seedling-establishment

Conifer Seedling Establishment in a mountaineous Landscape

This repository demonstrates where. how, and why conifer seedlings are present/not present in a post-wildfire landscape in Colorado FrontRange using spatial modeling framework:

1. A website to communicate your science to others.
2. A hub for sharing code within your group.

Template users: If you are using this repository as a template, start with TEMPLATE_GUIDE.md for the required name and link updates.

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1) Understanding the Repository

Think of this repository like a shared online folder. Inside it, there are a few important parts:

• README.md — This file (what you are reading now). It explains how things work.
• data/ — Optional. Small datasets can go here.
• outputs/ — Optional. Figures, results, and reports can go here.

Storage

• Code (code/) — Share scripts, notebooks, and analysis utilities. Keep filenames clear and include short comments at the top so teammates understand the purpose quickly.
• Documentation (docs/ and documentation/) — Everything inside docs/ powers the public website, while documentation/ can host internal notes or extended write-ups. Update these areas regularly so the story on the site and your working docs stay in sync.

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2) How to Update the Website

The website is built from the docs/ folder. Every time you change a file there, the website updates automatically.

Step by Step

1. In the repository, click the docs/ folder.
2. Click on index.md. This is the home page of your website.
3. In the top right, click the pencil icon (✏️) to edit.
4. Change the text to describe your project (for example, add your team’s name and a short description of what you’re studying).
5. Scroll down. In the Commit changes box, write a short message like updated homepage with project info.
6. Click Commit changes.

That’s it! In about a minute, refresh your website link and you’ll see your changes.

Note: If your website is not set up yet, go to Settings → Pages → Build and deployment. Set the Source to Deploy from a branch, then choose main and /docs. GitHub will give you a link to your site.

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3) How to Share Code

Code lives in the src/ folder. You can put scripts, Jupyter notebooks, or R files here.

Step by Step

1. In the repository, click the src/ folder.
2. Click Add file → Upload files (to add something from your computer), or Create new file.
3. Name your file something clear, like data_cleaning.py or fire_analysis.R.
4. At the top of the file, write a short comment about what the code does.
5. Scroll down, write a commit message like added first data cleaning script, and click Commit changes.

Now your teammates can see and use your code.

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4) Common Tasks

• Add a new webpage: Create a new .md file inside docs/ (like methods.md). It will become a new page on your site.
• Add a picture: Put the file in docs/assets/ and add it to a page with ![caption](assets/filename.png).
• Add team members: Edit docs/team.md to add names and roles.

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5) Tips for Beginners

• Don’t worry about breaking things — everything can be fixed, and old versions are saved.
• Small updates are valuable. Even a one-line change is a real contribution.
• Write commit messages as if explaining to your future self.
• Large data files (over ~50 MB) should not go in GitHub. Instead, link to them from the data/ page.

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6) Learn More

• GitHub Pages basics
• Editing files in your browser

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7) First Things to Try

1. Edit the docs/index.md file and add your project description.
2. Add yourself to the docs/team.md page.
3. Upload your first code file to the src/ folder.
4. Refresh your website link and see your changes live.

Congratulations — you’re now using GitHub to communicate your science and share code!

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Beginner Mode: From zero to website (no command line)

This section is written for someone who has never used GitHub. Follow it in order. You can do all of this in your web browser.

What you need

• A GitHub account (free). If you don’t have one: https://github.com → Sign up.
• A link to your group’s repository (ask your instructor/lead if you don’t have it).

Step 1 — Join your group’s repo

1. Open the invitation link you received by email or in GitHub notifications.
2. Click Accept invitation. You now have permission to edit.

Why this matters: GitHub only lets approved people change files. Accepting the invite gives you access.

Step 2 — Open the project home

1. Visit your repository link (it looks like https://github.com/ORG/Project_group_OASIS).
2. You’ll see folders like docs/, src/, and files like README.md.

Why this matters: This is the “front door” to your project’s files.

Step 3 — Turn on the website (GitHub Pages)

1. Click Settings (top menu of the repo).
2. In the left sidebar, click Pages.
3. Under Build and deployment → Source, choose Deploy from a branch.
4. Under Branch, choose main and /docs folder.
5. Click Save. A green box will show the site link after it builds (usually 1–2 minutes).

Why this matters: This tells GitHub to publish everything inside docs/ as a website.

Step 4 — Edit the homepage text

1. Click the Code tab to return to the file view.
2. Open the docs/ folder → click index.md.
3. Click the pencil icon to edit.
4. Change the title and first paragraph so they describe your project.
5. Scroll to the bottom, write a short Commit message (for example: update homepage).
6. Click Commit changes.

Why this matters: Saving (committing) creates a new version of your page and triggers the website to rebuild.

Step 5 — See your changes online

1. Go back to Settings → Pages (or use the link shown there).
2. Open your site in a new tab.
3. Refresh after a minute if you don’t see changes yet.

Why this matters: Now you can share a public link to your project.

Step 6 — Add a new page

1. In the docs/ folder, click Add file → Create new file.
2. Name it something like methods.md.
3. Paste a small outline (what, why, how) and click Commit changes.
4. To add it to the top navigation, open docs/_config.yml, find header_pages:, and add - methods.md on its own line. Commit.

Why this matters: You can grow your site one page at a time.

Step 7 — Add an image

1. Open docs/assets/ → Add file → Upload files → pick your image.
2. In a page (e.g., index.md), insert: ![Alt text](assets/your_image.png) and commit.

Why this matters: Images help explain your science.

Step 8 — Share code with the team

1. Open the src/ folder → Add file → upload a script or create a new file.
2. At the top of the file, write 2–3 lines that explain what it does, inputs, and outputs.
3. Commit changes.
4. In docs/code.md, add a short bullet linking to your file, e.g. - src/pipeline.py — end-to-end pipeline and commit.

Why this matters: The website becomes a clear map that points to your working code.

Step 9 — Post an update

1. Open docs/updates.md → pencil icon.
2. Add a new dated section (copy the example) with 1–3 bullets of what changed.
3. Commit.

Why this matters: Small updates build a readable project history.

Step 10 — Share the site link

• Copy the Pages URL from Settings → Pages and send it to your group or stakeholders.

You’re done. You’ve published a site and shared code without using the command line.

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Quick‑start checklist (printable)

• I can open the repo and see docs/, src/, and README.md.
• Pages is enabled: main + /docs.
• I edited docs/index.md and committed changes.
• I can open the public site link and see my edits.
• I added or uploaded one script to src/.
• I linked that script from docs/code.md.
• I posted one dated entry in docs/updates.md.

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Plain‑language glossary

• Repository (repo): Your project’s online folder.
• Commit: A saved change with a short note. Think “Save with a message.”
• Branch: A workspace for changes. Beginners can stay on main.
• Pull request (PR): A proposal to merge changes. Useful later; optional for now.
• GitHub Pages: A way to turn files in docs/ into a website.
• Markdown (.md): A simple text format for writing pages with headings, links, and images.

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Troubleshooting (common fixes)

I don’t see the Pages option. You might not have permission. Ask your lead to enable it, or ensure you’re in the repository’s Settings (not your user settings).

My site URL shows 404. Wait 1–2 minutes after enabling Pages or after a commit. Refresh. Confirm Source is set to Deploy from a branch and Branch = main and Folder = /docs.

My changes didn’t appear. Refresh the site. Confirm you edited a file inside docs/. Check commit history on the repo’s home page to see if your change saved.

Images don’t load. Make sure the image is inside docs/assets/ and the link is ![Alt text](assets/your_image.png) (no leading slash).

I uploaded a big file and got an error. GitHub limits file size. Keep data small in the repo. Link to external storage for big datasets.

I’m afraid of breaking things. Every change is tracked. You can always edit again or revert. Small, frequent commits are safest.

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Teaching notes (why this pedagogy works)

• Immediate reward: Editing index.md shows a visible website change fast.
• One mental model: “Files in docs/ become web pages.”
• Low friction: No installs or command line required.
• Narrated steps: Each action explains why it matters to build understanding.

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Next level (optional, later)

• Use branches + pull requests for review before merging to main.
• Add a requirements.txt or environment.yml to document software packages.
• Create a CONTRIBUTING.md with team norms (naming, reviews, issue labels).
• Add automatic checks (CI) to run tests when code changes.

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