PyPI - secondbrain-py - Versions diffs - 0.2.1__py3-none-any.whl - Mend

secondbrain-py 0.2.1__py3-none-any.whl

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brain/__init__.py +0 -0
brain/__main__.py +18 -0
brain/_capture_command.py +445 -0
brain/_compose.py +52 -0
brain/activity.py +206 -0
brain/ask.py +631 -0
brain/audio.py +591 -0
brain/backfill/__init__.py +12 -0
brain/backfill/search_extras.py +141 -0
brain/backfill/source_rows.py +101 -0
brain/bin/__init__.py +1 -0
brain/bin/_launcher.py +107 -0
brain/bin/down.py +8 -0
brain/bin/launchd.py +268 -0
brain/bin/monitor.py +570 -0
brain/bin/rebuild.py +8 -0
brain/bin/status.py +8 -0
brain/bin/up.py +8 -0
brain/brief.py +272 -0
brain/capture.py +49 -0
brain/chat.py +293 -0
brain/cli.py +9760 -0
brain/cli_claude.py +81 -0
brain/cli_connect.py +285 -0
brain/cli_demo.py +266 -0
brain/config.py +1949 -0
brain/connect.py +925 -0
brain/db.py +540 -0
brain/demo/__init__.py +452 -0
brain/demo/corpus/manifest.json +403 -0
brain/demo/embedder.py +74 -0
brain/durations.py +84 -0
brain/edit_session.py +156 -0
brain/editor.py +67 -0
brain/elicit/__init__.py +16 -0
brain/elicit/detectors.py +250 -0
brain/elicit/drafter.py +70 -0
brain/elicit/queue.py +220 -0
brain/elicit/schema.py +48 -0
brain/elicit/session.py +445 -0
brain/embedding_targets.py +54 -0
brain/embeddings.py +424 -0
brain/enrichment.py +808 -0
brain/errors.py +357 -0
brain/eval/__init__.py +129 -0
brain/eval/answer_eval.py +281 -0
brain/eval/baseline.py +265 -0
brain/eval/concept_extraction.py +378 -0
brain/eval/corpus.py +152 -0
brain/eval/errors.py +19 -0
brain/eval/graph_baseline.py +226 -0
brain/eval/graph_retrieval.py +202 -0
brain/eval/graph_runner.py +319 -0
brain/eval/metrics.py +101 -0
brain/eval/runner.py +223 -0
brain/format.py +783 -0
brain/gaps.py +390 -0
brain/graph_rag/__init__.py +94 -0
brain/graph_rag/_retrieval_common.py +113 -0
brain/graph_rag/aggregates.py +303 -0
brain/graph_rag/aliases/__init__.py +583 -0
brain/graph_rag/backends/__init__.py +10 -0
brain/graph_rag/backends/_age_helpers.py +473 -0
brain/graph_rag/backends/age.py +782 -0
brain/graph_rag/backends/base.py +272 -0
brain/graph_rag/build.py +344 -0
brain/graph_rag/communities.py +644 -0
brain/graph_rag/communities_summary.py +437 -0
brain/graph_rag/concepts.py +202 -0
brain/graph_rag/cooccur.py +193 -0
brain/graph_rag/cross_type.py +312 -0
brain/graph_rag/extract.py +885 -0
brain/graph_rag/fuse.py +371 -0
brain/graph_rag/global_.py +412 -0
brain/graph_rag/grouping.py +372 -0
brain/graph_rag/person_resolver.py +167 -0
brain/graph_rag/reconcile.py +792 -0
brain/graph_rag/relational.py +353 -0
brain/graph_rag/retrieve.py +526 -0
brain/graph_rag/router.py +288 -0
brain/graph_rag/schema.py +320 -0
brain/graph_rag/sync.py +237 -0
brain/graph_rag/tenancy.py +43 -0
brain/graph_rag/themes.py +501 -0
brain/graph_rag/weighting.py +202 -0
brain/ingest/__init__.py +1926 -0
brain/ingest/chunker.py +249 -0
brain/ingest/docx.py +40 -0
brain/ingest/gmail.py +621 -0
brain/ingest/markdown.py +37 -0
brain/ingest/pdf.py +61 -0
brain/ingest/stdin.py +22 -0
brain/ingest/sub_tokens.py +91 -0
brain/ingest/text.py +16 -0
brain/interactions.py +205 -0
brain/maintenance.py +355 -0
brain/mcp_server.py +3405 -0
brain/migrations/001_init.sql +43 -0
brain/migrations/002_qwen3_embedding.sql +17 -0
brain/migrations/003_vault_model.sql +41 -0
brain/migrations/004_relax_content_hash_uniqueness.sql +18 -0
brain/migrations/005_derived_links.sql +67 -0
brain/migrations/006_dedup_file_by_source_path.sql +25 -0
brain/migrations/007_email_thread_and_draft.sql +15 -0
brain/migrations/008_gmail_thread_unique.sql +11 -0
brain/migrations/009_chunks_weighted_tsv.sql +28 -0
brain/migrations/010_interactions.sql +30 -0
brain/migrations/011_documents_summary.sql +23 -0
brain/migrations/012_graphrag.sql +171 -0
brain/migrations/013_graphrag_communities.sql +125 -0
brain/migrations/014_graphrag_community_summary_hash.sql +33 -0
brain/migrations/015_interactions_graph_targets.sql +89 -0
brain/migrations/016_index_hygiene.sql +61 -0
brain/migrations/017_elicit.sql +30 -0
brain/migrations/018_review_gap_signal_kinds.sql +40 -0
brain/migrations/019_search_queries.sql +35 -0
brain/migrations/020_link_suggestions.sql +40 -0
brain/migrations/021_timeline_doc_date.sql +34 -0
brain/migrations/022_link_suggestions_undirected.sql +84 -0
brain/migrations/023_search_queries_fts_count.sql +28 -0
brain/quartz_overrides/__init__.py +8 -0
brain/quartz_overrides/quartz/bootstrap-cli.mjs +65 -0
brain/quartz_overrides/quartz/build.ts +568 -0
brain/quartz_overrides/quartz/cli/args.js +152 -0
brain/quartz_overrides/quartz/cli/build_partial_handler.js +544 -0
brain/quartz_overrides/quartz/cli/handlers.js +636 -0
brain/quartz_overrides/quartz/components/CommandPalette.tsx +172 -0
brain/quartz_overrides/quartz/components/Explorer.tsx +198 -0
brain/quartz_overrides/quartz/components/Footer.tsx +27 -0
brain/quartz_overrides/quartz/components/Graph.tsx +468 -0
brain/quartz_overrides/quartz/components/PageTitle.tsx +72 -0
brain/quartz_overrides/quartz/components/RelatedDocs.tsx +38 -0
brain/quartz_overrides/quartz/components/Search.tsx +161 -0
brain/quartz_overrides/quartz/components/SummaryLede.tsx +72 -0
brain/quartz_overrides/quartz/components/index.ts +92 -0
brain/quartz_overrides/quartz/components/pages/TagContent.tsx +272 -0
brain/quartz_overrides/quartz/components/scripts/commandPalette.inline.ts +665 -0
brain/quartz_overrides/quartz/components/scripts/explorer.inline.ts +768 -0
brain/quartz_overrides/quartz/components/scripts/graph.inline.ts +2302 -0
brain/quartz_overrides/quartz/components/scripts/relatedDocs.inline.ts +163 -0
brain/quartz_overrides/quartz/components/scripts/search.inline.ts +1011 -0
brain/quartz_overrides/quartz/plugins/emitters/contentIndex.ts +546 -0
brain/quartz_overrides/quartz/plugins/transformers/codeCopy.ts +94 -0
brain/quartz_overrides/quartz/plugins/transformers/derivedFenceMark.ts +302 -0
brain/quartz_overrides/quartz/plugins/transformers/emailThread.ts +148 -0
brain/quartz_overrides/quartz/plugins/transformers/emptyDoorFilter.ts +213 -0
brain/quartz_overrides/quartz/plugins/transformers/index.ts +114 -0
brain/quartz_overrides/quartz/plugins/transformers/linkKindMark.ts +205 -0
brain/quartz_overrides/quartz/plugins/transformers/linkSourceTag.ts +104 -0
brain/quartz_overrides/quartz/plugins/transformers/relativeDate.ts +100 -0
brain/quartz_overrides/quartz/plugins/transformers/reloadSignal.ts +131 -0
brain/quartz_overrides/quartz/processors/parse.ts +371 -0
brain/quartz_overrides/quartz/processors/parser_cache.ts +78 -0
brain/quartz_overrides/quartz/static/brain-logo-dark.png +0 -0
brain/quartz_overrides/quartz/static/brain-logo-light.png +0 -0
brain/quartz_overrides/quartz/static/codeCopy.js +196 -0
brain/quartz_overrides/quartz/static/emailThread.js +334 -0
brain/quartz_overrides/quartz/static/favicon.ico +0 -0
brain/quartz_overrides/quartz/static/icon.png +0 -0
brain/quartz_overrides/quartz/static/linkSourceTag.js +104 -0
brain/quartz_overrides/quartz/static/relativeDate.js +142 -0
brain/quartz_overrides/quartz/static/reload.js +168 -0
brain/quartz_overrides/quartz/styles/brain/_article.scss +252 -0
brain/quartz_overrides/quartz/styles/brain/_atmosphere.scss +113 -0
brain/quartz_overrides/quartz/styles/brain/_callouts.scss +180 -0
brain/quartz_overrides/quartz/styles/brain/_cmdk.scss +7 -0
brain/quartz_overrides/quartz/styles/brain/_code.scss +208 -0
brain/quartz_overrides/quartz/styles/brain/_command_palette.scss +369 -0
brain/quartz_overrides/quartz/styles/brain/_email_thread.scss +228 -0
brain/quartz_overrides/quartz/styles/brain/_explorer.scss +142 -0
brain/quartz_overrides/quartz/styles/brain/_home.scss +182 -0
brain/quartz_overrides/quartz/styles/brain/_links.scss +322 -0
brain/quartz_overrides/quartz/styles/brain/_marginalia.scss +117 -0
brain/quartz_overrides/quartz/styles/brain/_motion.scss +175 -0
brain/quartz_overrides/quartz/styles/brain/_people_hub.scss +100 -0
brain/quartz_overrides/quartz/styles/brain/_related_docs.scss +137 -0
brain/quartz_overrides/quartz/styles/brain/_search.scss +252 -0
brain/quartz_overrides/quartz/styles/brain/_sidebar.scss +468 -0
brain/quartz_overrides/quartz/styles/brain/_summary_lede.scss +56 -0
brain/quartz_overrides/quartz/styles/brain/_surface.scss +43 -0
brain/quartz_overrides/quartz/styles/brain/_tag_content.scss +118 -0
brain/quartz_overrides/quartz/styles/brain/_tokens.scss +197 -0
brain/quartz_overrides/quartz/styles/brain/_typography.scss +92 -0
brain/quartz_overrides/quartz/styles/custom.scss +89 -0
brain/quartz_overrides/quartz/styles/graph.scss +505 -0
brain/quartz_overrides/quartz/util/ctx.ts +92 -0
brain/quartz_overrides/quartz/util/fastpath_manifest.ts +608 -0
brain/quartz_overrides/quartz/util/path.ts +358 -0
brain/quartz_overrides/quartz/util/sourceIcons.ts +55 -0
brain/quartz_overrides/quartz.config.ts +270 -0
brain/quartz_overrides/quartz.layout.ts +314 -0
brain/queries.py +1188 -0
brain/rank_fusion.py +8 -0
brain/resurface.py +210 -0
brain/review/__init__.py +26 -0
brain/review/emit.py +27 -0
brain/review/queries.py +436 -0
brain/review/render.py +196 -0
brain/review/scans.py +355 -0
brain/review/weekly.py +413 -0
brain/search.py +704 -0
brain/set_similarity.py +15 -0
brain/setup.py +1205 -0
brain/tags.py +56 -0
brain/templates/Caddyfile.j2 +9 -0
brain/templates/__init__.py +1 -0
brain/templates/bin/__init__.py +1 -0
brain/templates/bin/_brain-brief-fg.sh +25 -0
brain/templates/bin/_brain-build-fg.sh +53 -0
brain/templates/bin/_brain-watcher-fg.sh +65 -0
brain/templates/bin/brain-down.sh +89 -0
brain/templates/bin/brain-status.sh +83 -0
brain/templates/bin/brain-up.sh +221 -0
brain/templates/docker/age/Dockerfile +79 -0
brain/templates/docker-compose.stock.yml.j2 +26 -0
brain/templates/docker-compose.yml.j2 +34 -0
brain/templates/env.example +190 -0
brain/templates/launchd/__init__.py +1 -0
brain/templates/launchd/com.brain.brief.plist.j2 +45 -0
brain/templates/launchd/com.brain.build.plist.j2 +46 -0
brain/templates/launchd/com.brain.watcher.plist.j2 +46 -0
brain/templates/skill/SKILL.md +63 -0
brain/templates/skill/__init__.py +1 -0
brain/timeline.py +834 -0
brain/todo.py +124 -0
brain/uninstall.py +185 -0
brain/vault/__init__.py +115 -0
brain/vault/_atomic.py +25 -0
brain/vault/daily_index.py +228 -0
brain/vault/derived_links/__init__.py +50 -0
brain/vault/derived_links/directory.py +683 -0
brain/vault/derived_links/fence.py +408 -0
brain/vault/derived_links/gws.py +64 -0
brain/vault/derived_links/participants.py +143 -0
brain/vault/derived_links/pass_runner.py +362 -0
brain/vault/derived_links/rules.py +137 -0
brain/vault/export.py +683 -0
brain/vault/frontmatter.py +165 -0
brain/vault/graph.py +620 -0
brain/vault/graph_format.py +388 -0
brain/vault/link_rewrite.py +235 -0
brain/vault/links.py +260 -0
brain/vault/note_builder.py +211 -0
brain/vault/paths.py +55 -0
brain/vault/quartz_overlay.py +236 -0
brain/vault/rename.py +591 -0
brain/vault/resolver.py +304 -0
brain/vault/slug.py +127 -0
brain/vault/sync.py +1513 -0
brain/vault/sync_summaries.py +264 -0
brain/vault/templates.py +145 -0
brain/vault/watch.py +1052 -0
brain/wiki/__init__.py +6 -0
brain/wiki/_github_slugger.py +76 -0
brain/wiki/_person_name.py +314 -0
brain/wiki/build_homepage.py +541 -0
brain/wiki/build_partial.py +273 -0
brain/wiki/build_people.py +934 -0
brain/wiki/build_related.py +758 -0
brain/wiki/build_swap.py +585 -0
brain/wiki/build_watcher.py +975 -0
brain/wiki/edit_classifier.py +215 -0
brain/wiki/errors.py +10 -0
brain/wiki/fastpath_manifest.py +475 -0
brain/wiki/fastpath_state.py +174 -0
brain/wiki/install.py +296 -0
brain/wiki/slug.py +111 -0
secondbrain_py-0.2.1.dist-info/METADATA +195 -0
secondbrain_py-0.2.1.dist-info/RECORD +273 -0
secondbrain_py-0.2.1.dist-info/WHEEL +5 -0
secondbrain_py-0.2.1.dist-info/entry_points.txt +11 -0
secondbrain_py-0.2.1.dist-info/licenses/LICENSE +21 -0
secondbrain_py-0.2.1.dist-info/top_level.txt +1 -0

brain/quartz_overrides/quartz/styles/graph.scss ADDED Viewed

@@ -0,0 +1,505 @@
+// Brain palette for the custom Quartz Graph component.
+//
+// This file is a TEMPLATE. It is installed at
+// `<vault>/.quartz/quartz/styles/graph.scss` by `brain vault render
+// --overlay`. It is brand-new — not a replacement for upstream's
+// `quartz/components/styles/graph.scss`, which carries the
+// component's box layout (sidebar sizing, modal positioning) and
+// is untouched by this overlay. The brain palette below loads
+// alongside it, imported as a sibling stylesheet by the custom
+// `Graph.tsx` and concatenated onto the component's `css` property.
+//
+// Tested against Quartz v4.5.x (April 2026). The CSS variables
+// defined here are referenced by name from
+// `components/scripts/graph.inline.ts` (via the `cssVars`
+// precompute list and the `cssVar()` helper) and by the
+// `D3Config.tierColors` / `sourceColors` defaults in
+// `components/Graph.tsx`. Renaming or removing a variable here
+// requires the matching update in those two files; the renderer
+// would otherwise resolve to an empty string and silently fall
+// through to `--gray`.
+// brain-extension: the `--brain-tier-*` and `--brain-source-*` tokens
+// formerly declared here moved to
+// `quartz/styles/brain/_tokens.scss` as part of the 2026-05-02
+// redesign (Lane A) so the graph palette and the ingested-link
+// styling (Lane B) share one source of truth.
+//
+// Note: the previous dark-mode block selected on `[data-theme="dark"]`,
+// which Quartz never sets (the dark-mode toggle writes
+// `<html saved-theme="dark">` — see `darkmode.inline.ts`). The new
+// tokens file uses the correct selector so dark-mode source colors
+// actually fire.
+//
+// Future graph-only tokens live alongside the palette in `_tokens.scss`.
+// brain-extension: in-graph controls (search input + filter chip rows).
+// Rendered as the first child of `.graph-container` / `.global-graph-container`
+// so they sit above the PixiJS canvas. Sized to take minimal vertical space
+// and to wrap if the sidebar is narrow.
+.brain-graph-controls {
+  display: flex;
+  flex-direction: column;
+  gap: 0.25rem;
+  margin-bottom: 0.4rem;
+  font-size: 0.75rem;
+  line-height: 1.2;
+  min-width: 0;
+}
+.brain-graph-toolbar {
+  flex-direction: row;
+  align-items: center;
+  gap: 0.45rem;
+  padding: 0.55rem 0.65rem;
+  margin-bottom: 0;
+  border-bottom: 1px solid var(--rule);
+  background: color-mix(in srgb, var(--surface-1) 94%, var(--dark) 6%);
+  position: relative;
+  z-index: 2;
+  .brain-graph-search {
+    max-width: 24rem;
+    min-width: 12rem;
+  }
+  .brain-graph-chip-row {
+    flex-wrap: nowrap;
+    overflow-x: auto;
+    scrollbar-width: thin;
+  }
+}
+.brain-graph-search {
+  width: 100%;
+  min-width: 0;
+  box-sizing: border-box;
+  // brain (Linear-variant feedback): bumped padding so the input
+  // stands ~28px tall, visually balancing the 24×24 graph icon
+  // buttons absolutely-positioned to its right. Was 0.25rem 0.5rem
+  // — too short, read as a stubby strip next to the buttons.
+  padding: 0.45rem 0.7rem;
+  border: 1px solid var(--lightgray);
+  border-radius: 4px;
+  background: var(--light);
+  color: var(--dark);
+  font: inherit;
+  // brain: explicit focus indicator for keyboard users — a border-color
+  // change alone wasn't enough at high-contrast settings. Outline-offset
+  // keeps the ring outside the rounded border so the visual cue is
+  // unambiguous.
+  &:focus {
+    outline: 2px solid var(--secondary);
+    outline-offset: 1px;
+    border-color: var(--secondary);
+  }
+}
+.brain-graph-chip-row {
+  display: flex;
+  flex-wrap: wrap;
+  align-items: center;
+  gap: 0.2rem;
+}
+.brain-graph-chip-label {
+  color: var(--darkgray);
+  margin-right: 0.15rem;
+  text-transform: capitalize;
+}
+// Each chip is a button by element so it remains keyboard-focusable. The
+// "active" class flips it to a filled state so the user reads which values
+// are currently included in the filter at a glance.
+.brain-graph-chip {
+  appearance: none;
+  border: 1px solid var(--lightgray);
+  background: transparent;
+  color: var(--darkgray);
+  border-radius: 999px;
+  padding: 0.1rem 0.55rem;
+  font: inherit;
+  cursor: pointer;
+  transition:
+    background-color 0.12s ease,
+    color 0.12s ease,
+    border-color 0.12s ease;
+  &:hover {
+    border-color: var(--gray);
+    color: var(--dark);
+  }
+  // brain: explicit focus ring for keyboard navigation. `:focus-visible`
+  // (vs plain `:focus`) keeps the indicator from showing on mouse-click,
+  // which feels noisy on a chip group, while still surfacing it for
+  // tab-traversed users.
+  &:focus-visible {
+    outline: 2px solid var(--secondary);
+    outline-offset: 1px;
+  }
+  &.active {
+    background: var(--secondary);
+    border-color: var(--secondary);
+    color: var(--light);
+  }
+  // The "all" chip gets a subtler accent so it doesn't compete with the
+  // value chips for attention — it's a reset affordance, not a filter
+  // value in its own right.
+  &.brain-graph-chip-all {
+    font-weight: 600;
+    text-transform: uppercase;
+    font-size: 0.65rem;
+    letter-spacing: 0.04em;
+    &.active {
+      background: var(--tertiary);
+      border-color: var(--tertiary);
+    }
+  }
+}
+// brain: stock Quartz renders the global-graph button as
+// `<button class="global-graph-icon">` directly inside `.graph-outer`,
+// but its own graph.scss only styles `.graph-icon` (no `global-` prefix
+// and inside a `.graph-icons` wrapper that doesn't exist in the markup).
+// Result on stock Quartz: the button sits unstyled in the top-left,
+// hard to see and easy to miss. We position + size it explicitly so
+// readers can actually find the "open global graph" affordance.
+//
+// brain-extension: `.brain-stock-graph-icon` is a sibling affordance that
+// opens the SAME global-graph modal but with the renderer's brain extensions
+// disabled (stock Quartz visuals). Same visual rules — only the absolute-
+// position offset differs.
+//
+// Layout note (Linear-variant feedback): the buttons are absolutely
+// positioned at the top-right corner. The `.brain-graph-controls`
+// below reserves a `padding-right` equal to both buttons' combined
+// horizontal footprint, so the search input shrinks to leave room
+// rather than slipping under the buttons.
+.graph > .graph-outer > .global-graph-icon,
+.graph > .graph-outer > .brain-stock-graph-icon,
+.graph > .graph-outer > .local-graph-fullscreen-icon,
+.graph > .graph-outer > .brain-graph-workbench-icon {
+  position: absolute;
+  top: 0;
+  margin: 0.3rem;
+  cursor: pointer;
+  background: none;
+  border: none;
+  color: var(--dark);
+  opacity: 0.5;
+  width: 24px;
+  height: 24px;
+  padding: 0.2rem;
+  border-radius: 4px;
+  background-color: transparent;
+  transition: background-color 0.2s ease, opacity 0.2s ease;
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  z-index: 1;
+  svg {
+    width: 100%;
+    height: 100%;
+  }
+  &:hover {
+    background-color: var(--lightgray);
+    opacity: 1;
+  }
+  &:focus-visible {
+    outline: 2px solid var(--secondary);
+    outline-offset: 1px;
+    opacity: 1;
+  }
+}
+.graph > .graph-outer > .global-graph-icon {
+  right: 0;
+}
+// brain-extension: dot-grid affordance sits 28px to the left of the globe so
+// the two icons read as a pair without visually colliding. Width-based offset
+// (`right: 28px`) keeps them aligned to the same right edge regardless of the
+// surrounding sidebar width.
+.graph > .graph-outer > .brain-stock-graph-icon {
+  right: 28px;
+}
+.graph > .graph-outer > .brain-graph-workbench-icon {
+  right: 56px;
+}
+// brain-extension: maximize affordance sits left of the diagnostic,
+// dot-grid, and global buttons. Order reads left-to-right as: local
+// fullscreen / diagnostic workbench / stock / global.
+.graph > .graph-outer > .local-graph-fullscreen-icon {
+  right: 84px;
+}
+// brain: keep upstream's `.graph-outer { height: 250px; overflow: hidden; }`
+// untouched. The compact `.brain-graph-controls` redesign above takes
+// only ~30px of vertical space (vs the previous ~94px), so a 250px
+// container leaves ~220px for the canvas — plenty of room for the
+// cluster — without growing the panel and pushing Table of Contents +
+// Backlinks past the viewport. The d3-zoom fit-to-bounds pass in
+// graph.inline.ts auto-scales the cluster to whatever canvas height
+// we end up with.
+//
+// Defense-in-depth: also let the right sidebar scroll internally if a
+// future content addition (e.g. a long ToC on a deeply-headed page)
+// pushes total content past the viewport. No-op when content fits;
+// gracefully scrolls when it doesn't.
+// brain (Linear variant): global/local graph modal — contrast +
+// positioning override.
+//
+// Stock paints `.global-graph-container` with `var(--light)` +
+// `var(--lightgray)` border, which makes the modal invisible in our
+// charcoal dark mode (page bg = `#0a0a0a` = same as `--light`). We
+// override to `--surface-1` so the panel has elevation, then layer in
+// `--scrim` for the backdrop.
+//
+// brain (Linear-variant feedback round 3): stock's modal centering
+// relies on `display: inline-block` on the outer wrapper plus
+// `transform: translate(-50%, -50%)` on the container, which together
+// have been rendering the modal as a narrow vertical strip on the
+// right edge of the viewport instead of a centered 80vw × 80vh panel.
+// Bypass the recipe entirely:
+//   1. `display: block` on `.global-graph-outer.active` kills the
+//      `inline-block` (stock's `width: 100vw` declaration only takes
+//      effect reliably on a block-level element).
+//   2. Replace the `transform: translate(-50%, -50%)` centering trick
+//      with explicit `left: 10vw; top: 10vh` offsets. No transforms
+//      means no chance of an accidental containing-block creation
+//      for the fixed-position container.
+.graph > .global-graph-outer,
+.graph > .local-graph-outer,
+.graph > .brain-graph-workbench-outer {
+  background: var(--scrim);
+}
+.graph > .brain-graph-workbench-outer {
+  backdrop-filter: blur(4px);
+  display: none;
+  height: 100%;
+  left: 0;
+  overflow: hidden;
+  position: fixed;
+  top: 0;
+  width: 100vw;
+  z-index: 9999;
+}
+.graph > .global-graph-outer.active,
+.graph > .local-graph-outer.active,
+.graph > .brain-graph-workbench-outer.active {
+  display: block;
+}
+.graph > .global-graph-outer > .global-graph-container,
+.graph > .local-graph-outer > .local-graph-container {
+  background-color: var(--surface-1);
+  border-color: var(--rule);
+  box-shadow: var(--shadow-md);
+  // Explicit positioning replaces stock's `top: 50%; left: 50%;
+  // transform: translate(-50%, -50%)` recipe.
+  left: 10vw;
+  top: 10vh;
+  transform: none;
+}
+.graph > .brain-graph-workbench-outer > .brain-graph-workbench-container {
+  background-color: var(--surface-1);
+  border: 1px solid var(--rule);
+  border-radius: 5px;
+  border-color: var(--rule);
+  box-sizing: border-box;
+  box-shadow: var(--shadow-md);
+  position: fixed;
+  left: 4vw;
+  top: 6vh;
+  width: 92vw;
+  height: 88vh;
+  transform: none;
+}
+.brain-graph-workbench-shell {
+  display: grid;
+  grid-template-areas:
+    "toolbar toolbar toolbar"
+    "rail graph inspector";
+  grid-template-columns: 9.5rem minmax(0, 1fr) 18rem;
+  grid-template-rows: auto minmax(0, 1fr);
+  height: 100%;
+  min-height: 0;
+  isolation: isolate;
+  overflow: hidden;
+}
+.brain-graph-workbench-shell > .brain-graph-toolbar {
+  grid-area: toolbar;
+}
+.brain-graph-mode-rail {
+  grid-area: rail;
+  border-right: 1px solid var(--rule);
+  background: var(--surface-1);
+  padding: 0.75rem;
+  display: flex;
+  flex-direction: column;
+  gap: 0.45rem;
+}
+.brain-graph-mode {
+  appearance: none;
+  border: 1px solid var(--lightgray);
+  background: transparent;
+  color: var(--dark);
+  border-radius: 6px;
+  padding: 0.55rem 0.6rem;
+  text-align: left;
+  cursor: pointer;
+  font: inherit;
+  small {
+    display: block;
+    color: var(--darkgray);
+    font-size: 0.68rem;
+    margin-top: 0.12rem;
+  }
+  &.active {
+    border-color: var(--secondary);
+    background: color-mix(in srgb, var(--secondary) 14%, transparent);
+  }
+}
+.brain-graph-inspector {
+  grid-area: inspector;
+  align-self: stretch;
+  box-sizing: border-box;
+  border-left: 1px solid var(--rule);
+  background: #202124;
+  background-color: #202124;
+  color: var(--dark);
+  height: 100%;
+  justify-self: stretch;
+  min-height: 0;
+  min-width: 18rem;
+  padding: 0.9rem;
+  overflow: auto;
+  position: relative;
+  z-index: 3;
+  h3 {
+    margin: 0 0 0.25rem;
+    font-size: 1rem;
+  }
+  h4 {
+    margin: 1rem 0 0.35rem;
+    color: var(--darkgray);
+    font-size: 0.72rem;
+    text-transform: uppercase;
+    letter-spacing: 0.04em;
+  }
+  ul {
+    margin: 0;
+    padding-left: 1rem;
+  }
+}
+.brain-graph-inspector-meta {
+  color: var(--darkgray);
+  margin: 0 0 0.75rem;
+}
+.brain-graph-metrics {
+  display: grid;
+  grid-template-columns: 1fr 1fr;
+  gap: 0.45rem;
+  > div {
+    border: 1px solid var(--lightgray);
+    border-radius: 6px;
+    padding: 0.45rem;
+  }
+  strong,
+  span {
+    display: block;
+  }
+}
+.brain-graph-canvas-pane {
+  grid-area: graph;
+  align-self: stretch;
+  contain: paint;
+  justify-self: stretch;
+  min-height: 0;
+  min-width: 0;
+  overflow: hidden;
+  position: relative;
+  z-index: 1;
+}
+.brain-graph-canvas-pane > canvas {
+  display: block;
+  max-height: 100%;
+  max-width: 100%;
+  min-width: 0;
+  overflow: hidden;
+}
+.brain-graph-workbench-shell > .brain-graph-tooltip {
+  grid-column: 2;
+  grid-row: 2;
+}
+@media (max-width: 900px) {
+  .brain-graph-workbench-shell {
+    grid-template-areas:
+      "toolbar"
+      "rail"
+      "graph"
+      "inspector";
+    grid-template-columns: 1fr;
+    grid-template-rows: auto auto minmax(22rem, 1fr) auto;
+  }
+  .brain-graph-mode-rail {
+    flex-direction: row;
+    overflow-x: auto;
+    border-right: 0;
+    border-bottom: 1px solid var(--rule);
+  }
+  .brain-graph-inspector {
+    border-left: 0;
+    border-top: 1px solid var(--rule);
+    max-height: 14rem;
+    min-width: 0;
+  }
+}
+.sidebar.right {
+  overflow-y: auto;
+  // Hide the scrollbar gutter so the sidebar reads as a clean column
+  // when content fits. Still scrollable via wheel / touchpad gestures.
+  scrollbar-width: thin;
+  scrollbar-color: var(--lightgray) transparent;
+  &::-webkit-scrollbar {
+    width: 4px;
+  }
+  &::-webkit-scrollbar-thumb {
+    background: var(--lightgray);
+    border-radius: 2px;
+  }
+}

brain/quartz_overrides/quartz/util/ctx.ts ADDED Viewed

@@ -0,0 +1,92 @@
+// Brain wiki — BuildCtx with parser-cache plumbing.
+//
+// This file is a TEMPLATE. It is installed at
+// `<vault>/.quartz/quartz/util/ctx.ts` by `brain vault render --overlay`,
+// overwriting the stock upstream module.
+//
+// Changes from upstream:
+//   * `Argv.noCache?: boolean` — opt-out flag. When true, parseMarkdown
+//     sets cacheDir to null and the parser cache is disabled for the run.
+//     The upstream Quartz CLI handler does not set this flag (it lives in
+//     upstream-only handlers.ts which we do not override), so in practice
+//     it is always undefined (falsy) and the cache is always active unless
+//     a future override of the CLI handler flips it. Wired in as
+//     `argv.noCache` so the flag propagates to workers via
+//     WorkerSerializableBuildCtx.argv without any additional plumbing.
+//   * `BuildCtx.cacheDir?: string | null` — on-disk path for the parser
+//     result cache. `null` disables the cache for the run.
+//     `undefined` means "not yet set by the caller"; parseMarkdown in
+//     parse.ts defaults it to `<argv.directory>/.quartz/.cache/parser`
+//     so it matches `bin/brain-rebuild --clean-cache`'s rm target.
+//     Optional so existing BuildCtx constructors (upstream handlers.ts
+//     and test fixtures) compile without modification.
+//     `WorkerSerializableBuildCtx = Omit<BuildCtx, "cfg" | "trie">` so
+//     cacheDir auto-propagates to workers via the type — no worker.ts
+//     edit needed. The serializableCtx literal in parse.ts does list
+//     fields by hand and explicitly includes `cacheDir`.
+import { QuartzConfig } from "../cfg"
+import { QuartzPluginData } from "../plugins/vfile"
+import { FileTrieNode } from "./fileTrie"
+import { FilePath, FullSlug } from "./path"
+export interface Argv {
+  directory: string
+  verbose: boolean
+  output: string
+  serve: boolean
+  watch: boolean
+  port: number
+  wsPort: number
+  remoteDevHost?: string
+  concurrency?: number
+  // brain: opt-out flag for the parser cache. When true, parseMarkdown
+  // sets cacheDir = null so no cache reads or writes occur for this run.
+  // Not currently wired from the upstream CLI handler (handlers.ts is not
+  // overridden); a future override can expose `--no-cache` via yargs and
+  // set this field. Until then it is always undefined = cache active.
+  noCache?: boolean
+}
+export type BuildTimeTrieData = QuartzPluginData & {
+  slug: string
+  title: string
+  filePath: string
+}
+export interface BuildCtx {
+  buildId: string
+  argv: Argv
+  cfg: QuartzConfig
+  allSlugs: FullSlug[]
+  allFiles: FilePath[]
+  trie?: FileTrieNode<BuildTimeTrieData>
+  incremental: boolean
+  // brain: on-disk directory for the parser result cache.
+  //   string  — active cache at this path
+  //   null    — cache explicitly disabled for this run (e.g. --no-cache)
+  //   undefined — not yet set; parseMarkdown.ts defaults to
+  //               <argv.directory>/.quartz/.cache/parser (matches
+  //               brain.maintenance._PARSER_CACHE_RELPATH; wiped by
+  //               `brain-rebuild --clean-cache`).
+  // Optional so existing BuildCtx constructors compile without change.
+  cacheDir?: string | null
+}
+export function trieFromAllFiles(allFiles: QuartzPluginData[]): FileTrieNode<BuildTimeTrieData> {
+  const trie = new FileTrieNode<BuildTimeTrieData>([])
+  allFiles.forEach((file) => {
+    if (file.frontmatter) {
+      trie.add({
+        ...file,
+        slug: file.slug!,
+        title: file.frontmatter.title,
+        filePath: file.filePath!,
+      })
+    }
+  })
+  return trie
+}
+export type WorkerSerializableBuildCtx = Omit<BuildCtx, "cfg" | "trie">