Organizing a new project with git and conda and synching it to GitHub (CC246)
ฝัง
- เผยแพร่เมื่อ 5 ก.พ. 2025
- To get going on a new reproducible project we're going to talk about project organization and set up the directory with git, create a conda environment, and sync everything to GitHub. Our conda environment will start out with an installation of R and the tidyverse package. The goal of this project is to highlight reproducible research practices using a number of tools. The specific output from this project will be a map-based visual that shows the level of drought across the globe.
You can find my blog post for this episode at www.riffomonas....
#conda #git #github #R #Rstats
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0:00 Introduction
2:44 Create repository on GitHub
4:36 Modify repository and push changes to GitHub
12:04 Create conda environment
18:10 Create directory organization
Dude, this is so sick its so clear and exactly what I needed
Wonderful!🤓
I've been silently watching and learning from your videos for a while now. Just wanted to give my thanks :)
Your videos have been really helpful for me as an MD student breaking into research!
Fantastic! Thanks so much for watching. Good luck with your studies 🤓
That one was extremally technical and very advanced. Thank you! just learning about git and its uses on the GitHub platform.
Hang in there! With practice I know you’ll get it
I am returning to this video to start a new SQL repository. This is pure gold PAtrick. I can't really thank you enough! You are amazing.
In the same series of videos I am learning git, github, using the command line and much much more.
Glad it helped! So happy to get the feedback - thanks!
Looking forward to the series! Great video love the way you teach!
Thanks Jason!
Thanks for these great videos - I really enjoy learning and improving my R skills through them. I was wondering if you could use Conda and Renv together? e.g. Conda to capture the system dependencies (rstudio version, tidytek) and Renv to capture r packages
Hey Neil! Maybe. In the past I’ve run into problems using both at the same time. I feel like it’s best to stick with one or the other to be safe. Give it a shot and let us know how it goes
Hi professor thanks for really work. Is possible to show customize this viscode terminal weather.
Thanks very much for drought project
Definitely - I did this in an earlier episode riffomonas.org/code_club/2020-08-13-customizing-bash
pretty cool!
Thanks! 🤓
Great Video!! I already have installed vs code a few days ago. Can´t wait for your next videos. You are the main reason I haven't went full Python yet. I truly love R and I seriously need to learn github. This videos are amazing to cover both ends. Also using vs Code helps me learn faster to use the terminal.
I have a question about reproducible research. I am presenting a paper next month and I uploaded the code I made to github to make it available for everyone. I didn't set a license when I created the repository as I didn't know which one to choose and didn't have the time to research about that. Can you make a video about licensing projects? Also, should I remade my work following along with your videos in order to make it more reproducible? How can I examine this quality of the work I have done? As you can tell, I am not a researcher per se, but I work in an industry that there is a lot to do with data, and there aren't enough data analyst, so I can contribute just by bringing the domains together.
Thanks for your amazing videos!
Hi Matias - you're asking all of the right questions! I'd suggest MIT for the code and CC-BY for the paper itself. These will make it as open as possible while still making sure you get proper attribution. I have a much earlier video about doing open science where I talk about licenses and such... th-cam.com/video/lXnetUbbGIc/w-d-xo.html. Ultimately, I'd encourage you to not be super hard on yourself, but to instead do better with each new project you start. That's what I try to do and am still finding new things to work on 🤓
@@Riffomonas Thanks for your response!! I really appreciate you take the time to answer all my questions. I have another one tho. Have you ever needed to deploy a visualization, as with shiny or kniting it in a HTML file?
@@mabenba Absolutely - everything you see at riffomonas.org is based on R markdown. Here's the github repository for the minimalR resources: github.com/riffomonas/minimalR
Great presentation , as you said you are UNIX BASH terminal , on windows it is very hard to configure something like that , can you show us how to do that on Windows environment , if possible everything using R studio as it is easy to keep everything at one place
Thanks for watching! I’m sorry but I don’t know windows. I’d encourage windows users to install git bash or the Linux subsystem. A lot more tools will be available in a Linux type environment
I use mac personally but I have Windows at work and there I install anaconda prompt (a gui for Windows) which mimics using conda in terminal. We can't use things like 'which' that are part of the bash universe but the rest of the conda stuff is available there
This is very interesting. You recommended Linux for serious data analysis, could you help us see how to install Linux for Windows subsystem. Thanks.
This is a tutorial that I’ve sent people to in the past itsfoss.com/install-bash-on-windows/
@@Riffomonas Thank you so much. I love your videos. They are very resourceful.
Hello Pat! Thank you for all your content, it is wonderful! I love it! I have been following your videos and now, I am working on a project using all your suggestions. I have found a particular problem when traying to make my environment.yml, with some packages that I need to use. In particular, this package is terra. The problem is as follows:
-Although mamba creates the environment with the proper packages, when I fire up R and try to load terra it seems that some dependencies can't find the installed package. The error message looks like shown bellow. Have you ever faced a similar problem with your conda environments? - Any guidance is much appreciated!
> library(terra)
Error: package or namespace load failed for ‘terra’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/grizzo/miniconda3/envs/mex/lib/R/library/terra/libs/terra.so':
libproj.so.15: cannot open shared object file: No such file or directory
Hi Pat, Thank you. R library is not loading from the created environment. Is there any stage I might skipped or something is missing?
Are you sure you're in the environment before starting R?
@ yes, i am sure.
@@EmouAcademy Sorry, it could be a lot of things and this interface is not the best for diagnosing problems. If you want to email me screenshots of wwhat's going on I can take a look - pat@riffomonas.org
Does mamba get installed with miniconda?
Looks like that is now the preferred way to install mamba - mamba.readthedocs.io/en/latest/installation/mamba-installation.html