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CBICA / niCHART

The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
https://cbica.github.io/niCHART/
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Instructions for creating a conda enviroment with python3.8.8 #181

Closed melhemr closed 2 years ago

melhemr commented 2 years ago

PR will add instructions for creating a conda environment to ensure python version is 3.8.8

melhemr commented 2 years ago

@AbdulkadirA

The only line I wasn't entirely sure how to deal with this line since I am using a mac:

Prepare environment for PowerShell (Windows 10 or 11)

Assuming conda enviroment with Python version 3.8.8 has been created

**& env/Scripts/Activate.ps1**
python -m pip install --upgrade pip
poetry install

In these instructions, I've outlined it so the users create a conda enviroment, so I'm not sure where or how the & env/Scripts/Activate.ps1 should be implemented for Windows users. Can you let me know?

ashishsingh18 commented 2 years ago

@melhemr In my conda env, I usually just do: python -m pip install -U -e . poetry install

ashishsingh18 commented 2 years ago

It might be clearer if we create 2 separate sections for installation: one using conda and the other using virtual env.

melhemr commented 2 years ago

@melhemr Thanks. Please leave the sections on setting up the PIP venv for Windows and Linux as they were and only add a section for conda. You could add the indication of PIP to the exiting section headers, though.

Can you clarify what you mean? I did leave the PIP section alone, and added conda sections as we discussed. Windows for example:

### Prepare environment for PowerShell (Windows 10 or 11)
Assuming current working directory is `NiBAx` and containing the source code
cloned from https://github.com/CBICA/NiBAx.git.

Virtual environment
```shell
python -m venv .env
& .env/Scripts/Activate.ps1
python -m pip install --upgrade pip
poetry install
Conda environment (assuming conda environment with Python version 3.8.8 or newer has been created)
```shell
conda activate NiBAx
python -m pip install --upgrade pip
poetry install
melhemr commented 2 years ago

@AbdulkadirA the changes look good. The only final concern I had is about Ashish's comment above. It seems that using a conda environment with a Windows OS still requires using the command poetry install. I don't know if that's 100% necessary, but if it is, how should we include that in the conda environment section?