Quartz sync: Mar 16, 2026, 1:40 AM

Author: kmaitreys

content/research/Denoising Astronomical Observations of Protoplanetary Disks.md

@@ -0,0 +1,14 @@
+---
+tags:
+  - machine-learning
+  - "#projects"
+  - "#gsoc"
+---
+# Motivation
+Gas kinematics reveals still-forming planets in images of disks through features called *kinks*. 
+
+# Basic Idea
+[[Denoising Astronomical Observations of Protoplanetary Disks#Bibliography|Terry et al. (2022)]] use [[Latin Hypercube|latin hypercube]] to distribute randomly-spaced data points evenly across the whole parameter space. 
+
+# Bibliography
+1. *Locating Hidden Exoplanets in ALMA Data Using Machine Learning*: https://iopscience.iop.org/article/10.3847/1538-4357/aca477

content/research/On inertial forces (indirect terms) in problems with a central body.md

@@ -39,6 +39,3 @@ abstract: |-
   generalized to other astrophysical systems.
 journal_logo: arxiv.svg
 ---
-$$
-\dfrac{}{}
-$$

content/tools/Hunting Planets Using Machine Learning.md

@@ -77,6 +77,7 @@ const config: QuartzConfig = {
       Plugin.Latex({ renderEngine: "mathjax" }),
       Plugin.Citations({
         linkCitations: true,
+        suppressBibliography: true,
       }),
       // Plugin.FootnotesToReferences(),
       Plugin.PaperPreviewInjector(),

quartz.config.ts

@@ -97,6 +97,7 @@ export default (() => {
             return resource
           }
         })}
+        <script src={`${baseDir}/static/citation-popover.js`}></script>
       </head>
     )
   }

quartz/components/Head.tsx

@@ -1,8 +1,43 @@
+import fs from "fs"
+import path from "path"
+
 import rehypeCitation from "rehype-citation"
 import { PluggableList } from "unified"
 import { visit } from "unist-util-visit"
 import { QuartzTransformerPlugin } from "../types"
 
+function field(body: string, name: string) {
+  const r = new RegExp(name + "\\s*=\\s*\\{([^}]+)\\}", "i")
+  const m = body.match(r)
+  return m ? m[1] : ""
+}
+
+function parseBibFile(filePath: string) {
+  const text = fs.readFileSync(filePath, "utf8")
+  const entries: Record<string, any> = {}
+
+  const entryRegex = /@.+?\{([^,]+),([\s\S]*?)\n\}/g
+
+  let match
+  while ((match = entryRegex.exec(text)) !== null) {
+    const key = match[1].trim().toLowerCase()
+    const body = match[2]
+
+    const doi = field(body, "doi")
+    const url = field(body, "url")
+
+    entries[key] = {
+      title: field(body, "title"),
+      author: field(body, "author"),
+      year: field(body, "year"),
+      journal: field(body, "journal") || field(body, "booktitle"),
+      link: doi ? `https://doi.org/${doi}` : url
+    }
+  }
+
+  return entries
+}
+
 export interface Options {
   bibliographyFile: string
   suppressBibliography: boolean
@@ -12,28 +47,27 @@ export interface Options {
 
 const defaultOptions: Options = {
   bibliographyFile: "./bibliography.bib",
-  suppressBibliography: false,
-  linkCitations: false,
+  suppressBibliography: true,
+  linkCitations: true,
   csl: "apa",
 }
 
 export const Citations: QuartzTransformerPlugin<Partial<Options>> = (userOpts) => {
   const opts = { ...defaultOptions, ...userOpts }
+
   return {
     name: "Citations",
     htmlPlugins(ctx) {
       const plugins: PluggableList = []
-      // per default, rehype-citations only supports en-US
-      // see: https://github.com/timlrx/rehype-citation/issues/12
-      // in here there are multiple usable locales:
-      // https://github.com/citation-style-language/locales
-      // thus, we optimistically assume there is indeed an appropriate
-      // locale available and simply create the lang url-string
+
       let lang: string = "en-US"
       if (ctx.cfg.configuration.locale !== "en-US") {
         lang = `https://raw.githubusercontent.com/citation-stylelanguage/locales/refs/heads/master/locales-${ctx.cfg.configuration.locale}.xml`
       }
-      // Add rehype-citation to the list of plugins
+
+      const bibPath = path.resolve(opts.bibliographyFile)
+      const citationData = parseBibFile(bibPath)
+
       plugins.push([
         rehypeCitation,
         {
@@ -45,13 +79,32 @@ export const Citations: QuartzTransformerPlugin<Partial<Options>> = (userOpts) =
         },
       ])
 
-      // Transform the HTML of the citattions; add data-no-popover property to the citation links
-      // using https://github.com/syntax-tree/unist-util-visit as they're just anochor links
       plugins.push(() => {
-        return (tree, _file) => {
-          visit(tree, "element", (node, _index, _parent) => {
-            if (node.tagName === "a" && node.properties?.href?.startsWith("#bib")) {
-              node.properties["data-no-popover"] = true
+        return (tree) => {
+          visit(tree, "element", (node: any) => {
+            if (
+              node.tagName === "a" &&
+              typeof node.properties?.href === "string" &&
+              node.properties.href.startsWith("#bib-")
+            ) {
+              const key = node.properties.href.replace("#bib-", "").toLowerCase()
+              const entry = citationData[key]
+
+              if (entry?.link) {
+                node.properties.href = entry.link
+                node.properties.target = "_blank"
+                node.properties.rel = "noopener noreferrer"
+
+                node.properties["data-cite-title"] = entry.title
+                node.properties["data-cite-author"] = entry.author
+                node.properties["data-cite-year"] = entry.year
+                node.properties["data-cite-journal"] = entry.journal
+
+                node.properties.className = [
+                  ...(node.properties.className || []),
+                  "citation-link",
+                ]
+              }
             }
           })
         }
@@ -60,4 +113,4 @@ export const Citations: QuartzTransformerPlugin<Partial<Options>> = (userOpts) =
       return plugins
     },
   }
-}
+}

quartz/plugins/transformers/citations.ts

@@ -0,0 +1,28 @@
+document.addEventListener("DOMContentLoaded", () => {
+    const pop = document.createElement("div")
+    pop.className = "citation-popover"
+    document.body.appendChild(pop)
+
+    document.querySelectorAll("a.citation-link").forEach((el) => {
+        el.addEventListener("mouseenter", () => {
+            const title = el.dataset.citeTitle || ""
+            const author = el.dataset.citeAuthor || ""
+            const year = el.dataset.citeYear || ""
+            const journal = el.dataset.citeJournal || ""
+
+            pop.innerHTML =
+                "<strong>" + title + "</strong><br>" +
+                author + " (" + year + ")<br>" +
+                journal
+
+            const rect = el.getBoundingClientRect()
+            pop.style.left = rect.left + window.scrollX + "px"
+            pop.style.top = rect.bottom + window.scrollY + 8 + "px"
+            pop.style.display = "block"
+        })
+
+        el.addEventListener("mouseleave", () => {
+            pop.style.display = "none"
+        })
+    })
+})

quartz/static/citation-popover.js

@@ -384,4 +384,18 @@ a.data-footnote-backref {
 .global-graph-container {
     width: 100vw;
     height: 100vh;
+}
+
+.citation-popover {
+    position: absolute;
+    max-width: 320px;
+    padding: 10px;
+    background: var(--light);
+    border: 1px solid var(--border);
+    border-radius: 6px;
+    font-size: 0.85rem;
+    line-height: 1.4;
+    box-shadow: 0 4px 10px rgba(0, 0, 0, 0.15);
+    display: none;
+    z-index: 1000;
 }