justthedocs template

Gemfile

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+source 'https://rubygems.org'
+
+gem "jekyll", "~> 4.3.4" # installed by `gem jekyll`
+# gem "webrick"        # required when using Ruby >= 3 and Jekyll <= 4.2.2
+
+gem "just-the-docs", "0.10.1" # pinned to the current release
+# gem "just-the-docs"        # always download the latest release

Gemfile.lock

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+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    bigdecimal (3.1.9)
+    colorator (1.1.0)
+    concurrent-ruby (1.3.4)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    forwardable-extended (2.6.0)
+    google-protobuf (4.29.2-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.2-x86_64-linux)
+      bigdecimal
+      rake (>= 13)
+    http_parser.rb (0.8.0)
+    i18n (1.14.6)
+      concurrent-ruby (~> 1.0)
+    jekyll (4.3.4)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
+      liquid (~> 4.0)
+      mercenary (>= 0.3.6, < 0.5)
+      pathutil (~> 0.9)
+      rouge (>= 3.0, < 5.0)
+      safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    just-the-docs (0.10.1)
+      jekyll (>= 3.8.5)
+      jekyll-include-cache
+      jekyll-seo-tag (>= 2.0)
+      rake (>= 12.3.1)
+    kramdown (2.5.1)
+      rexml (>= 3.3.9)
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.4.0)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (6.0.1)
+    rake (13.2.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.4.0)
+    rouge (4.5.1)
+    safe_yaml (1.0.5)
+    sass-embedded (1.83.1-arm64-darwin)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.1-x86_64-linux-gnu)
+      google-protobuf (~> 4.29)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    unicode-display_width (2.6.0)
+    webrick (1.9.1)
+
+PLATFORMS
+  arm64-darwin
+  x86_64-linux-gnu
+
+DEPENDENCIES
+  jekyll (~> 4.3.4)
+  just-the-docs (= 0.10.1)
+
+BUNDLED WITH
+   2.5.9

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023  Lifespan Informatics and Neuroimaging Center
+Copyright (c) 2022 just-the-docs
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,17 +1,174 @@
-# grmpy open data release curation
-
-## File organization on CUBIC
-
-```
-/cbica/projects/grmpy/
-    |-  code/           # Local clone of the GitHub repository
-        |- curation     # Scripts for bids curation
-        |-  figures/    # Any figures for the manuscript
-        |_  data/       # Tabular data that may be shared on GitHub
-    |-  data/
-    |-  results/        # Results that cannot be shared on GitHub
-    |_  reproduction/
-        |-  code/       # Local clone of reproducibilibuddy's fork of GitHub repository
-        |-  data/       # Any data that must be copied and not referenced
-        |_  results/
-```
+# just-the-docs-template
+
+This is a *bare-minimum* template to create a [Jekyll] site that:
+
+- uses the [Just the Docs] theme;
+- can be built and published on [GitHub Pages];
+- can be built and previewed locally, and published on other platforms.
+
+More specifically, the created site:
+
+- uses a gem-based approach, i.e. uses a `Gemfile` and loads the `just-the-docs` gem;
+- uses the [GitHub Pages / Actions workflow] to build and publish the site on GitHub Pages.
+
+To get started with creating a site, simply:
+
+1. click "[use this template]" to create a GitHub repository
+2. go to Settings > Pages > Build and deployment > Source, and select GitHub Actions
+
+If you want to maintain your docs in the `docs` directory of an existing project repo, see [Hosting your docs from an existing project repo](#hosting-your-docs-from-an-existing-project-repo).
+
+After completing the creation of your new site on GitHub, update it as needed:
+
+## Replace the content of the template pages
+
+Update the following files to your own content:
+
+- `index.md` (your new home page)
+- `README.md` (information for those who access your site repo on GitHub)
+
+## Changing the version of the theme and/or Jekyll
+
+Simply edit the relevant line(s) in the `Gemfile`.
+
+## Adding a plugin
+
+The Just the Docs theme automatically includes the [`jekyll-seo-tag`] plugin.
+
+To add an extra plugin, you need to add it in the `Gemfile` *and* in `_config.yml`. For example, to add [`jekyll-default-layout`]:
+
+- Add the following to your site's `Gemfile`:
+
+  ```ruby
+  gem "jekyll-default-layout"
+  ```
+
+- And add the following to your site's `_config.yml`:
+
+  ```yaml
+  plugins:
+    - jekyll-default-layout
+  ```
+
+Note: If you are using a Jekyll version less than 3.5.0, use the `gems` key instead of `plugins`.
+
+## Publishing your site on GitHub Pages
+
+1.  If your created site is `YOUR-USERNAME/YOUR-SITE-NAME`, update `_config.yml` to:
+
+    ```yaml
+    title: YOUR TITLE
+    description: YOUR DESCRIPTION
+    theme: just-the-docs
+
+    url: https://YOUR-USERNAME.github.io/YOUR-SITE-NAME
+
+    aux_links: # remove if you don't want this link to appear on your pages
+      Template Repository: https://github.com/YOUR-USERNAME/YOUR-SITE-NAME
+    ```
+
+2.  Push your updated `_config.yml` to your site on GitHub.
+
+3.  In your newly created repo on GitHub:
+    - go to the `Settings` tab -> `Pages` -> `Build and deployment`, then select `Source`: `GitHub Actions`.
+    - if there were any failed Actions, go to the `Actions` tab and click on `Re-run jobs`.
+
+## Building and previewing your site locally
+
+Assuming [Jekyll] and [Bundler] are installed on your computer:
+
+1.  Change your working directory to the root directory of your site.
+
+2.  Run `bundle install`.
+
+3.  Run `bundle exec jekyll serve` to build your site and preview it at `localhost:4000`.
+
+    The built site is stored in the directory `_site`.
+
+## Publishing your built site on a different platform
+
+Just upload all the files in the directory `_site`.
+
+## Customization
+
+You're free to customize sites that you create with this template, however you like!
+
+[Browse our documentation][Just the Docs] to learn more about how to use this theme.
+
+## Hosting your docs from an existing project repo
+
+You might want to maintain your docs in an existing project repo. Instead of creating a new repo using the [just-the-docs template](https://github.com/just-the-docs/just-the-docs-template), you can copy the template files into your existing repo and configure the template's Github Actions workflow to build from a `docs` directory. You can clone the template to your local machine or download the `.zip` file to access the files.
+
+### Copy the template files
+
+1.  Create a `.github/workflows` directory at your project root if your repo doesn't already have one. Copy the `pages.yml` file into this directory. GitHub Actions searches this directory for workflow files.
+
+2.  Create a `docs` directory at your project root and copy all remaining template files into this directory.
+
+### Modify the GitHub Actions workflow
+
+The GitHub Actions workflow that builds and deploys your site to Github Pages is defined by the `pages.yml` file. You'll need to edit this file to that so that your build and deploy steps look to your `docs` directory, rather than the project root.
+
+1.  Set the default `working-directory` param for the build job.
+
+    ```yaml
+    build:
+      runs-on: ubuntu-latest
+      defaults:
+        run:
+          working-directory: docs
+    ```
+
+2.  Set the `working-directory` param for the Setup Ruby step.
+
+    ```yaml
+    - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.3'
+          bundler-cache: true
+          cache-version: 0
+          working-directory: '${{ github.workspace }}/docs'
+    ```
+
+3.  Set the path param for the Upload artifact step:
+
+    ```yaml
+    - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_site/
+    ```
+
+4.  Modify the trigger so that only changes within the `docs` directory start the workflow. Otherwise, every change to your project (even those that don't affect the docs) would trigger a new site build and deploy.
+
+    ```yaml
+    on:
+      push:
+        branches:
+          - "main"
+        paths:
+          - "docs/**"
+    ```
+
+## Licensing and Attribution
+
+This repository is licensed under the [MIT License]. You are generally free to reuse or extend upon this code as you see fit; just include the original copy of the license (which is preserved when you "make a template"). While it's not necessary, we'd love to hear from you if you do use this template, and how we can improve it for future use!
+
+The deployment GitHub Actions workflow is heavily based on GitHub's mixed-party [starter workflows]. A copy of their MIT License is available in [actions/starter-workflows].
+
+----
+
+[^1]: [It can take up to 10 minutes for changes to your site to publish after you push the changes to GitHub](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/creating-a-github-pages-site-with-jekyll#creating-your-site).
+
+[Jekyll]: https://jekyllrb.com
+[Just the Docs]: https://just-the-docs.github.io/just-the-docs/
+[GitHub Pages]: https://docs.github.com/en/pages
+[GitHub Pages / Actions workflow]: https://github.blog/changelog/2022-07-27-github-pages-custom-github-actions-workflows-beta/
+[Bundler]: https://bundler.io
+[use this template]: https://github.com/just-the-docs/just-the-docs-template/generate
+[`jekyll-default-layout`]: https://github.com/benbalter/jekyll-default-layout
+[`jekyll-seo-tag`]: https://jekyll.github.io/jekyll-seo-tag
+[MIT License]: https://en.wikipedia.org/wiki/MIT_License
+[starter workflows]: https://github.com/actions/starter-workflows/blob/main/pages/jekyll.yml
+[actions/starter-workflows]: https://github.com/actions/starter-workflows/blob/main/LICENSE

_config.yml

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+title: Just the Docs Template
+description: A starter template for a Jeykll site using the Just the Docs theme!
+theme: just-the-docs
+
+url: https://just-the-docs.github.io
+
+aux_links:
+  Template Repository: https://github.com/just-the-docs/just-the-docs-template