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Initial commit: MuscleMimic blog with Jekyll Distill template
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‎.github/workflows/deploy.yml‎

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name: Deploy to GitHub Pages
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on:
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push:
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branches: [main]
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workflow_dispatch:
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: ruby/setup-ruby@v1
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with:
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ruby-version: '3.2'
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bundler-cache: true
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- name: Build site
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run: bundle exec jekyll build --future
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env:
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JEKYLL_ENV: production
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- uses: actions/upload-pages-artifact@v3
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deploy:
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needs: build
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runs-on: ubuntu-latest
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- uses: actions/deploy-pages@v4
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id: deployment

‎.gitignore‎

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# Jekyll build output
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_site/
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.sass-cache/
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.jekyll-cache/
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.jekyll-metadata
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# Dependencies
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vendor/
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Gemfile.lock
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node_modules/
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# OS files
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.DS_Store
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Thumbs.db
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references/
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# Source archives
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*.zip

‎Gemfile‎

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source "https://rubygems.org"
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gem "jekyll", "~> 4.3"
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gem "webrick", "~> 1.8"
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.12"
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gem "jekyll-scholar", "~> 7.0"
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gem "jekyll-sitemap", "~> 1.4"
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gem "jekyll-paginate-v2", "~> 3.0"
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end

‎LICENSE‎

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MIT License
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Copyright (c) 2026 Charlie Li
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# MuscleMimic Blog
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## Build
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```bash
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bundle install
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bundle exec jekyll serve --future
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```
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Visit `http://localhost:4000`.

‎_bibliography/references.bib‎

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@article{gregor2015draw,
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title={DRAW: A Recurrent Neural Network For Image Generation},
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author={Gregor, Karol and Danihelka, Ivo and Graves, Alex and Rezende, Danilo Jimenez and Wierstra, Daan},
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journal={arXiv preprint arXiv:1502.04623},
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year={2015},
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url={https://arxiv.org/abs/1502.04623}
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}
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@article{olah2017feature,
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title={Feature Visualization},
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author={Olah, Chris and Mordvintsev, Alexander and Schubert, Ludwig},
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journal={Distill},
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year={2017},
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url={https://distill.pub/2017/feature-visualization/}
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}
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@article{vaswani2017attention,
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title={Attention is All You Need},
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author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, {\L}ukasz and Polosukhin, Illia},
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journal={Advances in Neural Information Processing Systems},
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volume={30},
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year={2017}
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}

‎_config.yml‎

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# Site settings
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title: MuscleMimic
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description: Full-body musculoskeletal model for neuromuscular motor control research
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url: ""
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baseurl: ""
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lang: en
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# Build
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markdown: kramdown
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highlighter: rouge
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kramdown:
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input: GFM
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math_engine: null # MathJax handles math rendering
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# Plugins
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plugins:
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- jekyll-feed
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- jekyll-scholar
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- jekyll-sitemap
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- jekyll-paginate-v2
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# Scholar (BibTeX citation support)
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scholar:
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style: apa
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locale: en
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source: ./_bibliography
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bibliography: "*.bib"
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bibliography_template: ""
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sort_by: none
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# Feature toggles
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enable_math: true
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enable_dark_mode: true
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# Third-party CDN libraries
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third_party_libraries:
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mathjax:
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url: "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
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jquery:
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url: "https://cdn.jsdelivr.net/npm/jquery@3.6.0/dist/jquery.min.js"
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bootstrap:
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css: "https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css"
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js: "https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/js/bootstrap.bundle.min.js"
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# Include _pages directory
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include:
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- _pages
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# Collections
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collections:
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posts:
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output: true
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permalink: /blog/:title/
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# Pagination
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pagination:
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enabled: true
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per_page: 10
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permalink: "/page/:num/"
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# Defaults
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defaults:
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- scope:
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path: ""
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type: "posts"
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values:
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layout: "distill"
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# Exclude from build
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exclude:
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- references/
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- Gemfile
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- Gemfile.lock
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- README.md
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- node_modules/
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- vendor/

‎_includes/figure.html‎

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<figure {% if include.class %}class="{{ include.class }}"{% endif %}>
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<img
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src="{% if include.url %}{{ include.url }}{% else %}{{ include.path | relative_url }}{% endif %}"
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{% if include.alt %}alt="{{ include.alt }}"{% endif %}
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{% if include.width %}style="width: {{ include.width }}"{% endif %}
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loading="lazy"
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>
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{% if include.caption %}
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<figcaption>{{ include.caption | markdownify | remove: '<p>' | remove: '</p>' }}</figcaption>
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{% endif %}
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</figure>

‎_includes/footer.html‎

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<footer class="sticky-bottom mt-5" role="contentinfo">
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<div class="container">
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&copy; {{ site.time | date: '%Y' }} {{ site.title }}.
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Powered by <a href="https://jekyllrb.com/" target="_blank" rel="noopener">Jekyll</a> &amp;
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<a href="https://github.com/distillpub/template" target="_blank" rel="noopener">Distill</a>.
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</div>
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</footer>

‎_includes/head.html‎

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{% include metadata.html %}
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<!-- Bootstrap CSS -->
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<link rel="stylesheet" href="{{ site.third_party_libraries.bootstrap.css }}">
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<!-- Google Fonts -->
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<link rel="preconnect" href="https://fonts.googleapis.com">
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<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
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<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Roboto+Mono:wght@400;500&display=swap">
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<!-- Site CSS -->
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<link rel="stylesheet" href="{{ '/assets/css/main.css' | relative_url }}">
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{% if site.enable_dark_mode %}
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<!-- Dark mode (in head to prevent flash) -->
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<script src="{{ '/assets/js/theme.js' | relative_url }}"></script>
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<script>initTheme();</script>
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{% endif %}

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