Neurostuff Development Environment
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This post is a chronicle of how I’m setting up a development environment for neurostuff using VSCode (version 1.48.2 as of this writing).
Blog posts
2020
2019
Development Environment with VS Code
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Often times you have to choose between installing the complex web of dependencies to debug fmriprep from a graphical text editor and using a container where you can only debug from a terminal. VS Code has several extensions that make it easier to develop fmriprep and have the best of both worlds. The VS Code Docker and Remote Development extensions will give you a great experience running tests and debugging fmriprep on your laptop or work machine.
Rules for problem solving and understanding code
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- Create a minimal dataset to test the code
Python User Learning R
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Just as I’m getting a feel for python, why not tack on another language. R is very popular for statistical computing, and the number of packages R has for this functionality confirms that intuition.
2018
Automating Data Quality Assurance
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This is an ongoing process where we are attempting to collect data and visualize it quickly so we can see if anything looks off.
My Workflow
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We work with data on a lab server, basically network attached storage… There is no ftp access or any other web service integrations, so we do not treat it as our own private git server. However, I am “softly” mimicking that functionality in my current workflow. Once I’ve generated data I want to analyze/explore on the server (via some heavy data chugging analysis through the cluster), I can make the output directory a git repository and clone it locally. Since multiple people can access the server at the same time, this is useful as to not step on each other’s toes as we access/modify data. When I’m done fooling around locally, I can try to push, but since the repository I cloned from isn’t bare, I can’t. To get around that I had to use this command (that I stole from stack overflow):