kopia lustrzana https://github.com/jupyterhub/repo2docker
updating index, usage, and install docs
Chris Holdgraf
rodzic
46f056a4e2
commit
d6eea937ce
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@ -1,3 +1,7 @@
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img.logo {
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width:100%
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}
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div.body p.caption {
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font-size: 1.5em;
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}
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@ -44,7 +44,7 @@ source_parsers = {
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}
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def setup(app):
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app.add_stylesheet('custom.css') # may also be an URL
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app.add_stylesheet('_static/custom.css') # may also be an URL
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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@ -188,38 +188,31 @@ epub_copyright = copyright
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# A list of files that should not be packed into the epub file.
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epub_exclude_files = ['search.html']
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# Build the repo2docker test syntax
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import os
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s = ''
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FILE_ORDER_PREFERENCE = ['System', 'Python', 'Julia', 'Docker', 'Misc']
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SKIP_FOLDERS = ['binder-dir']
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FILES_DICT = {ii: [] for ii in FILE_ORDER_PREFERENCE}
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for root, _, files in os.walk(os.path.join('..', '..', 'tests')):
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depth = len(root.split('/')) - 3
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if 'README.rst' not in files or depth > 2:
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continue
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if any(folder in root for folder in SKIP_FOLDERS):
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continue
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header = files.pop(files.index('README.rst'))
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with open(os.path.join(root, header), 'r') as ff:
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this_s = ff.read() + '\n\n'
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title = this_s.split('\n')[0]
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for ifile in files:
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filename = os.path.basename(ifile)
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if filename == 'verify':
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continue
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with open(os.path.join(root, ifile), 'r') as ff:
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lines = ff.readlines()
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lines = [' ' + line for line in lines]
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this_s += 'File: ``{}``\n{}\n\n**Contents**::\n\n'.format(
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filename, '~' * (len(filename) + 10))
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this_s += '\n'.join(lines)
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this_s += '\n\n'
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usename = [ii for ii in FILE_ORDER_PREFERENCE if ii in title]
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usename = 'Misc' if len(usename) == 0 else usename[0]
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FILES_DICT[usename].append(this_s)
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for key in FILE_ORDER_PREFERENCE:
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for istring in FILES_DICT[key]:
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s += istring
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with open('./test_file_text.txt', 'w') as ff:
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ff.write(s)
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# Update the example_repos text file
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# import requests
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#
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# config_files = ['start', 'postBuild', 'apt.txt', 'runtime.txt',
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# 'environment.yml', 'requirements.txt', 'setup.py',
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# 'REQUIRE', 'install.R', 'Dockerfile']
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# config_dict = {ii: [] for ii in config_files}
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# repos = requests.get('https://api.github.com/orgs/jupyterhub/repos').json()
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# repo_names = [ii['full_name'].split('/')[-1] for ii in repos]
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# repo_descriptions = {name: repo['description'] for repo, name in zip(repos, repo_names)}
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#
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# files = {}
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# for repo_name in repo_names:
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# this_files = requests.get('https://api.github.com/repos/binder-examples/{}/contents'.format(repo_name)).json()
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# for ifile in this_files:
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# if ifile['name'] in config_dict:
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# config_dict[ifile['name']].append(repo_name)
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#
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# s = ''
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# for file_name, repos in config_dict.items():
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# header_chars = '=' * len(file_name)
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# s = '{}\n{}\n\n'.format(file_name, header_chars)
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# for repo_name in repos:
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# this_url = "https://github.com/binder-examples/{}".format(repo_name)
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# this_desc = repo_descriptions['repo_name']
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# s += '`{} <{}>`_\n'.format(this_desc, this_url)
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# with open('example_repos.txt', 'w') as ff:
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# ff.write(s)
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@ -1,9 +1,8 @@
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.. NOTE: the header characters are different in this file because it is 'included' in another site
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.. see https://raw.githubusercontent.com/jupyterhub/binder/master/doc/using.rst
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.. _config-files:
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===================
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Configuration Files
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-------------------
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===================
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``repo2docker`` looks for configuration files in the repository being built
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to determine how to build it. In general, ``repo2docker`` uses the same
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@ -13,14 +12,6 @@ rather than creating new custom configuration files.
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A number of ``repo2docker`` configuration files can be combined to compose more
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complex setups.
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``repo2docker`` will look for configuration files in either:
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* A folder named ``binder/`` in the root of the repository.
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* The root directory of the repository.
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If the folder ``binder/`` is located at the top level of the repository,
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**only configuration files in the** ``binder/`` **folder will be considered**.
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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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@ -32,74 +23,45 @@ Below is a list of supported configuration files (roughly in the order of build
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:local:
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:depth: 1
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``Dockerfile``
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~~~~~~~~~~~~~~
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In the majority of cases, providing your own Dockerfile is not necessary as the base
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images provide core functionality, compact image sizes, and efficient builds. We recommend
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trying the other configuration files before deciding to use your own Dockerfile.
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With Dockerfiles, a regular Docker build will be performed.
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**If a Dockerfile is present, all other configuration files will be ignored.**
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See the `Binder Documentation <https://mybinder.readthedocs.io/en/latest/dockerfile.html>`_ for
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best-practices with Dockerfiles.
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.. _environment-yml:
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``environment.yml``
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~~~~~~~~~~~~~~~~~~~
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``environment.yml`` - Install a Python environment
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==================================================
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``environment.yml`` is the standard configuration file used by Anaconda, conda,
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and miniconda that lets you install Python packages.
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You can also install files from pip in your ``environment.yml`` as well.
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Our example `environment.yml <https://github.com/binder-examples/python-conda_pip/blob/master/environment.yml>`_
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shows how one can specify a conda environment for repo2docker.
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and miniconda that lets you install packages in the data analytics stack (it
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primarily installs Python packages, though can be used to install a range of
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non-Python packages as well).
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.. note::
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You can install files from pip in your ``environment.yml`` as well.
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For example, see the `binder-examples environment.yml
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<https://github.com/binder-examples/python-conda_pip/blob/master/environment.yml>`_
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file.
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You can also specify which Python version to install in your built environment
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with ``environment.yml``. By default, ``repo2docker`` **installs
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Python 3.6** with your ``environment.yml`` unless you include the version of
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Python in the file. ``conda`` supports Python versions 3.6, 3.5, 3.4, and 2.7.
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``repo2docker`` support is best with Python 3.6, 3.5, and 2.7. If you include
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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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``repo2docker`` support is best with Python 3.6, 3.5, and 2.7.
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``requirements.txt``
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~~~~~~~~~~~~~~~~~~~~
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.. warning::
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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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``requirements.txt`` - Install a Python environment
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===================================================
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This specifies a list of Python packages that should be installed in your
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environment. Our
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`requirements.txt example <https://github.com/binder-examples/requirements/blob/master/requirements.txt>`_
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on GitHub shows a typical requirements file.
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``REQUIRE``
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~~~~~~~~~~~
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This specifies a list of Julia packages. Repositories with a ``REQUIRE`` file
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**must also contain an** ``environment.yml`` **file**. To see an example of a
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Julia repository with ``REQUIRE`` and ``environment.yml``,
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visit `binder-examples/julia-python <https://github.com/binder-examples/julia-python>`_.
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``install.R``
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~~~~~~~~~~~~~
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This is used to install R libraries pinned to a specific snapshot on
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`MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
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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/master/install.R>`_.
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``apt.txt``
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~~~~~~~~~~~
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A list of Debian packages that should be installed. The base image used is usually the latest released
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version of Ubuntu.
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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/master/apt.txt>`_.
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``setup.py``
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~~~~~~~~~~~~
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``setup.py`` - Install Python packages
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======================================
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To install your repository like a Python package, you may include a
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``setup.py`` file. repo2docker installs ``setup.py`` files by running
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@ -109,10 +71,39 @@ While one can specify dependencies in ``setup.py``,
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repo2docker **requires configuration files such as** ``environment.yml`` or
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``requirements.txt`` to install dependencies during the build process.
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``REQUIRE`` - Install a Julia environment
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=========================================
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This specifies a list of Julia packages. Repositories with a ``REQUIRE`` file
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**must also contain an** ``environment.yml`` **file**. To see an example of a
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Julia repository with ``REQUIRE`` and ``environment.yml``,
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visit `binder-examples/julia-python <https://github.com/binder-examples/julia-python>`_.
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``install.R`` - Install an R/RStudio environment
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================================================
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This is used to install R libraries pinned to a specific snapshot on
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`MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
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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/master/install.R>`_.
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``apt.txt`` - Install packages with apt-get
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===========================================
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A list of Debian packages that should be installed. The base image used is usually the latest released
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version of Ubuntu.
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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/master/apt.txt>`_.
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.. _postBuild:
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``postBuild``
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~~~~~~~~~~~~~
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``postBuild`` - Run code after installing the environment
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=========================================================
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A script that can contain arbitrary commands to be run after the whole repository has been built. If you
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want this to be a shell script, make sure the first line is ```#!/bin/bash``.
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@ -121,10 +112,11 @@ An example use-case of ``postBuild`` file is JupyterLab's demo on mybinder.org.
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It uses a ``postBuild`` file in a folder called ``binder`` to `prepare
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their demo for binder <https://github.com/jupyterlab/jupyterlab-demo/blob/master/binder/postBuild>`_.
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.. _start:
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``start``
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^^^^^^^^^
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``start`` - Run code before the user sessions starts
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====================================================
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A script that can contain simple commands to be run at runtime (as an
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`ENTRYPOINT <https://docs.docker.com/engine/reference/builder/#entrypoint>`
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@ -138,13 +130,14 @@ should at most take a few seconds to run.
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If you only need to run things once during the build phase use :ref:`postBuild`.
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.. TODO: Discuss runtime limits, best practices, etc.
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Also, point to an example.
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.. _runtime.txt:
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``runtime.txt``
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~~~~~~~~~~~~~~~
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``runtime.txt`` - Specifying runtimes
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=====================================
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This allows you to control the runtime of Python or R.
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@ -163,3 +156,17 @@ used for installing libraries.
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To see an example R repository, visit our `R
|
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example in binder-examples <https://github.com/binder-examples/r/blob/master/runtime.txt>`_.
|
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|
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|
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``Dockerfile`` - Advanced environments
|
||||
======================================
|
||||
|
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In the majority of cases, providing your own Dockerfile is not necessary as the base
|
||||
images provide core functionality, compact image sizes, and efficient builds. We recommend
|
||||
trying the other configuration files before deciding to use your own Dockerfile.
|
||||
|
||||
With Dockerfiles, a regular Docker build will be performed.
|
||||
**If a Dockerfile is present, all other configuration files will be ignored.**
|
||||
|
||||
See the `Binder Documentation <https://mybinder.readthedocs.io/en/latest/dockerfile.html>`_ for
|
||||
best-practices with Dockerfiles.
|
||||
|
|
|
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|
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@ -0,0 +1,8 @@
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.. _examples:
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|
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======================================
|
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Example repositories using repo2docker
|
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======================================
|
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|
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This page contains links to example repositories for each of the repo2docker
|
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configuration files.
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|
|
@ -1,26 +1,38 @@
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jupyter-repo2docker
|
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===================
|
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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 repository
|
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``jupyter-repo2docker`` is a tool to **build, run, and push Docker
|
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images from source code repositories** that run via a Jupyter server.
|
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|
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``repo2docker`` fetches a repository
|
||||
(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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constructed image of the repository, or as a means of building images that
|
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are pushed to a Docker registry.
|
||||
|
||||
Please report `Bugs <https://github.com/jupyter/repo2docker/issues>`_,
|
||||
`ask questions <https://gitter.im/jupyterhub/binder>`_ or
|
||||
`contribute to the project <https://github.com/jupyter/repo2docker/blob/master/CONTRIBUTING.md>`_.
|
||||
|
||||
|
||||
Site Contents
|
||||
-------------
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:maxdepth: 2
|
||||
:caption: Getting started with repo2docker
|
||||
|
||||
install
|
||||
usage
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
:caption: Configuration files and examples
|
||||
|
||||
config_files
|
||||
examples
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:caption: Advanced and developer information
|
||||
|
||||
faq
|
||||
deploy
|
||||
design
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ Installing ``repo2docker``
|
|||
repo2docker requires Python 3.4 and above on Linux and macOS. See
|
||||
:ref:`below <windows>` for more information about Windows support.
|
||||
|
||||
Prerequisite: docker
|
||||
Prerequisite: Docker
|
||||
--------------------
|
||||
|
||||
Install `Docker <https://www.docker.com>`_ as it is required
|
||||
|
|
@ -56,28 +56,3 @@ Bash on Windows) provides additional information about Windows and docker.
|
|||
|
||||
|
||||
.. _using Windows and the WSL: https://nickjanetakis.com/blog/setting-up-docker-for-windows-and-wsl-to-work-flawlessly
|
||||
|
||||
.. _jupyterhub_ready:
|
||||
|
||||
JupyterHub-ready images
|
||||
-----------------------
|
||||
|
||||
JupyterHub_ allows multiple
|
||||
users to collaborate on a shared Jupyter server. ``repo2docker`` can build
|
||||
Docker images that can be shared within a JupyterHub deployment. For example,
|
||||
`mybinder.org <https://mybinder.org>`_ uses JupyterHub and ``repo2docker``
|
||||
to allow anyone to build a Docker image of a git repository online and
|
||||
share an executable version of the repository with a URL to the built image.
|
||||
|
||||
To build JupyterHub_-ready Docker images with ``repo2docker``, the
|
||||
version of your JupterHub deployment must be included in the
|
||||
``environment.yml`` or ``requirements.txt`` of the git repositories you
|
||||
build.
|
||||
|
||||
If your instance of JupyterHub uses ``DockerSpawner``, you will need to set its
|
||||
command to run ``jupyterhub-singleuser`` by adding this line in your
|
||||
configuration file::
|
||||
|
||||
c.DockerSpawner.cmd = ['jupyterhub-singleuser']
|
||||
|
||||
.. _JupyterHub: https://github.com/jupyterhub/jupyterhub
|
||||
|
|
|
|||
|
|
@ -1,60 +1,50 @@
|
|||
.. _usage:
|
||||
|
||||
=====================
|
||||
Using ``repo2docker``
|
||||
=====================
|
||||
|
||||
`Docker <https://docs.docker.com/>`_ **must be running** in
|
||||
order to run ``repo2docker``. For more information on installing
|
||||
``repo2docker``, see :ref:`install`.
|
||||
.. note::
|
||||
|
||||
``repo2docker`` performs two steps:
|
||||
`Docker <https://docs.docker.com/>`_ **must be running** in
|
||||
order to run ``repo2docker``. For more information on installing
|
||||
``repo2docker``, see :ref:`install`.
|
||||
|
||||
1. builds a Docker image from a git repo
|
||||
2. runs a Jupyter server within the image to explore the repository
|
||||
``repo2docker`` is called with a URL/path to a git repository. It then
|
||||
performs these steps:
|
||||
|
||||
.. To ensure you can run the software in your repository, you must
|
||||
1. Inspects the repository for :ref:`configuration files <config-files>`. These will be used to build
|
||||
the environment needed to run the repository.
|
||||
2. Builds a Docker image with an environment specified in these :ref:`configuration files <config-files>`.
|
||||
3. Runs a Jupyter server within the image that lets you explore the
|
||||
repository interactively (optional)
|
||||
4. Pushes the images to a Docker registry so that it may be accessed remotely
|
||||
(optional)
|
||||
|
||||
Calling repo2docker
|
||||
===================
|
||||
|
||||
repo2docker is called with this command::
|
||||
|
||||
jupyter-repo2docker <URL-or-path to repository>
|
||||
|
||||
where ``<URL-or-path to repository>`` is a URL or path to the source repository.
|
||||
where ``<URL-or-path to repository>`` is a URL or path to the source repository
|
||||
for which you'd like to build an image.
|
||||
|
||||
For example, use the following to build an image of Peter Norvig's
|
||||
Pytudes_::
|
||||
For example, the following command will build an image of Peter Norvig's
|
||||
Pytudes_ repository::
|
||||
|
||||
jupyter-repo2docker https://github.com/norvig/pytudes
|
||||
|
||||
To build a particular branch and commit, use the argument ``--ref`` to
|
||||
specify the ``branch-name`` or ``commit-hash``::
|
||||
|
||||
jupyter-repo2docker https://github.com/norvig/pytudes --ref 9ced85dd9a84859d0767369e58f33912a214a3cf
|
||||
|
||||
.. tip::
|
||||
For reproducible research, we recommend specifying a commit-hash to
|
||||
deterministically build a fixed version of a repository. Not specifying a
|
||||
commit-hash will result in the latest commit of the repository being built.
|
||||
|
||||
Building the image may take a few minutes.
|
||||
|
||||
During building, ``repo2docker``
|
||||
clones the repository to obtain its contents and inspects the repository for
|
||||
:ref:`configuration files <config-files>`.
|
||||
|
||||
By default, ``repo2docker`` will assume you are using
|
||||
Python 3.6 unless you include the version of Python in your
|
||||
:ref:`configuration files <config-files>`. ``repo2docker`` support is best with
|
||||
Python 2.7, 3.5, and 3.6. In the case of this repository, a Python version is not
|
||||
specified in their configuration files and Python 3.6 is installed.
|
||||
|
||||
Pytudes_
|
||||
uses a `requirements.txt file <https://github.com/norvig/pytudes/blob/master/requirements.txt>`_
|
||||
to specify its Python environment. ``repo2docker`` uses ``pip`` to install
|
||||
dependencies listed in the ``requirement.txt`` in the image. To learn more about
|
||||
to specify its Python environment. Because of this, ``repo2docker`` will use
|
||||
``pip`` to install dependencies listed in this ``requirement.txt`` file, and
|
||||
these will be present in the generated Docker image. To learn more about
|
||||
configuration files in ``repo2docker`` visit :ref:`config-files`.
|
||||
|
||||
.. _Pytudes: https://github.com/norvig/pytudes
|
||||
|
||||
When the image is built, a message will be output to your terminal::
|
||||
|
||||
Copy/paste this URL into your browser when you connect for the first time,
|
||||
|
|
@ -64,25 +54,82 @@ When the image is built, a message will be output to your terminal::
|
|||
Pasting the URL into your browser will open Jupyter Notebook with the
|
||||
dependencies and contents of the source repository in the built image.
|
||||
|
||||
Because JupyterLab is a server extension of the classic Jupyter Notebook server,
|
||||
you can launch JupyterLab by opening Jupyter Notebook and visiting the
|
||||
```/lab`` to the end of the URL:
|
||||
|
||||
Building a specific branch / commit / tag
|
||||
=========================================
|
||||
|
||||
To build a particular branch and commit, use the argument ``--ref`` and
|
||||
specify the ``branch-name`` or ``commit-hash``. For example::
|
||||
|
||||
jupyter-repo2docker https://github.com/norvig/pytudes --ref 9ced85dd9a84859d0767369e58f33912a214a3cf
|
||||
|
||||
.. tip::
|
||||
For reproducible research, we recommend specifying a commit-hash to
|
||||
deterministically build a fixed version of a repository. Not specifying a
|
||||
commit-hash will result in the latest commit of the repository being built.
|
||||
|
||||
|
||||
Where to put configuration files
|
||||
================================
|
||||
|
||||
``repo2docker`` will look for configuration files in either:
|
||||
|
||||
* A folder named ``binder/`` in the root of the repository.
|
||||
* The root directory of the repository.
|
||||
|
||||
If the folder ``binder/`` is located at the top level of the repository,
|
||||
**only configuration files in the** ``binder/`` **folder will be considered**.
|
||||
|
||||
.. note::
|
||||
|
||||
``repo2docker`` builds an environment with Python 3.6 by default. If you'd
|
||||
like a different version, you can specify this in your
|
||||
:ref:`configuration files <config-files>`.
|
||||
|
||||
|
||||
.. _user_interface:
|
||||
|
||||
Specifying the user interface
|
||||
=============================
|
||||
|
||||
repo2docker can build several user interfaces into the resulting Docker image.
|
||||
This is controlled with various :ref:`configuration files <config-files>`.
|
||||
|
||||
JupyterLab
|
||||
----------
|
||||
|
||||
repo2docker does not need any extra configuration in order to allow the use
|
||||
of the JupyterLab interface. You can launch JupyterLab from within a repo2docker
|
||||
image by opening the Jupyter Notebook and appending ``/lab`` to the end of the URL
|
||||
like so:
|
||||
|
||||
.. code-block:: none
|
||||
|
||||
http(s)://<server:port>/<lab-location>/lab
|
||||
http(s)://<server:port>/lab
|
||||
|
||||
To switch back to the classic notebook, add ``/tree`` to the URL:
|
||||
To switch back to the classic notebook, add ``/tree`` to the URL like so:
|
||||
|
||||
.. code-block:: none
|
||||
|
||||
http(s)://<server:port>/<lab-location>/tree
|
||||
http(s)://<server:port>/tree
|
||||
|
||||
To learn more about URLs in JupyterLab and Jupyter Notebook, visit
|
||||
`starting JupyterLab <http://jupyterlab.readthedocs.io/en/latest/getting_started/starting.html>`_.
|
||||
|
||||
``--debug`` and ``--no-build``
|
||||
------------------------------
|
||||
RStudio
|
||||
-------
|
||||
|
||||
The RStudio user interface is enabled when repo2docker detects a configuration
|
||||
for R (an R version specified in ``runtime.txt``). If this is detected,
|
||||
RStudio will be accessible by appending ``/rstudio`` to the URL, like so:
|
||||
|
||||
.. code-block:: none
|
||||
|
||||
http(s)://<server:port>/rstudio
|
||||
|
||||
|
||||
Debugging repo2docker with ``--debug`` and ``--no-build``
|
||||
=========================================================
|
||||
|
||||
To debug the docker image being built, pass the ``--debug`` parameter:
|
||||
|
||||
|
|
@ -100,3 +147,28 @@ be used by docker directly.
|
|||
.. code-block:: bash
|
||||
|
||||
jupyter-repo2docker --no-build --debug https://github.com/norvig/pytudes
|
||||
|
||||
|
||||
Building JupyterHub-ready images
|
||||
================================
|
||||
|
||||
JupyterHub_ allows multiple
|
||||
users to collaborate on a shared Jupyter server. ``repo2docker`` can build
|
||||
Docker images that can be shared within a JupyterHub deployment. For example,
|
||||
`mybinder.org <https://mybinder.org>`_ uses JupyterHub and ``repo2docker``
|
||||
to allow anyone to build a Docker image of a git repository online and
|
||||
share an executable version of the repository with a URL to the built image.
|
||||
|
||||
To build JupyterHub_-ready Docker images with ``repo2docker``, the
|
||||
version of your JupterHub deployment must be included in the
|
||||
``environment.yml`` or ``requirements.txt`` of the git repositories you
|
||||
build.
|
||||
|
||||
If your instance of JupyterHub uses ``DockerSpawner``, you will need to set its
|
||||
command to run ``jupyterhub-singleuser`` by adding this line in your
|
||||
configuration file::
|
||||
|
||||
c.DockerSpawner.cmd = ['jupyterhub-singleuser']
|
||||
|
||||
.. _JupyterHub: https://github.com/jupyterhub/jupyterhub
|
||||
.. _Pytudes: https://github.com/norvig/pytudes
|
||||
|
|
|
|||
Ładowanie…
Reference in New Issue