px; + } +} diff --git a/people/andrew-scott.md b/people/andrew-scott.md new file mode 100644 index 0000000..dbe991a --- /dev/null +++ b/people/andrew-scott.md @@ -0,0 +1,6 @@ +--- +title: Andrew D. Scott +layout: person +person_id: andrew-scott +permalink: /people/andrew-scott/ +--- diff --git a/people/denis-doorly.md b/people/denis-doorly.md new file mode 100644 index 0000000..c8e20dd --- /dev/null +++ b/people/denis-doorly.md @@ -0,0 +1,6 @@ +--- +title: Denis J. Doorly +layout: person +person_id: denis-doorly +permalink: /people/denis-doorly/ +--- diff --git a/people/index.md b/people/index.md new file mode 100644 index 0000000..1c0670f --- /dev/null +++ b/people/index.md @@ -0,0 +1,4 @@ +--- +title: People +layout: people_index +--- diff --git a/people/jan-rose.md b/people/jan-rose.md new file mode 100644 index 0000000..f0d27fc --- /dev/null +++ b/people/jan-rose.md @@ -0,0 +1,10 @@ +--- +title: Jan Rose +layout: person +person_id: jan-rose +permalink: /people/jan-rose/ +--- + +## Profile + +Jan completed his PhD in 2021 with the thesis [Computational modelling of diffusion magnetic resonance imaging based on cardiac histology](https://doi.org/10.25560/100556), under the supervision of [Denis Doorly](/people/denis-doorly) and [Andrew Scott](/people/andrew-scott). diff --git a/publications/index.md b/publications/index.md new file mode 100644 index 0000000..48bac3a --- /dev/null +++ b/publications/index.md @@ -0,0 +1,4 @@ +--- +title: Publications +layout: publications_index +--- diff --git a/publications/novel-insights-dt-cmr-virtual-microstructure.md b/publications/novel-insights-dt-cmr-virtual-microstructure.md new file mode 100644 index 0000000..0b9df72 --- /dev/null +++ b/publications/novel-insights-dt-cmr-virtual-microstructure.md @@ -0,0 +1,12 @@ +--- +title: Novel insights into in-vivo diffusion tensor cardiovascular magnetic resonance using computational modeling and a histology-based virtual microstructure +layout: publication +publication_id: novel-insights-dt-cmr-virtual-microstructure +permalink: /publications/novel-insights-dt-cmr-virtual-microstructure/ +--- + +