/* =====================================================================
   Pipelines and reproducibility – styles for the terminal colours,
   the editor, Galaxy's workflow editor, the agent and the chapters.
   ===================================================================== */
:root {
  --smk-y: #e3c96b;
  --smk-g: #86d99a;
  --smk-r: #ff8f86;
}

/* ---------------- terminal: Snakemake's colours, hints, environment ---------------- */
.term-out .tl.cy { color: var(--smk-y); }
.term-out .tl.cg { color: var(--smk-g); }
.term-out .tl.cr { color: var(--smk-r); }
.term-out .tl.hint { color: #b9e6ff; font-family: var(--font); font-size: 12.5px; background: rgba(79, 157, 222, 0.12); border-left: 3px solid #4f9dde; padding: 3px 8px; margin: 3px 0; border-radius: 0 6px 6px 0; }
.term-out a.flink { color: inherit; text-decoration: underline dotted; cursor: pointer; }
.term-out a.flink:hover { color: #fff; }

/* ---------------- files & editor ---------------- */
#edRoot { height: 100%; min-height: 0; }
.ed { display: flex; height: 100%; min-height: 0; background: #fff; }
.ed-side { width: 230px; flex: none; display: flex; flex-direction: column; border-right: 1px solid var(--line); background: var(--panel-2); min-height: 0; }
.ed-treebar { display: flex; align-items: center; gap: 2px; padding: 6px 6px 6px 10px; border-bottom: 1px solid var(--line); flex: none; }
.ed-treebar b { font-size: 0.82rem; text-transform: uppercase; letter-spacing: 0.04em; color: var(--muted); }
.ed-treebar .grow, .ed-bar .grow { flex: 1; }
.ed-treebar .tbtn { padding: 3px 5px; }
.ed-treebar .tbtn.on { background: var(--accent-soft); color: var(--accent-2); }
.ed-tree { flex: 1; overflow: auto; padding: 4px 0 20px; font-size: 0.82rem; }
.ed-row { display: flex; align-items: center; gap: 4px; padding: 2px 8px; cursor: pointer; white-space: nowrap; color: var(--ink-2); border-radius: 4px; margin: 0 4px; }
.ed-row:hover { background: #e8edf3; }
.ed-row:focus-visible { outline: 2px solid var(--accent); outline-offset: -2px; }
.ed-row.on { background: var(--accent-soft); color: var(--accent-2); font-weight: 600; }
.ed-row.dir { color: #2d5f8a; }
.ed-row.fresh .ed-name { color: var(--good); }
.ed-caret { width: 10px; flex: none; color: var(--muted); font-size: 0.75rem; }
.ed-ic .ic { width: 14px; height: 14px; opacity: 0.75; }
.ed-name { flex: 1; overflow: hidden; text-overflow: ellipsis; font-family: var(--mono); font-size: 12px; }
.ed-size { color: var(--muted); font-size: 11px; }
.ed-lock .ic { width: 12px; height: 12px; opacity: 0.55; }
.ed-main { flex: 1; min-width: 0; display: flex; flex-direction: column; min-height: 0; }
.ed-tabs { display: flex; gap: 2px; padding: 4px 6px 0; background: var(--panel-2); border-bottom: 1px solid var(--line); overflow-x: auto; flex: none; min-height: 31px; }
.ed-tab { display: inline-flex; align-items: center; border: 1px solid var(--line); border-bottom: 0; border-radius: 7px 7px 0 0; background: #eef1f5; font-size: 0.8rem; }
.ed-tab.on { background: #fff; position: relative; top: 1px; }
.ed-tab.gone .ed-tab-l { text-decoration: line-through; }
.ed-tab-l { border: 0; background: none; padding: 4px 4px 4px 10px; cursor: pointer; font-family: var(--mono); font-size: 12px; }
.ed-tab-x { border: 0; background: none; padding: 2px 8px 2px 4px; cursor: pointer; color: var(--muted); }
.ed-tab.dirty .ed-tab-x { color: var(--act); }
.ed-tab-x:hover { color: var(--bad); }
.ed-bar { display: flex; align-items: center; gap: 6px; padding: 5px 10px; border-bottom: 1px solid var(--line); flex: none; min-height: 38px; }
.ed-path { font-family: var(--mono); font-size: 12px; color: var(--ink-2); overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
.ed-cm { flex: 1; min-height: 0; position: relative; }
.ed-cm .CodeMirror { position: absolute; inset: 0; height: auto; font-family: var(--mono); font-size: 13px; line-height: 1.5; }
.cm-flash { background: #fff3c4 !important; transition: background 1s; }
.ed-view { flex: 1; min-height: 0; overflow: auto; padding: 14px; background: #fafbfc; }
.ed-empty { flex: 1; min-height: 0; overflow: auto; }
.ed-img { background: #fff; border: 1px solid var(--line); border-radius: 8px; padding: 10px; display: inline-block; max-width: 100%; }
.ed-img img { max-width: 100%; height: auto; display: block; }
.ed-img.svg img { min-width: min(100%, 420px); }
.ed-frame { width: 100%; height: calc(100% - 10px); min-height: 400px; border: 1px solid var(--line); border-radius: 8px; background: #fff; }
.ed-tablebox { overflow: auto; max-height: 70vh; background: #fff; border: 1px solid var(--line); border-radius: 8px; }
.ed-table { border-collapse: collapse; }
.ed-table th, .ed-table td { padding: 3px 10px; border-bottom: 1px solid var(--line); text-align: left; font-family: var(--mono); font-size: 12px; white-space: nowrap; }
.ed-table th { position: sticky; top: 0; background: var(--panel-2); }
.ed-note { margin: 10px 0 0; }
/* PDF files (pdfview.js): the pages on a grey desk, a toolbar above them */
.ed-view.pdf { padding: 0; overflow: hidden; display: flex; flex-direction: column; background: #e7ebf0; }
.pdfv { flex: 1; min-height: 0; display: flex; flex-direction: column; }
.pdfv-bar { flex: none; display: flex; align-items: center; flex-wrap: wrap; gap: 6px; padding: 5px 10px; background: var(--panel); border-bottom: 1px solid var(--line); font-size: 0.8rem; color: var(--ink-2); }
.pdfv-pg { display: inline-flex; align-items: center; gap: 4px; white-space: nowrap; }
.pdfv-num { width: 3.6em; padding: 2px 4px; border: 1px solid var(--line-2); border-radius: 5px; font: inherit; text-align: right; }
.pdfv-sep { width: 1px; height: 18px; background: var(--line); margin: 0 4px; }
.pdfv-zoom { min-width: 3.6em; text-align: center; font-variant-numeric: tabular-nums; }
.pdfv-bar .tbtn.on { background: var(--accent-soft); color: var(--accent-2); border-color: var(--accent); }
.pdfv-scroll { flex: 1; min-height: 0; overflow: auto; scrollbar-gutter: stable; position: relative; outline: none; }
.pdfv-scroll:focus-visible { box-shadow: inset 0 0 0 2px var(--accent); }
/* (a page wider than the pane – zoomed in, or turned sideways – starts at its left edge and the pane scrolls sideways;
   narrower pages stay in the middle) */
.pdfv-pages { padding: 12px 16px 28px; }
.pdfv-page { position: relative; margin: 0 auto 12px; background: #fff; box-shadow: 0 0 0 1px rgba(16, 24, 40, 0.08), 0 2px 6px rgba(16, 24, 40, 0.14);
  --user-unit: 1; --total-scale-factor: calc(var(--scale-factor) * var(--user-unit)); --scale-round-x: 1px; --scale-round-y: 1px; }
.pdfv-page > canvas { position: absolute; inset: 0; width: 100%; height: 100%; display: block; }
.pdfv-links { position: absolute; inset: 0; z-index: 2; pointer-events: none; }
.pdfv-link { position: absolute; pointer-events: auto; border-radius: 2px; }
.pdfv-link:hover, .pdfv-link:focus-visible { background: rgba(11, 107, 138, 0.12); box-shadow: 0 0 0 1px rgba(11, 107, 138, 0.55); outline: none; }
.pdfv-msg { max-width: 34rem; margin: 40px auto; padding: 16px 18px; background: #fff; border: 1px solid var(--line); border-radius: 8px; color: var(--ink-2); font-size: 0.86rem; line-height: 1.5; }
.pdfv-msg p { margin: 6px 0 0; }
.pdfv-pass div { display: flex; gap: 6px; margin-top: 8px; }
.pdfv-pass input { flex: 1; padding: 4px 8px; border: 1px solid var(--line-2); border-radius: 6px; font: inherit; }
.pdfv-frame { width: 100%; height: 100%; min-height: 400px; border: 0; display: block; background: #fff; }
/* the text of a page, laid over its picture so that it can be selected and found (after PDF.js's own text_layer.css) */
.pdfv .textLayer { position: absolute; inset: 0; overflow: hidden; overflow: clip; text-align: initial; opacity: 1; line-height: 1; letter-spacing: normal; word-spacing: normal;
  -webkit-text-size-adjust: none; text-size-adjust: none; forced-color-adjust: none; transform-origin: 0 0; caret-color: CanvasText; z-index: 0;
  --min-font-size: 1; --text-scale-factor: calc(var(--total-scale-factor) * var(--min-font-size)); --min-font-size-inv: calc(1 / var(--min-font-size)); }
.pdfv .textLayer span, .pdfv .textLayer br { color: transparent; position: absolute; white-space: pre; cursor: text; transform-origin: 0% 0%; -webkit-user-select: text; user-select: text; }
.pdfv .textLayer > :not(.markedContent), .pdfv .textLayer .markedContent span:not(.markedContent) { z-index: 1; --font-height: 0; font-size: calc(var(--text-scale-factor) * var(--font-height));
  --scale-x: 1; --rotate: 0deg; transform: rotate(var(--rotate)) scaleX(var(--scale-x)) scale(var(--min-font-size-inv)); }
.pdfv .textLayer .markedContent { display: contents; }
.pdfv .textLayer span[role="img"] { -webkit-user-select: none; user-select: none; cursor: default; }
.pdfv .textLayer ::selection { background: rgba(11, 107, 138, 0.28); color: transparent; }
.pdfv .textLayer br::selection { background: transparent; }
.pdfv .textLayer .endOfContent { display: block; position: absolute; inset: 100% 0 0; z-index: 0; cursor: default; -webkit-user-select: none; user-select: none; }
.pdfv .textLayer.selecting .endOfContent { top: 0; }
.pill.small { font-size: 0.7rem; padding: 0 6px; }
.pill.warn { background: var(--warn-soft); color: var(--warn); }

@media (max-width: 700px) {
  .ed-side { width: 150px; }
}

/* ---------------- Galaxy: upload, history actions, editor side panel ---------------- */
.gx-upwrap { padding: 0 8px 8px; }
.gx-upload { width: 100%; justify-content: center; }
.gx-hacts { display: flex; gap: 4px; margin-top: 6px; flex-wrap: wrap; }
.gx-hacts .btn { font-size: 0.76rem; }
.gx-empty { padding: 14px 10px; text-align: center; color: var(--ink-2); font-size: 0.82rem; }
.gx-empty p { margin: 0 0 6px; }
.gx-dname { word-break: break-word; }
.gx-uplist { display: flex; flex-direction: column; gap: 2px; border: 1px solid var(--line); border-radius: 8px; padding: 6px; background: var(--panel-2); }
.gx-uprow { display: grid; grid-template-columns: auto 1fr auto auto; gap: 8px; align-items: center; padding: 4px 6px; border-radius: 6px; cursor: pointer; }
.gx-uprow:hover { background: #fff; }
.gx-uprow code { font-size: 12px; word-break: break-all; }
.gx-uprow select { font-size: 0.78rem; padding: 2px 4px; border: 1px solid var(--line-2); border-radius: 5px; background: #fff; }
.gx-uprow input[type='checkbox'] { width: 16px; height: 16px; }
.gx-canvas-empty { position: absolute; left: 20px; top: 20px; right: 20px; color: var(--muted); font-size: 0.86rem; pointer-events: none; }
.gx-sidecol .gx-ph { padding: 4px 0; }
.gx-pad { padding: 0 0 8px; }
.gx-pad .gx-field { margin-bottom: 8px; }
.gx-probs { margin: 4px 0 8px; padding-left: 18px; color: var(--warn); font-size: 0.8rem; }
.gx-probs li { margin-bottom: 3px; }
.gx-port.in.on .dot { background: #5b6b82; }
.gx-form .gx-uplist + .gx-runrow { padding-top: 8px; }
.gx-center .callout ul { margin: 4px 0 0; padding-left: 18px; }

/* ---------------- terminal: ask the AI about an error ---------------- */
.term-out .tl.ask { margin: 2px 0 6px; }
.term-ask { font-family: var(--font); font-size: 12px; border: 1px solid #6b5a8e; background: rgba(140, 95, 208, 0.16); color: #e3d4ff; border-radius: 99px; padding: 2px 11px; cursor: pointer; }
.term-ask:hover { background: rgba(140, 95, 208, 0.3); color: #fff; }
.term-ask:disabled { opacity: 0.5; cursor: default; }

/* ---------------- AI assistant: tabs, tables, code actions, agent ---------------- */
.ai-tabs { display: inline-flex; border: 1px solid var(--line-2); border-radius: 99px; overflow: hidden; margin-left: 4px; }
.ai-tab { display: inline-flex; align-items: center; gap: 5px; border: 0; background: var(--panel-2); padding: 3px 12px; font-size: 0.82rem; cursor: pointer; color: var(--ink-2); }
.ai-tab + .ai-tab { border-left: 1px solid var(--line-2); }
.ai-tab .ic { width: 14px; height: 14px; }
.ai-tab.on { background: #6b3fa0; color: #fff; }
.ai-threads { flex: 1; min-height: 0; display: flex; flex-direction: column; }
.ai-threads .ai-thread { flex: 1; min-height: 0; }
.ai.agent .ai-thread { background: #f7f9fb; }
.ai-tablewrap { overflow-x: auto; margin: 6px 0; }
.ai-table { border-collapse: collapse; font-size: 0.84rem; }
.ai-table th, .ai-table td { border: 1px solid var(--line); padding: 3px 8px; text-align: left; vertical-align: top; }
.ai-table th { background: var(--panel-2); }
.ai-code-file { font-family: var(--mono); font-size: 11.5px; color: var(--muted); padding: 4px 10px 0; background: #f6f8fa; }
.ai-codebox.example { border-style: dashed; }
.ai-codebox.example .ai-code { background: #fbfbfc; }
.ai-msg.ag { max-width: 96%; background: #fff; border: 1px solid #d7dfe8; }
.ag-head { display: flex; align-items: center; gap: 7px; color: #28405a; margin-bottom: 4px; }
.ag-head .ic { width: 16px; height: 16px; }
.ag-steps { list-style: none; margin: 4px 0 8px; padding: 0; display: flex; flex-direction: column; gap: 3px; font-size: 0.84rem; }
.ag-step { display: flex; flex-wrap: wrap; align-items: baseline; gap: 7px; padding: 3px 8px; border-radius: 6px; background: #f3f6f9; }
.ag-step.run { background: #fff8e0; }
.ag-step.bad { background: var(--bad-soft); }
.ag-step code { font-size: 0.82rem; }
/* the terminal while the real agent uses it; a step of several lines */
.term.locked .term-inputline { opacity: 0.6; }
.term.locked .term-input::placeholder { color: #c9b6f2; font-family: var(--font); font-size: 12.5px; }
.ag-step code.ag-cmd { display: inline-block; white-space: pre-wrap; word-break: break-word; vertical-align: top; }
.ag-ic { width: 16px; flex: none; text-align: center; color: var(--good); font-weight: 700; }
.ag-step.bad .ag-ic { color: var(--bad); }
.ag-out { flex-basis: 100%; margin: 2px 0 2px 23px; }
.ag-out summary { cursor: pointer; font-size: 0.76rem; color: var(--muted); }
.ag-out pre { margin: 4px 0; max-height: 220px; overflow: auto; background: #0f1720; color: #dbe4ee; border-radius: 6px; padding: 6px 8px; font-size: 11.5px; white-space: pre-wrap; word-break: break-word; }
.ag-file { display: flex; align-items: center; gap: 8px; flex-wrap: wrap; border: 1px solid var(--line); border-radius: 8px; padding: 6px 8px; margin-top: 8px; background: #fbfcfe; }
.ag-file .grow { flex: 1; }
.ag-fname { display: inline-flex; align-items: center; gap: 5px; font-family: var(--mono); font-size: 12px; }
.ag-fname .ic { width: 14px; height: 14px; }

/* ---------------- files and code in the instructions ---------------- */
.codefile { border: 1px solid var(--line); border-radius: 8px; margin: 0.8em 0; background: #fff; overflow: hidden; }
.cf-head { display: flex; align-items: center; gap: 6px; padding: 5px 8px 5px 10px; background: var(--panel-2); border-bottom: 1px solid var(--line); flex-wrap: wrap; }
.cf-head .grow { flex: 1; }
.cf-name { font-family: var(--mono); font-size: 12.5px; font-weight: 600; color: var(--ink-2); }
.codefile .codeblock { margin: 0; border: 0; border-radius: 0; background: #fbfcfd; max-height: 420px; overflow: auto; white-space: pre; font-size: 12.3px; line-height: 1.5; }
.codefile.snippet .cf-head { padding: 3px 8px; background: #fbfcfd; border-bottom: 1px dashed var(--line); }
.codefile.nbcode .cf-name { font-family: var(--font); color: #5b2f94; }
.cf-note { font-size: 0.8rem; color: var(--muted); padding: 5px 10px; border-top: 1px solid var(--line); background: var(--panel-2); }
.tut blockquote.quote { margin: 0.2em 0 0.5em; font-size: 1.02rem; font-style: italic; line-height: 1.5; }
.tut table.route td:first-child { white-space: nowrap; font-weight: 600; }
.tut table.compare th { text-align: left; vertical-align: top; }
.tut table.compare td { vertical-align: top; }
.tut .table { margin: 0.6em 0; }
.tut .steps code, .tut p code { overflow-wrap: anywhere; }
.tut .table td:first-child code { white-space: nowrap; }