Merge pull request #59 from kir-rescomp/dev

fix typo on mkdir as directory name was wrong

Author: DininduSenanayake

docs/4.git_model_commands.md

@@ -22,7 +22,7 @@ They begin their project as they would a new experiment — setting up a clean w
 !!! terminal ""
 
     ```bash
-    mkdir CellCulsterFlow
+    mkdir CellClusterFlow
     cd CellClusterFlow
     ```
 
@@ -58,13 +58,14 @@ The `git init` command created a hidden `.git` directory — the heart of your r
     .git/
     ├── HEAD              # Points to current branch
     ├── config            # Repository settings
-    ├── description       # Repository description
+    ├── description       # Repository description (rarely used)
+    ├── branches/         # (deprecated, legacy Git)
     ├── hooks/            # Scripts triggered by Git events
+    ├── info/             # Additional repository information (excludes, attributes)
     ├── objects/          # Database of all file versions (commits, trees, blobs)
-    ├── refs/             # Pointers to commits (branches, tags)
-    │   ├── heads/        # Local branches
-    │   └── tags/         # Version tags
-    └── index             # Staging area (will be created on first 'git add')
+    └── refs/             # Pointers to commits (branches, tags)
+        ├── heads/        # Local branches
+        └── tags/         # Version tags
     ```
 
 !!! warning "Never delete `.git`!"
@@ -132,9 +133,27 @@ Just like checking which samples are unprocessed, they inspects their project’
     ```bash
     git status
     ```
+    
+    ??? success "Output"
+
+        ```bash
+        On branch main
+
+        No commits yet
 
+        Untracked files:
+          (use "git add <file>..." to include in what will be committed)
+        	LICENSE
+        	README.md
+        	clustering.R
+        	data_preprocessing.py
+        	qc_filtering.py
+        	visualization.ipynb
+
+        nothing added to commit but untracked files present (use "git add" to track)
+        ```
 Git reports untracked files — nothing is committed yet.
-This command becomes a habit; they run it before almost every operation.
+This command should become a habit; they run it before almost every operation.
 
 ```mermaid
 flowchart LR
@@ -165,27 +184,41 @@ Only staged files will be committed.
 
 They  capture their first snapshot.
 
-```bash
-git commit -m "Initial commit: basic pipeline structure"
-```
+!!! terminal ""
+    ```bash
+    git commit -m "Initial commit: basic pipeline structure"
+    ```
 
-This is their first “frozen sample” — They can always revert to it later.
+    ??? success "Output"
 
-<center>
-```mermaid
-%%{init: {'theme':'base'}}%%
-gitGraph
-  commit id: "Initial commit"
-```
-</center>
+        ```bash
+        [main (root-commit) 40eb049] Initial commit: basic pipeline structure
+         6 files changed, 0 insertions(+), 0 deletions(-)
+         create mode 100644 LICENSE
+         create mode 100644 README.md
+         create mode 100644 clustering.R
+         create mode 100644 data_preprocessing.py
+         create mode 100644 qc_filtering.py
+         create mode 100644 visualization.ipynb
+        ```
+
+    This is their first “frozen sample” — They can always revert to it later.
+
+    <center>
+    ```mermaid
+    %%{init: {'theme':'base'}}%%
+    gitGraph
+      commit id: "Initial commit"
+    ```
+    </center>
 
 ### 5. `git branch` — Designing new experiments
 
 To test a new normalization method, they create a new branch — a safe environment to experiment without contaminating their main results.
 
 ```bash
-git branch normalization
-git checkout normalization
+git branch normalisation
+git checkout normalisation
 ```
 
 Branches in Git are like running parallel experiments in separate tubes.
@@ -244,50 +277,7 @@ gitGraph
 ```
 </center>
 
-### 8. `git fetch` — Getting updates from collaborators
-
-Their collaborator Dr. Y pushes changes to **qc_filtering.py** on the shared repository.
-Before pulling them in, they fetches to see what’s changed.
-
-```bash
-git fetch origin
-```
-
-
-Fetching updates to their remote tracking branches (like checking a shared Google Sheet without overwriting your own copy).
-
-<center>
-```mermaid
-%%{init: {'theme': 'base'}}%%
-gitGraph
-  commit id: "A"
-  commit id: "B" tag: "origin/main"
-```
-</center>
-
-### 9. `git pull` — Syncing the latest version
-
-Now they merge Dr.Y's updates into their local repository.
 
-```bash
-git pull origin main
-```
-
-This performs a `fetch` + `merge`.
-Their local branch is now aligned with the shared main.
-
-<center>
-```mermaid
-%%{init: {'theme': 'base'}}%%
-gitGraph
-  commit id: "A"
-  commit id: "B"
-  branch feature
-  commit id: "C"
-  checkout main
-  merge feature
-```
-</center>
 
 ### 10. `git checkout` — Switching branches
 

docs/5.from_git_to_github.md

@@ -336,4 +336,54 @@ Now that Dr. X's pipeline is on GitHub:
 ---
 
 !!! quote "Remember"
-    "Science is not a solo sport. Git tracks your journey; GitHub shares it with the world." 🚀
+    "Science is not a solo sport. Git tracks your journey; GitHub shares it with the world." 🚀
+
+
+
+
+## Draft material
+
+### 8. `git fetch` — Getting updates from collaborators
+
+Their collaborator Dr. Y pushes changes to **qc_filtering.py** on the shared repository.
+Before pulling them in, they fetches to see what’s changed.
+
+```bash
+git fetch origin
+```
+
+
+Fetching updates to their remote tracking branches (like checking a shared Google Sheet without overwriting your own copy).
+
+<center>
+```mermaid
+%%{init: {'theme': 'base'}}%%
+gitGraph
+  commit id: "A"
+  commit id: "B" tag: "origin/main"
+```
+</center>
+
+### 9. `git pull` — Syncing the latest version
+
+Now they merge Dr.Y's updates into their local repository.
+
+```bash
+git pull origin main
+```
+
+This performs a `fetch` + `merge`.
+Their local branch is now aligned with the shared main.
+
+<center>
+```mermaid
+%%{init: {'theme': 'base'}}%%
+gitGraph
+  commit id: "A"
+  commit id: "B"
+  branch feature
+  commit id: "C"
+  checkout main
+  merge feature
+```
+</center>