/* mad-lab.org
   Palette from the Ziehl-Neelsen acid-fast stain: M. tuberculosis takes up
   carbol fuchsin (magenta) against a methylene blue counterstain. */

:root {
  --paper: #ffffff;
  --ink: #161a1e;
  --muted: #5a6270;
  --track: #8f99a6;
  --gene: #dde2e8;
  --fuchsin: #b3175c;
  --blue: #1c5a9e;

  --sans: 'Jost', 'Futura', 'Century Gothic', system-ui, sans-serif;
  --serif: 'Newsreader', 'Iowan Old Style', 'Palatino Linotype', Georgia, serif;
  --measure: 38rem;
}

html {
  font-size: clamp(17px, 16px + 0.25vw, 19px);
}

/* Author display rules (e.g. .track-tip's flex) would otherwise override the
   hidden attribute and leave "hidden" elements on screen. */
[hidden] {
  display: none !important;
}

body {
  margin: 0;
  background: var(--paper);
  color: var(--ink);
  font: 400 1rem/1.6 var(--serif);
  font-optical-sizing: auto;
  -webkit-font-smoothing: antialiased;
}

.wrap {
  max-width: 56rem;
  margin: 0 auto;
  padding-inline: clamp(1.25rem, 5vw, 2.5rem);
}

a {
  color: var(--blue);
  text-decoration-thickness: 1px;
  text-underline-offset: 0.18em;
}

a:hover {
  text-decoration-thickness: 2px;
}

:focus-visible {
  outline: 2px solid var(--blue);
  outline-offset: 3px;
  border-radius: 2px;
}

h1, h2 {
  font-family: var(--sans);
  font-weight: 500;
  line-height: 1.15;
}

h1 {
  font-size: clamp(2rem, 1.3rem + 2.6vw, 2.8rem);
  letter-spacing: -0.01em;
  margin: clamp(1.5rem, 5vw, 3rem) 0 0.75rem;
}

h2 {
  font-size: 1.35rem;
  margin: 2.75rem 0 1.1rem;
}

p {
  margin: 0 0 1em;
}

/* Header and footer */

.site-header {
  display: flex;
  flex-wrap: wrap;
  align-items: center;
  justify-content: space-between;
  gap: 0.75rem 2rem;
  padding-block: 1.25rem;
  font-family: var(--sans);
}

.brand {
  display: block;
  color: var(--ink);
  text-decoration: none;
}

.brand img {
  display: block;
  width: auto;
  height: 1.6rem;
}

.site-header nav > ul {
  display: flex;
  flex-wrap: wrap;
  gap: 0.4rem 1.6rem;
  margin: 0;
  padding: 0;
  list-style: none;
}

.site-header nav > ul > li > a,
.menu-toggle {
  display: inline-block;
  padding-block: 0.2rem;
  border-bottom: 2px solid transparent;
  color: var(--ink);
  font-size: 0.95rem;
  text-decoration: none;
}

.site-header nav > ul > li > a:hover,
.menu-toggle:hover {
  border-bottom-color: var(--track);
}

.site-header nav > ul > li > a[aria-current="page"] {
  border-bottom-color: var(--ink);
}

/* The GitHub menu: hover opens it where there is a mouse; nav.js adds
   click, tap and keyboard (it sets .is-open). */

.menu {
  position: relative;
}

.menu-toggle {
  margin: 0;
  padding-inline: 0;
  border-top: 0;
  border-inline: 0;
  background: none;
  font-family: inherit;
  cursor: pointer;
}

.menu-toggle::after {
  content: "";
  display: inline-block;
  width: 0.36em;
  height: 0.36em;
  margin-left: 0.45em;
  border-right: 1.5px solid currentColor;
  border-bottom: 1.5px solid currentColor;
  transform: translateY(-0.2em) rotate(45deg);
}

.menu-list {
  position: absolute;
  top: 100%;
  left: -0.9rem;
  z-index: 10;
  display: none;
  min-width: 9.5rem;
  margin: 0;
  padding: 0.35rem 0;
  border: 1px solid var(--gene);
  border-radius: 4px;
  background: var(--paper);
  list-style: none;
}

.menu.is-open .menu-list {
  display: block;
}

.menu.is-open .menu-toggle::after {
  transform: translateY(0.05em) rotate(225deg);
}

@media (hover: hover) {
  .menu:hover .menu-list {
    display: block;
  }

  /* The arrow follows the menu: up whenever it is showing. */
  .menu:hover .menu-toggle::after {
    transform: translateY(0.05em) rotate(225deg);
  }
}

.menu-list a {
  display: flex;
  flex-direction: column;
  padding: 0.4rem 0.9rem;
  color: var(--ink);
  text-decoration: none;
}

.menu-list a:hover {
  background: #f3f5f7;
}

.menu-name {
  font-size: 0.95rem;
}

.menu-note {
  color: var(--muted);
  font-size: 0.78rem;
}

.site-footer {
  margin-top: 4.5rem;
  padding-block: 1.25rem 2.5rem;
  border-top: 1px solid var(--gene);
  color: var(--muted);
  font-family: var(--sans);
  font-size: 0.8rem;
}

.site-footer a {
  color: inherit;
}

/* Home */

.hero {
  display: grid;
  grid-template-columns: minmax(8rem, 12.5rem) 1fr;
  align-items: center;
  gap: clamp(1.25rem, 4vw, 3rem);
  margin-block: clamp(1.5rem, 6vw, 4rem) 2rem;
}

/* The logos have different proportions; a fixed frame keeps the hero steady
   as they rotate. */
.hero img {
  width: 100%;
  height: auto;
  aspect-ratio: 3 / 2;
  object-fit: contain;
  object-position: left center;
}

.hero h1 {
  margin: 0 0 0.7rem;
  font-size: clamp(2.3rem, 1.2rem + 4vw, 3.8rem);
  line-height: 1.02;
}

.hero .role,
.hero .place {
  margin: 0;
  font-family: var(--sans);
}

.hero .role {
  font-size: 1.15rem;
}

.hero .place {
  color: var(--muted);
}

.track-figure {
  position: relative;
  margin: 0 0 2.5rem;
}

.track {
  display: block;
  width: 100%;
  height: 4.75rem;
  overflow: visible;
  touch-action: pan-y;
}

.track .insertions line {
  stroke: var(--track);
  stroke-width: 1.6px;
  vector-effect: non-scaling-stroke;
}

.track .insertions line.is-active {
  stroke: var(--ink);
  stroke-width: 2.4px;
}

.track .axis {
  stroke: var(--ink);
  stroke-width: 1px;
  vector-effect: non-scaling-stroke;
}

.track .gene {
  fill: var(--gene);
  outline: none;
}

.track .gene.is-active {
  fill: var(--track);
}

.track .gene:focus-visible {
  stroke: var(--blue);
  stroke-width: 2px;
  vector-effect: non-scaling-stroke;
}

.track .essential,
.track .essential.is-active {
  fill: var(--fuchsin);
}

.track .band {
  fill: var(--ink);
  opacity: 0;
}

.track .band.is-shown {
  opacity: 0.04;
}

.track .band.is-essential {
  fill: var(--fuchsin);
  opacity: 0.08;
}

.track-tip {
  position: absolute;
  z-index: 1;
  display: flex;
  flex-direction: column;
  padding: 0.3rem 0.55rem;
  border-radius: 3px;
  background: var(--ink);
  color: var(--paper);
  font-family: var(--sans);
  font-size: 0.75rem;
  line-height: 1.35;
  white-space: nowrap;
  transform: translateX(-50%);
  pointer-events: none;
}

.track-tip-detail {
  color: #c3c9d1;
}

.track-figure figcaption {
  max-width: var(--measure);
  margin-top: 0.6rem;
  color: var(--muted);
  font-family: var(--sans);
  font-size: 0.8rem;
  line-height: 1.5;
}

@media (prefers-reduced-motion: no-preference) {
  /* The one moment of motion: insertions accumulate across the genome,
     then the gene they avoided takes the stain. */
  .track .insertions {
    animation: sweep 1.6s cubic-bezier(0.25, 0.7, 0.25, 1) both;
  }

  .track .essential {
    animation: stain 0.6s ease-out 1.35s both;
  }
}

@keyframes sweep {
  from { clip-path: inset(0 100% 0 0); }
  to { clip-path: inset(0 0 0 0); }
}

@keyframes stain {
  from { fill: var(--gene); }
  to { fill: var(--fuchsin); }
}

.prose {
  max-width: var(--measure);
  font-size: 1.1rem;
}

.software {
  display: grid;
  grid-template-columns: 7rem 1fr;
  gap: 1rem 1.5rem;
  max-width: 44rem;
  margin: 0;
}

.software dt {
  font-family: var(--sans);
  font-weight: 500;
}

.software dd {
  margin: 0;
}

.software dd p {
  margin-bottom: 0.3rem;
}

.links {
  display: flex;
  flex-wrap: wrap;
  gap: 0.25rem 1.25rem;
  margin: 0;
  padding: 0;
  font-family: var(--sans);
  font-size: 0.9rem;
  list-style: none;
}

.links.stacked {
  flex-direction: column;
}

.more {
  font-family: var(--sans);
  font-size: 0.95rem;
}

/* Publications */

.lede {
  max-width: var(--measure);
  color: var(--muted);
}

.pub-list {
  margin: 0;
  padding: 0;
  list-style: none;
}

.pub {
  max-width: 40rem;
  margin-bottom: 1.6rem;
}

.pub p {
  margin: 0;
}

.pub-title {
  margin-bottom: 0.3rem !important;
  font-size: 1.05rem;
  font-weight: 500;
  line-height: 1.35;
}

.pub-title a {
  color: var(--ink);
  text-decoration: none;
}

.pub-title a:hover {
  color: var(--blue);
  text-decoration: underline;
}

.pub-authors,
.pub-venue,
.pub-notes {
  font-size: 0.88rem;
  line-height: 1.5;
}

.pub-authors {
  color: var(--muted);
}

.pub-authors b {
  color: var(--ink);
  font-weight: 600;
}

.pub-notes {
  color: var(--muted);
}

.pub-label {
  margin-left: 0.35em;
  color: var(--muted);
  font-family: var(--sans);
  font-size: 0.78rem;
}

.pub .scite-badge {
  margin-top: 0.45rem;
}

.pubs-year {
  display: grid;
  grid-template-columns: 5rem 1fr;
  gap: 0 1.5rem;
  margin-top: 2.5rem;
}

.pubs-year h2 {
  position: sticky;
  top: 1rem;
  align-self: start;
  margin: 0;
  color: var(--muted);
  font-size: 1.15rem;
  font-variant-numeric: tabular-nums;
}

/* Contact */

.contact {
  display: grid;
  grid-template-columns: 7rem 1fr;
  gap: 1rem 1.5rem;
  margin: 1.75rem 0 0;
}

.contact dt {
  font-family: var(--sans);
  font-weight: 500;
}

.contact dd {
  margin: 0;
}

.contact .links {
  gap: 0.55rem;
  font-family: var(--serif);
  font-size: 1rem;
}

.with-icon {
  display: inline-flex;
  align-items: center;
  gap: 0.6rem;
}

.with-icon .icon {
  flex: none;
  width: 1.15em;
  height: 1.15em;
  color: var(--muted);
}

/* Profile icons keep their brand colors. */
.scholar .icon { color: #4285f4; }
.orcid .icon { color: #a6ce39; }
.github .icon { color: #181717; }
.linkedin .icon { color: #0a66c2; }
.researchgate .icon { color: #00ccbb; }

/* Narrow screens */

@media (max-width: 36rem) {
  .hero {
    grid-template-columns: 1fr;
  }

  .hero img {
    width: 10rem;
  }

  .software,
  .contact,
  .pubs-year {
    grid-template-columns: 1fr;
  }

  .software dd,
  .contact dd {
    margin-bottom: 0.5rem;
  }

  .pubs-year h2 {
    position: static;
    margin-bottom: 0.9rem;
  }
}