npyx 1.0

Python routines dealing with Neuropixels data.

routines

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Formal Definition of a "routine" -> a python function with the following properties:

• short memorable name
• computes a commonly used Variable from a raw dataset directory.
• when called, looks for the Variable in dir/routinesMemory where dir is the directory of the dataset. If not found, the routine saves the variable after having computed it.

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Python version has to be >=3.7 ot there will be imports issues!

Useful link to create a python package from a git repository

Installation:

Using a conda environment is very much advised. Instructions here: manage conda environments

• from a local repository (recommended if plans to work on it/regularly pull upgrades)

$ conda activate env_name
$ cd path/to/save_dir # any directory where your code will be accessible by your editor and safe. NOT downloads folder.
$ git clone https://github.com/Npix-routines/NeuroPyxels
$ cd NeuroPyxels
$ python setup.py develop # this will create an egg link to save_dir, which means that you do not need to reinstall the package each time you pull an udpate from github.

• from the remote repository (recommended for easy passive install)

$ conda activate env_name
$ pip install git+https://github.com/Npix-routines/NeuroPyxels@master

• Now test that the installation works. If it doesn't, figure out which packages are missing from the error log.

$ conda activate env_name
$ python
>>> import npix # NO ERROR OMG THIS PACKAGE IS SO AWESOME

Pull remote updates (after Maxime's updates :)):

$ conda activate env_name
$ cd path/to/save_dir/NeuroPyxels
$ git pull
# And that's it, thanks to the egg link no need to reinstall the package!

Push local updates:

# DO NOT DO THAT WITHOUT CHECKING WITH MAXIME FIRST
# ONLY ON DEDICATED BRANCH CREATED WITH THE GITHUB BROWSER INTERFACE

$ cd path/to/save_dir/NeuroPyxels
$ git checkout DEDICATED_BRANCH_NAME # ++++++ IMPORTANT
$ git add.
$ git commit -m "commit details - try to be specific"
$ git push origin DEDICATED_BRANCH_NAME # ++++++ IMPORTANT

# Then pull request to master branch using the online github green button! Do not forget this last step, to allow the others repo to sync.