/*
 * jserizay.com's own styles, loaded after chromokit's (config.yml > params.css).
 *
 * Every colour, size and shadow is a chromokit token (`--cx-*`), so both
 * palettes follow the theme toggle; change a token here to change it
 * everywhere (e.g. `:root { --cx-accent: … }`). The kit's prose rules style
 * bare elements inside `.cx-prose`, so the rules below are scoped under each
 * component's own class to win over them.
 */

/* ---- the frame: no header (config.yml > params.header), a thin sidebar --- */
body.cx-page {
  --cx-sidebar-w: 200px;
  /* "On this page" (Papers: the years; Software: the themes) */
  --cx-toc-w: 210px;
}

.cx-sidebar {
  padding: 24px 12px 20px 14px;
}

/* ---- the pages with grids of cards: a wider column ----------------------- */
.site-wide {
  --cx-content-w: 1040px;
}

/* ---- home ---------------------------------------------------------------- */
.site-home {
  position: relative;
  min-height: calc(100vh - var(--cx-header-h));
  /* The sequence behind stays hoverable around the column */
  pointer-events: none;
}

.site-home__inner {
  position: relative;
  z-index: 1;
  box-sizing: border-box;
  max-width: 50rem;
  margin: 0 auto;
  padding: 3rem 16px 3rem;
}

.site-home__inner > * {
  pointer-events: auto;
}

.site-intro {
  padding: 28px 32px 22px;
  background: color-mix(in srgb, var(--cx-bg-raised) 88%, transparent);
  -webkit-backdrop-filter: blur(6px);
  backdrop-filter: blur(6px);
  border: 1px solid var(--cx-border);
  border-radius: 12px;
  box-shadow: var(--cx-shadow-2);
}

.site-intro__head {
  display: flex;
  align-items: center;
  gap: 24px;
}

.site-portrait {
  flex: none;
  width: 112px;
  height: 112px;
  object-fit: cover;
  background: #fff;
  border: 1px solid var(--cx-border);
  border-radius: 50%;
  box-shadow: var(--cx-shadow-1);
}

.site-intro .site-name {
  margin: 0;
  font-size: clamp(1.9rem, 5vw, 2.5rem);
  font-weight: 650;
  line-height: 1.1;
  letter-spacing: -0.02em;
  color: var(--cx-text);
}

.site-intro .site-role {
  margin: 8px 0 0;
  font-size: var(--cx-step-0);
  color: var(--cx-text-dim);
}

.site-intro__text {
  margin-top: 20px;
}

.site-intro__text > :first-child {
  margin-top: 0;
}

.site-intro__text hr {
  margin: 22px 0;
}

.site-intro .site-links {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
  margin: 14px 0 0;
}

/* A button for each page of the menu, at the foot of the introduction */
.site-pages {
  display: flex;
  flex-wrap: wrap;
  gap: 8px;
  margin-top: 24px;
  padding-top: 20px;
  border-top: 1px solid var(--cx-border);
}

/* The sequence (layouts/partials/atgc-background.html, static/site.js) */
#atgc-background {
  position: fixed;
  inset: var(--cx-header-h) 0 0;
  overflow: hidden;
  padding: 18px 22px;
  font: 400 13px / 1.55 var(--cx-mono);
  letter-spacing: 0.14em;
  word-break: break-all;
  pointer-events: none;
  background: var(--cx-bg);
  opacity: 0;
  transition: opacity 1.2s ease;
  /* The sequence fades out towards the bottom of the screen */
  -webkit-mask-image: linear-gradient(to bottom, #000 45%, rgb(0 0 0 / 0.2) 100%);
  mask-image: linear-gradient(to bottom, #000 45%, rgb(0 0 0 / 0.2) 100%);

  /* Nucleotides, in muted genome-browser colours */
  --nt-a: #409162;
  --nt-c: #4270aa;
  --nt-g: #bf7900;
  --nt-t: #ba5246;
  --nt-alpha: 42%;
}

#atgc-background.is-ready {
  opacity: 1;
}

.atgc-letter {
  cursor: crosshair;
  pointer-events: auto;
  transition:
    color 0.15s ease,
    background-color 0.15s ease;
}

.atgc-letter.a { color: color-mix(in srgb, var(--nt-a) var(--nt-alpha), transparent); }
.atgc-letter.c { color: color-mix(in srgb, var(--nt-c) var(--nt-alpha), transparent); }
.atgc-letter.g { color: color-mix(in srgb, var(--nt-g) var(--nt-alpha), transparent); }
.atgc-letter.t { color: color-mix(in srgb, var(--nt-t) var(--nt-alpha), transparent); }

.atgc-letter:hover,
.atgc-letter.highlight {
  font-weight: 700;
  color: var(--cx-accent);
  background-color: var(--cx-accent-soft);
}

#atgc-tooltip {
  position: fixed;
  z-index: 20;
  padding: 2px 10px;
  font: 600 12px / 1.6 var(--cx-mono);
  letter-spacing: 0.08em;
  color: var(--cx-accent);
  white-space: nowrap;
  pointer-events: none;
  background: var(--cx-bg-raised);
  border: 1px solid var(--cx-border-strong);
  border-radius: 999px;
  box-shadow: var(--cx-shadow-2);
  transform: translate(-50%, calc(-100% - 8px));
}

/* Brighter letters on the dark palette, on each switch chromokit reads */
@media (prefers-color-scheme: dark) {
  :root:not([data-theme='light']) #atgc-background {
    --nt-a: #5fbf86;
    --nt-c: #79a6e0;
    --nt-g: #e0a33b;
    --nt-t: #e07b6e;
    --nt-alpha: 38%;
  }
}

:root[data-theme='dark'] #atgc-background {
  --nt-a: #5fbf86;
  --nt-c: #79a6e0;
  --nt-g: #e0a33b;
  --nt-t: #e07b6e;
  --nt-alpha: 38%;
}

@media (prefers-reduced-motion: reduce) {
  #atgc-background {
    transition: none;
  }
}

/* {{< fish >}}: a phrase that shows a picture */
.fish-hover {
  font-weight: 600;
  color: var(--cx-text);
  cursor: help;
  border-bottom: 1px dotted var(--cx-text-faint);
}

.fish-popup {
  position: fixed;
  z-index: 30;
  padding: 8px;
  pointer-events: none;
  background: var(--cx-bg-raised);
  border: 1px solid var(--cx-border);
  border-radius: 8px;
  box-shadow: var(--cx-shadow-2);
}

.fish-popup img {
  display: block;
  max-width: 250px;
  max-height: 200px;
  object-fit: contain;
}

/* ---- filter chips (layouts/partials/filter-chips.html, assets/js/filters.js) */
.filter-chips {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
  margin: 4px 0 28px;
}

.filter-chips[hidden] {
  display: none;
}

.filter-chip {
  display: inline-flex;
  align-items: center;
  gap: 6px;
  padding: 4px 6px 4px 11px;
  font: 500 var(--cx-step--1) / 1.2 var(--cx-sans);
  color: var(--cx-text-dim);
  cursor: pointer;
  background: var(--cx-bg-raised);
  border: 1px solid var(--cx-border-strong);
  border-radius: 999px;
  transition:
    color 120ms,
    border-color 120ms,
    background 120ms;
}

.filter-chip:hover {
  color: var(--cx-text);
  border-color: var(--cx-text-faint);
}

.filter-chip:focus-visible {
  outline: 2px solid var(--cx-accent);
  outline-offset: 2px;
}

.filter-chip[aria-pressed='true'] {
  color: var(--cx-accent);
  background: var(--cx-accent-soft);
  border-color: color-mix(in srgb, var(--cx-accent) 55%, transparent);
}

.filter-chip .cx-count {
  border-radius: 999px;
}

.filter-chip[aria-pressed='true'] .cx-count {
  color: var(--cx-accent);
  border-color: color-mix(in srgb, var(--cx-accent) 55%, transparent);
}

.filter-chip svg {
  width: 14px;
  height: 14px;
}

/* ---- year rail: items grouped by year along a vertical line (Papers, Courses) */
.year-rail {
  --year-w: 52px;
  --rail-gap: 34px;
  --marker-y: 22px;
  position: relative;
}

.year-rail::before {
  position: absolute;
  top: var(--marker-y);
  bottom: 0;
  left: calc(var(--year-w) + var(--rail-gap) / 2);
  width: 2px;
  content: '';
  background: linear-gradient(to bottom, var(--cx-border-strong), var(--cx-border) 70%, transparent);
  border-radius: 1px;
  transform: translateX(-50%);
}

.year-rail__year {
  display: grid;
  grid-template-columns: var(--year-w) minmax(0, 1fr);
  column-gap: var(--rail-gap);
}

.year-rail__year + .year-rail__year {
  margin-top: 28px;
}

.year-rail__year[hidden] {
  display: none;
}

.year-rail .year-rail__label {
  position: relative;
  margin: 0;
  padding-top: 11px;
  font: 600 var(--cx-step-1) / 1.3 var(--cx-sans);
  font-variant-numeric: tabular-nums;
  text-align: right;
  color: var(--cx-text-faint);
}

/* The marker on the rail; its halo cuts the line */
.year-rail__label::after {
  position: absolute;
  top: var(--marker-y);
  left: calc(100% + var(--rail-gap) / 2);
  width: 11px;
  height: 11px;
  box-sizing: border-box;
  content: '';
  background: var(--cx-bg);
  border: 2px solid var(--cx-text-faint);
  border-radius: 50%;
  box-shadow: 0 0 0 4px var(--cx-bg);
  transform: translate(-50%, -50%);
}

/* The latest year shown: a filled marker in the accent */
.year-rail:not(:has([data-filter-first])) .year-rail__year:first-child .year-rail__label,
.year-rail__year[data-filter-first] .year-rail__label {
  color: var(--cx-text);
}

.year-rail:not(:has([data-filter-first])) .year-rail__year:first-child .year-rail__label::after,
.year-rail__year[data-filter-first] .year-rail__label::after {
  background: var(--cx-accent);
  border-color: var(--cx-accent);
}

/* ---- papers -------------------------------------------------------------- */
.paper-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(17rem, 1fr));
  gap: 12px;
}

.paper {
  display: flex;
  flex-direction: column;
  gap: 6px;
}

.paper[hidden] {
  display: none;
}

.paper .paper__title {
  margin: 0;
  font: 600 var(--cx-step-0) / 1.4 var(--cx-sans);
  letter-spacing: -0.005em;
  color: var(--cx-text);
}

.paper .paper__title a {
  color: inherit;
  text-decoration: none;
}

.paper .paper__title a:hover {
  color: var(--cx-accent);
  text-decoration: underline;
  text-underline-offset: 0.2em;
}

.paper .paper__authors {
  margin: 0;
  font-size: var(--cx-step--1);
  line-height: 1.5;
  color: var(--cx-text-dim);
}

/* This site's author, as a highlighter would mark it */
.paper .paper__me,
.paper-page .paper__me {
  font-weight: 600;
  color: var(--cx-text);
  background: linear-gradient(to top, var(--cx-accent-soft) 45%, transparent 45%);
}

.paper .paper__meta {
  display: flex;
  flex-wrap: wrap;
  gap: 4px 8px;
  align-items: center;
  margin: 0;
  font-size: var(--cx-step--1);
  line-height: 1.4;
  color: var(--cx-text-faint);
}

.paper .cx-badge {
  padding: 2px 8px;
  font-size: var(--cx-step--2);
}

.paper .paper__links {
  display: flex;
  flex-wrap: wrap;
  gap: 6px 14px;
  align-items: center;
  margin: auto 0 0;
  padding-top: 9px;
  font-size: var(--cx-step--1);
  border-top: 1px solid var(--cx-border);
}

.paper .paper__links a:not(.cx-chip),
.package .package__links a {
  font-weight: 500;
  color: var(--cx-accent);
  text-decoration: none;
}

.paper .paper__links a:not(.cx-chip):hover,
.package .package__links a:hover {
  text-decoration: underline;
  text-underline-offset: 0.2em;
}

/* A package of the Software page, cited by a paper or named in a workflow */
.paper a.cx-chip,
.software-flow a.cx-chip {
  color: var(--cx-text);
  text-decoration: none;
  transition:
    color 120ms,
    border-color 120ms;
}

.paper a.cx-chip:hover,
.software-flow a.cx-chip:hover {
  color: var(--cx-accent);
  border-color: var(--cx-accent);
}

.paper .cx-chip svg {
  width: 12px;
  height: 12px;
  color: var(--cx-text-faint);
}

/* All the papers' citations, above the filters */
.papers .papers__downloads {
  display: flex;
  flex-wrap: wrap;
  gap: 4px 6px;
  align-items: center;
  margin: 0 0 14px;
  font-size: var(--cx-step--1);
  color: var(--cx-text-dim);
}

.papers__downloads svg {
  width: 13px;
  height: 13px;
  color: var(--cx-text-faint);
}

/* ---- a paper's page (layouts/partials/paper-page.html) -------------------- */
.paper-page .paper-page__authors {
  margin: 0;
  font-size: var(--cx-step-0);
  line-height: 1.65;
  color: var(--cx-text-dim);
}

.paper-page__authors sup,
.paper-page__note sup {
  margin-left: 1px;
  color: var(--cx-accent);
}

.paper-page .paper-page__note {
  margin: 4px 0 0;
  font-size: var(--cx-step--1);
  color: var(--cx-text-faint);
}

.paper-page .paper-page__meta {
  display: flex;
  flex-wrap: wrap;
  gap: 4px 16px;
  align-items: center;
  margin: 14px 0 0;
  font-size: var(--cx-step-0);
  color: var(--cx-text-dim);
}

.paper-page__meta em {
  color: var(--cx-text);
}

.paper-page__meta span:not(.cx-badge) {
  display: inline-flex;
  gap: 5px;
  align-items: center;
}

.paper-page__meta svg {
  width: 13px;
  height: 13px;
  color: var(--cx-text-faint);
}

.paper-page .cx-badge {
  padding: 3px 9px;
  font-size: var(--cx-step--2);
}

.paper-page .paper-page__actions,
.paper-page .paper-page__downloads {
  display: flex;
  flex-wrap: wrap;
  gap: 8px;
  margin: 22px 0 0;
}

.paper-page .paper-page__downloads {
  margin-top: 12px;
}

.paper-page .paper-page__software {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
}

.paper-page__software a.cx-chip {
  color: var(--cx-text);
  text-decoration: none;
}

.paper-page__software a.cx-chip:hover {
  color: var(--cx-accent);
  border-color: var(--cx-accent);
}

.paper-page__software .cx-chip svg {
  width: 12px;
  height: 12px;
  color: var(--cx-text-faint);
}

.paper-page .paper-page__reference {
  margin: 0 0 14px;
  padding: 12px 16px;
  font-size: var(--cx-step-0);
  line-height: 1.6;
  background: var(--cx-bg-raised);
  border: 1px solid var(--cx-border);
  border-left: 3px solid var(--cx-accent);
  border-radius: var(--cx-radius);
}

/* The BibTeX entry wraps, so that its long author line can be read */
.paper-page__bibtex pre {
  font-size: var(--cx-step--1);
  white-space: pre-wrap;
  overflow-wrap: anywhere;
}

/* ---- software ------------------------------------------------------------ */
.software-section {
  scroll-margin-top: calc(var(--cx-header-h) + 16px);
}

.software-section + .software-section {
  margin-top: 48px;
}

.software-section[hidden] {
  display: none;
}

.software .software-section__head h2 {
  margin: 0 0 4px;
  font-size: var(--cx-prose-h3);
}

.software .software-section__head p {
  margin: 0 0 16px;
  font-size: var(--cx-step-0);
  line-height: 1.55;
}

.software-flow {
  margin: 0 0 14px;
  padding: 14px 16px;
  background: color-mix(in srgb, var(--cx-bg-sunken) 60%, transparent);
  border: 1px dashed var(--cx-border-strong);
  border-radius: var(--cx-radius);
}

.software-flow[hidden] {
  display: none;
}

.software .software-flow__steps {
  display: flex;
  flex-wrap: wrap;
  gap: 10px 12px;
  align-items: flex-end;
  margin: 0;
  padding: 0;
  list-style: none;
}

.software .software-flow__steps li + li {
  margin-top: 0;
}

.software-flow__step {
  display: flex;
  flex-direction: column;
  gap: 6px;
}

.software-flow__label {
  font: 600 var(--cx-label) / 1.2 var(--cx-sans);
  letter-spacing: 0.1em;
  text-transform: uppercase;
  color: var(--cx-text-faint);
}

.software-flow__packages {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
}

.software-flow__arrow {
  display: grid;
  place-items: center;
  height: 1.55rem;
  color: var(--cx-text-faint);
}

.software-flow__arrow svg {
  width: 16px;
  height: 16px;
}

.software-flow__extras {
  display: flex;
  flex-wrap: wrap;
  gap: 12px 32px;
  margin-top: 14px;
  padding-top: 12px;
  border-top: 1px dashed var(--cx-border);
}

.software-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(21rem, 1fr));
  gap: 12px;
}

.package {
  display: flex;
  flex-direction: column;
  gap: 8px;
  scroll-margin-top: calc(var(--cx-header-h) + 16px);
}

.package[hidden] {
  display: none;
}

/* The card a link points to (a workflow step, a paper) */
.package:target {
  border-color: var(--cx-accent);
  box-shadow:
    0 0 0 3px var(--cx-accent-soft),
    var(--cx-shadow-2);
}

.package .package__head {
  display: flex;
  gap: 10px;
  align-items: baseline;
  justify-content: space-between;
}

.package .package__name {
  margin: 0;
  font: 600 var(--cx-step-1) / 1.3 var(--cx-mono);
  letter-spacing: -0.01em;
  color: var(--cx-text);
}

.package .package__name a {
  color: inherit;
  text-decoration: none;
}

.package .package__name a:hover {
  color: var(--cx-accent);
  text-decoration: underline;
  text-underline-offset: 0.2em;
}

.package__language {
  display: inline-flex;
  flex: none;
  gap: 5px;
  align-items: center;
  font-size: var(--cx-step--2);
  color: var(--cx-text-faint);
  white-space: nowrap;
}

.package__language svg {
  width: 13px;
  height: 13px;
}

.package .package__tagline {
  margin: 0;
  font-size: var(--cx-step-0);
  line-height: 1.55;
}

.package .package__meta {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
  align-items: center;
  margin: 0;
  font-size: var(--cx-step--1);
  color: var(--cx-text-faint);
}

.package .cx-badge {
  padding: 3px 8px;
  font-size: var(--cx-step--2);
}

.package .package__links {
  display: flex;
  flex-wrap: wrap;
  gap: 4px 14px;
  margin: 0;
  font-size: var(--cx-step--1);
}

.package .package__install {
  margin: auto 0 0;
  box-shadow: none;
}

.package .package__install pre {
  padding: 7px 42px 7px 12px;
  font-size: var(--cx-step--1);
  line-height: 1.5;
  /* A command breaks only after its bracket (the <wbr> in software.html) */
  white-space: pre-wrap;
}

.package .package__install .cx-code__copy {
  top: 50%;
  width: 26px;
  height: 26px;
  transform: translateY(-50%);
}

/* ---- courses ------------------------------------------------------------- */
.course-list {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(20rem, 1fr));
  gap: 10px;
}

.course {
  display: flex;
  flex-direction: column;
  gap: 8px;
}

.course .course__title {
  margin: 0;
  font: 600 var(--cx-step-0) / 1.4 var(--cx-sans);
  color: var(--cx-text);
}

.course .course__title a {
  color: inherit;
  text-decoration: none;
}

.course .course__title a:hover {
  color: var(--cx-accent);
  text-decoration: underline;
  text-underline-offset: 0.2em;
}

.course .course__meta,
.book .book__meta {
  display: flex;
  flex-wrap: wrap;
  gap: 4px 14px;
  align-items: center;
  margin: auto 0 0;
  font-size: var(--cx-step--1);
  color: var(--cx-text-dim);
}

.course__meta span,
.book__meta span:not(.cx-badge) {
  display: inline-flex;
  gap: 5px;
  align-items: center;
}

.course__meta svg,
.book__meta svg {
  width: 13px;
  height: 13px;
  color: var(--cx-text-faint);
}

/* ---- books --------------------------------------------------------------- */
.book-list {
  display: grid;
  gap: 16px;
}

.book {
  display: grid;
  grid-template-columns: 200px minmax(0, 1fr);
  gap: 28px;
  padding: 22px;
}

.book .book__cover {
  margin: 0;
}

.book .book__cover img {
  display: block;
  width: 100%;
  height: auto;
  border: 1px solid var(--cx-border);
  border-radius: 4px;
  box-shadow: var(--cx-shadow-2);
}

.book .book__title {
  margin: 0 0 10px;
  font-size: var(--cx-prose-h2);
  line-height: 1.25;
}

.book .book__title a {
  color: var(--cx-text);
  text-decoration: none;
}

.book .book__title a:hover {
  color: var(--cx-accent);
}

.book .book__meta {
  margin: 0 0 14px;
}

.book .cx-badge {
  padding: 3px 9px;
  font-size: var(--cx-step--2);
}

.book .book__description {
  margin: 0;
}

.book .book__actions {
  justify-content: flex-start;
  margin: 20px 0 0;
}

/* ---- career timeline (data/timeline.yaml; the timeline shortcode) -------- */
.timeline {
  margin: 24px 0;
  padding: 0;
  list-style: none;
  border-left: 2px solid var(--cx-border);
}

.timeline__item {
  display: grid;
  gap: 2px;
  padding: 0 0 16px 18px;
}

.timeline__period {
  font-size: var(--cx-step--1);
  color: var(--cx-accent);
}

.timeline__description {
  font-size: var(--cx-step--1);
  color: var(--cx-text-dim);
}

/* ---- phones -------------------------------------------------------------- */
@media (max-width: 640px) {
  .site-home__inner {
    padding-top: 1.5rem;
  }

  .site-intro {
    padding: 22px 18px 16px;
  }

  .site-intro__head {
    flex-direction: column;
    gap: 14px;
    text-align: center;
  }

  .site-portrait {
    width: 96px;
    height: 96px;
  }

  .site-intro .site-links,
  .site-pages {
    justify-content: center;
  }

  #atgc-background {
    font-size: 12px;
  }

  /* The years above their items, with no rail */
  .year-rail::before,
  .year-rail__label::after {
    display: none;
  }

  .year-rail__year {
    grid-template-columns: minmax(0, 1fr);
  }

  .year-rail .year-rail__label {
    padding: 0 0 8px;
    text-align: left;
  }

  .book {
    grid-template-columns: minmax(0, 1fr);
    gap: 18px;
  }

  .book .book__cover img {
    max-width: 180px;
  }
}