Adam2392's Blog

Week 2 - Check In

Adam2392
Published: 06/21/2021

I've successfully coordinate with one of my MNE mentors in getting the CI setup correctly, such that docs are being deployed, unit tests are occurring and build tests are occurring during every commit to a new PR. The next step is figuring out how to make a release properly by having the CI build the docs and deploy them for a release when wanted. In terms of coding, I have been discussing and perusing the existing mne.connectivity code base to understand what sort of "Connectivity" data structure containers I want to implement to provide to the user. We have decided on a few and I will be implementing their functionality and tests this week!
View Blog Post

Week 2 – Blog Post

Adam2392
Published: 06/14/2021

What Have I Been Working On: This week, I’ve been primarily working on refactoring existing MNE-Python code in their connectivity submodule into the new “mne-connectivity” repository. In order to simplify the code changes, I have kept everything in terms of the API and examples the same name without changing any real code functionality. Instead, this week is dedicated to setting up the repository successfully. Thus, I have been working on setting up the documentation via sphinx, and setting up the continuous integration (CI) and unit tests. What Have I Been Struggling With: For the CI, I have ported over the code from an existing MNE repository, “mne-realtime”. This has multiple CI pipelines, such as Azure, Github Actions and CircleCI. However, getting the CI to properly work is a bit tedious since each pipeline run requires a Github push. Thus, a major time investment is on perusing over CI code line-by-line to either i) get rid of any unnecessary procedures that only mne-realtime needed, or ii) adjust the pipeline to be mne-connectivity specific. What Solutions Have I Found: I have also been looking at other MNE repositories, such as “mne-bids”, which has a very simple CI and documentation setup. Thus, to directly port the CI and documentation code into “mne-connectivity” is a bit easier. I have been using bits and pieces of code from “mne-bids” in order to i) get the unit tests working locally, ii) simplify the documentation setup via sphinx and then iii) simplifying the CI workflows.
View Blog Post

Initial Week - Getting Started

Adam2392
Published: 06/10/2021

I've been talking with my MNE mentors and reviewing some of the existing connectivity code for neural data. I have begun refactoring existing code from the "mne.connectivity" submodule into a new repository "mne-connectivity" housed under the mne-tools organization. Next week, I plan on finalizing this push with a working CI pipeline that confirms equivalent functionality to the original mne-python code. Things are progressing as expected so far!
View Blog Post