From 3ce94dc9c86b3347d9ca70f1b95769b500d41479 Mon Sep 17 00:00:00 2001
From: Marvin Albert <marvin.albert@gmail.com>
Date: Wed, 28 Jun 2023 22:11:31 +0200
Subject: [PATCH] WIP

---
 book/setup_environment.md | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/book/setup_environment.md b/book/setup_environment.md
index fda6b32..d554a07 100644
--- a/book/setup_environment.md
+++ b/book/setup_environment.md
@@ -54,31 +54,33 @@ The following assumes that you have installed python using Mambaforge as [descri
 	- **Linux**: Open your terminal application
 
 
-2. We use an environment to encapsulate the python tools used for this workshop. This ensures that the requirements for this workshop do not interfere with your other python projects. To create the environment (named `pyimagecourse`), enter the following command.
+2. Navigate to the `notebooks` subdirectory of the `bioimage_analysis_with_python_course` directory you downloaded.
 
 	```bash
-	mamba create -n pyimagecourse python=3.10
+	cd <path to bioimage_analysis_with_python_course>/notebooks
 	```
 
-3. Once the environment setup has finished, activate the environment. If you successfully activated the environment, you should now see `(pyimagecourse)` to the left of your command prompt.
+
+3. The file `environment.yml` contains the dependencies needed to run the notebooks, and it specifies a `conda` environment named `pyimagecourse`. Create this environment from the file by entering the following command.
 
 	```bash
-	mamba activate pyimagecourse
+	mamba create --file environment.yml
 	```
 
-4. Install the dependencies with the commands below
+4. Once the environment setup has finished, activate the environment. If you successfully activated the environment, you should now see `(pyimagecourse)` to the left of your command prompt.
 
 	```bash
-	mamba env update -n pyimagecourse --file environment.yml
+	mamba activate pyimagecourse
 	```
 
-6. Test that your notebook installation is working. We will be using notebook for interactive analysis. Enter the command below and it should launch jupyter notebook book in a web browser.
+
+5. Test that your notebook installation is working. We will be using notebook for interactive analysis. Enter the command below and it should launch jupyter notebook book in a web browser.
 
 	```bash
 	jupyter notebook
 	```
 
-7. Test your napari installation. Enter the command below and an empty napari viewer should open. You can close the window after it opens. Please note that it takes a bit of extra time to launch napari the first time.
+6. Test your napari installation. Enter the command below and an empty napari viewer should open. You can close the window after it opens. Please note that it takes a bit of extra time to launch napari the first time.
 	
 	```bash
 	napari
-- 
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