Merge pull request #8 from biosustain/main

push latest changes

Author: enryH

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,4 @@
+
+
+See the preview for the last modified PR:
+- https://biosustain.github.io/git-tutorial/dev/index.html

.github/workflows/build_website.yaml

@@ -0,0 +1,48 @@
+# Build website and save it on gh-pages branch
+name: build-and-save-website
+
+# Only run this when the master branch is ch
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  # workflow_dispatch:
+
+# This job installs dependencies, builds the website and pushes it to `gh-pages`
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build the site
+        run: |
+          sphinx-build -nW --keep-going -b html .  _build
+
+      # If we've pushed to main, push the book's HTML to github-pages
+      - if: ${{ github.ref == 'refs/heads/main' }}
+        name: Save to gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build
+          # # set it to a subfolder of the root to keep all PR previews:
+          # destination_dir: latest
+          # cname: website.com
+      - name: Save to gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build
+          # # create a version for an PR
+          # # will be automatically deleted in case the build in on the root
+          destination_dir: dev

.gitignore

@@ -1,3 +1,23 @@
+# Byte-compiled Python files
+__pycache__/
+
+# data
+*.csv
+*.json
+*.parquet
+
+# C extensions
+*.so
+
+# Mac OS
+.DS_Store
+*/.DS_Store
+
+# Distribution / packaging
+dist/
+eggs/
+
+
 .npm
 .yarn
 .cache
@@ -9,3 +29,5 @@
 .jupyter
 .bash_logout
 .profile
+.DS_Store
+_build

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, Tim Head
+Copyright (c) 2025, Henry Webel
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,66 +1,71 @@
-# Git Tutorial using
+# Git Tutorial
 
-> VS Code on Binder  
-> VS Code on Binder, because sometimes you need a real editor.  
+Sign-Up to the workshop here (being logged in with your DTU Microsoft account): [Sign-Up Form](https://forms.office.com/e/62H1nV61R0)
 
-[![PyPI](https://img.shields.io/pypi/v/jupyter-vscode-proxy)](https://pypi.org/project/jupyter-vscode-proxy/)
-[![Install with conda](https://anaconda.org/conda-forge/jupyter-vscode-proxy/badges/installer/conda.svg)](https://github.com/conda-forge/jupyter-vscode-proxy-feedstock)
+## Announcement
 
-Start:
- - lab: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/RasmussenLab/git-tutorial/master?urlpath=lab)
- - vscode: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/RasmussenLab/git-tutorial/master?urlpath=vscode?folder=/home/jovyan/examples)
+This workshop will give you the opportunity to practice git as a version control system
+and Github as a website to host your repositories. Using git you can track changes in
+folders. It allows you track your progress and to spot random typos when working on
+many projects and tasks in parallel. In the workshop you will get the time to practice
+the fundamental concepts and actions directly in your browser - either using VSCode in
+GitHub Codespaces or in using the GitHub web interface. If you want, you can also try
+everything on your local computer.
 
+I will give a brief introduction to git. Then you will specific workflows by
+collaboratively work on extending a [recipe book](https://biosustain.github.io/recipe-book/)
+(please bring a recipe you like).
+You will learn how to work on
+[branches](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches),
+review [Pull Requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests)
+and merge them into the main branch. If you have specific requests, feel free to reach out to me.
 
-## Explore
+If you have specific requests, feel free to reach out to [me](mailto:heweb@dtu.dk) and/or write it down in the sign-up form.
 
-You will need to setup your git email and user-name
-(replace with yours in case you want to commit something, otherwise use copy-paste)
+What you'll learn:
 
-```bash
-git config --global user.email "you@example.com"
-git config --global user.name "Your Name"
-``` 
-> could be added to local config using `git config user...`
+- Basic tasks and actions to perform with git (in VSCode or in the browser)
+- How to branch and tag
+- Follow trunk-based development
+- See how to merge and comment a Pull Request based on a branch
+- Solve merge conflicts
+- Familiarize yourself with VSCode’s and GitHub’s interface and user experience
+- Get to know new recipes
 
-### Steps
+Minimal prerequisite: A [GitHub account](https://github.com/signup).
+If you want to follow along locally, please install
+[GitHub Desktop](https://desktop.github.com/download/) and
+[VSCode](https://code.visualstudio.com/) on your machine.
 
-- create a folder with an empty repository (default `examples`)
-- `git init` in console to initialize repo
-- setup user.name and user.email
-- create files, stage them and see what files are created in `.git/objects`
-- commit files and check `.git/objects`
-- create branches and checkout `.git/refs` and `git/branches` folder
-- look at `git/HEAD` (maybe `git/ORIG_HEAD` if it exists)
+### Brief timeline of the workshop:
 
-> try to create your own fork, and try to lauch it on [mybinder](https://mybinder.org/)
+| Time          | Activity                                   |
+| ------------- | ------------------------------------------ |
+| 10:00 - 10:15 | Coffee and snacks 🥐                       |
+| 10:15 - 10:45 | Introduction and example workflow          |
+| 10:45 - 12:00 | Working collaboratively on the recipe book |
+| 12:00 - 12:30 | lunch break (not included)                 |
+| 12:30 - 13:30 | Your question and advanced content         |
 
-## Links
+## Slides
 
+<iframe 
+src="https://docs.google.com/presentation/d/1RsKMiKquE4wqncrAv9LEtjivGE_dGiHoJ8nKCxgVKeY/embed" 
+frameborder="0"
+width="100%" height="480" 
+allowfullscreen="true"
+mozallowfullscreen="true" 
+webkitallowfullscreen="true">
+</iframe>
+
+## Local Setup
+
+See [local_setup](local_setup.md) for instructions to setup git on your local computer.
+
+## Links to learn more
+
+- [git-intro by coderefinery](https://coderefinery.github.io/git-intro/#)
 - [git-moji](https://gitmoji.dev/)
-- [curious git](https://matthew-brett.github.io/curious-git/) - detailed intro to the inner workings
-- [git parable](http://practical-neuroimaging.github.io/git_parable.html) - why git came to exist
-- Videos: 
-    - [Python-Git-Client](https://www.youtube.com/watch?v=xvzo_nV9PjU)
-    - [Git-Interals](https://www.youtube.com/watch?v=MYP56QJpDr4)
-    - [Git PyData Global 2021 talk](https://www.youtube.com/watch?v=rBYC3dEOOyI)
-
-## Inspect git objects
-
-```bash
-git log --format=raw
-git cat-file -p <hash> # pretty print
-git cat-file -t <hash> # type
-
-# the binary object can also be inspected using different tools,
-# which might make it easier to navigate to certain blobs:
-cat .git/objects/<2c>/<38c> | zlib-flate -uncompress
-```
-
-## Note
-
-> Should be Run the Python Tsunami notebooks on binder.
-?urlpath=vscode/?folder
-Go directly to Python Tsunami repository in
- - VSCode [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/RasmussenLab/git-tutorial/master?urlpath=vscode/?folder=/home/jovyan/PythonTsunami)
- - JupyterLab [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/RasmussenLab/git-tutorial/master?urlpath=lab/tree/PythonTsunami)
- - Jupyter Notebook [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/RasmussenLab/git-tutorial/master?urlpath=tree/PythonTsunami)
+- [Git Internals - Plumbing and Porcelain](https://git-scm.com/book/en/v2/Git-Internals-Plumbing-and-Porcelain)
+- [Glossary of terms for git](https://www.git-scm.com/docs/gitglossary)
+- [Glossary terms for GitHub](https://docs.github.com/en/get-started/learning-about-github/github-glossary)

advanced.md

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+
+# Git under the hood
+
+> Extended content for those interested in how git works under the hood
+
+You can find a recording of the
+[talk](https://www.youtube.com/watch?v=cAU3BCUkHxM)
+([slides](https://docs.google.com/presentation/d/1RsKMiKquE4wqncrAv9LEtjivGE_dGiHoJ8nKCxgVKeY/edit?usp=sharing))
+and [hands-on tutorial](https://www.youtube.com/watch?v=5iB7qc5zRjQ)
+on YouTube which was done for the Data Club seminar
+between DTU biosustain and DTU bioengineering (see sections in description of Video).
+
+Talk:
+[![Recording of talk](https://img.youtube.com/vi/cAU3BCUkHxM/maxresdefault.jpg)](https://www.youtube.com/watch?v=cAU3BCUkHxM)
+
+Live Demo:
+[![Live Demo of Hands On part](https://img.youtube.com/vi/5iB7qc5zRjQ/maxresdefault.jpg)](https://www.youtube.com/watch?v=5iB7qc5zRjQ)
+
+The above Live Demo is not pulling the merge commit after merging the branch on GitHub:
+[github.com/biosustain/git_training_henry_recording](https://github.com/biosustain/git_training_henry_recording)
+
+I show the merge commit in the video below, cloining the recording repository in a newly
+create VSCode sandbox environment above:
+
+[![Live Demo Hand on Addon](https://img.youtube.com/vi/gcfzruIJ-rw/sddefault.jpg)](https://www.youtube.com/watch?v=gcfzruIJ-rw)
+
+## Instructions
+
+- create a folder with an empty repository (default `examples`
+  directly openend in VSCode on binder)
+- open instruction: `code-server ../README.md` (local computer: `code ../README.md`)
+- `git init` in console to initialize repo (or via command palette "Git: Initialize Repository")
+- setup user.name and user.email (see above)
+- create files, stage them and see what files are created in `.git/objects`
+- commit files and check `.git/objects`
+- create branches and checkout `.git/refs` (`git/branches` is a legacy folder,see
+  [here](https://stackoverflow.com/a/10398507/9684872))
+- look at `git/HEAD` (maybe `git/ORIG_HEAD` if it exists)
+
+> try to create your own fork, and try to lauch it on [mybinder](https://mybinder.org/)
+
+## Inspect git objects
+
+```bash
+git log --format=raw
+git cat-file -p <hash> # pretty print
+git cat-file -t <hash> # type
+
+# the binary object can also be inspected using different tools,
+# which might make it easier to navigate to certain blobs:
+cat .git/objects/<2c>/<38c> | zlib-flate -uncompress
+```
+
+You can find the latest objects and compare it to the log
+
+```bash
+find .git/objects  -type f -exec ls -lt {} + | head -n 10
+git log --format=raw -n 3
+```
+
+If you wonder what the codes in a tree mean, check this stackexchange
+[answer](https://unix.stackexchange.com/a/450488/349761)
+
+## What's happening?
+
+Can you explain what happens in the following scenarios?
+
+- You committed ten commits and did not yet push. Git complains about too much data.
+  You realize that you committed your source data. You delete it and commit again,
+  but the problem still persists.
+- You commit something and push. You realize your last commit was wrong. You undo it
+  and commit again. Git complains that you cannot push.
+
+## Git internals resources
+
+- [curious git](https://matthew-brett.github.io/curious-git/) - detailed intro to the
+  inner workings
+- [git parable](http://practical-neuroimaging.github.io/git_parable.html) - why git came to exist
+- Videos:
+  - [Python-Git-Client](https://www.youtube.com/watch?v=xvzo_nV9PjU)
+  - [Git-Interals](https://www.youtube.com/watch?v=MYP56QJpDr4) - shows how git works
+  - [Git PyData Global 2021 talk](https://www.youtube.com/watch?v=rBYC3dEOOyI)
+  - Scoot Chacon’s [“So you thin you know git” talk](https://www.youtube.com/watch?v=aolI_Rz0ZqY) (FOSDEM 2024),
+    notes on [blog](https://blog.gitbutler.com/git-tips-1-theres-a-git-config-for-that/)