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# Configuration for datascience workflows
(environment-yml)=
## `environment.yml` - Install a conda environment
@ -30,7 +29,6 @@ If you include a Python version in a `runtime.txt` file in addition to your
`environment.yml`, your `runtime.txt` will be ignored.
:::
(require)=
## `REQUIRE` - Install a Julia environment (legacy)
@ -47,8 +45,6 @@ This is used to install R libraries pinned to a specific snapshot on
To set the date of the snapshot add a [runtime.txt].
For an example `install.R` file, visit our [example install.R file](https://github.com/binder-examples/r/blob/HEAD/install.R).
(description)=
## `DESCRIPTION` - Install an R package

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@ -20,7 +20,6 @@ Python and R installation in a repository.
A list of supported configuration files (roughly in the order of build priority)
can be found on this page (and to the right).
```{toctree}
:maxdepth: 2
./datascience

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# System-wide configuration
(apt-txt)=
## `apt.txt` - Install packages with apt-get
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We use `apt.txt`, for example, to install LaTeX in our
[example apt.txt for LaTeX](https://github.com/binder-examples/latex/blob/HEAD/apt.txt).
(runtime-txt)=
## `runtime.txt` - Specifying runtimes

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@ -39,7 +39,6 @@ Mercurial and hg-evolve), one can use the environment variable
Some of the tests have non-python requirements for your development machine. They are:
- `git-lfs` must be installed ([instructions](https://github.com/git-lfs/git-lfs)). It need not be activated -- there is no need to run the `git lfs install` command. It just needs to be available to the test suite.
- If your test failure messages include "`git-lfs filter-process: git-lfs: command not found`", this step should address the problem.
- Minimum Docker Image size of 128GB is required. If you are not running docker on a linux OS, you may need to expand the runtime image size for your installation. See Docker's instructions for [macOS](https://docs.docker.com/docker-for-mac/space/) or [Windows 10](https://docs.docker.com/docker-for-windows/#resources) for more information.
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### Conda dependencies
1. There are two files related to conda dependencies. Edit as needed.
- `repo2docker/buildpacks/conda/environment.yml`
Contains list of packages to install in Python3 conda environments,

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@ -74,7 +74,6 @@ Python itself releases a new version every year now, and repo2docker will follow
If you choose not to specify a Python version, your repository is _guaranteed_ to stop working, eventually.
We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.)
## The R Language
repo2docker supports R, the open source [RStudio IDE](https://www.rstudio.com/) as well
@ -90,7 +89,7 @@ installed by default for all R versions.
[packagemanager.posit.co](https://packagemanager.posit.co/client/#/)
will be used to provide much faster installations via [binary packages](https://www.rstudio.com/blog/package-manager-v1-1-no-interruptions/).
For *some* packages, this might require you install underlying system libraries
For _some_ packages, this might require you install underlying system libraries
using [apt.txt](#apt-txt) - look at the page for the CRAN package you are interested in at
[packagemanager.posit.co](https://packagemanager.posit.co/client/#/) to find
a list.
@ -105,7 +104,6 @@ file.
We support R versions 3.4, 3.5, 3.6, 4.0, 4.1 and 4.2.
## Julia
To build an environment with Julia, include a configuration file called
@ -122,7 +120,6 @@ file, and this is the recommended way to install Julia environments.
Julia < 1.3 and the older Julia REQUIRE file is no longer supported because required infrastructure has been removed.
## Languages not covered here
If a language is not "officially" supported by a build pack, it can often be

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../howto/breaking_changes
```
```{toctree}
:maxdepth: 2
:caption: Learn about repo2docker

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`repo2docker` will look for configuration files in the following order:
* The root directory of the repository.
* A folder named `binder/` or `.binder/` in the root of the repository.
- The root directory of the repository.
- A folder named `binder/` or `.binder/` in the root of the repository.
If one of these folders exists, only configuration files in that folder are considered, configuration in the root directory will be ignored.
Having both `binder/` and `.binder/` folders is not allowed.
@ -16,6 +16,7 @@ Check the complete list of [configuration files](#config-files) supported
by `repo2docker` to see how to configure the build process.
(repository-providers)=
## Supported repository providers
repo2docker can fetch repositories from a number of repositories. Here are the ones we support:
@ -35,7 +36,6 @@ In each case you can build from these repository sources like so:
jupyter-repo2docker <URL-ID-or-path>
```
## Supported version control systems
These Version Control Systems are supported by `repo2docker`.