[pre-commit.ci] auto fixes from pre-commit.com hooks

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pre-commit-ci[bot] 2025-07-25 22:42:15 +00:00
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@ -30,4 +30,4 @@ should at most take a few seconds to run.
If you only need to run things once during the build phase use {ref}`postBuild`. If you only need to run things once during the build phase use {ref}`postBuild`.
% TODO: Discuss runtime limits, best practices, etc. % TODO: Discuss runtime limits, best practices, etc.

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@ -1,6 +1,5 @@
# Configuration for datascience workflows # Configuration for datascience workflows
(environment-yml)= (environment-yml)=
## `environment.yml` - Install a conda environment ## `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. `environment.yml`, your `runtime.txt` will be ignored.
::: :::
(require)= (require)=
## `REQUIRE` - Install a Julia environment (legacy) ## `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]. 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). For an example `install.R` file, visit our [example install.R file](https://github.com/binder-examples/r/blob/HEAD/install.R).
(description)= (description)=
## `DESCRIPTION` - Install an R package ## `DESCRIPTION` - Install an R package

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@ -20,11 +20,10 @@ Python and R installation in a repository.
A list of supported configuration files (roughly in the order of build priority) A list of supported configuration files (roughly in the order of build priority)
can be found on this page (and to the right). can be found on this page (and to the right).
```{toctree} ```{toctree}
:maxdepth: 2 :maxdepth: 2
./datascience ./datascience
./development ./development
./system ./system
./actions ./actions
``` ```

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@ -1,6 +1,5 @@
# System-wide configuration # System-wide configuration
(apt-txt)= (apt-txt)=
## `apt.txt` - Install packages with apt-get ## `apt.txt` - Install packages with apt-get
@ -11,8 +10,6 @@ version of Ubuntu.
We use `apt.txt`, for example, to install LaTeX in our 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). [example apt.txt for LaTeX](https://github.com/binder-examples/latex/blob/HEAD/apt.txt).
(runtime-txt)= (runtime-txt)=
## `runtime.txt` - Specifying runtimes ## `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: 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. - `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. - 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. - 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.
@ -69,7 +68,6 @@ See the subsections below for more detailed instructions.
### Conda dependencies ### Conda dependencies
1. There are two files related to conda dependencies. Edit as needed. 1. There are two files related to conda dependencies. Edit as needed.
- `repo2docker/buildpacks/conda/environment.yml` - `repo2docker/buildpacks/conda/environment.yml`
Contains list of packages to install in Python3 conda environments, 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. 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.) We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.)
## The R Language ## The R Language
repo2docker supports R, the open source [RStudio IDE](https://www.rstudio.com/) as well 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/#/) [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/). 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 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 [packagemanager.posit.co](https://packagemanager.posit.co/client/#/) to find
a list. a list.
@ -105,7 +104,6 @@ file.
We support R versions 3.4, 3.5, 3.6, 4.0, 4.1 and 4.2. We support R versions 3.4, 3.5, 3.6, 4.0, 4.1 and 4.2.
## Julia ## Julia
To build an environment with Julia, include a configuration file called 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. Julia < 1.3 and the older Julia REQUIRE file is no longer supported because required infrastructure has been removed.
## Languages not covered here ## Languages not covered here
If a language is not "officially" supported by a build pack, it can often be If a language is not "officially" supported by a build pack, it can often be

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@ -34,7 +34,6 @@ repository
../howto/breaking_changes ../howto/breaking_changes
``` ```
```{toctree} ```{toctree}
:maxdepth: 2 :maxdepth: 2
:caption: Learn about repo2docker :caption: Learn about repo2docker

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@ -6,8 +6,8 @@
`repo2docker` will look for configuration files in the following order: `repo2docker` will look for configuration files in the following order:
* The root directory of the repository. - The root directory of the repository.
* A folder named `binder/` or `.binder/` in the root 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. 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. 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. by `repo2docker` to see how to configure the build process.
(repository-providers)= (repository-providers)=
## Supported repository providers ## Supported repository providers
repo2docker can fetch repositories from a number of repositories. Here are the ones we support: 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> jupyter-repo2docker <URL-ID-or-path>
``` ```
## Supported version control systems ## Supported version control systems
These Version Control Systems are supported by `repo2docker`. These Version Control Systems are supported by `repo2docker`.