seedling-establishment

Template Customization Checklist

This repository is a template for new project groups. After you generate a project-specific copy, walk through the sections below before adding new content. The checklist is written so you can copy/paste the steps into Codex (or any coding assistant) to make the required edits for you.

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1. Prepare the repository

1. Rename the repo – On GitHub go to Settings → General → Repository name and rename it to match your project. If you already cloned the repo locally, update the remote with git remote set-url origin <new_repo_url>.
2. Enable GitHub Actions – When GitHub shows the banner “Workflows aren’t being run,” open the Actions tab and click I understand, enable workflows so deployment jobs can start.

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2. Update configuration and metadata

MkDocs configuration (mkdocs.yml)

Ask Codex to open mkdocs.yml and update the following keys so the published site shows the correct project details:

• site_name: plain-language project or group name (e.g., "Mountain Snow Analysis").
• site_url: https://<org>.github.io/<repo> (replace with your organization/user and new repo name).
• repo_name: short display label such as "ORG/Project".
• repo_url: the full GitHub URL to the repository.
• Confirm the theme, nav, and plugins look right for your project. Update any navigation labels that still reference “Project Group OASIS.”
• Update the nav item labeled Your persistent storage so it links to your team’s CyVerse folder. Replace Group_1 in the URL with the number that matches your repository name (for example, a repo ending in _5 should use Group_5). If the shared link needs a unique resourceId, grab the correct link directly from the Data Store interface while viewing your group’s folder.

Top-level files

• README.md: change the title, short description, and any sample URLs to your new project name.
• CITATION.cff: edit title, abstract, author list, and other metadata to reflect your team.
• LICENSE: confirm the license you want to use and update the copyright line if needed.

Search-and-replace the old name

Run a repository-wide search for Project_group_OASIS and replace it with your new repo name. Pay attention to:

• Front-matter in the Markdown files inside docs/ (for example, hero images or repo links).
• Any sample links in documentation under docs/orientation/.
• YAML config files in .github/ and workflows/ if you copied them forward.

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3. Refresh the website content

Use the bullets below as prompts for Codex so it can edit each file.

• docs/index.md
  • Update the first-level heading to your project name.
  • Rewrite the intro section with your project summary, goals, or call to action.
  • Review the resources block between <!--RESOURCES_START--> and <!--RESOURCES_END-->; set the repository link, storage link, and any other quick links you want to feature.
• docs/project_template.md
  • Adjust the front-matter fields (repo_owner, repo_name, contact_slack, contact_email, etc.).
  • Replace placeholder hero images, figures, and descriptive text with your team’s content.
• docs/team.md
  • Add each team member with name, role, and contact info.
• docs/code.md
  • List important analysis scripts or notebooks and link to their paths in the repo.
• docs/updates.md
  • Add your first status entry or remove the placeholder timeline.
• docs/resources/
  • Add links to shared drives, data catalogs, or collaboration tools relevant to your group.

If you are using any of the orientation materials, skim the files in docs/orientation/ and swap in screenshots or instructions that match your environment.

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4. Persistent storage instructions

Update docs/instructions/save-to-persistent-storage.md so it points to your team’s storage location. Edit the GROUP_NAME, base path, and any screenshots that mention the original template.

Reminder: The template ships with Group_1 placeholders for the navigation link and shell snippets. Swap these for your group’s identifier (matching the number in your repo name). If your team has a custom share link from the Data Store, copy it from the CyVerse web UI to keep the resourceId accurate.

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5. Turn on GitHub Pages with MkDocs

1. Open Settings → Pages.
2. Under Build and deployment → Source, choose GitHub Actions. This tells GitHub to use the provided Deploy site (MkDocs) workflow.
3. Still on the Pages screen, make sure Allow GitHub Actions to deploy to GitHub Pages is enabled (GitHub may prompt you automatically on first deploy).
4. Go to the Actions tab, open the Deploy site (MkDocs) workflow, and run it (click Run workflow → main). The workflow builds the MkDocs site and publishes it to Pages.
5. Once the job succeeds, your site will be available at https://<org>.github.io/<repo>/. Update the site_url in mkdocs.yml if the link differs.

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6. Final checks

• Confirm all navigation links in the live site work as expected.
• Delete any leftover placeholder sections or TODO comments.
• Share the Pages URL with your team once you verify the site renders correctly.

Keep this file for future reference so anyone (or any assistant) can re-run the setup steps if needed.

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