Quality-of-life improvements

.github/workflows/pages.yml

@@ -22,6 +22,14 @@ jobs:
       - name: Setup Pages
         uses: actions/configure-pages@v4
 
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Generate sidebar tree
+        run: python3 scripts/generate_tree.py
+
       - name: Build with Jekyll
         uses: actions/jekyll-build-pages@v1
 

Gemfile

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# gem "rails"
+
+gem "github-pages", "~> 232"
+gem "jekyll-readme-index"

Gemfile.lock

@@ -0,0 +1,284 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (8.1.2)
+      base64
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.3.1)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      json
+      logger (>= 1.4.2)
+      minitest (>= 5.1)
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0, >= 2.0.5)
+      uri (>= 0.13.1)
+    addressable (2.8.8)
+      public_suffix (>= 2.0.2, < 8.0)
+    base64 (0.3.0)
+    bigdecimal (4.0.1)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
+    colorator (1.1.0)
+    commonmarker (0.23.12)
+    concurrent-ruby (1.3.6)
+    connection_pool (3.0.2)
+    csv (3.3.5)
+    dnsruby (1.73.1)
+      base64 (>= 0.2)
+      logger (~> 1.6)
+      simpleidn (~> 0.2.1)
+    drb (2.2.3)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    ethon (0.15.0)
+      ffi (>= 1.15.0)
+    eventmachine (1.2.7)
+    execjs (2.10.0)
+    faraday (2.14.1)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.2)
+      net-http (~> 0.5)
+    ffi (1.17.3-x86_64-linux-gnu)
+    forwardable-extended (2.6.0)
+    gemoji (4.1.0)
+    github-pages (232)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.10.0)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
+      jekyll-commonmark-ghpages (= 0.5.1)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.16.1)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.13.0)
+      kramdown (= 2.4.0)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.16.2, < 2.0)
+      rouge (= 3.30.0)
+      terminal-table (~> 1.4)
+      webrick (~> 1.8)
+    github-pages-health-check (1.18.2)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
+      typhoeus (~> 1.3)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
+    http_parser.rb (0.8.1)
+    i18n (1.14.8)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.10.0)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      csv (~> 3.0)
+      em-websocket (~> 0.5)
+      i18n (>= 0.7, < 2)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (>= 1.17, < 3)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+      webrick (>= 1.0)
+    jekyll-avatar (0.8.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.2.2)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.12)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.5.1)
+      commonmarker (>= 0.23.7, < 1.1.0)
+      jekyll (>= 3.9, < 4.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 5.0)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-feed (0.17.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.16.1)
+      jekyll (>= 3.4, < 5.0)
+      octokit (>= 4, < 7, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    jemoji (0.13.0)
+      gemoji (>= 3, < 5)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
+    json (2.18.1)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.10.0)
+      logger
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.7.0)
+    mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    minitest (6.0.1)
+      prism (~> 1.5)
+    net-http (0.9.1)
+      uri (>= 0.11.1)
+    nokogiri (1.19.0-x86_64-linux-gnu)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    prism (1.9.0)
+    public_suffix (5.1.1)
+    racc (1.8.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.4.4)
+    rouge (3.30.0)
+    rubyzip (2.4.1)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.3)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    securerandom (0.4.1)
+    simpleidn (0.2.3)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    typhoeus (1.5.0)
+      ethon (>= 0.9.0, < 0.16.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (1.8.0)
+    uri (1.1.1)
+    webrick (1.9.2)
+
+PLATFORMS
+  x86_64-linux-gnu
+
+DEPENDENCIES
+  github-pages (~> 232)
+  jekyll-readme-index
+
+BUNDLED WITH
+   2.4.20

Input_peak_lists_for_4D-GraFID/peak_list_full_format_guide.md

@@ -1,3 +1,8 @@
+---
+title: "peak list full format guide"
+layout: default
+---
+
 # Submitting peak lists for 4D-GraFID
 
 ## Experiment type reference

NMR_Pipe/Readme.md

@@ -1,3 +1,9 @@
+---
+title: "Single line NMR Pipe installation"
+permalink: /NMR_Pipe/
+layout: default
+---
+
 # Single line NMR Pipe installation
 
 Download, install and set up [NMRPipe](https://spin.niddk.nih.gov/bax/NMRPipe/) on Ubuntu with the single line!
@@ -46,4 +52,3 @@ Simple as that!
 
 
 
-

NMR_theory/NMR_Spectrometer.md

@@ -1,3 +1,8 @@
+---
+title: "NMR Spectrometer"
+layout: default
+---
+
 NMR spectrometers consist of three main components: a superconducting magnet, a probe and a complex electronic system 
 (console) controlled by a workstation (Figure 3).