update install instructions to prefer building cupy (#108)

* switch install preference due to significant speed-up building can offer

* update text

* Update README.md

Co-authored-by: Sander Roet <[email protected]>

---------

Co-authored-by: Sander Roet <[email protected]>

README.md

@@ -12,35 +12,40 @@ nvidia-cuda-toolkit
 
 ## Installation
 
-There are 2 options for creating a conda environment:
+There are 2 options for creating a conda environment. We recommend option (1) which will later allow cupy to build 
+against a system installed cuda-toolkit. Compared to option (2) this can give an almost two-fold speedup:
 
-1. **(recommended)** Create a new environment with a prebuild cupy version and complete CUDA-toolkit. This is reliable but takes more disk space.
+1. **(recommended)** Create a new python 3 environment:
 
     ```commandline
-    conda create -n pytom_tm -c conda-forge python=3 cupy cuda-version=11.8
+    conda create -n pytom_tm python=3
     ```
 
-2. Create a new environment without cupy and let pip build against a system installed CUDA-toolkit.
+2.  Create a new environment with a prebuild cupy version and complete CUDA-toolkit. This is more reliable, but takes more 
+    disk space and has less optimal performance.
 
     ```commandline
-    conda create -n pytom_tm python=3
+    conda create -n pytom_tm -c conda-forge python=3 cupy cuda-version=11.8
     ```
 
+
 Once the environment is created, activate it:
 
 ```commandline
 conda activate pytom_tm
 ```
 
-Then clone the repository and install it with pip: 
+Then clone the repository and install it with pip (building cupy can take a while!): 
 
 ```commandline
 git clone https://github.com/SBC-Utrecht/pytom-template-matching-gpu.git
 cd pytom-template-matching-gpu
 python -m pip install '.[plotting]'
 ```
 
-The installation above also adds the optional dependencies `[matplotlib, seaborn]` which are required to run `pytom_estimate_roc.py`. They are not essential to the core template matching fucntionality, so for some systems (such as certain cluster environments) it might be desirable to skip them. In that case remove `[plotting]` from the pip install command:
+The installation above also adds the optional dependencies `[matplotlib, seaborn]` which are required to run 
+`pytom_estimate_roc.py`. They are not essential to the core template matching functionality, so for some systems 
+(such as certain cluster environments) it might be desirable to skip them. In that case remove `[plotting]` from the pip install command:
 
 ```commandline
 python -m pip install .