First blog post, added theming

Coffee-themed, font changes and a first post.

.gitignore

@@ -2,3 +2,5 @@ public/
 out/
 __pycache__/
 */template.md
+.crossnote/
+WIP

build.py

@@ -64,7 +64,13 @@ def parse(path):
         "date": when,
         "topic": rel.parts[0] if len(rel.parts) > 1 else meta.get("topic"),
         "slug": slugify(meta.get("slug") or re.sub(r"^\d{4}-\d{2}-\d{2}-", "", path.stem)),
-        "body": markdown.markdown(text, extensions=["fenced_code", "tables", "footnotes"]),
+        "body": markdown.markdown(
+            text,
+            extensions=[
+                "fenced_code", "tables", "footnotes", "codehilite", "abbr",
+            ],
+            extension_configs={"codehilite": {"guess_lang": False}},
+        ),
     }
 
 

static/OFL.txt

@@ -0,0 +1,93 @@
+Copyright 2020 The Poltawski Nowy Project Authors (https://github.com/kosmynkab/Poltawski-Nowy)
+
+This Font Software is licensed under the SIL Open Font License, Version 1.1.
+This license is copied below, and is also available with a FAQ at:
+https://openfontlicense.org
+
+
+-----------------------------------------------------------
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+-----------------------------------------------------------
+
+PREAMBLE
+The goals of the Open Font License (OFL) are to stimulate worldwide
+development of collaborative font projects, to support the font creation
+efforts of academic and linguistic communities, and to provide a free and
+open framework in which fonts may be shared and improved in partnership
+with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves. The
+fonts, including any derivative works, can be bundled, embedded, 
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works. The fonts and derivatives,
+however, cannot be released under any other type of license. The
+requirement for fonts to remain under this license does not apply
+to any document created using the fonts or their derivatives.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components as
+distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to a
+new environment.
+
+"Author" refers to any designer, engineer, programmer, technical
+writer or other person who contributed to the Font Software.
+
+PERMISSION & CONDITIONS
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,
+in Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+redistributed and/or sold with any software, provided that each copy
+contains the above copyright notice and this license. These can be
+included either as stand-alone text files, human-readable headers or
+in the appropriate machine-readable metadata fields within text or
+binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+Name(s) unless explicit written permission is granted by the corresponding
+Copyright Holder. This restriction only applies to the primary font name as
+presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+Software shall not be used to promote, endorse or advertise any
+Modified Version, except to acknowledge the contribution(s) of the
+Copyright Holder(s) and the Author(s) or with their explicit written
+permission.
+
+5) The Font Software, modified or unmodified, in part or in whole,
+must be distributed entirely under this license, and must not be
+distributed under any other license. The requirement for fonts to
+remain under this license does not apply to any document created
+using the Font Software.
+
+TERMINATION
+This license becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+OTHER DEALINGS IN THE FONT SOFTWARE.

template.html

@@ -4,48 +4,158 @@
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <title>Pascal Maas · Blog</title>
-<style>
-  :root {
-    --bg: #fbfaf7; --fg: #1d1d1b; --muted: #6b6a66; --line: #e4e1da;
-    --accent: #2f5d8a; --code-bg: #f1eee7;
-  }
-  @media (prefers-color-scheme: dark) {
-    :root {
-      --bg: #161616; --fg: #e8e6e1; --muted: #9a978f; --line: #2c2b29;
-      --accent: #8ab4dc; --code-bg: #222120;
+<script>
+  // Runs before the page is drawn, so a saved dark choice doesn't flash.
+  try {
+    if (localStorage.getItem("theme") === "dark") {
+      document.documentElement.dataset.theme = "dark";
     }
+  } catch (error) {}
+</script>
+<style>
+  /* Served from static/; Georgia shows until these have loaded. */
+  @font-face {
+    font-family: "Poltawski Nowy"; font-weight: 400; font-style: normal;
+    src: url("static/PoltawskiNowy-Regular.ttf"); font-display: swap;
+  }
+  @font-face {
+    font-family: "Poltawski Nowy"; font-weight: 400; font-style: italic;
+    src: url("static/PoltawskiNowy-Italic.ttf"); font-display: swap;
+  }
+  @font-face {
+    font-family: "Poltawski Nowy"; font-weight: 700; font-style: normal;
+    src: url("static/PoltawskiNowy-Bold.ttf"); font-display: swap;
+  }
+  @font-face {
+    font-family: "Poltawski Nowy"; font-weight: 700; font-style: italic;
+    src: url("static/PoltawskiNowy-BoldItalic.ttf"); font-display: swap;
+  }
+  :root {
+    --latte: #f4f2ee; --espresso: #231c15;
+    --espresso-button: #4a3326; --latte-button: #e3d9cb;
+    --bg: var(--latte); --fg: #1d1d1b; --muted: #6b6a66; --line: #dbd6cc;
+    --accent: #2f5d8a; --code-bg: #eae6e0;
+    /* Pinned header; the side list pins just below it. */
+    --header-height: 3.25rem; --header-bg: #ebe8e1;
+    --code-block-bg: #eae6e0; --code-text: #1d1d1b;
+    --code-comment: #7a7a7a; --code-keyword: #a85a1e; --code-string: #4f6b3f;
+    --code-number: #4a6f8f; --code-function: #8a6500;
+  }
+  :root[data-theme="dark"] {
+    --bg: var(--espresso); --fg: #e8e6e1; --muted: #9a978f; --line: #3d3227;
+    --accent: #8ab4dc; --code-bg: #2f261d; --header-bg: #2c231a;
+    --code-block-bg: #2e2822; --code-text: #d6d4cf;
+    --code-comment: #808080; --code-keyword: #cc7832; --code-string: #6a8759;
+    --code-number: #6897bb; --code-function: #ffc66d;
   }
   * { box-sizing: border-box; }
   body {
     margin: 0; background: var(--bg); color: var(--fg);
-    font: 17px/1.65 Georgia, "Iowan Old Style", "Times New Roman", serif;
+    font: 17px/1.65 "Poltawski Nowy", Georgia, "Iowan Old Style",
+      "Times New Roman", serif;
   }
-  .wrap { max-width: 44rem; margin: 0 auto; padding: 3rem 1rem 4rem; }
+  .wrap { max-width: 56rem; margin: 0 auto; padding: 0 1rem 4rem; }
   a { color: var(--accent); }
-  h1, h2, h3, .meta, nav, footer { font-family: system-ui, -apple-system, "Segoe UI", sans-serif; }
-  .site-header h1 { margin: 0; font-size: 1.6rem; letter-spacing: -0.01em; }
-  .site-header p { margin: .25rem 0 0; color: var(--muted); }
+  .site-header h1 {
+    margin: 0; font-size: 1.6rem; line-height: 1.2; letter-spacing: -0.01em;
+  }
+  .site-header p { display: none; margin: 0; color: var(--muted); }
+  .site-header {
+    display: flex; justify-content: space-between;
+    align-items: center; gap: 1rem;
+    position: sticky; top: 0; z-index: 2; background: var(--header-bg);
+    height: var(--header-height); padding: .5rem 0;
+    /* Stretches the colour and the line under it to the full window width
+       while the contents stay in the column. */
+    box-shadow: 0 0 0 100vmax var(--header-bg), 0 1px 0 100vmax var(--line);
+    clip-path: inset(0 -100vmax -1px);
+  }
+  .header-actions { display: flex; align-items: center; gap: .75rem; }
+  .site-header p, .header-actions { font-size: 15px; }
+  /* Same font as the tagline; buttons don't inherit it by default. */
+  .header-actions a, .theme-toggle { font: inherit; }
+  .header-actions a { color: var(--fg); text-decoration: none; }
+  .header-actions a:hover { text-decoration: underline; }
+  /* Espresso brown in light mode, latte beige in dark mode. */
+  .theme-toggle {
+    color: var(--latte); background: var(--espresso-button); cursor: pointer;
+    border: 1px solid var(--espresso-button); border-radius: 999px;
+    /* Fixed width fits "Espresso", so the Git link doesn't shift. */
+    width: 6em; padding: .2rem 0; text-align: center;
+  }
+  :root[data-theme="dark"] .theme-toggle {
+    color: var(--espresso); background: var(--latte-button);
+    border-color: var(--latte-button);
+  }
+  .theme-toggle:hover { opacity: .85; }
+  /* Wide enough for the tagline next to the name; hidden below this. */
+  @media (min-width: 52rem) {
+    .site-title { display: flex; align-items: baseline; gap: .75rem; }
+    .site-header p { display: block; }
+  }
 
-  nav { margin: 2.5rem 0 1rem; padding: 1rem 0; border-top: 1px solid var(--line); border-bottom: 1px solid var(--line); }
+  nav { margin: 2.5rem 0 1rem; padding: 1rem 0; border-bottom: 1px solid var(--line); }
   nav h2 { margin: 0 0 .5rem; font-size: .8rem; text-transform: uppercase; letter-spacing: .08em; color: var(--muted); }
   nav ol { margin: 0; padding: 0; list-style: none; }
   nav li { display: flex; justify-content: space-between; gap: 1rem; padding: .2rem 0; }
   nav li time { color: var(--muted); font-size: .85rem; white-space: nowrap; }
   nav a { text-decoration: none; }
   nav a:hover { text-decoration: underline; }
+  nav a.current { font-weight: 700; color: var(--fg); }
+
+  /* Side column (14rem) + gap (3rem) + posts (56rem) + padding (2rem). */
+  @media (min-width: 75rem) {
+    .wrap { max-width: 75rem; }
+    .layout { display: grid; grid-template-columns: 14rem 56rem; gap: 3rem; }
+    nav {
+      position: sticky; top: var(--header-height); align-self: start;
+      max-height: calc(100vh - var(--header-height)); overflow-y: auto;
+      margin: 0; padding: 2.5rem 0 1rem; border: none;
+    }
+    nav li, nav li time { display: block; }
+  }
 
   article { padding: 2.5rem 0; border-bottom: 1px solid var(--line); scroll-margin-top: 1rem; }
+  /* Keeps in-page jumps (footnotes) clear of the pinned header. */
+  html { scroll-padding-top: calc(var(--header-height) + 1rem); }
   article header h2 { margin: 0; font-size: 1.45rem; line-height: 1.25; }
   article header h2 a { color: inherit; text-decoration: none; }
   article header h2 a:hover { color: var(--accent); }
   .meta { margin: .35rem 0 1.25rem; font-size: .85rem; color: var(--muted); display: flex; gap: .75rem; align-items: center; }
   .tag { border: 1px solid var(--line); border-radius: 999px; padding: 0 .55rem; }
 
-  img { max-width: 100%; height: auto; }
+  /* Defined terms (Markdown "*[term]: definition"); the script below fills
+     data-definition with the text for the bubble. */
+  abbr[data-definition] {
+    position: relative; cursor: help;
+    text-decoration: underline dotted; text-underline-offset: .2em;
+  }
+  abbr[data-definition]:is(:hover, :focus)::after {
+    content: attr(data-definition);
+    position: absolute; left: 50%; bottom: 100%; z-index: 3;
+    transform: translateX(-50%); margin-bottom: .35rem;
+    width: max-content; max-width: 16rem; padding: .35rem .6rem;
+    background: var(--header-bg); color: var(--fg);
+    border: 1px solid var(--line); border-radius: 6px;
+    font-size: .85rem; line-height: 1.4;
+  }
+
+  img { display: block; margin: 0 auto; max-width: 100%; height: auto; }
   pre, code { font-family: ui-monospace, "Cascadia Code", Menlo, Consolas, monospace; font-size: .88em; }
   code { background: var(--code-bg); padding: .1em .3em; border-radius: 4px; }
-  pre { background: var(--code-bg); padding: 1rem; border-radius: 6px; overflow-x: auto; }
+  pre { background: var(--code-block-bg); color: var(--code-text); padding: 1rem; border-radius: 6px; overflow-x: auto; }
   pre code { background: none; padding: 0; }
+  /* Pygments token classes, Darcula colours: comments, keywords, strings,
+     numbers, function names. */
+  .codehilite :is(.c, .c1, .cm, .ch, .cs) {
+    color: var(--code-comment); font-style: italic;
+  }
+  .codehilite :is(.k, .kc, .kd, .kn, .kr, .kt) { color: var(--code-keyword); }
+  .codehilite :is(.s, .s1, .s2, .sa, .sd, .se, .si) {
+    color: var(--code-string);
+  }
+  .codehilite :is(.m, .mi, .mf, .mh, .il) { color: var(--code-number); }
+  .codehilite :is(.nf, .nb, .fm) { color: var(--code-function); }
   blockquote { margin: 1.25rem 0; padding-left: 1rem; border-left: 3px solid var(--line); color: var(--muted); }
   table { border-collapse: collapse; width: 100%; display: block; overflow-x: auto; }
   th, td { border: 1px solid var(--line); padding: .4rem .6rem; text-align: left; }
@@ -56,22 +166,102 @@
 <body>
 <div class="wrap">
   <header class="site-header">
-    <h1>Pascal Maas</h1>
-    <p>Notes and writing.</p>
+    <div class="site-title">
+      <h1>Pascal Maas</h1>
+      <p>A blog about bioinformatics in metabolomics</p>
+    </div>
+    <div class="header-actions">
+      <a href="https://git.pascal-maas.nl/pascalmaas" target="_blank"
+         rel="me noopener">Git</a>
+      <a href="mailto:contact@pascal-maas.nl">Contact</a>
+      <button class="theme-toggle" type="button"
+              title="Switch to dark mode">Espresso</button>
+    </div>
   </header>
 
-  <nav aria-label="Posts">
-    <h2>Posts</h2>
-    <ol>
+  <div class="layout">
+    <nav aria-label="Posts">
+      <h2>Posts</h2>
+      <ol>
 {{toc}}
-    </ol>
-  </nav>
+      </ol>
+    </nav>
 
-  <main>
+    <main>
 {{posts}}
-  </main>
+    </main>
+  </div>
 
   <footer>© {{year}} Pascal Maas</footer>
 </div>
+<script>
+  const root = document.documentElement;
+  const button = document.querySelector(".theme-toggle");
+
+  // The button names the mode it switches to, not the current one.
+  function applyTheme(theme) {
+    root.dataset.theme = theme;
+    if (theme === "dark") {
+      button.textContent = "Latte";
+      button.title = "Switch to light mode";
+    } else {
+      button.textContent = "Espresso";
+      button.title = "Switch to dark mode";
+    }
+  }
+
+  applyTheme(root.dataset.theme || "light");
+  button.addEventListener("click", function () {
+    const theme = root.dataset.theme === "dark" ? "light" : "dark";
+    applyTheme(theme);
+    try {
+      localStorage.setItem("theme", theme);
+    } catch (error) {}
+  });
+
+  const header = document.querySelector(".site-header");
+  const articles = Array.from(document.querySelectorAll("main article"));
+  const links = document.querySelectorAll("nav a");
+
+  // First use of each term per post keeps its definition, moved out of
+  // "title" so the browser's plain tooltip doesn't show beside the bubble.
+  for (const article of articles) {
+    const seen = new Set();
+    for (const term of article.querySelectorAll("abbr[title]")) {
+      if (seen.has(term.textContent)) {
+        term.replaceWith(term.textContent);
+        continue;
+      }
+      seen.add(term.textContent);
+      term.dataset.definition = term.title;
+      term.removeAttribute("title");
+      term.tabIndex = 0;
+    }
+  }
+
+  // The current post is the last one whose top has passed a line 3rem
+  // (48px) below the header; at the very bottom, it is always the last post.
+  function markCurrentPost() {
+    if (articles.length === 0) {
+      return;
+    }
+    const line = header.getBoundingClientRect().bottom + 48;
+    const viewBottom = window.innerHeight + window.scrollY;
+    const atBottom = viewBottom >= root.scrollHeight - 2;
+    let current = articles[0];
+    for (const article of articles) {
+      if (atBottom || article.getBoundingClientRect().top <= line) {
+        current = article;
+      }
+    }
+    for (const link of links) {
+      link.classList.toggle("current", link.hash === "#" + current.id);
+    }
+  }
+
+  markCurrentPost();
+  window.addEventListener("scroll", markCurrentPost, { passive: true });
+  window.addEventListener("resize", markCurrentPost);
+</script>
 </body>
 </html>

topics/starting-a-blog.md

@@ -0,0 +1,16 @@
+---
+title: Starting a blog
+date: 2026-10-04
+---
+
+Hi there! This is my first post in hopefully many. I'm Pascal and work as a bioinformatician in the field of metabolomics. I studied bioinformatics, getting my master degree in 2020 at the University of Amsterdam and since then I work at the Metabolomics Analytical Centre, which is part of the University of Leiden. Here I develop software to support the data analysis of large volumes of samples. This however, remains a challenge for reasons that hopefully become clear through posts on this blog. Ofcourse, I will also attempt to provide solutions for practical challenges I've encounted.
+
+I decided to start this blog to share my experience with data analysis in metabolomics as publishing articles is a slow process, and might not be the right platform for sharing everyday encounters. I've been enjoying reading other blogs like [yet another metabolomics club](https://metabolomics.blog) & [Notes from a data witch](https://blog.djnavarro.net), and it seemed the right fit to share my thoughts, ideas and code snippets. I'll post those to my [git](https://git.pascal-maas.nl/explore/repos). Except to see code mostly written in R, Python and perhaps some C++.
+
+In the office I'm known for drinking way too much coffee (although I don't see anything wrong with my consumption..). For this reason I called the light/dark mode after coffee drinks and themed the blog as such. I'm genuinely curious how big the caffeine spike would be on our LC-MS systems, but since the assay uses plasma it will remain a mystery to this day. Perhaps DBS based metabolomics would be my best bet..
+
+Anyways, enjoy your stay!
+
+
+*[bioinformatics]: An interdisciplinary field of science that develops computational methods and software tools for understanding biological data
+*[DBS]: Dried Blood Spots, a promising, minimally invasive techninique for blood sampling.