narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

don't install requirements.txt if environment.yml is present The most likely cause of both being present is equivalent dependencies for two use cases, not a single multi-stage conda environment. If deps should be installed in conda with pip, they will be in `environment.yml` under `pip`.

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -554,7 +554,7 @@ class CondaBuildPack(BuildPack): conda clean -tipsy """ )) - if os.path.exists('requirements.txt'): + elif os.path.exists('requirements.txt'): assembly_scripts.append(( '${NB_USER}', 'pip install --no-cache-dir -r requirements.txt' MODIFY tests/conda/requirements/README.rst tests/conda/requirements/README.rst Python - Mixed Requirements --------------------------- -You can specify both a ``requirements.txt`` and an ``environment.yml`` file, -and both of these will be used to build your environment. +An ``environment.yml`` takes precedence over ``requirements.txt``. +To install files into a conda environment with pip, use the ``pip`` key in ``environment.yml``: + +.. sourcecode:: yaml + + dependencies: + - numpy + - pip: + - tornado MODIFY tests/conda/requirements/environment.yml tests/conda/requirements/environment.yml dependencies: - numpy + - pip: + - simplejson MODIFY tests/conda/requirements/verify tests/conda/requirements/verify @@ -4,4 +4,9 @@ import sys assert sys.version_info[:2] == (3, 6) import numpy +try: import there +except ImportError: + print('ok') +else: + raise Exception("'there' shouldn't have been installed from requirements.txt")

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conda's not Python specific

MODIFY tests/conda/requirements/README.rst tests/conda/requirements/README.rst -Python - Mixed Requirements ---------------------------- +Conda - Mixed Requirements +-------------------------- An ``environment.yml`` takes precedence over ``requirements.txt``. -To install files into a conda environment with pip, use the ``pip`` key in ``environment.yml``: +To install Python packages into a conda environment with pip, use the ``pip`` key in ``environment.yml``: .. sourcecode:: yaml MODIFY tests/conda/requirements/verify tests/conda/requirements/verify #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 6) +assert sys.version_info[:2] == (3, 6), sys.version import numpy try: import there except ImportError: - print('ok') + pass else: raise Exception("'there' shouldn't have been installed from requirements.txt") MODIFY tests/conda/simple/README.rst tests/conda/simple/README.rst -Python - Conda Environment --------------------------- +Conda Environment +----------------- Conda environments files may allow for more complex builds and dependencies. You -can specify them in the standard YAML structure. +can specify them in the standard `environment.yml` files. MODIFY tests/conda/simple/verify tests/conda/simple/verify #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 6) +assert sys.version_info[:2] == (3, 6), sys.version import numpy

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typo: --print-dockerfile ended up falling under --debug

MODIFY repo2docker/app.py repo2docker/app.py @@ -168,7 +168,7 @@ class Repo2Docker(Application): '--no-build', dest='build', action='store_false', - help="Do not actually build the image. Useful in conjugation with --print-dockerfile." + help="Do not actually build the image. Useful in conjunction with --debug." ) argparser.add_argument(

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fix legacy docker appendix was just skipped

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -707,6 +707,7 @@ class JuliaBuildPack(BuildPack): class DockerBuildPack(BuildPack): name = "Dockerfile" + dockerfile = "Dockerfile" def detect(self): return os.path.exists('Dockerfile') @@ -719,6 +720,7 @@ class DockerBuildPack(BuildPack): client = docker.APIClient(version='auto', **docker.utils.kwargs_from_env()) for line in client.build( path=os.getcwd(), + dockerfile=self.dockerfile, tag=image_spec, buildargs={ 'JUPYTERHUB_VERSION': self.jupyterhub_version, @@ -730,6 +732,7 @@ class DockerBuildPack(BuildPack): class LegacyBinderDockerBuildPack(DockerBuildPack): name = 'Legacy Binder Dockerfile' + dockerfile = '._binder.Dockerfile' dockerfile_appendix = Unicode(dedent(r""" USER root @@ -754,6 +757,11 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): with open('Dockerfile') as f: return f.read() + self.dockerfile_appendix + def build(self, image_spec): + with open(self.dockerfile, 'w') as f: + f.write(self.render()) + return super().build(image_spec) + def detect(self): try: with open('Dockerfile', 'r') as f:

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ensure composed buildpacks inherit application config so that configurable buildpacks can be configured

MODIFY repo2docker/app.py repo2docker/app.py @@ -33,13 +33,13 @@ from .utils import execute_cmd from . import __version__ -def c(args): +def compose(buildpacks, parent=None): """ Shortcut to compose many buildpacks together """ - image = args[0]() - for arg in args[1:]: - image = image.compose_with(arg()) + image = buildpacks[0](parent=parent) + for buildpack in buildpacks[1:]: + image = image.compose_with(buildpack(parent=parent)) return image @@ -310,10 +310,10 @@ class Repo2Docker(Application): ) os.chdir(checkout_path) - picked_buildpack = c(self.default_buildpack) + picked_buildpack = compose(self.default_buildpack, parent=self) for bp_spec in self.buildpacks: - bp = c(bp_spec) + bp = compose(bp_spec, parent=self) if bp.detect(): picked_buildpack = bp break

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allow setting JUPYTERHUB_VERSION via env

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -149,8 +149,12 @@ class BuildPack(LoggingConfigurable): and the Hub itself should have the same version number. """ ) + @default('jupyterhub_version') + def _jupyterhub_version_default(self): + """Allow setting JUPYTERHUB_VERSION via env""" + return os.environ.get('JUPYTERHUB_VERSION') or '0.7.2' + packages = Set( - set(), help=""" List of packages that are installed in this BuildPack by default.

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document `--debug`

MODIFY README.md README.md @@ -52,6 +52,15 @@ After building (it might take a while!), it should output in your terminal somet If you copy paste that URL into your browser you will see a Jupyter Notebook with the contents of the repository you had just built! +### Displaying the image Dockerfile +Repo2Docker will generate a Dockerfile that composes the created Docker image. +To see the contents of this Dockerfile without building the image use `--debug` and `--no-build` +flags like so: + +```bash +jupyter-repo2docker --debug --no-build https://github.com/jakevdp/PythonDataScienceHandbook +``` + ## Repository specifications Repo2Docker looks for various files in the repository being built to figure out how to build it.

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remove impossible elif condition

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -554,11 +554,6 @@ class CondaBuildPack(BuildPack): conda clean -tipsy """ )) - elif os.path.exists('requirements.txt'): - assembly_scripts.append(( - '${NB_USER}', - 'pip install --no-cache-dir -r requirements.txt' - )) return assembly_scripts def detect(self):

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Update detectors to use jupyterlab 0.27

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -503,7 +503,7 @@ class PythonBuildPack(BuildPack): notebook==5.0.0 \ jupyterhub==${JUPYTERHUB_VERSION} \ ipywidgets==6.0.0 \ - jupyterlab==0.24.1 && \ + jupyterlab==0.27 && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ jupyter serverextension enable --py jupyterlab --sys-prefix """

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raise on non-executable postBuild instead of ignoring the file

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -3,7 +3,7 @@ Generates a variety of Dockerfiles based on an input matrix """ import textwrap from traitlets.config import LoggingConfigurable -from traitlets import Unicode, Set, List, Dict, Tuple, Bool, default +from traitlets import Unicode, Set, List, Dict, Tuple, default from textwrap import dedent import jinja2 import tarfile @@ -11,7 +11,6 @@ import io import os import stat import re -import json import docker TEMPLATE = r""" @@ -466,7 +465,8 @@ class BaseImage(BuildPack): def setup_post_build_scripts(self): post_build = self.binder_path('postBuild') if os.path.exists(post_build): - if stat.S_IXUSR & os.stat(post_build)[stat.ST_MODE]: + if not stat.S_IXUSR & os.stat(post_build).st_mode: + raise ValueError("%s is not executable" % post_build) return [post_build] return []

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Try to make expanded matrix of tests work properly

MODIFY .travis.yml .travis.yml @@ -8,11 +8,11 @@ install: - pip install -e . - pip install pytest-xdist pyyaml -jobs: - include: - - stage: test script: - pytest -s -v -n4 tests/${REPO_TYPE} + +jobs: + include: - stage: deploy script: skip if: type = push

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Use proper environment name for docker username

MODIFY travis/travis-script.bash travis/travis-script.bash @@ -6,6 +6,6 @@ VERSION=$(git rev-parse --short HEAD) docker build -t jupyter/repo2docker:${VERSION} . if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then - docker login -u ${DOCKER_USERNAME} -p "${DOCKER_PASSWORD}" + docker login -u ${DOCKER_LOGIN} -p "${DOCKER_PASSWORD}" docker push jupyter/rep2docker:${VERSION} fi

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Switch to using alpine based image for repo2docker This cuts image size from under 300MB to under 100MB. Plus we will never actually need this to have additional libraries installed, since it's talking to the docker socket directly to build new images. So switching to alpine here is worth it.

MODIFY Dockerfile Dockerfile -FROM ubuntu:17.04 +FROM python:3.6.3-alpine3.6 -RUN apt-get update && \ - apt-get install --yes --no-install-recommends \ - python3 \ - python3-pip \ - python3-setuptools \ - git && \ - apt-get clean && apt-get purge RUN mkdir /tmp/src ADD . /tmp/src

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Explicitly echo what image is built

MODIFY travis/travis-script.bash travis/travis-script.bash @@ -3,9 +3,11 @@ set -eu -o pipefail VERSION=$(git rev-parse --short HEAD) -docker build -t jupyter/repo2docker:${VERSION} . +IMAGE="jupyter/repo2docker:${VERSION}" +docker build -t ${IMAGE} . if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then docker login -u ${DOCKER_LOGIN} -p "${DOCKER_PASSWORD}" - docker push jupyter/rep2docker:${VERSION} + docker push ${IMAGE} + echo "Pushed new repo2docker image: ${IMAGE}" fi

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Explicitly add a .dockerignore rather than symlink Alpine linux seems very confused by symlinks

DELETE .dockerignore -.gitignore \ No newline at end of file ADD .dockerignore +.#* +dist +build +*.tar.gz +*.egg-info +*.py[co] +__pycache__ +MANIFEST + +.DS_Store +.cache + +repo2docker/s2i + +^bin/ +lib/ +lib64/ +share/ +include/ + +# Docs +generated/ +test_file_text.txt MODIFY .gitignore .gitignore @@ -14,6 +14,7 @@ repo2docker/s2i ^bin/ lib/ +lib64/ share/ include/

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yuvi comments

MODIFY tests/venv/postBuild/README.rst tests/venv/postBuild/README.rst @@ -8,7 +8,12 @@ Jupyter extension. .. note:: - This file needs to be executable in order to work with ``repo2docker``. The - easiest way to do this is to run the following command with ``git``:: + This file needs to be executable in order to work with ``repo2docker``. If + you're on Linux or macOS, run:: + + chmod +x postBuild + + If you're on windows, you can accomplish the same behavior with this + ``git`` command:: git update-index --chmod=+x postBuild

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avoid producing non-JSON output on errors register a custom excepthook that is called instead of the default traceback formatter. This produces a phase: failed message with the error.

MODIFY repo2docker/app.py repo2docker/app.py @@ -179,6 +179,17 @@ class Repo2Docker(Application): return argparser + def json_excepthook(self, etype, evalue, traceback): + """Called on an uncaught exception when using json logging + + Avoids non-JSON output on errors when using --json-logs + """ + self.log.error("Error during build: %s", evalue, + exc_info=(etype, evalue, traceback), + extra=dict(phase='failed'), + ) + + def initialize(self): args = self.get_argparser().parse_args() @@ -200,6 +211,8 @@ class Repo2Docker(Application): self.cleanup_checkout = args.clean if args.json_logs: + # register JSON excepthook to avoid non-JSON output on errors + sys.excepthook = self.json_excepthook # Need to reset existing handlers, or we repeat messages logHandler = logging.StreamHandler() formatter = jsonlogger.JsonFormatter()

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Upgrade to notebook 5.2.0

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -510,10 +510,10 @@ class PythonBuildPack(BuildPack): "${NB_USER}", r""" pip install --no-cache-dir \ - notebook==5.0.0 \ + notebook==5.2.0 \ jupyterhub==${JUPYTERHUB_VERSION} \ ipywidgets==6.0.0 \ - jupyterlab==0.27 && \ + jupyterlab==0.28 && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ jupyter serverextension enable --py jupyterlab --sys-prefix """ MODIFY repo2docker/files/conda/environment.yml repo2docker/files/conda/environment.yml dependencies: - python==3.6.1 - - notebook==5.0.0 + - notebook==5.2.0 - ipython==6.0.0 - ipykernel==4.6.0 - ipywidgets==6.0.0

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Only parse `REQUIRE` file in `binder` (if exists)

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -704,7 +704,7 @@ class JuliaBuildPack(BuildPack): cat "%s" >> ${JULIA_PKGDIR}/v0.6/REQUIRE && \ julia -e ' \ Pkg.resolve(); \ - for pkg in keys(Pkg.Reqs.parse("REQUIRE")) \ + for pkg in keys(Pkg.Reqs.parse("%s")) \ eval(:(using $(Symbol(pkg)))) \ end \ '

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Fixed missing string interpolation argument

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -701,14 +701,14 @@ class JuliaBuildPack(BuildPack): # Pre-compile all libraries if they've opted into it. `using {libraryname}` does the # right thing r""" - cat "%s" >> ${JULIA_PKGDIR}/v0.6/REQUIRE && \ + cat "%(require)s" >> ${JULIA_PKGDIR}/v0.6/REQUIRE && \ julia -e ' \ Pkg.resolve(); \ - for pkg in keys(Pkg.Reqs.parse("%s")) \ + for pkg in keys(Pkg.Reqs.parse("%(require)s")) \ eval(:(using $(Symbol(pkg)))) \ end \ ' - """ % require + """ % { "require" : require } )] def detect(self):

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Replace theme with alabaster

MODIFY docs/source/conf.py docs/source/conf.py @@ -33,9 +33,7 @@ import recommonmark.parser # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = [ - 'jupyter_alabaster_theme', -] +extensions = [] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -92,7 +90,7 @@ todo_include_todos = False # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'jupyter_alabaster_theme' +html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the

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Re-order arguments to make more intuitive sense

MODIFY repo2docker/app.py repo2docker/app.py @@ -138,16 +138,22 @@ class Repo2Docker(Application): ) argparser.add_argument( - '--push', - dest='push', + '--debug', + help="Turn on debug logging", action='store_true', - help='Push docker image to repository' ) argparser.add_argument( - '--debug', - help="Turn on debug logging", - action='store_true', + '--no-build', + dest='build', + action='store_false', + help="Do not actually build the image. Useful in conjunction with --debug." + ) + + argparser.add_argument( + 'cmd', + nargs='*', + help='Custom command to run after building container' ) argparser.add_argument( @@ -165,16 +171,10 @@ class Repo2Docker(Application): ) argparser.add_argument( - '--no-build', - dest='build', - action='store_false', - help="Do not actually build the image. Useful in conjunction with --debug." - ) - - argparser.add_argument( - 'cmd', - nargs='*', - help='Custom command to run after building container' + '--push', + dest='push', + action='store_true', + help='Push docker image to repository' ) return argparser

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Fix handling of 'cmd' nargs='*' made a lot of other parsing fail with strange errors.

MODIFY repo2docker/app.py repo2docker/app.py @@ -152,7 +152,7 @@ class Repo2Docker(Application): argparser.add_argument( 'cmd', - nargs='*', + action='append', help='Custom command to run after building container' )

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Use argparse.REMAINDER instead of action=append This gathers up all the remaining parameters without misinterpreting parameters like --no-build etc as part of cmd

MODIFY repo2docker/app.py repo2docker/app.py @@ -152,7 +152,7 @@ class Repo2Docker(Application): argparser.add_argument( 'cmd', - action='append', + nargs=argparse.REMAINDER, help='Custom command to run after building container' )

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Add doc badge

MODIFY README.md README.md [![Build Status](https://travis-ci.org/jupyter/repo2docker.svg?branch=master)](https://travis-ci.org/jupyter/repo2docker) +[![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) **jupyter-repo2docker** is a tool to build, run and push docker images from source code repositories.

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Remove jupyterhub from miniconda bash script

MODIFY repo2docker/files/conda/install-miniconda.bash repo2docker/files/conda/install-miniconda.bash @@ -30,7 +30,7 @@ ${CONDA_DIR}/bin/conda config --system --set update_dependencies false ${CONDA_DIR}/bin/conda config --system --set show_channel_urls true ${CONDA_DIR}/bin/conda env update -n root -f /tmp/environment.yml -${CONDA_DIR}/bin/pip install --no-cache-dir jupyterhub==${JUPYTERHUB_VERSION} + # Clean things out! ${CONDA_DIR}/bin/conda clean -tipsy

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update docstring to include binderhub

MODIFY repo2docker/app.py repo2docker/app.py """repo2docker: convert git repositories into jupyter-suitable docker images -Images produced by repo2docker can be used with Jupyter notebooks standalone or via JupyterHub. +Images produced by repo2docker can be used with Jupyter notebooks standalone, +with BinderHub, or with JupyterHub. Usage:

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Remove jupyterhub from buildpack and default build script

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -64,9 +64,6 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* {% endif -%} -# make JUPYTERHUB_VERSION a build argument -ARG JUPYTERHUB_VERSION=0.7.2 - EXPOSE 8888 {% if env -%} @@ -139,21 +136,6 @@ class BuildPack(LoggingConfigurable): and there are *some* general guarantees of ordering. """ - - jupyterhub_version = Unicode( - '0.7.2', - config=True, - help="""JupyterHub version to install. - - In general, the JupyterHub version in the image - and the Hub itself should have the same version number. - """ - ) - @default('jupyterhub_version') - def _jupyterhub_version_default(self): - """Allow setting JUPYTERHUB_VERSION via env""" - return os.environ.get('JUPYTERHUB_VERSION') or '0.7.2' - packages = Set( help=""" List of packages that are installed in this BuildPack by default. @@ -511,7 +493,6 @@ class PythonBuildPack(BuildPack): r""" pip install --no-cache-dir \ notebook==5.2.0 \ - jupyterhub==${JUPYTERHUB_VERSION} \ ipywidgets==6.0.0 \ jupyterlab==0.28 && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \

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Remove jupyterhub from buildargs except leave for legacy

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -398,9 +398,7 @@ class BuildPack(LoggingConfigurable): fileobj=tarf, tag=image_spec, custom_context=True, - buildargs={ - 'JUPYTERHUB_VERSION': self.jupyterhub_version, - }, + buildargs={}, decode=True, ): yield line @@ -714,9 +712,7 @@ class DockerBuildPack(BuildPack): path=os.getcwd(), dockerfile=self.binder_path(self.dockerfile), tag=image_spec, - buildargs={ - 'JUPYTERHUB_VERSION': self.jupyterhub_version, - }, + buildargs={}, decode=True, ): yield line

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Remove jupyterhub from test dockerfiles

MODIFY tests/dockerfile/binder-dir/binder/Dockerfile tests/dockerfile/binder-dir/binder/Dockerfile FROM python:3.5 -ARG JUPYTERHUB_VERSION -RUN pip3 install jupyterhub==$JUPYTERHUB_VERSION - ENTRYPOINT "/bin/sh" ADD sayhi.sh /usr/local/bin/sayhi.sh MODIFY tests/dockerfile/jupyter-stack/Dockerfile tests/dockerfile/jupyter-stack/Dockerfile FROM jupyter/base-notebook:b4dd11e16ae4 -ARG JUPYTERHUB_VERSION -RUN pip install jupyterhub==$JUPYTERHUB_VERSION - RUN pip install there ADD verify verify MODIFY tests/dockerfile/simple/Dockerfile tests/dockerfile/simple/Dockerfile FROM python:3.5 -ARG JUPYTERHUB_VERSION -RUN pip3 install jupyterhub==$JUPYTERHUB_VERSION - ENTRYPOINT "/bin/sh" ADD sayhi.sh /usr/local/bin/sayhi.sh

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Add a basic FAQ doc + 1 entry We get lots of questions that can be answered here!

ADD docs/source/faq.md +# Frequently Asked Questions (FAQ) + +A collection of frequently asked questions with answers! + +If you have a question & have found an answer, send a PR to add it here! + +## Can I use repo2docker to bootstrap my own Dockerfile? + +If you pass the `--debug` flag to `repo2docker`, it outputs the intermediate +Dockerfile it is using to build the docker image. While it is tempting to copy +this as a base for your own Dockerfile, that is not supported & in most cases +will not work. The `--debug` output is just our intermediate generated +Dockerfile, and is meant to be built in +[a very specific way](https://github.com/jupyter/repo2docker/blob/master/repo2docker/detectors.py#L381). +Hence the output of `--debug` can not be built with a normal `docker build -t .` +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! MODIFY docs/source/index.rst docs/source/index.rst @@ -11,4 +11,5 @@ Site Contents :maxdepth: 2 design + faq samples

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Use stdlib tempfile module The tempfile module can take care of finding a good temporary directory for us on paltforms where `/tmp` does not exist.

MODIFY repo2docker/app.py repo2docker/app.py @@ -14,6 +14,7 @@ import logging import uuid import shutil import argparse +import tempfile from pythonjsonlogger import jsonlogger import escapism @@ -53,10 +54,10 @@ class Repo2Docker(Application): return logging.INFO git_workdir = Unicode( - "/tmp", + tempfile.mkdtemp(prefix='repo2docker'), config=True, help=""" - The directory to use to check out git repositories into. + Working directory to check out git repositories to. Should be somewhere ephemeral, such as /tmp """ @@ -315,7 +316,7 @@ class Repo2Docker(Application): if self.repo_type == 'local': checkout_path = self.repo else: - checkout_path = os.path.join(self.git_workdir, str(uuid.uuid4())) + checkout_path = self.git_workdir self.fetch( self.repo, self.ref,

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Doc fixes per

MODIFY docs/source/faq.md docs/source/faq.md @@ -6,8 +6,10 @@ If you have a question & have found an answer, send a PR to add it here! ## Can I use repo2docker to bootstrap my own Dockerfile? +No, you can't. + If you pass the `--debug` flag to `repo2docker`, it outputs the intermediate -Dockerfile it is using to build the docker image. While it is tempting to copy +Dockerfile that is used to build the docker image. While it is tempting to copy this as a base for your own Dockerfile, that is not supported & in most cases will not work. The `--debug` output is just our intermediate generated Dockerfile, and is meant to be built in

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Add limit on git clone depth Only checkout last 50 commits from a remote repository. This helps speed up the cloning for large repositories.

MODIFY repo2docker/app.py repo2docker/app.py @@ -92,7 +92,8 @@ 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', '--depth', '50', + url, checkout_path], capture=self.json_logs): self.log.info(line, extra=dict(phase='fetching')) except subprocess.CalledProcessError:

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Add test for unshallowing repositories

MODIFY tests/external/datasci-shallow-clone.repos.yaml tests/external/datasci-shallow-clone.repos.yaml # Check that we correctly detect that this ref is more than 50 commits ago # and trigger a full clone of the repository - name: Jake's Data Science Book - url: https://github.com/jakevdp/PythonDataScienceHandbook - ref: 8761de29a853f0c187286b7c7bc1e4767e7c5574 - verify: python -c 'import matplotlib' + url: https://github.com/betatim/repo2docker-ci-clone-depth + ref: f702ae5c612ca0dcaf77954f9f5dd4ede7cb9b5f + verify: python -c "commit = open('COMMIT').read(); assert int(commit) == 1, 'this is not the first commit'"

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Add handling for no ref being provided We do not need to checkout a specific ref if none is provided. Added a test to check the behaviour.

MODIFY repo2docker/app.py repo2docker/app.py @@ -144,6 +144,9 @@ class Repo2Docker(Application): # create a shallow clone first _clone(depth=50) + # ref == None means we want to use HEAD so no need to checkout a + # specific revision + if ref is not None: if not _contains(ref): # have to create a full clone _unshallow() MODIFY tests/conftest.py tests/conftest.py @@ -51,9 +51,8 @@ class RemoteRepoTest(pytest.Item): self.verify = verify def runtest(self): - subprocess.check_call([ - 'jupyter-repo2docker', - '--ref', self.ref, - self.url, - '--', - ] + shlex.split(self.verify)) + if self.ref is not None: + cmd = ['jupyter-repo2docker', '--ref', self.ref, self.url, '--'] + else: + cmd = ['jupyter-repo2docker', self.url, '--'] + subprocess.check_call(cmd + shlex.split(self.verify)) MODIFY tests/external/shallow-clone.repos.yaml tests/external/shallow-clone.repos.yaml # we checkout the second to last commit, hence the log has 49 entries at a # max clone depth of 50 verify: /bin/bash -c '[ $(git log --oneline | wc -l) == "49" ]' + +- name: A dummy repo with 100 commits - live at HEAD + url: https://github.com/betatim/repo2docker-ci-clone-depth + # provide no ref, aka use HEAD, aka the 100th commit + ref: NULL + verify: python -c "commit = open('COMMIT').read(); assert int(commit) == 100, 'this is not the 100th commit'"

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Fix argument definition

MODIFY repo2docker/app.py repo2docker/app.py @@ -55,6 +55,7 @@ class Repo2Docker(Application): git_workdir = Unicode( None, config=True, + allow_none=True, help=""" Working directory to check out git repositories to.

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Ignore "julia" in REQUIRE file when precompiling

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -686,7 +686,7 @@ class JuliaBuildPack(BuildPack): julia -e ' \ Pkg.resolve(); \ for pkg in keys(Pkg.Reqs.parse("%(require)s")) \ - eval(:(using $(Symbol(pkg)))) \ + pkg != "julia" && eval(:(using $(Symbol(pkg)))) \ end \ ' """ % { "require" : require }

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Fix binder/apt.txt detection

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -421,7 +421,7 @@ class BaseImage(BuildPack): def setup_assembly(self): assemble_scripts = [] try: - with open('apt.txt') as f: + with open(self.binder_path('apt.txt')) as f: extra_apt_packages = [l.strip() for l in f] # Validate that this is, indeed, just a list of packages # We're doing shell injection around here, gotta be careful.

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add git-credential-env and configure git to use it by default `git-credential-env` only echoes the $GIT_CREDENTIAL_ENV environment variable when git asks for https credentials. with this, setting GIT_CREDENTIAL_ENV="username=name\npassword=xxx" sets the credentials that will be used. e.g. docker run -e GIT_CREDENTIAL_ENV="username=name\npassword=xxx" jupyter/repo2docker

MODIFY Dockerfile Dockerfile @@ -5,5 +5,6 @@ RUN apk add --no-cache git RUN mkdir /tmp/src ADD . /tmp/src -RUN pip3 install --no-cache-dir /tmp/src - +RUN pip3 install --no-cache-dir /tmp/src && \ + cp /tmp/src/docker/git-credential-env /usr/local/bin/git-credential-env && \ + git config --system credential.helper env ADD docker/git-credential-env +#!/bin/sh +echo -e $GIT_CREDENTIAL_ENV

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Add tests for binder/apt.txt and binder/postBuild

ADD tests/venv/binder-dir/apt.txt +thiswontwork ADD tests/venv/binder-dir/binder/apt.txt +gfortran ADD tests/venv/binder-dir/postBuild +#!/bin/bash +echo "This should never run" +exit 1 MODIFY tests/venv/binder-dir/verify tests/venv/binder-dir/verify #!/bin/bash +which gfortran test -z $(pip list | grep scipy) jupyter nbextension list jupyter nbextension list | grep 'jupyter-leaflet' | grep enabled

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Make all bash verify scripts fail on error Bash scripts by default continue on executing even if any command errors. That's not the behavior we want for our scripts, so let's explicitly get them to fail if: 1. Any command exits with non 0 exit code 2. An undefined variable is referenced

MODIFY tests/dockerfile/binder-dir/verify tests/dockerfile/binder-dir/verify #!/bin/sh -set -e +set -euo pipefail /usr/local/bin/sayhi.sh MODIFY tests/dockerfile/simple/verify tests/dockerfile/simple/verify #!/bin/sh -set -e +set -euo pipefail /usr/local/bin/sayhi.sh MODIFY tests/venv/apt-packages/verify tests/venv/apt-packages/verify #!/bin/bash +set -euo pipefail which gfortran MODIFY tests/venv/binder-dir/verify tests/venv/binder-dir/verify #!/bin/bash +set -euo pipefail which gfortran test -z $(pip list | grep scipy) jupyter nbextension list MODIFY tests/venv/postBuild/verify tests/venv/postBuild/verify #!/bin/bash -set -e +set -euo pipefail jupyter nbextension list | grep 'jupyter-leaflet' | grep enabled

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separate RUN for git-credential-env

MODIFY Dockerfile Dockerfile @@ -5,6 +5,6 @@ RUN apk add --no-cache git RUN mkdir /tmp/src ADD . /tmp/src -RUN pip3 install --no-cache-dir /tmp/src && \ - cp /tmp/src/docker/git-credential-env /usr/local/bin/git-credential-env && \ +RUN pip3 install --no-cache-dir /tmp/src +RUN cp /tmp/src/docker/git-credential-env /usr/local/bin/git-credential-env && \ git config --system credential.helper env

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Bump notebook version to 5.2.2 Brings in to fix

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -492,7 +492,7 @@ class PythonBuildPack(BuildPack): "${NB_USER}", r""" pip install --no-cache-dir \ - notebook==5.2.0 \ + notebook==5.2.2 \ ipywidgets==6.0.0 \ jupyterlab==0.28 && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ @@ -733,7 +733,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): USER main WORKDIR /home/main/notebooks ENV PATH /home/main/anaconda2/envs/python3/bin:$PATH - RUN conda install -yq -n python3 notebook==5.0.0 ipykernel==4.6.0 && \ + RUN conda install -yq -n python3 notebook==5.2.2 ipykernel==4.6.0 && \ conda remove -yq -n python3 nb_conda_kernels && \ conda install -yq -n root ipykernel==4.6.0 && \ /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \ MODIFY repo2docker/files/conda/environment.yml repo2docker/files/conda/environment.yml dependencies: - python==3.6.1 - - notebook==5.2.0 + - notebook==5.2.2 - ipython==6.0.0 - ipykernel==4.6.0 - ipywidgets==6.0.0

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Suggest editable install when installed from source

MODIFY README.md README.md @@ -21,12 +21,12 @@ To install from pypi, the python packaging index: pip install jupyter-repo2docker ``` -To install from source: +To install from source and start contributing: ```bash git clone https://github.com/jupyter/repo2docker.git cd repo2docker -pip install . +pip install -e . ``` ## Usage

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Bump legacy Dockerfile notebook down to 5.2.0 5.2.2 doesn't exist in anaconda channels...

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -733,7 +733,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): USER main WORKDIR /home/main/notebooks ENV PATH /home/main/anaconda2/envs/python3/bin:$PATH - RUN conda install -yq -n python3 notebook==5.2.2 ipykernel==4.6.0 && \ + RUN conda install -yq -n python3 notebook==5.2.0 ipykernel==4.6.0 && \ conda remove -yq -n python3 nb_conda_kernels && \ conda install -yq -n root ipykernel==4.6.0 && \ /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \

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Bump anaconda notebook down to 5.0 again Doesn't have 5.2 either

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -733,7 +733,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): USER main WORKDIR /home/main/notebooks ENV PATH /home/main/anaconda2/envs/python3/bin:$PATH - RUN conda install -yq -n python3 notebook==5.2.0 ipykernel==4.6.0 && \ + RUN conda install -yq -n python3 notebook==5.0.0 ipykernel==4.6.0 && \ conda remove -yq -n python3 nb_conda_kernels && \ conda install -yq -n root ipykernel==4.6.0 && \ /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \

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verbose env update

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -562,7 +562,7 @@ class CondaBuildPack(BuildPack): assembly_scripts.append(( '${NB_USER}', r""" - conda env update -n root -f "{}" && \ + conda env update -v -n root -f "{}" && \ conda clean -tipsy """.format(environment_yml) ))

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Move conda support files next to the code Better than in a separate files dir IMO

MODIFY MANIFEST.in MANIFEST.in include *.md include LICENSE include setup.cfg -recursive-include repo2docker/files * +recursive-include repo2docker/buildpacks * MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -381,7 +381,7 @@ class BuildPack(LoggingConfigurable): for src in sorted(self.build_script_files): src_parts = src.split('/') - src_path = os.path.join(os.path.dirname(__file__), '..', 'files', *src_parts) + src_path = os.path.join(os.path.dirname(__file__), *src_parts) tar.add(src_path, src, filter=_filter_tar) tar.add('.', 'src/', filter=_filter_tar) RENAME repo2docker/buildpacks/conda.py repo2docker/buildpacks/conda/__init__.py @@ -3,7 +3,7 @@ Generates a variety of Dockerfiles based on an input matrix """ from traitlets import default import os -from .base import BuildPack +from ..base import BuildPack class CondaBuildPack(BuildPack): RENAME repo2docker/files/conda/environment.yml repo2docker/buildpacks/conda/environment.yml RENAME repo2docker/files/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash RENAME repo2docker/buildpacks/python.py repo2docker/buildpacks/python/__init__.py @@ -3,7 +3,7 @@ Generates a variety of Dockerfiles based on an input matrix """ from traitlets import default import os -from .base import BuildPack +from ..base import BuildPack class PythonBuildPack(BuildPack):

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Use requirements.txt for installing base packages in requirements.txt Lets us move to a frozen requirements.txt that can be automated soon.

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -26,6 +26,11 @@ class PythonBuildPack(BuildPack): "${VENV_PATH}/bin" ] + + build_script_files = { + 'python/requirements.txt': '/tmp/requirements.txt', + } + build_scripts = [ ( "root", @@ -43,10 +48,7 @@ class PythonBuildPack(BuildPack): ( "${NB_USER}", r""" - pip install --no-cache-dir \ - notebook==5.2.2 \ - ipywidgets==6.0.0 \ - jupyterlab==0.28 && \ + pip install --no-cache-dir -r /tmp/requirements.txt && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ jupyter serverextension enable --py jupyterlab --sys-prefix """ @@ -92,6 +94,10 @@ class Python2BuildPack(BuildPack): 'virtualenv' } + build_script_files = { + 'python/requirements2.txt': '/tmp/requirements2.txt', + } + env = [ ('VENV2_PATH', '${APP_BASE}/venv2') ] @@ -117,8 +123,7 @@ class Python2BuildPack(BuildPack): ( "${NB_USER}", r""" - pip2 install --no-cache-dir \ - ipykernel==4.6.1 && \ + pip2 install --no-cache-dir -r /tmp/requirements2.txt && \ python2 -m ipykernel install --prefix=${NB_PYTHON_PREFIX} """ ) ADD repo2docker/buildpacks/python/requirements.txt +notebook==5.2.2 +ipywidgets==6.0.0 +jupyterlab==0.28 ADD repo2docker/buildpacks/python/requirements2.txt +ipykernel==4.6.1

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don't run tests in parallel on travis parallel tests might have been the cause of spurious travis failures plus, not running concurrently should result in reusing the cache for the initial stages, which might even save time

MODIFY .travis.yml .travis.yml @@ -6,10 +6,10 @@ python: - 3.4 install: - pip install -e . -- pip install pytest-xdist pyyaml +- pip install pyyaml script: - - pytest -s -v -n4 tests/${REPO_TYPE} + - pytest -s -v tests/${REPO_TYPE} jobs: include:

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Update JupyterLab version

MODIFY repo2docker/buildpacks/python/requirements.frozen.txt repo2docker/buildpacks/python/requirements.frozen.txt # AUTO GENERATED FROM requirements.txt, DO NOT MANUALLY MODIFY -# Frozen on Thu Nov 30 08:51:37 UTC 2017 +# Frozen on Thu Nov 30 11:49:16 UTC 2017 bleach==2.1.1 decorator==4.1.2 entrypoints==0.2.3 @@ -13,8 +13,8 @@ Jinja2==2.10 jsonschema==2.6.0 jupyter-client==5.1.0 jupyter-core==4.4.0 -jupyterlab==0.28.0 -jupyterlab-launcher==0.6.0 +jupyterlab==0.29.2 +jupyterlab-launcher==0.5.5 MarkupSafe==1.0 mistune==0.8.1 nbconvert==5.3.1 MODIFY repo2docker/buildpacks/python/requirements.txt repo2docker/buildpacks/python/requirements.txt notebook==5.2.2 ipywidgets==6.0.0 -jupyterlab==0.28 +jupyterlab==0.29.2 MODIFY repo2docker/buildpacks/python/requirements2.frozen.txt repo2docker/buildpacks/python/requirements2.frozen.txt # AUTO GENERATED FROM requirements2.txt, DO NOT MANUALLY MODIFY -# Frozen on Thu Nov 30 08:51:48 UTC 2017 +# Frozen on Thu Nov 30 11:49:30 UTC 2017 backports-abc==0.5 backports.shutil-get-terminal-size==1.0.0 certifi==2017.11.5

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fix cd to python dir in freeze.bash cd was missing, instead the directory was being printed readlink doesn't exist on BSD

MODIFY repo2docker/buildpacks/python/freeze.bash repo2docker/buildpacks/python/freeze.bash @@ -5,7 +5,14 @@ set -euo pipefail # Does the same for requirements2.txt to requirements2.frozen.txt... # cd to the directory where the freeze script is located -dirname "$(readlink -f "$0")" +if [[ ! -z "$(which realpath 2>/dev/null)" ]]; then + realpath=realpath +else + realpath="readlink -f" +fi + +cd $(dirname "$($realpath "$0")") + function freeze-requirements { # Freeze a requirements file $2 into a frozen requirements file $3

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sync conda versions with venv versions

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml dependencies: - python==3.6.1 - notebook==5.2.2 - - ipython==6.0.0 - - ipykernel==4.6.0 - - ipywidgets==6.0.0 - - jupyterlab==0.28 + - ipython==6.2.1 + - ipykernel==4.6.1 + - ipywidgets==6.0.1 + - jupyterlab==0.29.2

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fixing empty lines and comments in apt.txt

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -418,13 +418,19 @@ class BaseImage(BuildPack): assemble_scripts = [] try: with open(self.binder_path('apt.txt')) as f: - extra_apt_packages = [l.strip() for l in f] + + extra_apt_packages = [] + for l in f: + package = l.partition('#')[0].strip() + if not package: + continue # Validate that this is, indeed, just a list of packages # We're doing shell injection around here, gotta be careful. # FIXME: Add support for specifying version numbers - for p in extra_apt_packages: - if not re.match(r"^[a-z0-9.+-]+", p): - raise ValueError("Found invalid package name {} in apt.txt".format(p)) + if not re.match(r"^[a-z0-9.+-]+", package): + raise ValueError("Found invalid package name {} in apt.txt".format(package)) + extra_apt_packages.append(package) + assemble_scripts.append(( 'root', MODIFY tests/venv/apt-packages/apt.txt tests/venv/apt-packages/apt.txt +# testing to skip comments in this file gfortran \ No newline at end of file

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s/memoryswap/memswap/ Since clearly the equivalent of 'memory' is 'memswap' grumble

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -392,7 +392,7 @@ class BuildPack(LoggingConfigurable): limits = { # Always disable memory swap for building, since mostly # nothing good can come of that. - 'memoryswap': -1 + 'memswap': -1 } if memory_limit: limits['memory'] = memory_limit MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py @@ -22,7 +22,7 @@ class DockerBuildPack(BuildPack): limits = { # Always disable memory swap for building, since mostly # nothing good can come of that. - 'memoryswap': -1 + 'memswap': -1 } if memory_limit: limits['memory'] = memory_limit

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Remove extra - in argparse definition

MODIFY repo2docker/app.py repo2docker/app.py @@ -163,7 +163,7 @@ class Repo2Docker(Application): ) argparser.add_argument( - '---build-memory-limit', + '--build-memory-limit', help='Total Memory that can be used by the docker build process' )

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Add tests for checking if memlimit is enforced

ADD tests/memlimit.py +import subprocess + +def test_memlimit_nondockerfile(): + """ + Test if memory limited builds are working for non dockerfile builds + """ + try: + subprocess.check_call([ + 'repo2docker', + '--no-run', + '--build-memory-limit', '4M', + 'tests/memlimit/non-dockerfile' + ]) + # If this doesn't throw an exception, then memory limit was + # not enforced! + assert False + except subprocess.CalledProcessError as e: + assert True + + +def test_memlimit_dockerfile(): + """ + Test if memory limited builds are working for non dockerfile builds + """ + try: + subprocess.check_call([ + 'repo2docker', + '--no-run', + '--build-memory-limit', '4M', + 'tests/memlimit/dockerfile' + ]) + # If this doesn't throw an exception, then memory limit was + # not enforced! + assert False + except subprocess.CalledProcessError as e: + assert True ADD tests/memlimit/dockerfile/Dockerfile +FROM python:3.6 + +COPY postBuild /usr/local/bin/postBuild +RUN ./postBuild ADD tests/memlimit/dockerfile/postBuild +#!/usr/bin/env python3 + +array = [] +for i in range(1024 * 1024 * 64): + array.append(i) ADD tests/memlimit/non-dockerfile/postBuild +#!/usr/bin/env python3 + +array = [] +for i in range(1024 * 1024 * 64): + array.append(i)

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More idiomatic way of checking if all items on a list are same

MODIFY tests/memlimit.py tests/memlimit.py @@ -96,4 +96,5 @@ def test_memlimit_same_postbuild(): for fp in filepaths: with open(fp) as f: file_contents.append(f.read()) - assert all(c == file_contents[0] for c in file_contents) + # Make sure they're all the same + assert len(set(file_contents)) == 1

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update conda to 4.3.30

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -CONDA_VERSION=4.3.14 +CONDA_VERSION=4.3.30 URL="https://repo.continuum.io/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -12,7 +12,7 @@ chmod +x ${INSTALLER_PATH} # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="fc6fc37479e3e3fcf3f9ba52cae98991" +MD5SUM="0b80a152332a4ce5250f3c09589c7a81" if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!" @@ -26,7 +26,8 @@ ${CONDA_DIR}/bin/conda config --system --add channels conda-forge # Do not attempt to auto update conda or dependencies ${CONDA_DIR}/bin/conda config --system --set auto_update_conda false -${CONDA_DIR}/bin/conda config --system --set update_dependencies false +# bug in conda 4.3.>15 prevents --set update_dependencies +echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc ${CONDA_DIR}/bin/conda config --system --set show_channel_urls true ${CONDA_DIR}/bin/conda env update -n root -f /tmp/environment.yml

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adding runtime to preparing

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -57,6 +57,9 @@ Supported configuration files Below is a list of supported configuration files. +.. contents:: + :local: + ``requirements.txt`` ^^^^^^^^^^^^^^^^^^^^ @@ -101,6 +104,13 @@ This specifies a list of Julia packages! Using a ``REQUIRE`` file also requires that the repository contain an ``environment.yml`` file. +``runtime.txt`` +^^^^^^^^^^^^^^^ + +This allows you to control the runtime of Python. To use Python 2, +put the line ``python-2.7`` in the file. A Python 2 kernel will be installed +alongside Python 3. + ``Dockerfile`` ^^^^^^^^^^^^^^

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Set default for volumes in argparse This prevents code from failing when volumes are not specified

MODIFY repo2docker/app.py repo2docker/app.py @@ -217,7 +217,8 @@ class Repo2Docker(Application): '--volume', '-v', dest='volumes', action='append', - help='Volumes to mount inside the container, in form src:dest' + help='Volumes to mount inside the container, in form src:dest', + default=[] ) return argparser

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Add simple test for volume mounting

ADD tests/volumes.py +""" +Test that volume mounts work when running +""" +import os +import subprocess +import tempfile +import time + +def test_volume_home(): + """ + Validate that you can bind mount a volume onto homedirectory & write to it + """ + ts = str(time.time()) + with tempfile.TemporaryDirectory() as tmpdir: + subprocess.check_call([ + 'repo2docker', + '-v', '{}:/home/jovyan'.format(tmpdir), + tmpdir, + '--', + '/bin/bash', + '-c', 'echo -n {} > ts'.format(ts) + ]) + + with open(os.path.join(tmpdir, 'ts')) as f: + assert f.read() == ts

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Fix error message + fix some formatting

MODIFY repo2docker/app.py repo2docker/app.py @@ -334,7 +334,7 @@ class Repo2Docker(Application): if args.volumes and not args.run: # Can't mount if we aren't running - print("Can not mount volumes when not running container") + print("To Mount volumes with -v, you also need to run the container") sys.exit(1) for v in args.volumes: @@ -373,8 +373,6 @@ class Repo2Docker(Application): def run_image(self): client = docker.from_env(version='auto') - api_client = docker.APIClient(version='auto', - **docker.utils.kwargs_from_env()) port = self._get_free_port() if not self.run_cmd: port = str(self._get_free_port()) @@ -386,6 +384,10 @@ class Repo2Docker(Application): ports = {} container_volumes = {} if self.volumes: + api_client = docker.APIClient( + version='auto', + **docker.utils.kwargs_from_env() + ) image = api_client.inspect_image(self.output_image_spec) image_workdir = image['ContainerConfig']['WorkingDir']

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Add tests for user options

ADD tests/users.py +""" +Test that User name and ID mapping works +""" +import os +import subprocess +import tempfile +import time + +def test_user(): + """ + Validate user id and name setting + """ + ts = str(time.time()) + with tempfile.TemporaryDirectory() as tmpdir: + username = os.getlogin() + subprocess.check_call([ + 'repo2docker', + '-v', '{}:/home/{}'.format(tmpdir, username), + '--user-id', '1000', + '--user-name', 'yuvipanda', + tmpdir, + '--', + '/bin/bash', + '-c', 'id -u > id && pwd > pwd && whoami > name'.format(ts) + ]) + + with open(os.path.join(tmpdir, 'id')) as f: + assert f.read().strip() == '1000' + with open(os.path.join(tmpdir, 'pwd')) as f: + assert f.read().strip() == '/home/yuvipanda' + with open(os.path.join(tmpdir, 'name')) as f: + assert f.read().strip() == 'yuvipanda'

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Set $USER environment variable in built images Lots of code looks for this. This is generally set by PAM or somesuch I believe. Let's set it explicitly!

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -32,6 +32,7 @@ ENV SHELL /bin/bash # Set up user ARG NB_USER ARG NB_UID +ENV USER ${NB_USER} ENV HOME /home/${NB_USER} RUN adduser --disabled-password \ MODIFY tests/users.py tests/users.py @@ -21,7 +21,7 @@ def test_user(): tmpdir, '--', '/bin/bash', - '-c', 'id -u > id && pwd > pwd && whoami > name'.format(ts) + '-c', 'id -u > id && pwd > pwd && whoami > name && echo -n $USER > env_user'.format(ts) ]) with open(os.path.join(tmpdir, 'id')) as f: @@ -30,3 +30,5 @@ def test_user(): assert f.read().strip() == '/home/yuvipanda' with open(os.path.join(tmpdir, 'name')) as f: assert f.read().strip() == 'yuvipanda' + with open(os.path.join(tmpdir, 'env_user')) as f: + assert f.read().strip() == 'yuvipanda'

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Fix username check

MODIFY tests/users.py tests/users.py @@ -11,13 +11,13 @@ def test_user(): Validate user id and name setting """ ts = str(time.time()) + username = 'yuvipanda' with tempfile.TemporaryDirectory() as tmpdir: - username = os.getlogin() subprocess.check_call([ 'repo2docker', '-v', '{}:/home/{}'.format(tmpdir, username), '--user-id', '1000', - '--user-name', 'yuvipanda', + '--user-name', username, tmpdir, '--', '/bin/bash', @@ -27,8 +27,8 @@ def test_user(): with open(os.path.join(tmpdir, 'id')) as f: assert f.read().strip() == '1000' with open(os.path.join(tmpdir, 'pwd')) as f: - assert f.read().strip() == '/home/yuvipanda' + assert f.read().strip() == '/home/{}'.format(username) with open(os.path.join(tmpdir, 'name')) as f: - assert f.read().strip() == 'yuvipanda' - with open(os.path.join(tmpdir, 'env_user')) as f: - assert f.read().strip() == 'yuvipanda' + assert f.read().strip() == username + with open(os.path.join(tmpdir, 'name')) as f: + assert f.read().strip() == username

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Fix legacydockerbuilder to also take args

MODIFY repo2docker/buildpacks/legacy.py repo2docker/buildpacks/legacy.py @@ -31,10 +31,10 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): with open('Dockerfile') as f: return f.read() + self.dockerfile_appendix - def build(self, image_spec, memory_limit): + def build(self, image_spec, memory_limit, build_args): with open(self.dockerfile, 'w') as f: f.write(self.render()) - return super().build(image_spec, memory_limit) + return super().build(image_spec, memory_limit, build_args) def detect(self): try:

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Fix user name test to run on computers that isn't mine

MODIFY tests/users.py tests/users.py @@ -11,12 +11,14 @@ def test_user(): Validate user id and name setting """ ts = str(time.time()) - username = 'yuvipanda' + # FIXME: Use arbitrary login here, We need it now since we wanna put things to volume. + username = os.getlogin() + userid = str(os.geteuid()) with tempfile.TemporaryDirectory() as tmpdir: subprocess.check_call([ 'repo2docker', '-v', '{}:/home/{}'.format(tmpdir, username), - '--user-id', '1000', + '--user-id', userid, '--user-name', username, tmpdir, '--', @@ -25,7 +27,7 @@ def test_user(): ]) with open(os.path.join(tmpdir, 'id')) as f: - assert f.read().strip() == '1000' + assert f.read().strip() == userid with open(os.path.join(tmpdir, 'pwd')) as f: assert f.read().strip() == '/home/{}'.format(username) with open(os.path.join(tmpdir, 'name')) as f:

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Added lowercase validation for image name argument

MODIFY repo2docker/app.py repo2docker/app.py @@ -122,6 +122,17 @@ class Repo2Docker(Application): extra=dict(phase='failed')) sys.exit(1) + def validate_image_name(self, image_name): + """ + Validate that the image_name read by argparse contains only lowercase characters + :param image_name: string argument read by argparse + :return: test and return image_name if it only contains lowercase characters else raise error + """ + if not image_name.islower(): + msg = "%r is not a valid docker image name. Image name can contain only lowercase characters." % image_name + raise argparse.ArgumentTypeError(msg) + return image_name + def get_argparser(self): argparser = argparse.ArgumentParser() argparser.add_argument( @@ -146,7 +157,8 @@ class Repo2Docker(Application): argparser.add_argument( '--image-name', help=('Name of image to be built. If unspecified will be ' - 'autogenerated') + 'autogenerated'), + type=self.validate_image_name ) argparser.add_argument(

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Add default command to base Dockerfile template

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -112,6 +112,10 @@ USER ${NB_USER} RUN ./{{ s }} {% endfor %} {% endif -%} + +# Specify the default command to run +CMD jupyter notebook --ip 0.0.0.0 + """ DOC_URL = "http://repo2docker.readthedocs.io/en/latest/samples.html"

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Changed to google style docstrings. Added image_name validation test.

MODIFY repo2docker/app.py repo2docker/app.py @@ -124,10 +124,18 @@ class Repo2Docker(Application): def validate_image_name(self, image_name): """ - Validate that the image_name read by argparse contains only lowercase characters - :param image_name: string argument read by argparse - :return: test and return image_name if it only contains lowercase characters else raise error + Validate image_name read by argparse contains only lowercase characters + + Args: + image_name: string argument read by the argument parser + + Returns: + unmodified image_name + + Raises: + ArgumentTypeError: if image_name contains characters that are not lowercase """ + if not image_name.islower(): msg = "%r is not a valid docker image name. Image name can contain only lowercase characters." % image_name raise argparse.ArgumentTypeError(msg) ADD tests/argumentvalidation.py +""" +Tests that runs validity checks on arguments passed in from shell +""" + +import os +import subprocess + +def does_validate_image_name(builddir, image_name): + try: + output = subprocess.check_output( + [ + 'repo2docker', + '--no-run', + '--image-name', + str(image_name), + builddir + ], + stderr=subprocess.STDOUT, + ).decode() + print(output) + return True + except subprocess.CalledProcessError as e: + output = e.output.decode() + print(output) + if "error: argument --image-name: %r is not a valid docker image name. " \ + "Image name can contain only lowercase characters." % image_name in output: + return False + else: + raise + +def test_image_name_fail(): + builddir = os.path.dirname(__file__) + + assert not does_validate_image_name(builddir, 'Test/Invalid_name:1.0.0') +

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Added docstring for image_name validation test

MODIFY tests/argumentvalidation.py tests/argumentvalidation.py @@ -17,11 +17,9 @@ def does_validate_image_name(builddir, image_name): ], stderr=subprocess.STDOUT, ).decode() - print(output) return True except subprocess.CalledProcessError as e: output = e.output.decode() - print(output) if "error: argument --image-name: %r is not a valid docker image name. " \ "Image name can contain only lowercase characters." % image_name in output: return False @@ -29,6 +27,10 @@ def does_validate_image_name(builddir, image_name): raise def test_image_name_fail(): + """ + Test to check if repo2docker throws image_name validation error on --image-name argument containing uppercase characters. + """ + builddir = os.path.dirname(__file__) assert not does_validate_image_name(builddir, 'Test/Invalid_name:1.0.0')

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Add multiple packages to apt.txt to check if all are parsed and installed

MODIFY tests/venv/apt-packages/apt.txt tests/venv/apt-packages/apt.txt # testing to skip comments in this file gfortran + +# testing to see if all packages get installed +rolldice +moo + MODIFY tests/venv/apt-packages/verify tests/venv/apt-packages/verify #!/bin/bash set -euo pipefail which gfortran +which rolldice +which sl

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Revise apt.txt and verify to install programs that install to /usr/bin instead of /usr/games

MODIFY tests/venv/apt-packages/apt.txt tests/venv/apt-packages/apt.txt gfortran # testing to see if all packages get installed -rolldice -sl +unp +byacc MODIFY tests/venv/apt-packages/verify tests/venv/apt-packages/verify #!/bin/bash set -euo pipefail which gfortran -which rolldice -which sl +which unp +which byacc

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test conda with python 2 env

ADD tests/conda/simple-py2/README.rst +Conda Environment +----------------- + +Conda environments files may allow for more complex builds and dependencies. You +can specify them in the standard `environment.yml` files. ADD tests/conda/simple-py2/environment.yml +dependencies: + - python=2 + - numpy ADD tests/conda/simple-py2/verify +#!/usr/bin/env python +import sys + +assert sys.version_info[:2] == (2, 7), sys.version + +import numpy

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change parameter handling to 'action=append'

MODIFY repo2docker/app.py repo2docker/app.py @@ -300,7 +300,7 @@ class Repo2Docker(Application): argparser.add_argument( '--env', '-e', dest='environment', - nargs='+', + action='append', help='Environment variables to define at container run time', default=[] ) MODIFY tests/env.py tests/env.py @@ -16,7 +16,8 @@ def test_env(): subprocess.check_call([ 'repo2docker', '-v', '{}:/home/{}'.format(tmpdir, username), - '-e', 'FOO={}'.format(ts), 'BAR=baz', + '-e', 'FOO={}'.format(ts), + '--env', 'BAR=baz', '--', tmpdir, '/bin/bash',

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Bump to artful Zesty fell out of support on Jan 13, and the packages have started disappearing from and other mirrors as of today. This will totally screw up our build processes whenever it hits the mirror we use.

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -10,7 +10,7 @@ import re import docker TEMPLATE = r""" -FROM buildpack-deps:zesty +FROM buildpack-deps:artful # Set up locales properly RUN apt-get update && \ @@ -151,7 +151,6 @@ class BuildPack(LoggingConfigurable): # FIXME: Use npm from nodesource! # Everything seems to depend on npm these days, unfortunately. "npm", - "nodejs-legacy" }, help=""" Base set of apt packages that are installed for all images.

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Bump version checks to work with new python 3.6

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, 5) +assert sys.version_info[:2] == (3, 6) import jupyter MODIFY tests/venv/numpy/verify tests/venv/numpy/verify #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 5) +assert sys.version_info[:2] == (3, 6) import numpy

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Remove DataScienceHandbook from our CI It'll be broken by python3.6 move, needs to be fixed before we can re-enable.

DELETE tests/external/datasci.repos.yaml -# A bunch of external datascience related repos we care about! -- name: Jake's Data Science Book - url: https://github.com/jakevdp/PythonDataScienceHandbook - ref: de0cc6bd31 - verify: python -c 'import matplotlib'

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Clarify that --debug and --no-build are for debugging only They output a Dockerfile that can not be used outside of repo2docker, so are only useful as debugging aids. Fixes

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -95,17 +95,26 @@ After building (it might take a while!), it should output a message in your term If you copy/paste that URL into your browser you will see a Jupyter Notebook with the contents of the repository you have just built! -Displaying the image Dockerfile -------------------------------- +Debugging the build process +--------------------------- + +If you want to debug and understand the details of the docker image being built, +you can pass the ``debug`` parameter to the commandline. This will print the +generated ``Dockerfile`` before building and running it. + + .. code-block:: bash + + jupyter-repo2docker --debug https://github.com/jakevdp/PythonDataScienceHandbook + + +If you only want to see the ``Dockerfile`` output but not actually build it, +you can also pass ``--no-build`` to the commandline. This ``Dockerfile`` output +is for **debugging purposes** only - it can not be used by docker directly. -``repo2docker`` will generate a Dockerfile that composes the created Docker image. -To see the contents of this Dockerfile without building the image use -the ``--debug`` and ``--no-build`` flags like so:: + .. code-block:: bash - jupyter-repo2docker --debug --no-build https://github.com/jakevdp/PythonDataScienceHandbook + jupyter-repo2docker --no-build --debug https://github.com/jakevdp/PythonDataScienceHandbook -This will output the contents of the Dockerfile in your console. Note that it -will **not** build the image. Accessing help from the command line ------------------------------------

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Move labels from traitlet to method

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -183,12 +183,11 @@ class BuildPack(LoggingConfigurable): """ return [] - labels = Dict( - {}, - help=""" + def get_labels(self): + """ Docker labels to set on the built image. """ - ) + return {} build_script_files = Dict( {}, @@ -283,15 +282,12 @@ class BuildPack(LoggingConfigurable): for resolving them. """ result = BuildPack(parent=self) - labels = {} - labels.update(self.labels) - labels.update(other.labels) - result.labels = labels # FIXME: Temporary hack so we can refactor this piece by piece instead of all at once! result.get_packages = lambda: self.get_packages().union(other.get_packages()) result.get_base_packages = lambda: self.get_base_packages().union(other.get_base_packages()) result.get_path = lambda: self.get_path() + other.get_path() result.get_env = lambda: self.get_env() + other.get_env() + result.get_labels = lambda: self.get_labels() + other.get_labels() result.build_scripts = self.build_scripts + other.build_scripts result.assemble_scripts = (self.assemble_scripts + @@ -350,7 +346,7 @@ class BuildPack(LoggingConfigurable): packages=sorted(self.get_packages()), path=self.get_path(), env=self.get_env(), - labels=self.labels, + labels=self.get_labels(), build_script_directives=build_script_directives, assemble_script_directives=assemble_script_directives, build_script_files=self.build_script_files,

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Fix python version detection in conda

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -78,9 +78,11 @@ class CondaBuildPack(BuildPack): Will return 'x.y' if found, or Falsy '' if not. """ if not hasattr(self, '_python_version'): + py_version = None environment_yml = self.binder_path('environment.yml') if not os.path.exists(environment_yml): self._python_version = '' + return self._python_version with open(environment_yml) as f: env = YAML().load(f) for dep in env.get('dependencies', []):

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Fix postBuild to work properly

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -417,8 +417,7 @@ class BaseImage(BuildPack): def detect(self): return True - @default('assemble_scripts') - def setup_assembly(self): + def get_assemble_scripts(self): assemble_scripts = [] try: with open(self.binder_path('apt.txt')) as f: MODIFY tests/venv/apt-packages/verify tests/venv/apt-packages/verify #!/bin/bash -set -euo pipefail +set -exuo pipefail which gfortran which unp which byacc

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Remove all traitlets from Legacy Dockerfile buildpack

MODIFY repo2docker/buildpacks/legacy.py repo2docker/buildpacks/legacy.py """ Generates a variety of Dockerfiles based on an input matrix """ -from traitlets import Unicode from textwrap import dedent from .docker import DockerBuildPack @@ -9,7 +8,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): dockerfile = '._binder.Dockerfile' - dockerfile_appendix = Unicode(dedent(r""" + dockerfile_appendix = dedent(r""" USER root COPY . /home/main/notebooks RUN chown -R main:main /home/main/notebooks @@ -24,7 +23,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): /home/main/anaconda2/bin/ipython kernel install --sys-prefix ENV JUPYTER_PATH /home/main/anaconda2/share/jupyter:$JUPYTER_PATH CMD jupyter notebook --ip 0.0.0.0 - """), config=True) + """) def render(self): with open('Dockerfile') as f:

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Remove traitlet imports from all buildpacks

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py import textwrap from traitlets.config import LoggingConfigurable -from traitlets import Unicode, Set, List, Dict, Tuple, default import jinja2 import tarfile import io MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -6,7 +6,6 @@ import os import re from ruamel.yaml import YAML -from traitlets import default, Unicode from ..base import BaseImage MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py """ Generates a variety of Dockerfiles based on an input matrix """ -from traitlets import default import os from .conda import CondaBuildPack MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py """ Generates a variety of Dockerfiles based on an input matrix """ -from traitlets import default import os from ..base import BaseImage

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Remove usage of LoggingConfigurable in BuildPack

MODIFY repo2docker/app.py repo2docker/app.py @@ -344,6 +344,7 @@ class Repo2Docker(Application): logHandler = logging.StreamHandler() formatter = jsonlogger.JsonFormatter() logHandler.setFormatter(formatter) + self.log = logging.getLogger("repo2docker") self.log.handlers = [] self.log.addHandler(logHandler) self.log.setLevel(logging.INFO) MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py import textwrap -from traitlets.config import LoggingConfigurable import jinja2 import tarfile import io import os import stat import re +import logging import docker TEMPLATE = r""" @@ -117,7 +117,7 @@ RUN ./{{ s }} DOC_URL = "http://repo2docker.readthedocs.io/en/latest/samples.html" -class BuildPack(LoggingConfigurable): +class BuildPack: """ A composable BuildPack. @@ -133,6 +133,10 @@ class BuildPack(LoggingConfigurable): and there are *some* general guarantees of ordering. """ + + def __init__(self): + self.log = logging.getLogger('repo2docker') + def get_packages(self): """ List of packages that are installed in this BuildPack.

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Fix tautology

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -152,5 +152,5 @@ class Python2BuildPack(PythonBuildPack): with open(runtime_txt) as f: runtime = f.read().strip() if runtime == 'python-2.7': - return True and super().detect() + return True return False

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ensure python=3.5 is tested

MODIFY tests/conda/binder-dir/binder/environment.yml tests/conda/binder-dir/binder/environment.yml dependencies: + - python=3.5 - numpy MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 6), sys.version +assert sys.version_info[:2] == (3, 5), sys.version import numpy

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conda: fix Python version detection detecting Python 3.5 wasn't happening properly

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -100,7 +100,7 @@ class CondaBuildPack(BuildPack): self._python_version = self.major_pythons.get(py_version[0]) else: # return major.minor - self._python_version = '.'.join(py_version[:2]) + self._python_version = '.'.join(py_version.split('.')[:2]) else: self._python_version = ''

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add nteract_on_jupyter via pip in conda

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml dependencies: - - python==3.6.* + - python=3.6.* - ipywidgets==6.0.1 - jupyterlab==0.30.6 - notebook==5.2.2 + - pip: + - nteract_on_jupyter==1.3.1 MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -31,6 +31,8 @@ echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc ${CONDA_DIR}/bin/conda config --system --set show_channel_urls true ${CONDA_DIR}/bin/conda env update -n root -f /tmp/environment.yml +# enable nteract-on-jupyter, which was installed with pip +jupyter serverextension enable nteract_on_jupyter --sys-prefix if [[ -f /tmp/kernel-environment.yml ]]; then # install kernel env and register kernelspec

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avoid pip cache in install-miniconda

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -30,6 +30,9 @@ ${CONDA_DIR}/bin/conda config --system --set auto_update_conda false echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc ${CONDA_DIR}/bin/conda config --system --set show_channel_urls true +# disable pip cache for conda-triggered pip installs +export PIP_CACHE_DIR=0 + ${CONDA_DIR}/bin/conda env update -n root -f /tmp/environment.yml # enable nteract-on-jupyter, which was installed with pip jupyter serverextension enable nteract_on_jupyter --sys-prefix

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support freezing one Python at a time

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py Freeze the conda environment.yml Run in a continuumio/miniconda3 image to ensure portability + +Usage: + +python freeze.py [3.5] """ from datetime import datetime @@ -10,6 +14,7 @@ import os import pathlib import shutil from subprocess import check_call +import sys from ruamel.yaml import YAML @@ -39,6 +44,7 @@ def freeze(env_file, frozen_file): Result will be stored in frozen_file """ + print(f"Freezing {env_file} -> {frozen_file}") with open(HERE / frozen_file, 'w') as f: f.write(f"# AUTO GENERATED FROM {env_file}, DO NOT MANUALLY MODIFY\n") @@ -73,6 +79,8 @@ def set_python(py_env_file, py): text = f.read() if text and 'GENERATED' not in text: return + + print(f"Regenerating {py_env_file} from {ENV_FILE}") with open(ENV_FILE) as f: env = yaml.load(f) for idx, dep in enumerate(env['dependencies']): @@ -89,7 +97,9 @@ def set_python(py_env_file, py): if __name__ == '__main__': - for py in ('2.7', '3.5', '3.6'): + # allow specifying which Pythons to update on argv + pys = sys.argv[1:] or ('2.7', '3.5', '3.6') + for py in pys: env_file = ENV_FILE_T.format(py=py) set_python(env_file, py) frozen_file = os.path.splitext(env_file)[0] + '.frozen.yml'

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Fix venv test failure caused by r buildpack addition

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -50,10 +50,8 @@ class RBuildPack(PythonBuildPack): match = re.match(r'r-(\d\d\d\d)-(\d\d)-(\d\d)', self.runtime) if not match: self._checkpoint_date = False - - year, month, day = [int(s) for s in match.groups()] - - self._checkpoint_date = datetime.date(year, month, day) + else: + self._checkpoint_date = datetime.date(*[int(s) for s in match.groups()]) return self._checkpoint_date

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Fix curl commandline parameters

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -146,7 +146,7 @@ class RBuildPack(PythonBuildPack): "root", # Install RStudio! r""" - curl --quiet -L --fail {rstudio_url} > /tmp/rstudio.deb && \ + curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \ echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \ dpkg -i /tmp/rstudio.deb && \ rm /tmp/rstudio.deb

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adding R README file

ADD tests/r/simple/README.rst +R environment - install.R +------------------------- + +You can install an R environment with the following two files: + +* ``install.R``: a script that will be run from an R installation. This is + generally used to install and set up packages. +* ``runtime.txt``: include a line that specifies a date for the appropriate + MRAN repository version for packages. It should have the structure + ``r-YYYY-MM-DD``.

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improving readme

MODIFY tests/r/simple/README.rst tests/r/simple/README.rst R environment - install.R ------------------------- -You can install an R environment with the following two files: +You can install an R, RStudio, and IRKernel environment with the following +two files: -* ``install.R``: a script that will be run from an R installation. This is - generally used to install and set up packages. -* ``runtime.txt``: include a line that specifies a date for the appropriate - MRAN repository version for packages. It should have the structure - ``r-YYYY-MM-DD``. +* A ``runtime.txt`` file with the text:: + + r-YYYY-MM-DD + + Where 'YYYY', 'MM' and 'DD' refer to a specific + date snapshot of https://mran.microsoft.com/timemachine + from which libraries will be installed. +* An optional ``install.R`` file that will be executed at build time and can + be used for installing packages from both MRAN and GitHub. + +The presence of ``runtime.txt`` is enough to set up R, RStudio, and IRKernel. It +uses the ``r-base`` package from the Ubuntu apt repositories to install +R itself.

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willingc comment on r readme

MODIFY tests/r/simple/README.rst tests/r/simple/README.rst @@ -11,8 +11,8 @@ two files: Where 'YYYY', 'MM' and 'DD' refer to a specific date snapshot of https://mran.microsoft.com/timemachine from which libraries will be installed. -* An optional ``install.R`` file that will be executed at build time and can - be used for installing packages from both MRAN and GitHub. +* An optional ``install.R`` file that will be executed by an R installation + at build time. It can be used for installing packages from MRAN or GitHub. The presence of ``runtime.txt`` is enough to set up R, RStudio, and IRKernel. It uses the ``r-base`` package from the Ubuntu apt repositories to install

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Switch freeze guidance to not be a directive

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py """ Freeze the conda environment.yml -Run in a continuumio/miniconda3 image to ensure portability +It runs the freeze in a continuumio/miniconda3 image to ensure portability Usage:

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Install from wheel when testing in travis This helps us catch issues with MANIFEST.in and friends that might cause problems with files not being included in the final built package, removing a step from the release process.

MODIFY .travis.yml .travis.yml @@ -5,8 +5,9 @@ services: python: - 3.4 install: -- pip install -e . -- pip install pyyaml +- pip install --no-cache-dir pyyaml pytest wheel +- python setup.py bdist_wheel +- pip install dist/*.whl script: - pytest -s -v tests/${REPO_TYPE}

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