Changed the order of the guide and polished it

Author: Schronding

LINUX_SETUP.md

@@ -1,14 +1,51 @@
 # Developer setup (Linux)
 
-To get setup for development, see [this video if you prefer VS Code](https://youtu.be/zddl3n1DCFM), or [this older video if you prefer PyCharm](https://youtu.be/QniQi-Hoo9A), and the instructions below.
+## 1. Install Git
+
+Choose the command for your Linux distribution:
+
+**Ubuntu, Debian, and Mint:**
+
+```bash
+sudo apt update
+sudo apt install -y git
+```
+
+**Fedora:**
+
+```bash
+sudo dnf install -y git
+```
+
+**Arch Linux:**
 
-## 1. Fork and clone this repo
 ```bash
-git clone git@github.com:[username]/malariagen-data-python.git
+sudo pacman -S sudo
+sudo pacman -S git
+sudo pacman -S openssh
+```
+
+If your Arch install does not have `sudo` configured yet, run the commands above as `root`, then configure `sudo` for your user.
+
+## 2. Fork and clone this repo
+
+After forking the repository on GitHub, clone your fork.
+
+Use SSH if your SSH keys are set up:
+
+```bash
+git clone git@github.com:[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
 cd malariagen-data-python
 ```
 
-## 2. Install pipx
+Use HTTPS if you prefer, or if you do not have SSH keys configured (common on WSL):
+
+```bash
+git clone https://github.com/[YOUR_GITHUB_USERNAME]/malariagen-data-python.git
+cd malariagen-data-python
+```
+
+## 3. Install pipx
 
 Choose the command for your Linux distribution:
 
@@ -23,7 +60,7 @@ pipx ensurepath
 **Fedora:**
 
 ```bash
-sudo dnf install pipx
+sudo dnf install -y pipx
 pipx ensurepath
 ```
 
@@ -34,9 +71,14 @@ sudo pacman -S python-pipx
 pipx ensurepath
 ```
 
-*(Note: You may need to open a new terminal or run `source ~/.profile` to apply PATH changes after this step).*
+Close and reopen your terminal to apply PATH changes.
+If you prefer to reload the shell in-place, run:
+
+```bash
+exec bash
+```
 
-## 3. Install Poetry and Python 3.12
+## 4. Install Poetry and Python 3.12
 
 The package requires `>=3.10,<3.13`. We use Poetry's built-in installer to handle the Python version universally across all distributions.
 
@@ -45,15 +87,14 @@ pipx install poetry
 poetry python install 3.12
 ```
 
-## 4. Create and activate development environment
+## 5. Create development environment
 
 ```bash
 poetry env use 3.12
 poetry install --extras dev
-poetry shell
 ```
 
-## 5. Install pre-commit hooks
+## 6. Install pre-commit hooks
 
 ```bash
 pipx install pre-commit
@@ -66,15 +107,15 @@ Run pre-commit checks manually:
 pre-commit run --all-files
 ```
 
-## 6. Run tests
+## 7. Run tests
 
 Run fast unit tests using simulated data:
 
 ```bash
 poetry run pytest -v tests/anoph
 ```
 
-## 7. Google Cloud authentication (for legacy tests)
+## 8. Google Cloud authentication (for legacy tests)
 
 To run legacy tests which read data from GCS, you'll need to [request access to MalariaGEN data on GCS](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html).