Submission of Microcredential Github project

.gitignore

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+#the files listed below can be ignored
+Github_UsernameSara.png

LICENSE.md

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+Copyright (c) 2025 GitHub, Inc.
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

Markdown-concepts/Markdown_Sheat-cheet.md

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+# Markdown cheat sheet
+
+# Header 1
+`use # HEADER`
+## Header 2
+`use ## HEADER`
+### Header 3 
+`use ### HEADER`
+
+
+**Bold text** (place text in between `** TEXT **`)
+
+**Italic text** (place text in between `* TEXT *` or `_ TEXT _`)
+
+## lists
+
+### ordered lists
+1. first list item
+2. second list item
+3. third list item
+
+
+### Unordered lists
+- A list item
+- Another list item
+- yet another list item
+
+
+## links and images
+
+### Links
+[Visible URL](https://www.google.com)
+
+### Images
+![Alternative text when image is not there](../images/ImageInMarkdown.png)
+
+`![Alternative text](pathToFile)`

Markdown-concepts/Markdown_concepts.md

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+# Markdown concepts
+
+Markdown is a markup language used for adding formatting elements to a text document.
+
+It is often used for web development, documentation, blogging, etc

README.md

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 -------------------------------------------------------------------------------------------------
 
 This project is part the first evaluation of the micro-credetial that is offered by [VIB](https://vib.be/en#/) and [UGent](https://www.ugent.be/en) with the aim to improve data analysis reproducbility in science. A micro-credential is like a mini-diploma that you have followed a course and learnd a new skill that is valuable for your carrear. If you are interested to register you can find more detais in the [UGent registration page](https://studiekiezer.ugent.be/2025/micro-credential-reproducible-data-analysis-an-essential-capability-in-modern-science-en).
+
+
+collaboration strategy: 
+1. every collaborator creates a separate branch (leena, rafael, sara, main)
+2. Leena works on git concepts, Rafael on github concepts, Sara on Markdown concepts
+3. We communicate via Teams to update each other on the process and conflict creation/resolving.
+4. second meeting on Thursday 27th at 2PM

git_and_github_concepts/git_cheat_sheet.md

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+# This is a cheat sheet for git and github
+
+## Setup
+This commands are for configuring user information used across all local repositories:
+
+`git config --global user.name "[firstname lastname]"`: set a name that is identifiable for credit when review version history
+
+`git config --global user.email "[valid-email]"`: set an email adress that will be associated with each history marker
+
+`git config --global color.ui auto`: set automatic command line coloring for git for easy reviewing.
+
+## Git setup & init
+Commands to config user information, initialization and cloning repositories.
+
+`git init`: to initialize an existing directory as a Git repository.  
+
+`git clone [url]`: retrieve an entire remote repository via URL
+
+## Stage and snapshot
+These are common commands used for working with snapshots and the Git staging area:
+
+`git status`: to show current status. Use it to show modified files in the working directory, staged for your next commit. 
+
+`git add`: to add files to the staging area. See usage details for staging area in the [git concepts](/git_and_github_concepts/git_concepts.md) file.
+
+`git reset [file]`: unstage a file while retaining the changes in your working directory
+
+`git commit -m "meaningful message"`: to commit files from the staging area.  
+
+## Branch and merge
+Commands to isolate work in branches, change context and integrate changes 
+
+`git branch <branch_name>`: create a new branch at the current commit
+
+`git checkout <branch_name>`: switch to another branch 
+
+`git merge <branch_name>`: merge the specified branch's history into the current one.
+
+## Inspect and compare
+Commands to examine logs, diffs and object information  
+
+`git log`: to see the log of all commits (for the currently active branch). Can be used with `-n #` where `#` is the number of commits in the past to show. `--abbrev-commits` will provide the abbreviated SHA for the commits.  
+
+`git log branchA..branchB`: show the commits on branchA that are not on branchB.
+
+`git log --follow [file]`: show the commits that changed the specified file, even across renames
+
+`git diff`: to show the difference between changes in your working directory and staged area.
+
+`git diff --staged`: to show differences between staging area in all local files and the repository. If you add a filename, you will only see the staged changes in a certain file. Alternative: `git diff --cached`
+
+`git diff <commit1> <commit2>`: to show differences between commits. Where <commit1> and <commit2> are the SHA of the commits to be compared. First will be compared to second.  
+
+`git diff <branch1> <branch2>`: show differences between two branches. 
+
+`git show [SHA]`: show any object in Git in human-readable format.
+
+## Tracking path changes
+Commands to version file removes and path changes
+
+`git rm [file]`: delete the file from project and stage the removal of the commit
+
+`git mv [existing-path] [new-path]`: change an existing file path and stage the move
+
+`git log --stat -M`: show all commit logs with indication of any paths that were moved.
+
+## Redo commits
+Commands to erase mistakes and craft replacement history
+
+`git revert [commit SHA]`: create a new commit, reverting changes from the specified commit. It generates an inversion of changes (safest option)
+
+------ more dangerous option:
+
+`git reset [commit]`: Undoes all commits after [commit], preserving changes locally. It switches the current branch to the target commit, leaving a difference as an uncommited change. 
+
+`git reset --hard [commit]`: Discards all history and changes back to the specified command. 
+
+**CAUTION**: changing history can have nasty side effects. If you need to change commits that exist on GitHub, proceed with caution. 
+
+
+## Share and update
+Commands to retrieve updates from another repository and updating local repository
+
+`git remove add [alias] [url]`: add a git URL as an alias
+
+`git fetch [alias]`: fetch down all the branches from that Git remote. It downloads all history from the remote tracking branches.
+
+`git merge [alias]/[branch]`: merge a remote branch into your current local branch to bring it up to date.
+
+`git push [alias] [branch]`: transmit local branch commits to the remote repository branch. 
+
+`git pull`: Updates your current local working branch with all new commits from the corresponding remote branch on GitHub. It is a combination of git fetch and git merge.  
+
+## Tagging commits
+
+`git tag`: list all tags
+
+`git tag [name] [commit SHA]`: create a tag reference named 'name' for current commit. Add commit SHA to tag a specific commit instead of current one.
+
+`git tag -d [name]`: remove a tag from local repository.  

git_and_github_concepts/git_concepts.md

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+# GIT AND GITHUB CONCEPTS
+
+## What is Git and Github?
+**Git:** 
+Git is a software to create a timeline of your projects. It keeps track of all changes you make during your project development and allows you to go back to each version at any point in time. You can save changes, and once you commit them to a version that is a snapshot in time.
+
+**GitHub:**
+Online repository to collect different git projects. GitHub can be used as an online backup of all your timelines that were created in git. As a web-based platform, GitHub offers several features that extend beyond the basic functionalities of git. These include:  
+- Repository Hosting: GitHub hosts Git repositories online, making them accessible from anywhere. 
+- Pull Requests: This feature allows developers to propose changes to a codebase, review code, and discuss modifications before merging.  
+- Issues and Bug Tracking: GitHub provides a built-in issue tracker to manage bugs, feature requests, and other tasks. 
+- Project Management Tools: GitHub offers project boards, milestones, and other tools to help manage and organize development tasks. 
+- Code Reviews: GitHub facilitates code reviews with inline comments and discussions on pull requests.  
+- Actions and CI/CD: GitHub Actions allows you to automate workflows, including continuous integration and continuous deployment (CI/CD). 
+
+## How to start your timeline/repository?
+**Start a local repository:**  
+When you are in your local project folder, you can start the timeline by initializing git, this will create a .git file. Git tracks every subfolder in your root folder, so no need to initialize it twice.  
+`git init`
+
+**Start from a remote repository:**  
+1. On github, you can go to a remote repository, and clone it to your local machine. No need to initialize the timeline again.  
+`git clone ssh-address-repository`
+
+2. You can also first 'fork' to create a personal copy of a repository on GitHub. It allows you to freely experiment with changes without affecting the original repository.
+
+## Where is Git/GitHub? Three conceptual areas:
+**1. Developing area**  
+My computer: developing area with local folder where project is developed. 
+
+**2. Preparation: staging area?**  
+If we do `git add`, we send it to the staging area, which is the place where you add files to prepare for commit. Location to prepare new snapshots to the timeline (before commit). 
+
+**3. Local repository: where is the timeline?**  
+The local repository on your computer is where all the versions live. It is the .git folder you have initialized. Typically only text files. 
+
+**4. Remote area (GitHub):**  
+It is the remote repository. In the context of this course, we use GitHub. You first need to make a repository in GitHub, then you can use the ssh address of the repository to make a bridge on your computer to the remote repository. After that, you can push your local repository to the remote one. Make sure to always clean up your working tree first (check with `git status`).
+
+GIT WORKFLOW:
+1. adjust your files and save (developing area)
+
+2. once you are ready, you should do:  
+`git add file_A`: records the changes made to file_A and adds it to the staging area  
+`git add *`: records the changes made to all files and adds it to the staging area  
+
+3. commit changes:  
+`git commit -m "message"`: you send from staging area to local commit, linked to a meaningful message.  
+
+4. push changes to remote repository:  
+`git push`: send commit to remote area  
+
+5. retrieve remote changes locally:  
+`git pull`: get updates
+
+## Collaborations:
+**Adding collaborators:** You can grant other GitHub users access to your repository as collaborators, allowing them to push changes.
+
+**Fetching changes:** Fetching changes from a remote repository downloads changes but does not apply them to your local branch.
+
+**Pulling changes:** Pulling changes from a remote repository downloads and merges them to your local branch.
+
+**Conflicts:** If you are working with someone simultaneously and somebody pushes it before you, this will create a conflict, because Git cannot automatically merge changes. When you try to push your modifications, you will get an error. You need to manually resolve conflicts by editing the conflicting files. For this, you first need to pull the latest version (containing the commit of your collaborator), then you can modify the file and look at the conflict closely and resolve. After that, you need to git add, commit and push it again. 
+
+**Pull requests:** A pull request is a way to propose changes to a repository and facilitate collaborations. While a request for a pull exists as a git concept, the formalized pull request is a feature of web-based git hosting services like GitHub. You create a pull request when you want to merge changes from one branch into another, and you need someone to review and approve them before merging.  
+    1. Push your changes to GitHub  
+    2. Open GitHub and navigate to your repository  
+    3. Click the "Pull Requests" tab and create a new pull request, selecting your feature branch and the main branch  
+    4. Once reviewed, the pull request can be merged.  
+
+GitHub provides extensive documentation on pull requests in their [GitHub Docs platform](https://docs.github.com/en/pull-requests).  
+
+## Tag a commit
+Git allows to create tags to mark specific points in the timeline of your repository. Tags can be used to specify specific versions of the code in a project. They can also be used to denote significant milestones in the development process.  
+You can use `git tag <tag_name>` to add a tag to a commit in your timeline.  
+It is important to note that tags must be included in the push command. When you push, you need to add `<tag_name>`to push a specific tag or `--tags` to push all tags. 
+To remove a tag, use `git tag -d <tag_name>` to delete a specific tag, but you also need to delete it manually on github.  
+
+**A note on releases:** Releases are a GitHub feature. They work on top of the tags feature and provide a way of packaging and distributing specific versions of the project. In addition to including release notes, releases can also have downloadable assets, like software source code.  
+
+## Branches
+A branch is an independent timeline that roots from the main timeline. You can use it to work independently on same project, to experiment without risk, etc.
+`git branch <name>`: initiate a new branch
+
+To move between branches you need to do git checkout.  
+`git checkout <branch_name>`: switches between branches.
+
+Once you’ve completed work on a branch, you can merge it back into the main branch:  
+- first switch to the main branch: `git checkout main`  
+- merge your branch with main: `git merge <your_branch>`  
+
+Once merged, you can delete the branch:  
+`git branch -d <your_branch>`
+
+**A note on direct merging and pull requests**
+While you can directly merge a branch into your main branch, the commands described above do not include a review process. In collaborative projects that are hosted in web-platforms such as GitHub, the use of a pull request to bring code changes from a branch into the main branch of a project is advisable. Pull requests allow for collaborators to review and comment on changes, giving chance for useful feedback and code improvements.   
+
+## What is a .gitignore file?
+In many cases, the project creates a lot of logs and other irrelevant files which are to be ignored. So to ignore those files, we have to put their names in“.gitignore” file.  
+The .gitignore file specifies files and directories that should be ignored by Git. It is used to prevent certain files from being tracked or committed.
+
+## GitHub history and keeping track of commits
+You can create an overview of what commits have been done in the entire history of your project. It shows you the commit hashes (IDs), the author and date of the commit, and the message that was assigned to it. It is great for reviewing past changes or finding a specific commit.
+`git log`: display commit history
+
+You can keep track of what is going on in your working directory and staging area using git status.
+`git status`: it shows you which files have been modified, which files are staged and which are untracked (new and not in git yet)
+
+To compare different commits or files you can use git diff.
+1. `git diff`: see unstaged changes (working directory vs last commit)
+2. `git diff --cached` or `git diff --staged`: see staged changes (staging area vs last commit)
+3. `git diff <commit1> <commit2>`: compare two commits 

references.md

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+# This file gives an overview of the references used in this project.
+
+## Git and Github concepts and cheat sheet:
+- Training material: [VIB training_material](https://github.com/vibbits/introduction-github)
+- [Medium git and github guide](https://medium.com/@ramadan123sayed/a-comprehensive-guide-to-git-and-github-from-beginner-to-advanced-with-practical-use-cases-8e1ad98b48db)
+- [Git lab Cheat Sheet](https://about.gitlab.com/images/press/git-cheat-sheet.pdf)
+- [GitHub documentation portal](https://docs.github.com/en)
+- [Git cheat sheet from GitHub Education](https://education.github.com/git-cheat-sheet-education.pdf)
+- [GitHub Education](https://github.com/education)
+
+## Images:
+- [git and github logo](https://pngimg.com/d/github_PNG65.png)
+- [git diff schematic](https://lafkblogs.wordpress.com/2015/12/08/why-git-diff-shows-nothing/)
+
+## Markdown
+- [Markdown cheat sheet](https://www.markdownguide.org/cheat-sheet/)