halvarsu/cinpla-base

Installation

Install GIT Windows

Install Github Desktop, if you do not like to use the terminal so much.

Setup

Install Atom

Start by cloning this repository, this can either be done with Github Desktop or with a terminal. When we say terminal, in Windows we mean Anaconda prompt. However, all code that starts with git can be done with Github Desktop.

With the terminal run

git clone https://github.com/CINPLA/cinpla-base.git

Anaconda

Windows: Search for anaconda and open Anaconda prompt Mac: open a terminal

Installing python and pyqt

In order to use phy (a spikesorter) we have to

conda install python=3.5 pyqt=4

Installing expipe for CINPLA

Navigate to where you have cloned cinpla-base, then install the cinpla-base requirements

cd cinpla-base
pip install -r requirements.txt

Getting started

Register a Gitea account

Contact Mikkel, Alessio or Svenn-Arne
Navigate to Gitea and expipe on NIRD

Create an expipe repository

Initialize with .gitignore, licence and README

Clone repository

from notebook (see example below)
with git desktop

git clone https://gitea.expipe.sigma2.no/user_name/my_project_name.git

Open jupyter notebook inside repository

Navigate to my_project_name and write in the terminal

jupyter notebook

In stead of using the terminal from now on, commands can be run from within the notebook if it is begun with an exclamation mark. That is, if you would write expipe init in the terminal, you would write in the notebook

expipe init

This command adds actions, entities and templates folders together with an expipe.yaml, this is necesarry so that my_project_name will be recognized as a expipe project.

Next, we need to add some information to git LFS which is helping us handling large files (LFS stands for Large File Storage)

expipe init-lfs

This command adds two files, .gitattributes and .lfsconfig, the latter is not so interesting but the former deserves some explanation. Inside it says

actions/*/data/**/* filter=lfs diff=lfs merge=lfs -text
*.yaml !filter !diff !merge

The first line says that all the contents in all data directories whithin every action should be handeled by git LFS. The second line says that even though all the data directories should be handeled by LFS, all files ending with .yaml should not be handeled by LFS.

In short, these lines ensures that all file except .yaml files will be downloaded as LFS files when the repository is cloned or pulled if nothing else is specified. This means that all files in data except .yaml files will be text files pointing to the real data files on NIRD.

git add -A
git commit -am "init expipe and LFS"

Add templates

Navigate to cinpla-base/src/expipe-templates-cinpla/templates, where you'll find a bunch of example templates, copy some you want to use or write your own. If you want to write your own template the filename must on the form filename.yaml and at a minimum contain

name: filename
identifier: filename

It is probably wise to commit after you add the templates.

git add -A
git commit -am "added some templates"

Working with expipe

Now you are ready to start using expipe

Open cinpla browser

from expipe_plugin_cinpla.widgets import browser
browser.display('workshop')

Open expipe browser

import expipe
expipe.Browser('workshop').display()

halvarsu / cinpla-base