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SITE_STRUCTURE.md

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Repository structure

This document identifies the role and ownership of each major file group. “Authored” files are edited directly. “Generated” files are replaced by scripts and should not be edited manually.

Root files

Path Type Purpose
index.html Authored Homepage with lab introduction, recent publications, and recent Lab Life posts.
research.html Authored Research overview and program areas.
people.html Authored template People index. Reads the _people collection.
software.html Authored Software and resource cards.
publications.html Authored wrapper Loads _includes/publications_page.html.
pub_bib.html Authored template Human-readable BibTeX page generated from site.papers.
jobs.html Authored template Reads the _jobs collection.
contact.html Authored Locations, maps, and contact information.
pub.bib Generated Combined downloadable bibliography.
CV.md Documentation CV source, generation, and deployment guide.
_config.yml Configuration Jekyll collections, pagination, defaults, and build exclusions.
CNAME Deployment Custom domain for GitHub Pages.
Gemfile Build GitHub Pages-compatible Ruby dependencies.
requirements-publications.txt Build Python dependencies for generation and tests.
Makefile Build Local maintenance commands.

Jekyll content collections

_people/

One Markdown file per current or former lab member. The front matter is the source of truth for the person’s Michigan umid, membership categories, lab roles, education, links, current position, and profile image. See PEOPLE.md.

_posts/

Lab Life posts, grouped in year directories for maintainability. Jekyll uses the filename and front-matter date to create the public URL. See NEWS_POSTS.md.

_jobs/

Job announcements. Only records with publish: true appear on the Jobs page. See JOBS.md.

_papers/

Generated publication records. Each filename is the stable BibTeX key, for example _papers/VanDeynze2025HMMSTR.yml. These files are committed because GitHub Pages and member pages consume them, but they must be regenerated rather than edited. See PUBLICATIONS.md.

Publication sources

Path Ownership Purpose
bibliography/publications.bib Authored Definitive bibliographic citation data.
publication_metadata/*.yml Authored Website-only metadata, including member umid relationships, featured summaries, and supplemental links.
scripts/publication_tools.py Code BibTeX parser, validation, person matching, and record construction.
scripts/build_publications.py Code Generates _papers/*.yml and pub.bib; validates stale or obsolete output.
scripts/scaffold_publication_metadata.py Code Creates a new sidecar template for an existing BibTeX key.

Curriculum vitae

Path Ownership Purpose
cv/cv.tex Authored CV sections other than the generated publication and patent lists.
cv/patents.bib Authored Patent records not represented in the website publication bibliography.
cv/generated/publications.tex Generated Full publication list with website-derived author highlighting.
cv/generated/patents.tex Generated Patent list included by cv/cv.tex.
scripts/cv_tools.py Code CV citation formatting and member highlighting built on the publication pipeline.
scripts/build_cv.py Code Generates CV TeX inputs and optionally compiles assets/ABoyle_CV.pdf.
assets/ABoyle_CV.pdf Generated Public CV linked from the People section.

See CV.md.

Presentation files

_layouts/

  • default.html: shared shell for normal pages.
  • member.html: individual people profile.
  • post.html: individual Lab Life story.

_includes/

  • header.html: document head, CSS, analytics, and navigation script.
  • nav.html: lab and university marks plus desktop/mobile navigation.
  • footer.html: compact institutional footer.
  • tracking.html: Google Analytics configuration.
  • person_card.html: reusable People-page card.
  • publication_authors.html: full publication byline.
  • publication_citation.html: complete or compact publication record.
  • publication_featured.html: featured-publication card.
  • publications_page.html: full Publications page.

css/

  • main_style.css: site-wide layout and component styles.
  • mobile_navigation.css: only the responsive navigation behavior.
  • academicons.css: minimal local Academic Icons subset used by member profiles.

assets/js/

  • site-navigation.js: accessible mobile-menu interaction. The site has no publication search or sorting JavaScript.

Assets

Directory Purpose
assets/images/ Primary-page graphics, logos, and featured paper screenshots.
assets/people/ Profile photographs and placeholder image.
assets/news_graphics/ Lab Life teasers, event photographs, and legacy post galleries.
assets/job_PDFs/ PDFs linked by active job records.
pubs/ Local publication PDFs linked from BibTeX or metadata.
fonts/ Local Academic Icons WOFF font.

Large Lab Life and publication archives are retained when a post, public URL, or download may still refer to them. Do not remove media solely because a literal path is not present in a template; some older Lab Life galleries discover files dynamically.

Tests and automation

  • tests/test_publication_tools.py: parser, metadata, generated schema, and reproducibility.
  • tests/test_cv_tools.py: CV generation, author highlighting, TeX source, PDF output, and legacy-build removal.
  • tests/test_people_data.py: profile identities, dates, roles, and assets.
  • tests/test_news_data.py: Lab Life metadata and linked records.
  • tests/test_site_structure.py: layouts, includes, CSS, dependencies, and repository shape.
  • tests/test_workflow.py: GitHub Actions generation and deployment contract.
  • .github/workflows/site.yml: publication and CV regeneration, validation, Jekyll build, and Pages deployment.