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incf-nidash / nidmresults-fsl

A python library to export FSL's feat results to NIDM-Results
http://nidm.nidash.org/specs/nidm-results.html
MIT License
3 stars 11 forks source link

Compatibility with nidmresults 2.0.0 #123

Open cmaumet opened 6 years ago

cmaumet commented 6 years ago

A major update of the nidmresults library will soon be available, providing reading capability for NIDM-Results packs (cf. https://github.com/incf-nidash/nidmresults/pull/42).

We will have to update the FSL exporter to be compatible with this upcoming version. (The updated code will form a new release of nidmfsl.)

@TomMaullin: as discussed with @nicholst last week are you still up to give this a go?

If that's the case:

Thanks in advance!

cmaumet commented 6 years ago

@TomMaullin: I would recommend installing anaconda and setting up a specific environment for those developments. I can't remember if you have already done this in the past? If not, let me know and I can send you a few pointers.

Once the dev environment is set up, the command to install nidmresults 2.0.0-rc1 is:

pip install git+git://github.com/cmaumet/nidmresults.git@aa89327e5a2cc82959746b1c99baa9a23277779b
TomMaullin commented 6 years ago

Hi @cmaumet , Ah yes! This was next on my to do list! I've not set up an anaconda environment before so pointers would be much appreciated - once I have set up the environment I will make the WIP branch straight away!

cmaumet commented 6 years ago

Excellent! I have just finished 2.0.0-rc1. Note that this first prerelease does not yet include full JSON API support yet (only reading of NIDM-Results packs) but it is worth checking compatibility at this point.

To get started with conda environments, I really like this page: https://conda.io/docs/user-guide/tasks/manage-python.html#installing-a-different-version-of-python. The page explains how to manage multiple versions of python using conda environements. As a starting point, you will only need python 3 but the logic is the same.

Here are the commands you could use to create a new environement for those nidmfsl developments:

# Create the nidmfsl environment (with Python 3)
conda create -n nidmfsl python=3
# Activate the nidmfsl environment
source activate nidmfsl
# Install nidmresults 2.0.0-rc1 
pip install git+git://github.com/cmaumet/nidmresults.git@aa89327e5a2cc82959746b1c99baa9a23277779b
# All set!

pip works well with conda so when you use pip it only install the packages for the conda environement you are in (therefore above, nidmresults 2.0.0-rc1 will only be available in the nidmfsl environement).

Next time you want to go back to the nidmfsl environment (e.g. after restarting your machine). You will only need to reactivate it:

source activate nidmfsl

Let me know how this goes!

TomMaullin commented 6 years ago

I see! Ah okay thank you! I think I now have this working and should hopefully have a WIP PR by lunchtime!