narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Add comments to .travis.yml on why we do what we do

MODIFY .travis.yml .travis.yml @@ -5,12 +5,16 @@ services: python: - 3.4 install: +# Make a wheel and install it to test to catch possible +# issues with MANIFEST.in - pip install --no-cache-dir pyyaml pytest wheel - python setup.py bdist_wheel - pip install dist/*.whl script: - - pytest -s -v tests/${REPO_TYPE} + # cd into tests so CWD being repo2docker does not hide + # possible issues with MANIFEST.in + - cd tests && pytest -s -v ${REPO_TYPE} jobs: include:

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do not reuse BuildPack instances rather than instantiating all buildpacks ahead of time, only instantiate as needed. Makes it clear that a given BuildPack should only perform a single build and a new BuildPack should be created for a subsequent build.

MODIFY repo2docker/app.py repo2docker/app.py @@ -60,13 +60,13 @@ class Repo2Docker(Application): buildpacks = List( [ - LegacyBinderDockerBuildPack(), - DockerBuildPack(), - JuliaBuildPack(), - CondaBuildPack(), - Python2BuildPack(), - RBuildPack(), - PythonBuildPack() + LegacyBinderDockerBuildPack, + DockerBuildPack, + JuliaBuildPack, + CondaBuildPack, + Python2BuildPack, + RBuildPack, + PythonBuildPack, ], config=True, help=""" @@ -75,7 +75,7 @@ class Repo2Docker(Application): ) default_buildpack = Any( - PythonBuildPack(), + PythonBuildPack, config=True, help=""" The build pack to use when no buildpacks are found @@ -547,12 +547,14 @@ class Repo2Docker(Application): ) os.chdir(checkout_path) - picked_buildpack = self.default_buildpack - for bp in self.buildpacks: + for BP in self.buildpacks: + bp = BP() if bp.detect(): picked_buildpack = bp break + else: + picked_buildpack = self.default_buildpack() self.log.debug(picked_buildpack.render(), extra=dict(phase='building'))

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allow passing argv to repo2docker.initialize matching existing Applications

MODIFY repo2docker/app.py repo2docker/app.py @@ -320,8 +320,10 @@ class Repo2Docker(Application): exc_info=(etype, evalue, traceback), extra=dict(phase='failed')) - def initialize(self): - args = self.get_argparser().parse_args() + def initialize(self, argv=None): + if argv is None: + argv = sys.argv[1:] + args = self.get_argparser().parse_args(argv) if args.debug: self.log_level = logging.DEBUG

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enable coverage on Travis ensure pip is up to date enable pip caching run tests with Python 3.6 publish coverage to codecov

MODIFY .gitignore .gitignore @@ -9,6 +9,8 @@ MANIFEST .DS_Store .cache +.coverage +htmlcov repo2docker/s2i MODIFY .travis.yml .travis.yml language: python sudo: required +cache: pip services: - docker python: -- 3.4 +- 3.6 install: # Make a wheel and install it to test to catch possible -# issues with MANIFEST.in -- pip install --no-cache-dir -r dev-requirements.txt + # issues with releases + - pip install --upgrade setuptools pip + - pip install -r dev-requirements.txt - python setup.py bdist_wheel - pip install dist/*.whl script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in - - cd tests && pytest -s -v ${REPO_TYPE} + - cd tests && pytest --cov repo2docker -s -v ${REPO_TYPE} +after_success: + - pip install codecov + - codecov jobs: include: MODIFY dev-requirements.txt dev-requirements.txt pyyaml pytest wheel +pytest-cov

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improve failure message

MODIFY tests/conftest.py tests/conftest.py @@ -9,6 +9,7 @@ success. """ import os +import pipes import shlex import pytest @@ -36,13 +37,22 @@ def make_test_func(args): class Repo2DockerTest(pytest.Function): """A pytest.Item for running repo2docker""" def __init__(self, name, parent, args): + self.args = args + self.save_cwd = os.getcwd() f = parent.obj = make_test_func(args) super().__init__(name, parent, callobj=f) - self.save_cwd = os.getcwd() def reportinfo(self): return self.parent.fspath, None, "" + def repr_failure(self, excinfo): + err = excinfo.value + if isinstance(err, SystemExit): + cmd = "jupyter-repo2docker %s" % ' '.join(map(pipes.quote, self.args)) + return "%s | exited with status=%s" % (cmd, err.code) + else: + return super().repr_failure(excinfo) + def teardown(self): super().teardown() os.chdir(self.save_cwd)

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remove -s on Travis now that we have better reporting of failures

MODIFY .travis.yml .travis.yml @@ -16,7 +16,7 @@ install: script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in - - cd tests && pytest --cov repo2docker -s -v ${REPO_TYPE} + - cd tests && pytest --cov repo2docker -v ${REPO_TYPE} after_success: - pip install codecov - codecov

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clone recursively ensures submodules, if any, are included

MODIFY repo2docker/app.py repo2docker/app.py @@ -151,7 +151,7 @@ class Repo2Docker(Application): def fetch(self, url, ref, checkout_path): try: - for line in execute_cmd(['git', 'clone', url, checkout_path], + for line in execute_cmd(['git', 'clone', '--recursive', url, checkout_path], capture=self.json_logs): self.log.info(line, extra=dict(phase='fetching')) except subprocess.CalledProcessError:

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test appendix

MODIFY tests/conftest.py tests/conftest.py @@ -62,7 +62,11 @@ class LocalRepo(pytest.File): def collect(self): yield Repo2DockerTest( self.fspath.basename, self, - args=[self.fspath.dirname, './verify'], + args=[ + '--appendix', 'RUN echo "appendix" > /tmp/appendix', + self.fspath.dirname, + './verify', + ], ) MODIFY tests/venv/default/verify tests/venv/default/verify # Verify that the default just provides a py3 environment with jupyter import sys -assert sys.version_info[:2] == (3, 6) +assert sys.version_info[:2] == (3, 6), sys.version import jupyter + +with open('/tmp/appendix') as f: + assert f.read().strip() == 'appendix'

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update postBuild error checking to be more flexible if the postBuild line changes

MODIFY tests/memlimit.py tests/memlimit.py @@ -37,7 +37,7 @@ def does_build(builddir, mem_limit, mem_allocate_mb): except subprocess.CalledProcessError as e: output = e.output.decode() print(output) - if "The command '/bin/sh -c ./postBuild' returned a non-zero code: 137" in output: + if "/postBuild' returned a non-zero code: 137" in output: return False else: raise

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Start specifiying our plans for stability in repo2docker versions

MODIFY docs/source/design.md docs/source/design.md @@ -31,6 +31,27 @@ This provides a few advantages: multiple repositories, enabling better use of the Docker build cache. This also provides massive performance advantages. +## Reproducibility and version stability + +Many ingredients go into making an image from a repository: + +1. version of the base docker image +1. version of `repo2docker` itself +1. versions of the libraries installed by the repository + +`repo2docker` controls the first two, the user controls the third one. The current +policy for the version of the base image is that we will keep pace with Ubuntu +releases until we reach the next release with Long Term Support (LTS). We +currently use Artful Aardvark (17.10) and the next LTS version will be +Bionic Beaver (18.04). + +The version of `repo2docker` used to build an image can influence which packages +are installed by default and which features are supported during the build +process. We will periodically update those packages to keep step with releases +of jupyter notebook, jupyterlab, etc. For packages that are installed by +default but where you want to control the version we recommend you specify them +explicitly in your dependencies. + ## Unix principles "do one thing well" `repo2docker` should do one thing, and do it well. This one thing is:

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omit appendix on custom Dockerfiles using a custom Dockerfile means opting out of *all* repo2docker logic

MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py @@ -15,7 +15,7 @@ class DockerBuildPack(BuildPack): def render(self): Dockerfile = self.binder_path('Dockerfile') with open(Dockerfile) as f: - return '\n'.join([f.read(), self.appendix, '']) + return f.read() def build(self, image_spec, memory_limit, build_args): limits = {

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Setup R libraries path for RStudio This makes sure our base R install (used by the notebook kernel) and RStudio share the same packages.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -155,6 +155,16 @@ class RBuildPack(PythonBuildPack): rstudio_checksum=rstudio_checksum ) ), + ( + "root", + # Set paths so that RStudio shares libraries with base R + # install. This first comments out any R_LIBS_USER that + # might be set in /etc/R/Renviron and then sets it. + r""" + sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \ + echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron + """ + ), ( "${NB_USER}", # Install nbrsessionproxy

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make sure there's a newline before each 'File: ' heading

MODIFY docs/source/conf.py docs/source/conf.py @@ -202,7 +202,7 @@ for root, _, files in os.walk(os.path.join('..', '..', 'tests')): continue header = files.pop(files.index('README.rst')) with open(os.path.join(root, header), 'r') as ff: - this_s = ff.read() + '\n' + this_s = ff.read() + '\n\n' title = this_s.split('\n')[0] for ifile in files: filename = os.path.basename(ifile)

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Update base.py adding unzip to base packages so you can just run unzip on the terminal (closing https://github.com/jupyter/repo2docker/issues/251)

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -170,6 +170,8 @@ class BuildPack: # FIXME: Use npm from nodesource! # Everything seems to depend on npm these days, unfortunately. "npm", + + "unzip", } def get_env(self):

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Fix detecting dependency files in binder/ subidr

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py """ Buildpack for conda environments """ -import glob import os import re @@ -124,6 +123,5 @@ class CondaBuildPack(BaseImage): )) return super().get_assemble_scripts() + assembly_scripts - def detect(self): return os.path.exists(self.binder_path('environment.yml')) and super().detect() MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -85,7 +85,8 @@ class PythonBuildPack(BaseImage): return assemble_scripts def detect(self): - return os.path.exists('requirements.txt') and super().detect() + return (os.path.exists(self.binder_path('requirements.txt')) and + super().detect()) class Python2BuildPack(PythonBuildPack): @@ -96,7 +97,6 @@ class Python2BuildPack(PythonBuildPack): 'virtualenv' }) - def get_env(self): return super().get_env() + [ ('VENV2_PATH', '${APP_BASE}/venv2') MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -210,11 +210,12 @@ class RBuildPack(PythonBuildPack): ), ] - if os.path.exists('install.R'): + installR_path = self.binder_path('install.R') + if os.path.exists(installR_path): assemble_scripts += [ ( "${NB_USER}", - "Rscript install.R" + "Rscript %s" % installR_path ) ]

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edits for formatting

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -14,9 +14,8 @@ This section describes the general ways in which you can use :depth: 1 :local: -.. note:: - See the `Frequently Asked Questions <faq.html>`_ for more info. +See the `Frequently Asked Questions <faq.html>`_ for additional information. Preparing your repository ------------------------- @@ -59,13 +58,13 @@ of them in the same repository. There are a few notable rules for precedence: .. *** List of all configuration files *** .. include:: config_files.txt -Preparing a repo and ``repo2docker`` to build JupyterHub-ready images -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Preparing a repo to build JupyterHub-ready images +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ It is possible to use ``repo2docker`` to build JupyterHub-ready -Docker images. For this to work properly, **the version of the ``jupyterhub`` +Docker images. For this to work properly, the version of the ``jupyterhub`` package in your git repository must match the version in your JupyterHub -deployment**. For example, if your JupyterHub deployment runs ``jupyterhub==0.8``, +deployment. For example, if your JupyterHub deployment runs ``jupyterhub==0.8``, you should put the following in ``requirements.txt`` or ``environment.yml``:: jupyterhub==0.8.* @@ -88,11 +87,11 @@ The simplest invocation of ``repo2docker`` performs two steps: This two step process enable you to build an image and run it so you can explore the repository's contents. -The **command** used is: +The **command** used is:: juptyer-repo2docker <URL to repo> -where <URL to repo> provides a URL to the source repository. +where ``<URL to repo>`` provides a URL to the source repository. For example, use the following to build an image and launch a Jupyter Notebook server::

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add a bit of clarity to install instructions

MODIFY docs/source/install.rst docs/source/install.rst Installing ``repo2docker`` ========================== -1. Install `Docker <https://www.docker.com>`_ as it is required to build Docker images. +Prerequisite: docker +-------------------- -2. We recommend installing ``repo2docker`` with the ``pip`` tool:: +Install `Docker <https://www.docker.com>`_ as it is required to build Docker images. + +Installing with ``pip`` +----------------------- + +We recommend installing ``repo2docker`` with the ``pip`` tool:: python3 -m pip install jupyter-repo2docker For infomation on using ``repo2docker``, see :ref:`usage`. -Installing repo2docker from source code ---------------------------------------- +Installing from source code +--------------------------- Alternatively, you can install repo2docker from source, i.e. if you are contributing back to this project:: @@ -23,3 +29,14 @@ i.e. if you are contributing back to this project:: That's it! For information on using ``repo2docker``, see :ref:`usage`. + +Note about Windows support +-------------------------- + +Windows support by ``repo2docker`` is still in the experimental stage. + +An article about `using Windows and the WSL`_ (Windows Subsytem for Linux or +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

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remove outdated note

MODIFY docs/source/config_files.txt docs/source/config_files.txt Supported configuration files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Below is a list of supported configuration files. +Below is a list of supported configuration files (roughly in the order of build priority). .. contents:: :local: @@ -35,11 +35,6 @@ Example Contents - pip: - sphinx-gallery -.. important:: - - You must leave the ``environment.yml``'s name field empty for this - to work out of the box. - ``requirements.txt`` ^^^^^^^^^^^^^^^^^^^^

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MODIFY docs/source/usage.rst docs/source/usage.rst @@ -40,15 +40,17 @@ Locating and composing configuration files creating new custom configuration files. ``repodocker`` configuration files are all **composable** - you can use any number -of them in the same repository. There are a few notable rules for precedence: +of them in the same repository. + +There are a few notable rules for composition precedence and build priority: * ``Dockerfile``: If a Dockerfile is present in a repository, it will take precedence over all other configuration files (which will be ignored). * ``environment.yml`` with ``requirements.txt``: If both of these files are present, then ``environment.yml`` will be used to build the image, **not** ``requirements.txt``. If you wish to ``pip install`` packages using an - ``environment.yml`` file, `you should do so with the - *pip:* key <https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually>`_. + ``environment.yml`` file, you should do so with the + ``pip:`` key as described in the `conda documentation`_. .. note:: @@ -137,3 +139,5 @@ For a list of all the build configurations at your disposal, see the CLI help:: jupyter-repo2docker -h + +.. _conda documentation: https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually

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MODIFY docs/source/config_files.txt docs/source/config_files.txt @@ -38,7 +38,7 @@ Example Contents ``requirements.txt`` ^^^^^^^^^^^^^^^^^^^^ -This specifies a list of Python packages that would be installed in a virtualenv (or conda environment). +This specifies a list of Python packages that should be installed in a virtualenv (or conda environment). Example Contents ```````````````` MODIFY docs/source/usage.rst docs/source/usage.rst @@ -86,14 +86,14 @@ The simplest invocation of ``repo2docker`` performs two steps: 1. builds a Docker image from a git repo 2. runs a Jupyter server within the image -This two step process enable you to build an image and run it so you can +This two step process enables you to build an image and run it so you can explore the repository's contents. The **command** used is:: - juptyer-repo2docker <URL to repo> + juptyer-repo2docker <URL-or-path to repo> -where ``<URL to repo>`` provides a URL to the source repository. +where ``<URL-or-path to repo>`` provides a URL or path to the source repository. For example, use the following to build an image and launch a Jupyter Notebook server:: @@ -124,7 +124,7 @@ This will print the generated ``Dockerfile``, build it, and run it. To see the generated ``Dockerfile`` without actually building it, pass ``--no-build`` to the commandline. This ``Dockerfile`` output -is for **debugging purposes** for ``repo2docker`` only - it can not +is for **debugging purposes** of ``repo2docker`` only - it can not be used by docker directly. .. code-block:: bash

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Add comment about Dockerfiles vs config files

MODIFY docs/source/config_files.txt docs/source/config_files.txt @@ -15,6 +15,11 @@ Below is a list of supported configuration files (roughly in the order of build This will be treated as a regular Dockerfile and a regular Docker build will be performed. The presence of a Dockerfile takes priority over and ignores all other build behavior specified in other configuration files. + +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. + See the `Binder Documentation <https://mybinder.readthedocs.io/en/latest/dockerfile.html>`_ for best-practices with Dockerfiles.

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add docstrings for juliabuildpack

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py -""" -Generates a variety of Dockerfiles based on an input matrix -""" +"""Generates a Dockerfile based on an input matrix for Julia""" import os from .conda import CondaBuildPack class JuliaBuildPack(CondaBuildPack): """ - Julia + Conda build pack + Julia build pack which uses conda. + + The Julia build pack always uses the parent, `CondaBuildPack`, + since Julia does not work with Python virtual environments. + See https://github.com/JuliaPy/PyCall.jl/issues/410 - Julia does not work with Virtual Envs, - see https://github.com/JuliaPy/PyCall.jl/issues/410 """ def get_env(self): + """Get additional environment settings for Julia and Jupyter + + Returns: + an ordered list of environment setting tuples. + The tuple contains a string of the environment variable name and + a string of the environment setting. For example, + `('JULIA_VERSION', '0.6.0')` + + """ return super().get_env() + [ ('JULIA_PATH', '${APP_BASE}/julia'), ('JULIA_HOME', '${JULIA_PATH}/bin'), @@ -22,6 +31,13 @@ class JuliaBuildPack(CondaBuildPack): ] def get_path(self): + """Get path for Julia executables + + Returns: + an ordered list of path strings. The path to the Julia + executable is added to the list. + + """ return super().get_path() + ['${JULIA_PATH}/bin'] def get_build_scripts(self):

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add yuvipanda text suggestions

MODIFY repo2docker/app.py repo2docker/app.py @@ -46,7 +46,7 @@ class Repo2Docker(Application): @default('log_level') def _default_log_level(self): - """The system's default log level""" + """The application's default log level""" return logging.INFO git_workdir = Unicode( @@ -484,7 +484,7 @@ class Repo2Docker(Application): last_emit_time = time.time() def run_image(self): - """Run docker image""" + """Run docker container from built image""" client = docker.from_env(version='auto') if not self.run_cmd: port = str(self._get_free_port())

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refactor detect() to not call super

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py @@ -117,7 +117,11 @@ class JuliaBuildPack(CondaBuildPack): """ Check if current repo should be built with the Julia Build pack - super().detect() is called if Julia Build pack should be used. + super().detect() is not called in this function - it would return + false unless an `environment.yml` is present and we do not want to + require the presence of a `environment.yml` to use Julia. + + Instead we just check if the path to `REQUIRE` exists """ - return os.path.exists(self.binder_path('REQUIRE')) and super().detect() + return os.path.exists(self.binder_path('REQUIRE'))

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update validation logic error message and docstring

MODIFY repo2docker/app.py repo2docker/app.py @@ -190,7 +190,9 @@ class Repo2Docker(Application): """ Validate image_name read by argparse - Note: image_name contains only lowercase characters + Note: Container names must start with an alphanumeric character and + can then use _ . or - in addition to alphanumeric. + [a-zA-Z0-9][a-zA-Z0-9_.-]+ Args: image_name (string): argument read by the argument parser @@ -199,12 +201,16 @@ class Repo2Docker(Application): unmodified image_name Raises: - ArgumentTypeError: if image_name contains characters that are not - lowercase + ArgumentTypeError: if image_name contains characters that do not + meet the logic that container names must start + with an alphanumeric character and can then + use _ . or - in addition to alphanumeric. + [a-zA-Z0-9][a-zA-Z0-9_.-]+ """ if not is_valid_docker_image_name(image_name): - msg = ("%r is not a valid docker image name. Image name can " - "contain only lowercase characters." % image_name) + msg = ("%r is not a valid docker image name. Image name" + "must start with an alphanumeric character and" + "can then use _ . or - in addition to alphanumeric." % image_name) raise argparse.ArgumentTypeError(msg) return image_name

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expand julia docstrings

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py @@ -16,11 +16,10 @@ class JuliaBuildPack(CondaBuildPack): """Get additional environment settings for Julia and Jupyter Returns: - An ordered list of environment setting tuples. - The tuple contains a string of the environment variable name and - a string of the environment setting. For example, - `('JULIA_VERSION', '0.6.0')` + an ordered list of environment setting tuples + The tuples contain a string of the environment variable name and + a string of the environment setting: - `JULIA_PATH`: base path where all Julia Binaries and libraries will be installed - `JULIA_HOME`: path where all Julia Binaries will be installed @@ -29,6 +28,8 @@ class JuliaBuildPack(CondaBuildPack): - `JUPYTER`: environment variable required by IJulia to point to the `jupyter` executable + For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. + """ return super().get_env() + [ ('JULIA_PATH', '${APP_BASE}/julia'), @@ -55,11 +56,8 @@ class JuliaBuildPack(CondaBuildPack): All scripts found here should be independent of contents of a particular repository. - This installs: - - - the specified Julia version and path - - Julia packages with ownership granted to the notebook user - - IJulia + This creates a directory with permissions for installing julia packages + (from get_assemble_scripts). """ return super().get_build_scripts() + [

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Reword per review

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -7,7 +7,13 @@ from ..base import BaseImage class PythonBuildPack(BaseImage): """Setup Python 3 for use with a repository.""" def get_packages(self): - """Return list of Python3 packages to be installed.""" + """Return a list of the Python 3 core language packages to be installed + via apt-get for this BuildPack. + + Note: The packages specified here are for the core Python3 language. + Third party libraries are specified in other configuration files. + + """ return super().get_packages().union({ 'python3', 'python3-venv', @@ -137,7 +143,13 @@ class PythonBuildPack(BaseImage): class Python2BuildPack(PythonBuildPack): """Setup Python 2 for use with a repository.""" def get_packages(self): - """Return list of Python 2 packages to be installed.""" + """Return a list of the Python 2 core language packages to be installed + via apt-get for this BuildPack. + + Note: The packages specified here are for the core Python2 language. + Third party libraries are specified in other configuration files. + + """ return super().get_packages().union({ 'python', 'python-dev',

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add docstrings to docker buildpack

MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py -""" -Generates a variety of Dockerfiles based on an input matrix +"""Generates a variety of Dockerfiles based on an input matrix """ import os import docker @@ -7,17 +6,21 @@ from .base import BuildPack class DockerBuildPack(BuildPack): + """Docker BuildPack""" dockerfile = "Dockerfile" def detect(self): + """Check if current repo should be built with the Docker BuildPack""" return os.path.exists(self.binder_path('Dockerfile')) def render(self): + """Render the Dockerfile using by reading it from the source repo""" Dockerfile = self.binder_path('Dockerfile') with open(Dockerfile) as f: return f.read() def build(self, image_spec, memory_limit, build_args): + """Build a Docker image based on the Dockerfile in the source repo.""" limits = { # Always disable memory swap for building, since mostly # nothing good can come of that.

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fixing python2 search

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -238,10 +238,11 @@ class Python2BuildPack(PythonBuildPack): def get_assemble_scripts(self): """Return series of build-steps specific to this repository. """ + requirements_file = self.binder_path('requirements.txt') return super().get_assemble_scripts() + [ ( '${NB_USER}', - 'pip2 install --no-cache-dir -r requirements.txt' + 'pip2 install --no-cache-dir -r "{}"'.format(requirements_file) ) ]

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Updates comments on docstrings in freeze.py

MODIFY repo2docker/buildpacks/legacy/freeze.py repo2docker/buildpacks/legacy/freeze.py #!/usr/bin/env python3 """ -Freeze the conda environment.yml +Freeze the conda environment.yml for legacy dockerfiles. -It runs the freeze in a continuumio/miniconda3 image to ensure portability +It runs the freeze in the andrewosh/binder-base image used for legacy dockerfiles. Usage: @@ -58,7 +58,7 @@ def freeze(env_name, env_file, frozen_file): if __name__ == '__main__': - # allow specifying which Pythons to update on argv + # allow specifying which env(s) to update on argv env_names = sys.argv[1:] or ('root', 'python3') for env_name in env_names: env_file = env_name + ".yml"

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clarify render order

MODIFY repo2docker/buildpacks/legacy/__init__.py repo2docker/buildpacks/legacy/__init__.py @@ -46,7 +46,9 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): def render(self): """Render buildpack into a Dockerfile. - Render appendix (post-build commands) at the end of the Dockerfile. + Render legacy image source (andrewosh/binder-base at a specific commit) + and then prependix. Render appendix (post-build commands) at the end of + the Dockerfile. """ segments = [

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Add codecov configuration to enable PR comments

ADD .codecov.yml +# show coverage in CI status, not as a comment. Never consider it a failure. +comment: off +coverage: + status: + project: + default: + target: 0% + patch: + default: + target: 0%

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Add a mention of adding tests to CONTRIBUTING.md

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -83,7 +83,9 @@ Then you are good to go! ## Running tests We have a lot of tests for various cases supported by repo2docker in the `tests/` -subdirectory. These use [py.test](https://docs.pytest.org/). +subdirectory. If you fix a bug or add new functionality consider adding a new +test to prevent the bug from coming back. These use +[py.test](https://docs.pytest.org/). You can run all the tests with: @@ -196,7 +198,8 @@ See the subsections below for more detailed instructions. Once you've made the commit, please make a Pull Request to the `jupyter/repo2docker` repository, with a description of what versions were bumped / what new packages were -added and why. +added and why. If you fix a bug or add new functionality consider adding a new +test to prevent the bug from coming back/the feature breaking in the future. ## Creating a Release

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Corrects typos in Python buildpacks

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -142,7 +142,7 @@ class PythonBuildPack(BaseImage): if os.path.exists(runtime_txt): with open(runtime_txt) as f: runtime = f.read().strip() - if runtime.startswith("python"): + if runtime.startswith("python-3"): return True else: return False @@ -252,7 +252,7 @@ class Python2BuildPack(PythonBuildPack): if os.path.exists(requirements_txt): assemble_scripts.append(( '${NB_USER}', - 'pip3 install --no-cache-dir -r "{}"'.format(requirements_txt) + 'pip2 install --no-cache-dir -r "{}"'.format(requirements_txt) )) return assemble_scripts

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Add a test to select Python 3 via runtime.txt

ADD tests/venv/py3/README.rst +System - Specifying runtime environments +---------------------------------------- + +You can specify runtime environments (such as Python 2 or 3) with a +``runtime.txt`` file. + +This is an example that selects Python 3. Currently you can not use +this to select a sepcific version of Python 3 (e.g. 3.4 vs 3.6). If you +need this level of control we recommend you use a `environment.yml`. ADD tests/venv/py3/runtime.txt +python-3 ADD tests/venv/py3/verify +#!/usr/bin/env python3 +import sys + +print(sys.version_info) +assert sys.version_info[:1] == (3,)

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Use travis_retry to run tests

MODIFY .travis.yml .travis.yml @@ -16,7 +16,7 @@ install: script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in - - cd tests && pytest --cov repo2docker -v ${REPO_TYPE} + - cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE} after_success: - pip install codecov - codecov

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Add guidelines on merging work.

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -5,6 +5,7 @@ This document covers: - Setting up for Local Development - Running Tests - Updating and Freezing BuildPack Dependencies +- Merging a Pull Request - Creating a Release ## Setting up for Local Development @@ -201,6 +202,23 @@ repository, with a description of what versions were bumped / what new packages added and why. If you fix a bug or add new functionality consider adding a new test to prevent the bug from coming back/the feature breaking in the future. + +## Merging a Pull Request + +There are not a lot of rules around merging a Pull Request (PR), we rely on +individuals to be responsible and tread softly when doing so. Below a few +standard procedures that have proven useful over time that we do follow: + +* do not merge your own PR +* wait for travis to complete +* check if test coverage has gone up or down, consider discussing additional + tests to keep coverage at the same level or even increase it +* do use merge commits instead of merge-by-squashing/-rebasing. This makes it + easier to find all changes since the last deployment `git log --merges --pretty=format:"%h %<(10,trunc)%an %<(15)%ar %s" <deployed-revision>..` +* [when you merge do deploy to mybinder.org](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html) + + + ## Creating a Release We try to make a release of repo2docker every few months if possible.

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Corrects __init__.py It will install setup.py file only when binder folder does not exist.

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -117,7 +117,7 @@ class PythonBuildPack(BaseImage): # will be installed in python3 venv. This is less of a # surprise than requiring python2 to be requirements2.txt tho. assemble_scripts = super().get_assemble_scripts() - setup_py = self.binder_path('setup.py') + setup_py = 'setup.py' try: with open(self.binder_path('runtime.txt')) as f: runtime = f.read().strip() @@ -134,10 +134,10 @@ class PythonBuildPack(BaseImage): '${NB_USER}', 'pip3 install --no-cache-dir -r "{}"'.format(requirements_file) )) - if os.path.exists(setup_py): + if not os.path.exists('binder') and os.path.exists(setup_py): assemble_scripts.append(( '${NB_USER}', - '{} install . "{}"'.format(pip, setup_py) + '{} install --no-cache-dir .'.format(pip) )) return assemble_scripts

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split post build script command in Docker file `RUN chmod +x postBuild && ./postBuild` causes `./postBuild: Text file busy` error with Docker version 1.13.1

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -109,7 +109,8 @@ USER ${NB_USER} # Make sure that postBuild scripts are marked executable before executing them {% if post_build_scripts -%} {% for s in post_build_scripts -%} -RUN chmod +x {{ s }} && ./{{ s }} +RUN chmod +x {{ s }} +RUN ./{{ s }} {% endfor %} {% endif -%}

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document --e, --env command line flag

MODIFY docs/source/faq.md docs/source/faq.md @@ -24,3 +24,9 @@ or similar traditional docker command. Check out the [binder-examples](http://github.com/binder-examples/) github organization for example Dockerfiles you can copy & modify for your own use! + +## How do I set environment variables? + +Use the `-e` or `--env` flag for each variable that you want to define. + +For example `jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...` MODIFY docs/source/usage.rst docs/source/usage.rst @@ -131,6 +131,14 @@ be used by docker directly. jupyter-repo2docker --no-build --debug https://github.com/jakevdp/PythonDataScienceHandbook +Setting environment variables +----------------------------- + +If you want to define environment variables, you can pass the ``--env`` or ``-e`` parameter to the commandline: + + .. code-block:: bash + + jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ... Accessing help from the command line ------------------------------------

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Improve the error message for unsupported python2

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -266,4 +266,10 @@ class Python2BuildPack(PythonBuildPack): runtime = f.read().strip() if runtime == 'python-2.7': return True + elif runtime.startswith('python-2'): + raise ValueError( + "Only python-2.7 or python-3.x is supported in " + "runtime.txt, not '{}'".format(runtime_txt)) + else: + return False return False

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add KERNEL_PYTHON_PREFIX for py2 env and put it on PATH

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -25,17 +25,24 @@ class CondaBuildPack(BaseImage): the `NB_PYTHON_PREFIX` to the location of the jupyter binary. """ - return super().get_env() + [ + env = super().get_env() + [ ('CONDA_DIR', '${APP_BASE}/conda'), ('NB_PYTHON_PREFIX', '${CONDA_DIR}'), ] + if self.py2: + env.append(('KERNEL_PYTHON_PREFIX', '${CONDA_DIR}/envs/kernel')) + return env def get_path(self): """Return paths (including conda environment path) to be added to the PATH environment variable. """ - return super().get_path() + ['${CONDA_DIR}/bin'] + path = super().get_path() + if self.py2: + path.append('${KERNEL_PYTHON_PREFIX}/bin') + path.append('${CONDA_DIR}/bin') + return path def get_build_scripts(self): """

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verify that Python 3.5 works with venv

ADD tests/venv/py35/README.rst +System - Specifying runtime environments +---------------------------------------- + +You can specify runtime environments (such as Python 2 or 3) with a +``runtime.txt`` file. + +This is an example that selects Python 3. Currently you can not use +this to select a sepcific version of Python 3 (e.g. 3.4 vs 3.6). If you +need this level of control we recommend you use a `environment.yml`. ADD tests/venv/py35/runtime.txt +python-3.5 ADD tests/venv/py35/verify +#!/usr/bin/env python3 +import sys + +print(sys.version_info) +assert sys.version_info[:2] == (3, 5), sys.version

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kernel python prefix is always defined, even when it's the same as NB_PYTHON_PREFIX

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -31,6 +31,8 @@ class CondaBuildPack(BaseImage): ] if self.py2: env.append(('KERNEL_PYTHON_PREFIX', '${CONDA_DIR}/envs/kernel')) + else: + env.append(('KERNEL_PYTHON_PREFIX', '${NB_PYTHON_PREFIX}')) return env def get_path(self):

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Fix detect docstring for Python since it's not just about Python 3 anymore

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -69,7 +69,7 @@ class PythonBuildPack(CondaBuildPack): return assemble_scripts def detect(self): - """Check if current repo should be built with the Python 3 Build pack. + """Check if current repo should be built with the Python buildpack. """ requirements_txt = self.binder_path('requirements.txt') runtime_txt = self.binder_path('runtime.txt')

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readmes in py3 venv tests remove outdated note about not being able to pick a Python 3.x

MODIFY tests/venv/py3/README.rst tests/venv/py3/README.rst @@ -4,6 +4,5 @@ System - Specifying runtime environments You can specify runtime environments (such as Python 2 or 3) with a ``runtime.txt`` file. -This is an example that selects Python 3. Currently you can not use -this to select a sepcific version of Python 3 (e.g. 3.4 vs 3.6). If you -need this level of control we recommend you use a `environment.yml`. +This is an example that selects Python 3. +If you need this level of control we recommend you use a `environment.yml`. MODIFY tests/venv/py35/README.rst tests/venv/py35/README.rst @@ -4,6 +4,5 @@ System - Specifying runtime environments You can specify runtime environments (such as Python 2 or 3) with a ``runtime.txt`` file. -This is an example that selects Python 3. Currently you can not use -this to select a sepcific version of Python 3 (e.g. 3.4 vs 3.6). If you -need this level of control we recommend you use a `environment.yml`. +This is an example that selects Python 3.5. +If you need this level of control we recommend you use a `environment.yml`.

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clarify comments about requirements3.txt

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -31,18 +31,15 @@ class PythonBuildPack(CondaBuildPack): """Return series of build-steps specific to this repository. """ # If we have a runtime.txt & that's set to python-2.7, - # we will *not* install requirements.txt but will find & - # install a requirements3.txt file if it exists. - # This way, when using python2 env, requirements.txt will - # be installed in the python2 env, and requirements3.txt - # will be installed in python3 env. This is less of a - # surprise than requiring python2 to be requirements2.txt tho. + # requirements.txt will be installed in the *kernel* env + # and requirements3.txt (if it exists) + # will be installed in the python 3 notebook server env. assemble_scripts = super().get_assemble_scripts() setup_py = 'setup.py' pip = 'pip' if self.py2: # using python 2 kernel, - # requirements3.txt allows installation in the notebook env + # requirements3.txt allows installation in the notebook server env nb_requirements_file = self.binder_path('requirements3.txt') if os.path.exists(nb_requirements_file): assemble_scripts.append((

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always use $KERNEL_PYTHON_PREFIX/bin/pip it's always defined and always right for the pip for the kernel env, whether it's separate from the notebook or not.

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -36,7 +36,9 @@ class PythonBuildPack(CondaBuildPack): # will be installed in the python 3 notebook server env. assemble_scripts = super().get_assemble_scripts() setup_py = 'setup.py' - pip = 'pip' + # KERNEL_PYTHON_PREFIX is the env with the kernel, + # whether it's distinct from the notebook or the same. + pip = '${KERNEL_PYTHON_PREFIX}/bin/pip' if self.py2: # using python 2 kernel, # requirements3.txt allows installation in the notebook server env @@ -44,10 +46,8 @@ class PythonBuildPack(CondaBuildPack): if os.path.exists(nb_requirements_file): assemble_scripts.append(( '${NB_USER}', - 'pip install --no-cache-dir -r "{}"'.format(nb_requirements_file) + '${NB_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "{}"'.format(nb_requirements_file) )) - # subsequent `pip` calls should run in the kernel env - pip = '${KERNEL_PYTHON_PREFIX}/bin/pip' # install requirements.txt in the kernel env requirements_file = self.binder_path('requirements.txt')

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fix inverted path CONDA_DIR should come first, not last

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -42,8 +42,8 @@ class CondaBuildPack(BaseImage): """ path = super().get_path() if self.py2: - path.append('${KERNEL_PYTHON_PREFIX}/bin') - path.append('${CONDA_DIR}/bin') + path.insert(0, '${KERNEL_PYTHON_PREFIX}/bin') + path.insert(0, '${CONDA_DIR}/bin') return path def get_build_scripts(self):

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handle runtime not being Python in Python BuildPack because R buildpack subclasses the Python buildpack, where runtime.txt should be ignored for retrieving the Python version

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -16,7 +16,14 @@ class PythonBuildPack(CondaBuildPack): with open(self.binder_path('runtime.txt')) as f: runtime = f.read().strip() except FileNotFoundError: - runtime = 'python-' + self.major_pythons['3'] + runtime = '' + + if not runtime.startswith('python-'): + # not a Python runtime (e.g. R, which subclasses this) + # use the default Python + self._python_version = self.major_pythons['3'] + return self._python_version + py_version_info = runtime.split('-', 1)[1].split('.') py_version = '' if len(py_version_info) == 1:

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adding docs about ref

MODIFY repo2docker/app.py repo2docker/app.py @@ -176,6 +176,8 @@ class Repo2Docker(Application): sys.exit(1) if ref: + if len(ref.split('/')) != 2: + raise ValueError('--ref must be of the form remote/ref') try: for line in execute_cmd(['git', 'reset', '--hard', ref], cwd=checkout_path, @@ -245,7 +247,8 @@ class Repo2Docker(Application): argparser.add_argument( '--ref', - help='If building a git url, which ref to check out' + help=('If building a git url, which ref to check out. Must be of' + 'the form `remote/ref`. E.g., `origin/master`.') ) argparser.add_argument(

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adding warning for windows platform

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -6,6 +6,7 @@ import os import re import logging import docker +import sys TEMPLATE = r""" FROM buildpack-deps:artful @@ -144,6 +145,9 @@ class BuildPack: def __init__(self): self.log = logging.getLogger('repo2docker') self.appendix = '' + if sys.platform.startswith('win'): + self.log.warning("Windows environment detected. Note that Windows " + "support is experimental in repo2docker.") def get_packages(self): """

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adding test and more informative error

MODIFY repo2docker/app.py repo2docker/app.py @@ -177,7 +177,8 @@ class Repo2Docker(Application): if ref: if len(ref.split('/')) != 2: - raise ValueError('--ref must be of the form remote/ref') + raise ValueError('Expected --ref to be of the form ' + 'remote/reference, but got %s' % ref) try: for line in execute_cmd(['git', 'reset', '--hard', ref], cwd=checkout_path, @@ -247,8 +248,8 @@ class Repo2Docker(Application): argparser.add_argument( '--ref', - help=('If building a git url, which ref to check out. Must be of' - 'the form `remote/ref`. E.g., `origin/master`.') + help=('If building a git url, which reference to check out. Must ' + 'be of the form `remote/reference`. E.g., `origin/master`.') ) argparser.add_argument( MODIFY tests/argumentvalidation.py tests/argumentvalidation.py @@ -231,3 +231,12 @@ def test_docker_no_build_success(): assert validate_arguments(builddir, args_list, "", True) + +def test_ref_has_correct_form(): + """ + Test to check if --ref is given with the form `remote/reference` + """ + builddir = os.path.dirname(__file__) + args_list = ['--no-run', '--no-build', '--ref', 'myreference'] + + assert not validate_arguments(builddir, args_list, 'Expected --ref to be of the form remote/reference, but got myreference')

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fixing test for ref

MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml # A bunch of external repos that reproduce something cool we care about - name: LIGO Gravitational Waves url: https://github.com/minrk/ligo-binder/ - ref: b8259dac9eb + ref: origin/b8259dac9eb verify: python -c 'import matplotlib'

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remove _nb_ext_conf from legacy env _nb_ext_conf adds configuration that requires nb_conda_kernels, which has been removed, preventing launch

MODIFY repo2docker/buildpacks/legacy/__init__.py repo2docker/buildpacks/legacy/__init__.py @@ -23,7 +23,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): RUN conda install -yq conda>=4.3 && \ conda install -yq conda==4.4.11 && \ conda env update -n python3 -f /tmp/python3.frozen.yml && \ - conda remove -yq -n python3 nb_conda_kernels && \ + conda remove -yq -n python3 nb_conda_kernels _nb_ext_conf && \ conda env update -n root -f /tmp/root.frozen.yml && \ /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \ /home/main/anaconda2/bin/ipython kernel install --prefix=/home/main/anaconda2/envs/python3 && \

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set DEBIAN_FRONTEND=noninteractive avoids possible prompts during setup of apt packages

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -10,6 +10,9 @@ import docker TEMPLATE = r""" FROM buildpack-deps:bionic +# avoid prompts from apt +ENV DEBIAN_FRONTEND=noninteractive + # Set up locales properly RUN apt-get update && \ apt-get install --yes --no-install-recommends locales && \

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remove some duplicate READMEs from tests since we don't need every one included in the docs adds detail to the one that remains

MODIFY tests/venv/py2/README.rst tests/venv/py2/README.rst @@ -3,3 +3,7 @@ System - Specifying runtime environments You can specify runtime environments (such as Python 2 or 3) with a ``runtime.txt`` file. + +You can specify just the major version, +such as `python-2` or `python-3`, +or a minor version, such as `python-3.5`. DELETE tests/venv/py3/README.rst -System - Specifying runtime environments ----------------------------------------- - -You can specify runtime environments (such as Python 2 or 3) with a -``runtime.txt`` file. - -This is an example that selects Python 3. -If you need this level of control we recommend you use a `environment.yml`. DELETE tests/venv/py35/README.rst -System - Specifying runtime environments ----------------------------------------- - -You can specify runtime environments (such as Python 2 or 3) with a -``runtime.txt`` file. - -This is an example that selects Python 3.5. -If you need this level of control we recommend you use a `environment.yml`.

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Add bug, chat and contrib links to the front page It should be easier to find us to ask questions, report bugs and to get started contributing.

MODIFY docs/source/index.rst docs/source/index.rst @@ -5,6 +5,11 @@ jupyter-repo2docker images from source code repositories. See the list below for various ways in which you can use ``repo2docker``. +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:: @@ -17,4 +22,3 @@ Site Contents design architecture dev_newbuildpack -

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Allow for longer periods of no output during R tests

MODIFY .travis.yml .travis.yml @@ -16,7 +16,11 @@ install: script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in - - cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE} + - if [ ${REPO_TYPE} == "r" ]; + then cd tests && travis_wait pytest --cov repo2docker -v ${REPO_TYPE}; + else cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE}; + fi + after_success: - pip install codecov - codecov

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To add the user bin folder to the path Here thread

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -71,6 +71,9 @@ ENV {{item[0]}} {{item[1]}} {% endfor -%} {% endif -%} +# So users can move executables here with postBuild, issue #557 +ENV PATH {{ /home/jovyan/{local}/bin:${PATH}}} + {% if path -%} # Special case PATH ENV PATH {{ ':'.join(path) }}:${PATH}

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removing extra curly brackets

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -72,7 +72,7 @@ ENV {{item[0]}} {{item[1]}} {% endif -%} # So users can move executables here with postBuild, issue #557 -ENV PATH {{ '/home/jovyan/local/bin':${PATH}}} +ENV PATH '/home/jovyan/local/bin':${PATH} {% if path -%} # Special case PATH

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Use XDG standard ~/.local for user software installs ~/.local is also where things like pip install --user seem to install things, so we should use that instead of ~/local.

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -71,9 +71,6 @@ ENV {{item[0]}} {{item[1]}} {% endfor -%} {% endif -%} -# So users can move executables here with postBuild, issue #557 -ENV PATH '/home/jovyan/local/bin':${PATH} - {% if path -%} # Special case PATH ENV PATH {{ ':'.join(path) }}:${PATH} @@ -200,7 +197,10 @@ class BuildPack: Just sets the PATH environment variable. Separated out since it is very commonly set by various buildpacks. """ - return [] + # Allow local user installs into ~/.local, which is where the + # XDG desktop standard suggests these should be + # See https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html + return ['$HOME/.local/bin'] def get_labels(self): """

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Modify usr-bin test

MODIFY tests/venv/usr-bin/verify tests/venv/usr-bin/verify #!/usr/bin/env python -# Verify that ~/local/bin is on the PATH +# Verify that ~/.local/bin is on the PATH import os -PATH = os.getenv("PATH") -assert "/home/jovyan/local/bin" in PATH +assert "$HOME/.local/bin" in os.getenv("PATH") \ No newline at end of file

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short docs explanation

MODIFY docs/source/faq.md docs/source/faq.md @@ -9,6 +9,19 @@ If you have a question & have found an answer, send a PR to add it here! Currently the best way to do this is by using a conda ``environment.yml`` file and setting the language to whichever version of Python you like. +## Can I add binary files to the user's PATH? + +Yes! Using a ``postBuild`` file, you can place any files that should be called +from the command line in the folder ``~/.local/``. This folder will be +available in a user's PATH, and can be run from the command line (or as +a subsequent build step.) + +## How do I set environment variables? + +Use the `-e` or `--env` flag for each variable that you want to define. + +For example `jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...` + ## Can I use repo2docker to bootstrap my own Dockerfile? No, you can't. @@ -24,9 +37,3 @@ or similar traditional docker command. Check out the [binder-examples](http://github.com/binder-examples/) github organization for example Dockerfiles you can copy & modify for your own use! - -## How do I set environment variables? - -Use the `-e` or `--env` flag for each variable that you want to define. - -For example `jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...`

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nbrsessionproxy to 0.7 for shiny support!

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -4,6 +4,7 @@ import datetime from .python import PythonBuildPack + class RBuildPack(PythonBuildPack): """ Setup R for use with a repository @@ -169,7 +170,7 @@ class RBuildPack(PythonBuildPack): "${NB_USER}", # Install nbrsessionproxy r""" - pip install --no-cache-dir nbrsessionproxy==0.6.1 && \ + pip install --no-cache-dir nbrsessionproxy==0.7.0 && \ jupyter serverextension enable nbrsessionproxy --sys-prefix && \ jupyter nbextension install --py nbrsessionproxy --sys-prefix && \ jupyter nbextension enable --py nbrsessionproxy --sys-prefix

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Install shiny-server.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -128,6 +128,10 @@ class RBuildPack(PythonBuildPack): # This is MD5, because that is what RStudio download page provides! rstudio_checksum = '24cd11f0405d8372b4168fc9956e0386' + # Via https://www.rstudio.com/products/shiny/download-server/ + shiny_url = 'https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb' + shiny_checksum = '78371a8361ba0e7fec44edd2b8e425ac' + # Version of MRAN to pull devtools from. devtools_version = '2018-02-01' @@ -155,6 +159,20 @@ class RBuildPack(PythonBuildPack): rstudio_checksum=rstudio_checksum ) ), + ( + "root", + # Install Shiny Server! + r""" + curl --silent --location --fail {url} > {deb} && \ + echo '{checksum} {deb}' | md5sum -c - && \ + dpkg -i {deb} && \ + rm {deb} + """.format( + url=shiny_url, + checksum=shiny_checksum, + deb='/tmp/shiny.deb' + ) + ), ( "root", # Set paths so that RStudio shares libraries with base R

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Create shiny-server output directories.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -226,6 +226,16 @@ class RBuildPack(PythonBuildPack): echo "options(repos = c(CRAN='{mran_url}'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site """.format(mran_url=mran_url) ), + ( + # Not all of these locations are configurable; log_dir is + "root", + r""" + install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \ + install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \ + install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \ + install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid + """ + ), ] installR_path = self.binder_path('install.R')

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Checks if the environment.yml file is empty and if it contains a dictionary. If the environment.yml is empty, an empty dictionary is instantiated. This will rise an TypeError if the environment.yml file contains a list or other data structure different than a dictionary.

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -136,6 +136,12 @@ class CondaBuildPack(BaseImage): py_version = None with open(environment_yml) as f: env = YAML().load(f) + # check if the env file is empty, if so instantiate an empty dictionary. + if env is None: + env = {} + # check if the env file has a dictionary not a list or other data structure. + if not isinstance(env, dict): + raise TypeError("environment.yml should contain a dictionary. Got %r" % env) for dep in env.get('dependencies', []): if not isinstance(dep, str): continue ADD tests/test_env_yml.py +""" +Test if the environment.yml is empty or it constains other data structure than a dictionary +""" +import os +import sys +import pytest +from repo2docker import buildpacks + +#@pytest.mark.xfail(reason="Not yet implemented") +def test_empty_env_yml(tmpdir): + tmpdir.chdir() + p = tmpdir.join("environment.yml") + bp = buildpacks.CondaBuildPack() + with pytest.raises(Exception): + py_ver = bp.python_version() + +def test_no_dict_env_yml(tmpdir): + tmpdir.chdir() + q = tmpdir.join("environment.yml") + q.write("list/n ,string") + bq = buildpacks.CondaBuildPack() + with pytest.raises(Exception): + py_ver = bq.python_version() \ No newline at end of file

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Updated test_env_yml.py file

MODIFY tests/test_env_yml.py tests/test_env_yml.py @@ -6,18 +6,20 @@ import sys import pytest from repo2docker import buildpacks -#@pytest.mark.xfail(reason="Not yet implemented") + def test_empty_env_yml(tmpdir): tmpdir.chdir() p = tmpdir.join("environment.yml") + p.write("") bp = buildpacks.CondaBuildPack() - with pytest.raises(Exception): - py_ver = bp.python_version() + py_ver = bp.python_version + # If the environment.yml is empty python_version will get an empty string + assert py_ver == '' def test_no_dict_env_yml(tmpdir): tmpdir.chdir() q = tmpdir.join("environment.yml") q.write("list/n ,string") bq = buildpacks.CondaBuildPack() - with pytest.raises(Exception): - py_ver = bq.python_version() \ No newline at end of file + with pytest.raises(TypeError): + py_ver = bq.python_version \ No newline at end of file

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Install shiny library.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -203,6 +203,13 @@ class RBuildPack(PythonBuildPack): """.format( devtools_version=devtools_version, irkernel_version=irkernel_version + ), + ( + "${NB_USER}", + # Install a pinned version of IRKernel and set it up for use! + r""" + R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/{}', method='libcurl')" + """.format(self.checkpoint_date.isoformat()) ) ) ]

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Fix parentheses in the build scripts for R buildpack

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -204,15 +204,17 @@ class RBuildPack(PythonBuildPack): """.format( devtools_version=devtools_version, irkernel_version=irkernel_version + ) ), ( "${NB_USER}", # Install shiny library r""" R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/{}', method='libcurl')" - """.format(self.checkpoint_date.isoformat()) - ) + """.format( + self.checkpoint_date.isoformat() ) + ), ] def get_assemble_scripts(self):

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Update the TypeError message and example in the unit test.

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -141,7 +141,7 @@ class CondaBuildPack(BaseImage): env = {} # check if the env file has a dictionary not a list or other data structure. if not isinstance(env, dict): - raise TypeError("environment.yml should contain a dictionary. Got %r" % env) + raise TypeError("environment.yml should contain a dictionary. Got %r" % type(env)) for dep in env.get('dependencies', []): if not isinstance(dep, str): continue MODIFY tests/test_env_yml.py tests/test_env_yml.py @@ -19,7 +19,8 @@ def test_empty_env_yml(tmpdir): def test_no_dict_env_yml(tmpdir): tmpdir.chdir() q = tmpdir.join("environment.yml") - q.write("list/n ,string") + q.write("numpy\n " + "matplotlib\n") bq = buildpacks.CondaBuildPack() with pytest.raises(TypeError): py_ver = bq.python_version \ No newline at end of file

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Switch to miniconda v4.5.1

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -CONDA_VERSION=4.3.30 +CONDA_VERSION=4.5.1 URL="https://repo.continuum.io/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -12,7 +12,7 @@ chmod +x ${INSTALLER_PATH} # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="0b80a152332a4ce5250f3c09589c7a81" +MD5SUM="0c28787e3126238df24c5d4858bd0744" if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"

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Add root conda environment to expected output

MODIFY tests/conda/simple-py2/verify tests/conda/simple-py2/verify @@ -13,7 +13,7 @@ assert sorted(specs) == ['python2', 'python3'], specs.keys() import json from subprocess import check_output envs = json.loads(check_output(['conda', 'env', 'list', '--json']).decode('utf8')) -assert envs == {'envs': ['/srv/conda/envs/kernel']}, envs +assert envs == {'envs': ['/srv/conda', '/srv/conda/envs/kernel']}, envs pkgs = json.loads(check_output(['conda', 'list', '-n', 'kernel', '--json']).decode('utf8')) pkg_names = [pkg['name'] for pkg in pkgs]

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Split run_image into two steps for easier testing of image-running logic

MODIFY repo2docker/app.py repo2docker/app.py @@ -489,7 +489,18 @@ class Repo2Docker(Application): last_emit_time = time.time() def run_image(self): - """Run docker container from built image""" + """Run docker container from built image + + and wait for it to finish. + """ + container = self.start_container() + self.wait_for_container(container) + + def start_container(self): + """Start docker container from built image + + Returns running container + """ client = docker.from_env(version='auto') if not self.run_cmd: port = str(self._get_free_port()) @@ -504,6 +515,8 @@ class Repo2Docker(Application): ports = self.ports else: ports = {} + # store ports on self so they can be retrieved in tests + self.ports = ports container_volumes = {} if self.volumes: api_client = docker.APIClient( @@ -532,6 +545,14 @@ class Repo2Docker(Application): time.sleep(0.5) container.reload() + return container + + def wait_for_container(self, container): + """Wait for a container to finish + + Displaying logs while it's running + """ + try: for line in container.logs(stream=True): self.log.info(line.decode('utf-8'),

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checking for origin/ explicitly

MODIFY repo2docker/app.py repo2docker/app.py @@ -175,8 +175,10 @@ class Repo2Docker(Application): sys.exit(1) if ref: - if self.repo_type == "remote" and len(ref.split('/')) < 2: + if self.repo_type == "remote" and not ref.startswith('origin/'): # Ensure that the ref has `origin` in front + self.log.info("Ref did not have a remote specified, " + "adding 'origin/' to ref.") ref = '/'.join(["origin", ref]) try: for line in execute_cmd(['git', 'reset', '--hard', ref],

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sharing images with jhub and binder with r2d see

MODIFY docs/source/install.rst docs/source/install.rst @@ -57,9 +57,18 @@ 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: + JupyterHub-ready images ----------------------- +`JupyterHub <https://jupyterhub.readthedocs.io/en/stable/>`_ allows multiple +users to collaborate on a shared Jupyter server. ``repo2docker`` can build +Docker images that can be shared within a JupyterHub deployment. An example +of using JupyterHub with ``repo2docker`` is Project Jupyter's free online +service, `mybinder.org <https://mybinder.org>`_, which allows anyone to +build a Docker image of a git repo online share the image with a URL. + To build `JupyterHub <https://github.com/jupyterhub/jupyterhub>`_-ready Docker images with ``repo2docker``, the version of your JupterHub deployment must be included in the ``environment.yml`` or ``requiements.txt`` of the

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Bring the versions in sync

MODIFY .travis.yml .travis.yml @@ -50,6 +50,8 @@ matrix: deploy: provider: pypi user: betatim + # this line together with `setup.cfg` creates universal wheels as long as + # repo2docker is a python only module (no compiled code) distributions: sdist bdist_wheel on: tags: true MODIFY repo2docker/__init__.py repo2docker/__init__.py -__version__ = '0.2.0' +__version__ = '0.5.0' MODIFY setup.cfg setup.cfg +# used by our travis auto-deployment system +# needs changing if repo2docker ever stops being +# a pure python module [wheel] universal = 1 MODIFY setup.py setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages setup( name='jupyter-repo2docker', - version='0.5.0', + version='0.5.1', install_requires=[ 'docker', 'traitlets',

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Add comments back to travis config

MODIFY .travis.yml .travis.yml @@ -6,11 +6,15 @@ services: python: - 3.6 install: +# Make a wheel and install it to test to catch possible +# issues with releases - pip install --upgrade setuptools pip - pip install -r dev-requirements.txt - python setup.py bdist_wheel - pip install dist/*.whl script: +# cd into tests so CWD being repo2docker does not hide +# possible issues with MANIFEST.in - if [ ${REPO_TYPE} == "r" ]; then cd tests && travis_wait pytest --cov repo2docker -v ${REPO_TYPE}; else cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE}; fi MODIFY repo2docker/__init__.py repo2docker/__init__.py -__version__ = '0.5.0' - from ._version import get_versions __version__ = get_versions()['version'] del get_versions

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Add DockerSpawner command in JupyterHub config This may be useful to DockerSpawner users who want to create custom images using repo2docker

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -63,6 +63,11 @@ you should put the following in ``requirements.txt`` or ``environment.yml``:: jupyterhub==0.8.* +In your JupyterHub configuration, you may also need to pass a command to the Spawner +to run ``jupyterhub-singleuser``, for instance if using ``DockerSpawner``:: + + c.DockerSpawner.cmd = ['jupyterhub-singleuser'] + Running ``repo2docker`` locally -------------------------------

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Edit to be more affirmative

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -63,8 +63,8 @@ you should put the following in ``requirements.txt`` or ``environment.yml``:: jupyterhub==0.8.* -In your JupyterHub configuration, you may also need to pass a command to the Spawner -to run ``jupyterhub-singleuser``, for instance if using ``DockerSpawner``:: +If your instance of JupyterHub uses ``DockerSpawner``, you will need to set its +command to run ``jupyterhub-singleuser``:: c.DockerSpawner.cmd = ['jupyterhub-singleuser']

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Mention the jupyterhub config file

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -64,7 +64,7 @@ you should put the following in ``requirements.txt`` or ``environment.yml``:: jupyterhub==0.8.* If your instance of JupyterHub uses ``DockerSpawner``, you will need to set its -command to run ``jupyterhub-singleuser``:: +command to run ``jupyterhub-singleuser`` by adding this line in your configuration file:: c.DockerSpawner.cmd = ['jupyterhub-singleuser']

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Fixs dockerfile tests that did not work

MODIFY tests/dockerfile/binder-dir/binder/Dockerfile tests/dockerfile/binder-dir/binder/Dockerfile FROM python:3.5 -ENTRYPOINT "/bin/sh" +RUN pip install --no-cache notebook + +CMD "/bin/sh" ADD sayhi.sh /usr/local/bin/sayhi.sh ADD verify verify + +ARG NB_UID +ENV HOME /tmp +USER $NB_UID MODIFY tests/dockerfile/binder-dir/verify tests/dockerfile/binder-dir/verify -#!/bin/sh +#!/bin/bash set -euo pipefail /usr/local/bin/sayhi.sh MODIFY tests/dockerfile/simple/Dockerfile tests/dockerfile/simple/Dockerfile FROM python:3.5 -ENTRYPOINT "/bin/sh" +RUN pip install --no-cache notebook + +CMD "/bin/sh" ADD sayhi.sh /usr/local/bin/sayhi.sh ADD verify verify + +ARG NB_UID +ENV HOME /tmp +USER $NB_UID MODIFY tests/dockerfile/simple/verify tests/dockerfile/simple/verify -#!/bin/sh +#!/bin/bash set -euo pipefail /usr/local/bin/sayhi.sh

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Fix some rst weirdness in the uage docs

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -26,9 +26,9 @@ For example, use the following to build an image of the jupyter-repo2docker https://github.com/jakevdp/PythonDataScienceHandbook To build a particular branch and commit, use the argument ``--ref`` to -specify the ``branch-name/commit-hash``:: +specify the ``branch-name`` or ``commit-hash``:: - jupyter-repo2docker https://github.com/jakevdp/PythonDataScienceHandbook --ref master/599aa0fe3f882c0001670e676e5a8d43b92c35fc + jupyter-repo2docker https://github.com/jakevdp/PythonDataScienceHandbook --ref 599aa0fe3f882c0001670e676e5a8d43b92c35fc .. tip:: For reproducibile research, we recommend specifying a commit-hash to

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scinece -> science

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -21,7 +21,7 @@ repo2docker is called with this command:: where ``<URL-or-path to repo>`` is a URL or path to the source repository. For example, use the following to build an image of the -`Python Data Scinece Handbook <https://github.com/jakevdp/PythonDataScienceHandbook>`_:: +`Python Data Science Handbook <https://github.com/jakevdp/PythonDataScienceHandbook>`_:: jupyter-repo2docker https://github.com/jakevdp/PythonDataScienceHandbook @@ -47,7 +47,7 @@ Python 3.6 unless you include the version of Python in your Python 2.7, 3.5, and 3.6. In the case of this repo, a Python version is not specified in their configuation files and Python 3.6 is installed. -`Python Data Scinece Handbook <https://github.com/jakevdp/PythonDataScienceHandbook>`_ +`Python Data Science Handbook <https://github.com/jakevdp/PythonDataScienceHandbook>`_ uses a `requirements.txt file <https://github.com/jakevdp/PythonDataScienceHandbook/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

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install deps in same step

MODIFY .circleci/config.yml .circleci/config.yml @@ -44,18 +44,16 @@ jobs: pigz -d --stdout /tmp/cache/container.tar.gz | docker load fi docker images - - run: # install and activate virtual environment with pip - name: Install Repo2Docker + - run: + name: Generate Docker Image + no_output_timeout: 60m command: | + echo "0. Installing dependencies..." python3 -m venv venv . venv/bin/activate pip install jupyter-repo2docker export VERSION=$(python3 -c "import repo2docker; print(repo2docker.__version__)") echo "repo2docker version: ${VERSION}" - - run: - name: Generate Docker Image - no_output_timeout: 60m - command: | echo "1. Preparing building environment" echo "Working directory is ${PWD}" # If not set, define CONTAINER_NAME

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try setting username

MODIFY .circleci/config.yml .circleci/config.yml @@ -45,7 +45,7 @@ jobs: fi docker images - run: - name: Generate Docker Image + name: Run jupyter-repo2docker to generate Docker Container no_output_timeout: 60m command: | echo "0. Installing dependencies..." @@ -70,7 +70,7 @@ jobs: echo "Repository name is ${REPO_NAME}" echo "2. Running jupyter-repo2docker..." echo "jupyter-repo2docker --debug --image-name ${CONTAINER_NAME} ${REPO_NAME}" - jupyter-repo2docker --debug --image-name "${CONTAINER_NAME}" "${REPO_NAME}" + USER=username jupyter-repo2docker --debug --image-name "${CONTAINER_NAME}" "${REPO_NAME}" - run: name: Docker Save no_output_timeout: 40m

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try setting username and userid

MODIFY .circleci/config.yml .circleci/config.yml @@ -70,7 +70,7 @@ jobs: echo "Repository name is ${REPO_NAME}" echo "2. Running jupyter-repo2docker..." echo "jupyter-repo2docker --debug --image-name ${CONTAINER_NAME} ${REPO_NAME}" - USER=username jupyter-repo2docker --debug --image-name "${CONTAINER_NAME}" "${REPO_NAME}" + jupyter-repo2docker --debug --user-name username --user-id 1000 --image-name "${CONTAINER_NAME}" "${REPO_NAME}" - run: name: Docker Save no_output_timeout: 40m

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adding example with save

MODIFY .circleci/config.yml .circleci/config.yml @@ -3,7 +3,10 @@ jobs: # If you want to deploy your container to Docker Hub, you must # 1. define the CONTAINER_NAME environment variable for the project - # 2. Also define DOCKER_USER and DOCKER_PASS + # If not defined, will use the repo that is being built from. + # 2. define the REPO_NAME with the juypter notebook you want to build. If not + # defined, will use https://www.github.com/{CONTAINER_NAME} + # 2. Also define DOCKER_USER and DOCKER_PASS (for deploy, if wanted) setup: environment: - TZ: "/usr/share/zoneinfo/America/Los_Angeles" @@ -70,7 +73,11 @@ jobs: echo "Repository name is ${REPO_NAME}" echo "2. Running jupyter-repo2docker..." echo "jupyter-repo2docker --debug --image-name ${CONTAINER_NAME} ${REPO_NAME}" - jupyter-repo2docker --debug --user-name username --user-id 1000 --image-name "${CONTAINER_NAME}" "${REPO_NAME}" + jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name "${CONTAINER_NAME}" "${REPO_NAME}" + echo "3. Running without server (example)" + docker run -td --name repo2docker --entrypoint /bin/bash "${CONTAINER_NAME}" + docker ps + docker images - run: name: Docker Save no_output_timeout: 40m

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also deploy on branch non-master

MODIFY .circleci/config.yml .circleci/config.yml @@ -72,7 +72,7 @@ jobs: echo "Container name is ${CONTAINER_NAME}" echo "Repository name is ${REPO_NAME}" echo "2. Running jupyter-repo2docker..." - echo "jupyter-repo2docker --debug --image-name ${CONTAINER_NAME} ${REPO_NAME}" + echo "jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name ${CONTAINER_NAME} ${REPO_NAME}" jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name "${CONTAINER_NAME}" "${REPO_NAME}" echo "3. Running without server (example)" docker run -td --name repo2docker --entrypoint /bin/bash "${CONTAINER_NAME}" @@ -166,8 +166,5 @@ workflows: - deploy: requires: - build - filters: - branches: - only: master tags: only: /.*/

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adding version argument

MODIFY repo2docker/app.py repo2docker/app.py @@ -217,6 +217,7 @@ class Repo2Docker(Application): def get_argparser(self): """Get arguments that may be used by repo2docker""" argparser = argparse.ArgumentParser() + argparser.add_argument( '--config', default='repo2docker_config.py', @@ -342,6 +343,15 @@ class Repo2Docker(Application): type=str, help=self.traits()['appendix'].help, ) + + argparser.add_argument( + '--version', + dest='version', + action='store_true', + help='Print the repo2docker version and exit.' + ) + + return argparser def json_excepthook(self, etype, evalue, traceback): @@ -353,10 +363,16 @@ class Repo2Docker(Application): exc_info=(etype, evalue, traceback), extra=dict(phase='failed')) + def initialize(self, argv=None): """Init repo2docker configuration before start""" if argv is None: argv = sys.argv[1:] + + if '--version' in argv: + print(self.version) + sys.exit(0) + args = self.get_argparser().parse_args(argv) if args.debug:

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forgot to add tag to build step!

MODIFY .circleci/config.yml .circleci/config.yml @@ -79,10 +79,8 @@ jobs: echo "Container name is ${CONTAINER_NAME}" echo "Repository name is ${REPO_NAME}" echo "2. Running jupyter-repo2docker..." - echo "jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name ${CONTAINER_NAME} ${REPO_NAME}" - jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name "${CONTAINER_NAME}" "${REPO_NAME}" - echo "3. Running without server (example)" - docker run -td --name repo2docker --entrypoint /bin/bash "${CONTAINER_NAME}" + echo "jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name ${CONTAINER_NAME}:${DOCKER_TAG} ${REPO_NAME}" + jupyter-repo2docker --debug --user-name username --user-id 1000 --no-run --image-name "${CONTAINER_NAME}:${DOCKER_TAG}" "${REPO_NAME}" docker ps docker images - run:

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removing extra blank lines

MODIFY repo2docker/app.py repo2docker/app.py @@ -351,7 +351,6 @@ class Repo2Docker(Application): help='Print the repo2docker version and exit.' ) - return argparser def json_excepthook(self, etype, evalue, traceback): @@ -363,7 +362,6 @@ class Repo2Docker(Application): exc_info=(etype, evalue, traceback), extra=dict(phase='failed')) - def initialize(self, argv=None): """Init repo2docker configuration before start""" if argv is None:

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adding note to future developers about why version is checked first

MODIFY repo2docker/app.py repo2docker/app.py @@ -367,6 +367,8 @@ class Repo2Docker(Application): if argv is None: argv = sys.argv[1:] + # version must be checked before parse, as repo/cmd are required and + # will spit out an error if allowed to be parsed first. if '--version' in argv: print(self.version) sys.exit(0)

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good job wrong repo name!

MODIFY docs/source/deploy.rst docs/source/deploy.rst Deploy ``repo2docker`` ====================== -We've created for you the `continuous-build <https://www.github.com/jupyter/continuous-build/>`_ +We've created for you the `continuous-build <https://www.github.com/binder-examples/continuous-build/>`_ repository so that you can deploy a `Docker <https://docs.docker.com/>`_ container to `Docker Hub <https://hub.docker.com/>`_ directly from a Github repository that has a Jupyter notebook. Here are instructions to do this. @@ -24,7 +24,7 @@ to pull from Docker Hub. Step 1. Clone the Repository ............................ -First, fork the `continuous-build <https://www.github.com/jupyter/continuous-build/>`_ Github +First, fork the `continuous-build <https://www.github.com/binder-examples/continuous-build/>`_ Github repository to your account, and clone the branch. git clone https://www.github.com/<username>/continuous-build @@ -47,7 +47,7 @@ including: Also provided (or will be provided as they are requested) are other configuration templates in the subfolders of that repository. The README.md in each template example folder describes its functions. If you have a request for a template that is not provided, please -`let us know <https://www.github.com/jupyter/continuous-build/issues/>`_. +`let us know <https://www.github.com/binder-examples/continuous-build/issues/>`_. We will add templates as they are requested to do additional tasks like test containers, run nbconvert, etc.

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Updates the test_connect_url description and deletes print statements

MODIFY tests/test_connect_url.py tests/test_connect_url.py """ -Test if the environment.yml is empty or it constains other data structure than a dictionary +Test if the explict hostname is supplied correctly to the container """ import os import sys @@ -21,15 +21,11 @@ def test_env_yml(tmpdir): app.initialize(argv) app.run = False app.start() # This just build the image and does not run it. - detect = app.build - print("app.build",detect) container = app.start_container() port = app.port - print("port in test", port) hostname = app.hostname # wait a bit for the container to be ready container_url = 'http://{}:{}/api'.format(hostname, port) - print("print container url",container_url) # wait a bit for the container to be ready # give the container a chance to start time.sleep(1)

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Install nodejs/npm from nodesource

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -43,6 +43,11 @@ RUN adduser --disabled-password \ ${NB_USER} WORKDIR ${HOME} +RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - \ + DISTRO="$(lsb_release -s -c)" \ + echo "deb https://deb.nodesource.com/$VERSION $DISTRO main" | tee /etc/apt/sources.list.d/nodesource.list \ + echo "deb-src https://deb.nodesource.com/$VERSION $DISTRO main" | tee -a /etc/apt/sources.list.d/nodesource.list + RUN apt-get update && \ apt-get install --yes --no-install-recommends \ {% for package in base_packages -%} @@ -175,9 +180,7 @@ class BuildPack: # Utils! "less", - # FIXME: Use npm from nodesource! - # Everything seems to depend on npm these days, unfortunately. - "npm", + "nodejs", "unzip", }

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add start script test

ADD tests/venv/start/postBuild/README.rst +System - Post-build scripts +--------------------------- + +It is possible to run scripts after you've built the environment specified in +your other files. This could be used to, for example, download data or run +some configuration scripts. + +In this example, we download and install a Jupyter Notebook extension. ADD tests/venv/start/postBuild/postBuild +#!/bin/bash +jupyter nbextension enable --py --sys-prefix ipyleaflet ADD tests/venv/start/postBuild/requirements.txt +ipyleaflet ADD tests/venv/start/postBuild/start +#!/bin/bash + +export TEST_START_VAR="var is set" + +exec "$@" ADD tests/venv/start/postBuild/verify +#!/bin/bash +set -euo pipefail +jupyter nbextension list | grep 'jupyter-leaflet' | grep enabled + +if [ "$TEST_START_VAR" != "var is set" ] +then + echo "TEST_START_VAR is not set" + exit 1 +fi

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Include corrections in app and test_connect_url files

MODIFY tests/test_connect_url.py tests/test_connect_url.py """ Test if the explict hostname is supplied correctly to the container """ -import os -import sys -import pytest import requests import time -import urllib.parse from repo2docker.app import Repo2Docker def test_connect_url(tmpdir):

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Add missing version tag to DEB links

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -45,8 +45,8 @@ WORKDIR ${HOME} RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - \ DISTRO="$(lsb_release -s -c)" \ - echo "deb https://deb.nodesource.com/$VERSION $DISTRO main" | tee /etc/apt/sources.list.d/nodesource.list \ - echo "deb-src https://deb.nodesource.com/$VERSION $DISTRO main" | tee -a /etc/apt/sources.list.d/nodesource.list + echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" | tee /etc/apt/sources.list.d/nodesource.list \ + echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" | tee -a /etc/apt/sources.list.d/nodesource.list RUN apt-get update && \ apt-get install --yes --no-install-recommends \ @@ -187,9 +187,7 @@ class BuildPack: return { # Utils! "less", - "nodejs", - "unzip", }

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