nb-py-quarcs: Python computational notebooks to explore and learn
Online Analysis Environment
- To open a virtual Jupyter lab session, make sure you change you click on
Fileand change it to
URL. Then, write
labin the field
URL to open (optional). Finally, click on
launch. Alternatively, you could just click on this Binder badge:
Materials are licensed under CC BY-SA 4.0.
Conda environment with environment.yml
A Binder-compatible repo with an
Access this Binder by clicking the blue badge above or at the following URL:
environment.yml file should list all Python libraries on which your notebooks
depend, specified as though they were created using the following
conda activate example-environment conda env export --from-history -f environment.yml
Note that the only libraries available to you will be the ones specified in
environment.yml, so be sure to include everything that you need!
Also note that if you skip the
--from-history, conda may include OS-specific
environment.yml, which you would have to manually prune from
environment.yml. For example, confirmed macOS-specific packages that should
be removed are:
R environment with a runtime.txt file
Binder supports using R and RStudio, with libraries pinned to a specific snapshot on MRAN.
Note: We recommend to follow r-conda instead. Especially if you want to use a specific version of R or need faster build times.
Note: Another alternative is to use the holepunch package for R.
Requirements and suggestions
You need to have a
runtime.txt file that is formatted like:
where YYYY-MM-DD is a snapshot at MRAN that will be used for installing
libraries. In this line, you can request a specific
version of R. To do this list the version between the 'r'
and the year, as in
r-3.6-2019-09-24. Right now the default version of R is 3.6.
We recommend using https://github.com/binder-examples/r-conda for faster installs than using a
To install R libraries (or packages) you can add an
install.R file that specifies one library to install per line.
This repository also contains an example of a Shiny app.
URL addresses for RStudio and Shiny environments
The Binder repository can be used to allow anyone to access an RStudio environment containing our code and data right in their web browser. It also allows hosting a Shiny app. For those purposes, we have to append a bit of text to the URL of our Binder repository, which we can find out at mybinder.org when we enter the URL of our original repository from GitHub or Figshare, etc.
For the RStudio environment, we must add the following at the end of the URL:
For the Shiny app environment, we must add the following at the end of the URL:
?urlpath=shiny. In this case, we also have to note that if the Shiny app files are located in a folder, this folder should be specified in the URL, after a slash. We would then also have to put in a trailing slash at the end of the URL, and to avoid spaces in the name of the repository, placing instead a hyphen (the reason is that spaces are converted to