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# Configuration for datascience workflows
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(environment-yml)=
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## `environment.yml` - Install a conda environment
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@ -30,7 +29,6 @@ If you include a Python version in a `runtime.txt` file in addition to your
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`environment.yml`, your `runtime.txt` will be ignored.
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:::
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(require)=
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## `REQUIRE` - Install a Julia environment (legacy)
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@ -47,8 +45,6 @@ This is used to install R libraries pinned to a specific snapshot on
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To set the date of the snapshot add a [runtime.txt].
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For an example `install.R` file, visit our [example install.R file](https://github.com/binder-examples/r/blob/HEAD/install.R).
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(description)=
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## `DESCRIPTION` - Install an R package
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@ -20,7 +20,6 @@ Python and R installation in a repository.
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A list of supported configuration files (roughly in the order of build priority)
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can be found on this page (and to the right).
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```{toctree}
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:maxdepth: 2
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./datascience
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# System-wide configuration
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(apt-txt)=
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## `apt.txt` - Install packages with apt-get
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We use `apt.txt`, for example, to install LaTeX in our
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[example apt.txt for LaTeX](https://github.com/binder-examples/latex/blob/HEAD/apt.txt).
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(runtime-txt)=
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## `runtime.txt` - Specifying runtimes
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@ -39,7 +39,6 @@ Mercurial and hg-evolve), one can use the environment variable
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Some of the tests have non-python requirements for your development machine. They are:
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- `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.
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- If your test failure messages include "`git-lfs filter-process: git-lfs: command not found`", this step should address the problem.
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- 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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@ -69,7 +68,6 @@ See the subsections below for more detailed instructions.
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### Conda dependencies
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1. There are two files related to conda dependencies. Edit as needed.
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- `repo2docker/buildpacks/conda/environment.yml`
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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
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If you choose not to specify a Python version, your repository is _guaranteed_ to stop working, eventually.
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We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.)
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## The R Language
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repo2docker supports R, the open source [RStudio IDE](https://www.rstudio.com/) as well
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[packagemanager.posit.co](https://packagemanager.posit.co/client/#/)
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will be used to provide much faster installations via [binary packages](https://www.rstudio.com/blog/package-manager-v1-1-no-interruptions/).
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For *some* packages, this might require you install underlying system libraries
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For _some_ packages, this might require you install underlying system libraries
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using [apt.txt](#apt-txt) - look at the page for the CRAN package you are interested in at
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[packagemanager.posit.co](https://packagemanager.posit.co/client/#/) to find
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a list.
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@ -105,7 +104,6 @@ file.
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We support R versions 3.4, 3.5, 3.6, 4.0, 4.1 and 4.2.
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## Julia
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To build an environment with Julia, include a configuration file called
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@ -122,7 +120,6 @@ file, and this is the recommended way to install Julia environments.
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Julia < 1.3 and the older Julia REQUIRE file is no longer supported because required infrastructure has been removed.
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## Languages not covered here
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If a language is not "officially" supported by a build pack, it can often be
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@ -34,7 +34,6 @@ repository
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../howto/breaking_changes
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```
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```{toctree}
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:maxdepth: 2
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:caption: Learn about repo2docker
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@ -6,8 +6,8 @@
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`repo2docker` will look for configuration files in the following order:
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* The root directory of the repository.
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* A folder named `binder/` or `.binder/` in the root of the repository.
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- The root directory of the repository.
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- A folder named `binder/` or `.binder/` in the root of the repository.
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If one of these folders exists, only configuration files in that folder are considered, configuration in the root directory will be ignored.
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Having both `binder/` and `.binder/` folders is not allowed.
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@ -16,6 +16,7 @@ Check the complete list of [configuration files](#config-files) supported
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by `repo2docker` to see how to configure the build process.
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(repository-providers)=
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## Supported repository providers
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repo2docker can fetch repositories from a number of repositories. Here are the ones we support:
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@ -35,7 +36,6 @@ In each case you can build from these repository sources like so:
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jupyter-repo2docker <URL-ID-or-path>
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```
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## Supported version control systems
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These Version Control Systems are supported by `repo2docker`.
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