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Merge pull request #381 from evertrol/fix/documentation-typos
Clean up documentation
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CONTRIBUTING.md

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### Set up a local virtual environment
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After cloning the repository (or your fork of the repo), you should set up an
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After cloning the repository (or your fork of the repository), you should set up an
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isolated environment to install libraries required for running / developing
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repo2docker. There are many ways to do this, and a `virtual environment` is
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one of them.
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## Update and Freeze BuildPack Dependencies
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### Updating libraries installed for all repos
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### Updating libraries installed for all repositories
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For both the `conda` and `virtualenv` (`pip`) base environments in the **Conda BuildPack** and **Python BuildPack**,
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we install specific pinned versions of all dependencies. We explicitly list the dependencies
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standard procedures that have proven useful over time that we do follow:
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* do not merge your own PR
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* wait for travis to complete
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* wait for Travis to complete
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* check if test coverage has gone up or down, consider discussing additional
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tests to keep coverage at the same level or even increase it
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* do use merge commits instead of merge-by-squashing/-rebasing. This makes it
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1. Access to the PyPI package for repo2docker
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2. Access to push tags to the jupyter/repo2docker repository
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3. Acess to push images to dockerhub on jupyter/repo2docker
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3. Access to push images to dockerhub on jupyter/repo2docker
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If you do not have access to any of these, please contact a current maintainer of the project!
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README.md

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[![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest)
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**jupyter-repo2docker** takes as input a repository source, such as a GitHub
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repo. It then builds, runs, and/or pushes Docker images built from that source.
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repository. It then builds, runs, and/or pushes Docker images built from that source.
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See the [repo2docker documentation](http://repo2docker.readthedocs.io)
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for more information.
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## Pre-requisites
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## Prerequisites
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1. Docker to build & run the repositories. The [community edition](https://store.docker.com/search?type=edition&offering=community)
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is recommended.
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## Usage
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The core feature of repo2docker is to fetch a repo (from github or locally),
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build a container image based on the specifications found in the repo &
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The core feature of repo2docker is to fetch a repository (from GitHub or locally),
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build a container image based on the specifications found in the repository &
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optionally launch a local Jupyter Notebook you can use to explore it.
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**Note that Docker needs to be running on your machine for this to work.**

docs/source/architecture.md

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The **buildpack** concept comes from [Heroku](https://devcenter.heroku.com/articles/buildpacks)
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and Ruby on Rails' [Convention over Configuration](http://rubyonrails.org/doctrine/#convention-over-configuration)
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doctrine.
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doctrine.
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Instead of the user specifying a complete specification of exactly how they want
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their environment to be, they can focus only on how their environment differs from a conventional
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1. Look at the ordered list of `BuildPack` objects listed in `Repo2Docker.buildpacks`
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traitlet. This is populated with a default set of buildpacks in most-specific-to-least-specific
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order. Other applications using this can add / change this using traditional
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order. Other applications using this can add / change this using traditional
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[traitlet](http://traitlets.readthedocs.io/en/stable/) configuration mechanisms.
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2. Calls the `detect` method of each `BuildPack` object. This method assumes that the repository
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is present in the current working directory, and should return `True` if the repository is
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something that it should be used for. For example, a `BuildPack` that uses `conda` to install
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libraries can check for presence of an `environment.yml` file and say 'yes, I can handle this
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repository' by returning `True`. Usually buildpacks look for presence of specific files
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(`requirements.txt`, `environment.yml`, `install.R`, etc) to determine if they can handle a
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repository or not.
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repository or not.
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3. If no `BuildPack` returns true, then repo2docker will use the default `BuildPack` (defined in
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`Repo2Docker.default_buildpack` traitlet).
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## Build base environment
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Once a buildpack is chosen, it builds a **base environment** that is mostly the same for various
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repositories built with the same buildpack.
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repositories built with the same buildpack.
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For example, in `CondaBuildPack`, the base environment consists of installing [miniconda](https://conda.io/miniconda.html)
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and basic notebook packages (from `repo2docker/buildpacks/conda/environment.yml`). This is going
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to be the same for most repositories built with `CondaBuildPack`, so we want to use
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[docker layer caching](https://thenewstack.io/understanding-the-docker-cache-for-faster-builds/) as
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to be the same for most repositories built with `CondaBuildPack`, so we want to use
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[docker layer caching](https://thenewstack.io/understanding-the-docker-cache-for-faster-builds/) as
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much as possible for performance reasons. Next time a repository is built with `CondaBuildPack`,
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we can skip straight to the **copy** step (since the base environment docker image *layers* have
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already been built and cached).
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The `get_build_scripts` and `get_build_script_files` methods are primarily used for this.
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The `get_build_scripts` and `get_build_script_files` methods are primarily used for this.
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`get_build_scripts` can return arbitrary bash script lines that can be run as different users,
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and `get_build_script_files` is used to copy specific scripts (such as a conda installer) into
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the image to be run as pat of `get_build_scripts`. Code in either has following constraints:
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The **assemble** stage builds the specific environment that is requested by the repository.
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This usually means installing required libraries specified in a format native to the language
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(`requirements.txt`, `environment.yml`, `REQUIRE`, `install.R`, etc).
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(`requirements.txt`, `environment.yml`, `REQUIRE`, `install.R`, etc).
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Most of this work is done in `get_assemble_scripts` method. It can return arbitrary bash script
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lines that can be run as different users, and has access to the repository contents (unlike
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lines that can be run as different users, and has access to the repository contents (unlike
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`get_build_scripts`). The docker image layers produced by this usually can not be cached,
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so less restrictions apply to this than to `get_build_scripts`.
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docs/source/config_files.rst

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The `binder examples <https://github.com/binder-examples>`_ organization on
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GitHub contains a list of sample repositories for common configurations
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that ``repo2docker`` can build with various configuration files such as
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Python and R installation in a repo.
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Python and R installation in a repository.
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Below is a list of supported configuration files (roughly in the order of build priority):
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docs/source/deploy.rst

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If you navigate to the main `app page <https://circleci.com/dashboard/>`_ you
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should be able to click "Add Projects" and then select your repository. If you don't
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see it on the list, then select a different organization in the top left. Once
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you find the repository, you can click the button to "Start Building" adn accept
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you find the repository, you can click the button to "Start Building" and accept
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the defaults.
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Before you push or trigger a build, let's set up the following environment variables.
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Once the environment variables are set up, you can push or issue a pull request
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to see circle build the workflow. Remember that you only need the ``.circleci/config.yml``
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and not any other files in the repository. If your notebook is hosted in the same repo,
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and not any other files in the repository. If your notebook is hosted in the same repository,
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you might want to add these, along with your requirements.txt, etc.
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.. tip::

docs/source/design.md

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- using common configuration files for familiar installation and packaging tools
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- allowing configuration files to be combined to compose more complex setups
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- specifying default locations for configuration files
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(repo's root directory or .binder directory)
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(the repository's root directory or .binder directory)
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When designing `repo2docker` and adding to it in the future, the
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The version of `repo2docker` used to build an image can influence which packages
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are installed by default and which features are supported during the build
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process. We will periodically update those packages to keep step with releases
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of jupyter notebook, jupyterlab, etc. For packages that are installed by
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of Jupyter Notebook, JupyterLab, etc. For packages that are installed by
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default but where you want to control the version we recommend you specify them
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explicitly in your dependencies.
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docs/source/dev_newbuildpack.md

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2. How easy it is to use a given setup without support from repo2docker natively.
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There are two escape hatches here - `postBuild` and `Dockerfile`.
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3. How widely used is this language / package manager? This is the primary tradeoff
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with point (1). We (Binder / Jupyter) team do not want to make new formats
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as much as possible, so ideally we can just say 'X repos on binder already use
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with point (1). We (the Binder / Jupyter team) want to make new formats
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as little as possible, so ideally we can just say "X repositories on binder already use
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this using one of the escape hatches in (2), so let us make it easy and add
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native support'.
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native support".
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## Adding libraries or UI to existing buildpacks
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Note that this doesn't apply to adding additional libraries / UI to existing
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buildpacks. For example, if we had an R buildpack and it supported IRKernel,
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it is much easier to
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just support RStudio / Shiny with it, since those are library additions instead of entirely
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new buildpacks.

docs/source/faq.md

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## How should I specify another version of Python 3?
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One can specify a Python version in the ``environment.yml`` file of a repo.
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One can specify a Python version in the ``environment.yml`` file of a repository.
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## Can I add executable files to the user's PATH?
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Check out the [binder-examples](http://github.com/binder-examples/) GitHub
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organization for example repositories you can copy & modify for your own use!

docs/source/index.rst

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===================
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**jupyter-repo2docker** is a tool to build, run, and push Docker
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images from source code repositories. repo2docker fetches a repo
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(e.g., from GitHub or other locations) and builds a container image based
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on the configuration files found in the repo. It can be used to explore a
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repository locally by building and executing the constructed image of the
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repository.
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images from source code repositories. repo2docker fetches a repository
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(e.g., from GitHub or other locations) and builds a container image
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based on the configuration files found in the repository. It can be
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used to explore a repository locally by building and executing the
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constructed image of the repository.
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Please report `Bugs <https://github.com/jupyter/repo2docker/issues>`_,
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`ask questions <https://gitter.im/jupyterhub/binder>`_ or

docs/source/install.rst

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python3 -m pip install jupyter-repo2docker
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For infomation on using ``repo2docker``, see :ref:`usage`.
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For information on using ``repo2docker``, see :ref:`usage`.
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Installing from source code
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To build JupyterHub_-ready
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Docker images with ``repo2docker``, the version of your JupterHub deployment
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must be included in the ``environment.yml`` or ``requiements.txt`` of the
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git repositories you build.
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version of your JupterHub deployment must be included in the
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``environment.yml`` or ``requirements.txt`` of the git repositories you
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If your instance of JupyterHub uses ``DockerSpawner``, you will need to set its
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command to run ``jupyterhub-singleuser`` by adding this line in your

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