From a79f7c9cde75b46a0410684198f253ed840a94a0 Mon Sep 17 00:00:00 2001
From: Javier Garcia-Bernardo <j.garciabernardo@uu.nl>
Date: Tue, 11 Jun 2024 13:54:18 +0200
Subject: [PATCH] Update README.md with new instructirons

---
 README.md | 43 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 34 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 71ddb39..fb23546 100644
--- a/README.md
+++ b/README.md
@@ -6,17 +6,42 @@ There are a few packages that are installed by default (e.g., pandas, pyreadstat
 
 If you need specific versions, you need to email CBS a environment.yml file with your requirements. This repository has a standard environment.yml with most of the tools researchers use. Before sending it, open "environment.yml" and change the number (0000 in the example) for your project number.
 
-You can also create your own environment file locally, where 0000 is your project number:
-```sh
-conda create -n 0000 -c conda-forge python=3
-conda activate 0000
-conda install jupyter notebook scikit-learn pandas matplotlib seaborn jupyterlab notebook plotly IPython pyreadstat openpyxl dask vaex modin polars pyarrow numpy scipy statsmodels pymc3 eli5 SHAP LIME networkx igraph tensorflow keras pytorch pytorch_geometric 
-conda env export --from-history > ~/environment.yml
-```
 
-If you require specific versions, you can check `conda env export` and add the versions to the `environment.yml` file.
+To create the YML file, you need to create your own environment outside the RA environment, in Python on Windows, using Mambaforge installed in C:\mambaforge. Follow the steps below to generate a text file and send it to us via email as a reply. With the text file, we can make the environment available for you within RA.
+
+
+    On your own Windows system in Python, create a new environment named after the project code and activate it. As an example, we use project code 0000.
+
+a.       `conda create –n 0000`
+
+b.       `conda activate 0000`
+
+    Install pip.
+        `conda install pip`
+
+    Then, install the required packages with pip.
+        `pip install package_name`
+
+    Export the environment with pip.
+        `pip freeze > C:\temp\environment0000.txt`
+        Check that the file does not contain references to local paths (file://).
+        If it does, use the following command:
+        pip list --format=freeze > C:\temp\environment0000.txt
+
+    Test the environment by removing and recreating it.
+        `rd /q /s <path to python>\envs\0000`
+        `conda create –n 0000`
+        `conda activate 0000`
+        `conda install pip`
+        `pip install –r C:\temp\environment0000.txt`
+        Test the Python environment.
+
+    Send the environment text file to us via email.
+
+ 
+
+Note! If you want to use Jupyter Notebook or Spyder, you need to install them in the environment as well.
 
-Once CBS has installed it, you may see a new icon with the right version of Python. If this is not the case, you need to activate the Python environment manually. You can open a `Python Prompt`, and run the following code, where 0000 is your project number:
 
 ```sh
 conda activate 0000.