narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Remove notebook from list of conda packages

MODIFY repo2docker/buildpacks/conda/environment.py-3.5.frozen.yml repo2docker/buildpacks/conda/environment.py-3.5.frozen.yml @@ -36,7 +36,6 @@ dependencies: - nbconvert=5.4.0=1 - nbformat=4.4.0=py_1 - ncurses=6.1=hfc679d8_1 - - notebook=5.7.0=py35_0 - openssl=1.0.2p=h470a237_1 - pandoc=1.19.2=0 - pandocfilters=1.4.2=py_1 @@ -85,4 +84,3 @@ dependencies: - sqlalchemy==1.2.14 - urllib3==1.24.1 prefix: /opt/conda/envs/r2d -

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push tagged images on travis creates jupyter/repo2docker:0.7.0 when we release 0.7.0

MODIFY .travis.yml .travis.yml @@ -40,6 +40,7 @@ jobs: provider: script script: "./travis/travis-script.bash" on: + tags: true branch: master env: matrix: MODIFY travis/travis-script.bash travis/travis-script.bash @@ -10,4 +10,11 @@ if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then docker login -u ${DOCKER_LOGIN} -p "${DOCKER_PASSWORD}" docker push ${IMAGE} echo "Pushed new repo2docker image: ${IMAGE}" + if [[ ! -z "${TRAVIS_TAG}" ]]; then + # also push tagged versions + IMAGE_TAG="jupyter/repo2docker:${TRAVIS_TAG/v/}" + docker tag "${IMAGE}" "${IMAGE_TAG}" + docker push "${IMAGE_TAG}" + echo "Pushed new repo2docker image: ${IMAGE_TAG}" + fi fi

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Add Dockerfile repo2docker labels

MODIFY repo2docker/app.py repo2docker/app.py @@ -745,6 +745,11 @@ class Repo2Docker(Application): picked_buildpack = self.default_buildpack() picked_buildpack.appendix = self.appendix + picked_buildpack.labels = { + 'repo2docker.version': self.version, + 'repo2docker.repo': self.repo, + 'repo2docker.ref': self.ref, + } self.log.debug(picked_buildpack.render(), extra=dict(phase='building')) MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -120,8 +120,8 @@ ENV {{item[0]}} {{item[1]}} # Container image Labels! # Put these at the end, since we don't want to rebuild everything # when these change! Did I mention I hate Dockerfile cache semantics? -{% for k, v in labels.items() -%} -LABEL {{k}}={{v}} +{% for k, v in labels.items() %} +LABEL {{k}}="{{v}}" {%- endfor %} # We always want containers to run as non-root @@ -246,7 +246,7 @@ class BuildPack: """ Docker labels to set on the built image. """ - return {} + return getattr(self, 'labels', {}) def get_build_script_files(self): """

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Add test_labels

ADD tests/test_labels.py +""" +Test if labels are supplied correctly to the container +""" +import time +from repo2docker.app import Repo2Docker +from repo2docker import __version__ +import pytest + + +@pytest.mark.parametrize('ref', ['some-branch', None]) +def test_labels(ref, tmpdir): + app = Repo2Docker() + if ref is not None: + argv = ['--ref', ref, str(tmpdir)] + else: + argv = [str(tmpdir)] + app.initialize(argv) + app.debug = True + app.run = False + app.start() # This just build the image and does not run it. + container = app.start_container() + expected_labels = { + 'repo2docker.ref': str(ref), + 'repo2docker.repo': str(tmpdir), + 'repo2docker.version': __version__, + } + + # wait a bit for the container to be ready + # give the container a chance to start + time.sleep(1) + + try: + assert container.labels == expected_labels + finally: + # stop the container + container.stop() + app.wait_for_container(container)

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fix push-tags condition `on` conditions only fire when they are *all* met

MODIFY .travis.yml .travis.yml @@ -33,15 +33,15 @@ jobs: include: - stage: deploy script: skip - if: type = push + if: type = push AND (branch = master OR tag IS present) env: - REPO_TYPE= deploy: provider: script script: "./travis/travis-script.bash" on: - tags: true - branch: master + repo: jupyter/repo2docker + env: matrix: - REPO_TYPE=base

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Remove getattr usage

MODIFY repo2docker/app.py repo2docker/app.py @@ -745,11 +745,9 @@ class Repo2Docker(Application): picked_buildpack = self.default_buildpack() picked_buildpack.appendix = self.appendix - picked_buildpack.labels = { - 'repo2docker.version': self.version, - 'repo2docker.repo': self.repo, - 'repo2docker.ref': self.ref, - } + picked_buildpack.labels['repo2docker.version'] = self.version + picked_buildpack.labels['repo2docker.repo'] = self.repo + picked_buildpack.labels['repo2docker.ref'] = self.ref self.log.debug(picked_buildpack.render(), extra=dict(phase='building')) MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -171,6 +171,7 @@ class BuildPack: def __init__(self): self.log = logging.getLogger('repo2docker') self.appendix = '' + self.labels = {} if sys.platform.startswith('win'): self.log.warning("Windows environment detected. Note that Windows " "support is experimental in repo2docker.") @@ -246,7 +247,7 @@ class BuildPack: """ Docker labels to set on the built image. """ - return getattr(self, 'labels', {}) + return self.labels def get_build_script_files(self): """

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Update test_labels.py

MODIFY repo2docker/app.py repo2docker/app.py @@ -744,6 +744,8 @@ class Repo2Docker(Application): else: picked_buildpack = self.default_buildpack() + self._picked_buildpack = picked_buildpack + picked_buildpack.appendix = self.appendix picked_buildpack.labels['repo2docker.version'] = self.version picked_buildpack.labels['repo2docker.repo'] = self.repo MODIFY tests/test_labels.py tests/test_labels.py @@ -10,28 +10,20 @@ import pytest @pytest.mark.parametrize('ref', ['some-branch', None]) def test_labels(ref, tmpdir): app = Repo2Docker() + repo = str(tmpdir) if ref is not None: - argv = ['--ref', ref, str(tmpdir)] + argv = ['--ref', ref, repo] else: - argv = [str(tmpdir)] + argv = [repo] app.initialize(argv) - app.debug = True + app.build = False app.run = False - app.start() # This just build the image and does not run it. - container = app.start_container() + app.start() + labels = app._picked_buildpack.labels expected_labels = { - 'repo2docker.ref': str(ref), - 'repo2docker.repo': str(tmpdir), + 'repo2docker.ref': ref, + 'repo2docker.repo': repo, 'repo2docker.version': __version__, } - # wait a bit for the container to be ready - # give the container a chance to start - time.sleep(1) - - try: - assert container.labels == expected_labels - finally: - # stop the container - container.stop() - app.wait_for_container(container) + assert labels == expected_labels

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Add test for BuildPack label rendering

MODIFY tests/test_labels.py tests/test_labels.py @@ -3,10 +3,20 @@ Test if labels are supplied correctly to the container """ import time from repo2docker.app import Repo2Docker +from repo2docker.buildpacks import BuildPack from repo2docker import __version__ import pytest +def test_buildpack_labels_rendered(): + bp = BuildPack() + assert 'LABEL' not in bp.render() + bp.labels['first_label'] = 'firstlabel' + assert 'LABEL first_label="firstlabel"\n' in bp.render() + bp.labels['second_label'] = 'anotherlabel' + assert 'LABEL second_label="anotherlabel"\n' in bp.render() + + @pytest.mark.parametrize('ref', ['some-branch', None]) def test_labels(ref, tmpdir): app = Repo2Docker()

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Refactor test to use mock

MODIFY repo2docker/app.py repo2docker/app.py @@ -744,8 +744,6 @@ class Repo2Docker(Application): else: picked_buildpack = self.default_buildpack() - self._picked_buildpack = picked_buildpack - picked_buildpack.appendix = self.appendix picked_buildpack.labels['repo2docker.version'] = self.version picked_buildpack.labels['repo2docker.repo'] = self.repo MODIFY tests/test_labels.py tests/test_labels.py Test if labels are supplied correctly to the container """ import time +from unittest.mock import Mock from repo2docker.app import Repo2Docker from repo2docker.buildpacks import BuildPack from repo2docker import __version__ @@ -19,21 +20,26 @@ def test_buildpack_labels_rendered(): @pytest.mark.parametrize('ref', ['some-branch', None]) def test_labels(ref, tmpdir): - app = Repo2Docker() repo = str(tmpdir) if ref is not None: argv = ['--ref', ref, repo] else: argv = [repo] + + app = Repo2Docker() + # Add mock BuildPack to app + mock_buildpack = Mock() + mock_buildpack.return_value.labels = {} + app.buildpacks = [mock_buildpack] + app.initialize(argv) app.build = False app.run = False app.start() - labels = app._picked_buildpack.labels expected_labels = { 'repo2docker.ref': ref, 'repo2docker.repo': repo, 'repo2docker.version': __version__, } - assert labels == expected_labels + assert mock_buildpack().labels == expected_labels

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Move cleanup_checkout automatic determination to main() This is automaticaly determined only from commandline args, so it should be in __main__

MODIFY repo2docker/__main__.py repo2docker/__main__.py import argparse import sys +import os from .app import Repo2Docker from . import __version__ from .utils import validate_and_generate_port_mapping @@ -299,6 +300,12 @@ def make_r2d(argv=None): r2d.environment = args.environment + # if the source exists locally we don't want to delete it at the end + if os.path.exists(args.repo): + r2d.cleanup_checkout = False + else: + r2d.cleanup_checkout = args.clean + return r2d MODIFY repo2docker/app.py repo2docker/app.py @@ -391,12 +391,6 @@ class Repo2Docker(Application): fmt='%(message)s' ) - # if the source exists locally we don't want to delete it at the end - if os.path.exists(self.repo): - self.cleanup_checkout = False - else: - self.cleanup_checkout = args.clean - if self.output_image_spec == "": # Attempt to set a sane default! # HACK: Provide something more descriptive?

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Split 'build' function out of start

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -237,15 +237,18 @@ def make_r2d(argv=None): if args.image_name: r2d.output_image_spec = args.image_name - r2d.push = args.push - r2d.run = args.run r2d.json_logs = args.json_logs r2d.build = args.build - if not r2d.build: + + if not args.build: # Can't push nor run if we aren't building - r2d.run = False - r2d.push = False + args.run = False + args.push = False + + r2d.build = args.build + r2d.run = args.run + r2d.push = args.push # check against r2d.run and not args.run as r2d.run is false on # --no-build MODIFY repo2docker/app.py repo2docker/app.py @@ -551,6 +551,10 @@ class Repo2Docker(Application): raise e sys.exit(1) + def build(self): + """ + Build docker image + """ # If the source to be executed is a directory, continue using the # directory. In the case of a local directory, it is used as both the # source and target. Reusing a local directory seems better than @@ -620,6 +624,9 @@ class Repo2Docker(Application): if self.cleanup_checkout: shutil.rmtree(checkout_path, ignore_errors=True) + def start(self): + self.build() + if self.push: self.push_image()

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Add test for proper failure when ref isn't found in git repo

MODIFY tests/contentproviders/test_git.py tests/contentproviders/test_git.py from contextlib import contextmanager import os import subprocess +import pytest from tempfile import TemporaryDirectory from repo2docker.contentproviders import Git @@ -34,6 +35,16 @@ def test_clone(): pass assert os.path.exists(os.path.join(clone_dir, 'test')) +def test_bad_ref(): + """ + Test trying to checkout a ref that doesn't exist + """ + with git_repo() as upstream: + with TemporaryDirectory() as clone_dir: + spec = {'repo': upstream, 'ref': 'does-not-exist'} + with pytest.raises(ValueError): + for _ in Git().fetch(spec, clone_dir): + pass def test_always_accept(): # The git content provider should always accept a spec

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Add test for cleanup_checkout

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -306,6 +306,7 @@ def make_r2d(argv=None): r2d.environment = args.environment # if the source exists locally we don't want to delete it at the end + # FIXME: Find a better way to figure out if repo is 'local'. Push this into ContentProvider? if os.path.exists(args.repo): r2d.cleanup_checkout = False else: MODIFY tests/test_args.py tests/test_args.py @@ -62,3 +62,18 @@ def test_run_required(): # Can't publish any ports while running if we don't specify a command explicitly with pytest.raises(SystemExit): make_r2d(['-p', '8000:8000', '.']) + +def test_clean(): + """ + Test checkout is cleaned appropriately + """ + + # Don't clean when repo isn't local and we explicitly ask it to not clean + assert not make_r2d(['--no-clean', 'https://github.com/blah.git']).cleanup_checkout + # Do clean repo when repo isn't localj + assert make_r2d(['https://github.com/blah.git']).cleanup_checkout + + # Don't clean by default when repo exists locally + assert not make_r2d(['.']).cleanup_checkout + # Don't clean when repo exists locally and we explicitly ask it to not clean + assert not make_r2d(['--no-clean', '.']).cleanup_checkout \ No newline at end of file

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Add test for valid & invalid docker image names

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -5,7 +5,7 @@ import logging import docker from .app import Repo2Docker from . import __version__ -from .utils import validate_and_generate_port_mapping +from .utils import validate_and_generate_port_mapping, is_valid_docker_image_name def validate_image_name(image_name): """ MODIFY tests/test_args.py tests/test_args.py @@ -77,3 +77,11 @@ def test_clean(): assert not make_r2d(['.']).cleanup_checkout # Don't clean when repo exists locally and we explicitly ask it to not clean assert not make_r2d(['--no-clean', '.']).cleanup_checkout + + +def test_invalid_image_name(): + """ + Test validating image names + """ + with pytest.raises(SystemExit): + make_r2d(['--image-name', '_invalid', '.']) \ No newline at end of file

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Use pytest's capsys to test for stdout values Works better with pytest's output capturing system

MODIFY tests/test_args.py tests/test_args.py @@ -6,18 +6,15 @@ import pytest import logging from repo2docker.__main__ import make_r2d from repo2docker import __version__ -from contextlib import redirect_stdout -import io -def test_version(): + +def test_version(capsys): """ Test passing '--version' to repo2docker """ - stdout = io.StringIO() - with redirect_stdout(stdout): with pytest.raises(SystemExit): make_r2d(['--version']) - assert stdout.getvalue().strip() == __version__ + assert capsys.readouterr().out == f"{__version__}\n" def test_simple(): """

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Fix typos and syntax errors in the documentation

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -113,7 +113,7 @@ used for your R installation. It is powered by the open file format `Dar <https://github.com/substance/dar>`_. If your repository contains a Stencila document, repo2docker detects it based on the file ``manifest.xml``. -The required `execution contexts <https://stenci.la/learn/intro.html>` are extracted from a Dar article (i.e. +The required `execution contexts <https://stenci.la/learn/intro.html>`_ are extracted from a Dar article (i.e. files named ``*.jats.xml``). You may also have a ``runtime.txt`` and/or an ``install.R`` to manually configure your R installation. @@ -141,9 +141,9 @@ their demo for binder <https://github.com/jupyterlab/jupyterlab-demo/blob/master ==================================================== A script that can contain simple commands to be run at runtime (as an -`ENTRYPOINT <https://docs.docker.com/engine/reference/builder/#entrypoint>` +`ENTRYPOINT <https://docs.docker.com/engine/reference/builder/#entrypoint>`_ to the docker container). If you want this to be a shell script, make sure the -first line is ```#!/bin/bash``. The last line must be ```exec "$@"``` +first line is ``#!/bin/bash``. The last line must be ``exec "$@"`` equivalent. Use this to set environment variables that software installed in your container

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Update CHANGES.rst [skip travis]

MODIFY CHANGES.rst CHANGES.rst -The ``repo2docker`` changelog has been moved to https://repo2docker.readthedocs.io/en/latest/changelog.html +The ``repo2docker`` changelog has been moved. It can be viewed online at https://repo2docker.readthedocs.io/en/latest/changelog.html. In the ``repo2docker`` repository, the changelog is located at ``docs/source/changelog.rst``.

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report top 10 slowest tests in each group

MODIFY .travis.yml .travis.yml @@ -17,9 +17,9 @@ script: # possible issues with MANIFEST.in - pushd tests; if [ ${REPO_TYPE} == "r" ] || [ ${REPO_TYPE} == "stencila-r" ] || [ ${REPO_TYPE} == "stencila-py" ]; then - travis_wait 30 pytest --cov repo2docker -v ${REPO_TYPE} || exit 1; + travis_wait 30 pytest --durations 10 --cov repo2docker -v ${REPO_TYPE} || exit 1; else - travis_retry pytest --cov repo2docker -v ${REPO_TYPE} || exit 1; + travis_retry pytest --durations 10 --cov repo2docker -v ${REPO_TYPE} || exit 1; fi; popd; - pip install -r docs/doc-requirements.txt

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Update new contributing guide changelog ref [skip travis]

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -31,7 +31,7 @@ to help you make a contribution. * describe why you are proposing the changes you are proposing; * try to not rush changes (the definition of rush depends on how big your changes are); -* Enter your changes into the [change log](https://github.com/jupyter/repo2docker/blob/master/CHANGES.rst); +* Enter your changes into the [changelog](https://repo2docker.readthedocs.io/en/latest/changelog.html) in `docs/source/changelog.rst`; * someone else has to merge your PR; * new code needs to come with a test; * apply [PEP8](https://www.python.org/dev/peps/pep-0008/) as much

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Use relative link to changelog [skip travis]

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -31,7 +31,7 @@ to help you make a contribution. * describe why you are proposing the changes you are proposing; * try to not rush changes (the definition of rush depends on how big your changes are); -* Enter your changes into the [changelog](https://repo2docker.readthedocs.io/en/latest/changelog.html) in `docs/source/changelog.rst`; +* Enter your changes into the [changelog](./../../changelog.html) in `docs/source/changelog.rst`; * someone else has to merge your PR; * new code needs to come with a test; * apply [PEP8](https://www.python.org/dev/peps/pep-0008/) as much

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Add CLI API docs

MODIFY dev-requirements.txt dev-requirements.txt @@ -4,3 +4,4 @@ pyyaml pytest wheel pytest-cov +sphinxcontrib-autoprogram MODIFY docs/source/conf.py docs/source/conf.py @@ -33,7 +33,9 @@ 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 = ['sphinx.ext.extlinks'] +extensions = ['sphinx.ext.extlinks', + 'sphinxcontrib.autoprogram', + ] extlinks = { 'issue': ('https://github.com/jupyter/repo2docker/issues/%s', 'Issue #'), MODIFY docs/source/usage.rst docs/source/usage.rst @@ -107,4 +107,12 @@ be used by docker directly. jupyter-repo2docker --no-build --debug https://github.com/norvig/pytudes + +Command line API +================ + +.. autoprogram:: repo2docker.__main__:argparser + :prog: jupyter-repo2docker + + .. _Pytudes: https://github.com/norvig/pytudes MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -194,6 +194,8 @@ def get_argparser(): return argparser +argparser = get_argparser() + def make_r2d(argv=None): if argv is None:

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Add ArgumentParser description

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -37,7 +37,9 @@ def validate_image_name(image_name): def get_argparser(): """Get arguments that may be used by repo2docker""" - argparser = argparse.ArgumentParser() + argparser = argparse.ArgumentParser( + description='Fetch a repository and build a container image', + ) argparser.add_argument( '--config',

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Move autoprogram to doc requirements

MODIFY Pipfile Pipfile @@ -11,6 +11,7 @@ recommonmark = "*" alabaster = "*" Sphinx = ">=1.4,!=1.5.4" alabaster_jupyterhub = "*" +sphinxcontrib-autoprogram = "*" [packages] repo2docker = {path=".", editable=true} MODIFY dev-requirements.txt dev-requirements.txt @@ -4,4 +4,3 @@ pyyaml pytest wheel pytest-cov -sphinxcontrib-autoprogram MODIFY docs/doc-requirements.txt docs/doc-requirements.txt @@ -4,3 +4,4 @@ sphinx>=1.4, !=1.5.4 recommonmark alabaster alabaster_jupyterhub +sphinxcontrib-autoprogram

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Add pip install repo

MODIFY .circleci/config.yml .circleci/config.yml @@ -15,6 +15,7 @@ jobs: - restore_cache: keys: - cache-pip + - run: pip install --user -e . # Install the packages needed to build our documentation # This will depend on your particular package! - run: pip install --user -r docs/doc-requirements.txt

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Provide help text for commandline arguments

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -169,13 +169,13 @@ def get_argparser(): argparser.add_argument( '--appendix', type=str, - #help=self.traits()['appendix'].help, + help=Repo2Docker.appendix.help ) argparser.add_argument( '--subdir', type=str, - #help=self.traits()['subdir'].help, + help=Repo2Docker.subdir.help ) argparser.add_argument( @@ -189,7 +189,7 @@ def get_argparser(): '--cache-from', action='append', default=[], - #help=self.traits()['cache_from'].help + help=Repo2Docker.cache_from.help ) return argparser

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Redirect apt-get install output to /dev/null `apt-get install` calls `dpkg` underneath to do the installation. Unfortunately, `-qq` does not get passed through, and we end up with a lot of log output even with `-qq`. Redirecting stdout to /dev/null stops this output. Errors come out to stderr, so those will be displayed.

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -17,7 +17,7 @@ ENV DEBIAN_FRONTEND=noninteractive # Set up locales properly RUN apt-get -qq update && \ - apt-get -qq install --yes --no-install-recommends locales && \ + apt-get -qq install --yes --no-install-recommends locales > /dev/null && \ apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* @@ -56,18 +56,19 @@ RUN apt-get -qq update && \ {% for package in base_packages -%} {{ package }} \ {% endfor -%} - && apt-get -qq purge && \ + > /dev/null && \ + apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* -# This apt-get install is *not* quiet, so users see their packages being installed {% if packages -%} RUN apt-get -qq update && \ apt-get -qq install --yes \ {% for package in packages -%} {{ package }} \ {% endfor -%} - && apt-get -qq purge && \ + > /dev/null && \ + apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* {% endif -%} @@ -552,6 +553,7 @@ class BaseImage(BuildPack): assemble_scripts.append(( 'root', + # This apt-get install is *not* quiet, since users explicitly asked for this r""" apt-get -qq update && \ apt-get install --yes --no-install-recommends {} && \

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Remove f-strings

MODIFY repo2docker/app.py repo2docker/app.py @@ -426,7 +426,8 @@ class Repo2Docker(Application): self.log.info('Pushing image\n', extra=dict(progress=layers, phase='pushing')) last_emit_time = time.time() - self.log.info(f'Successfully pushed {self.output_image_spec}', extra=dict(phase='pushing')) + self.log.info('Successfully pushed {}'.format(self.output_image_spec), + extra=dict(phase='pushing')) def run_image(self): """Run docker container from built image @@ -568,7 +569,7 @@ class Repo2Docker(Application): if not os.path.isdir(checkout_path): self.log.error('Subdirectory %s does not exist', self.subdir, extra=dict(phase='failure')) - raise FileNotFoundError(f'Could not find {checkout_path}') + raise FileNotFoundError('Could not find {}'.format(checkout_path)) with chdir(checkout_path): for BP in self.buildpacks:

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Another f-string

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -38,7 +38,7 @@ class Git(ContentProvider): if hash is None: self.log.error('Failed to check out ref %s', ref, extra=dict(phase='failed')) - raise ValueError(f'Failed to check out ref {ref}') + raise ValueError('Failed to check out ref {}'.format(ref)) # If the hash is resolved above, we should be able to reset to it for line in execute_cmd(['git', 'reset', '--hard', hash], cwd=output_dir,

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Remove f-string in test

MODIFY tests/unit/test_args.py tests/unit/test_args.py @@ -14,7 +14,7 @@ def test_version(capsys): """ with pytest.raises(SystemExit): make_r2d(['--version']) - assert capsys.readouterr().out == f"{__version__}\n" + assert capsys.readouterr().out == "{}\n".format(__version__) def test_simple(): """

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Set REPO_PATH as late as possible Leads to maximum cache re-use

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -38,15 +38,10 @@ ARG NB_UID ENV USER ${NB_USER} ENV HOME /home/${NB_USER} -# Allow target path repo is cloned to be configurable -ARG REPO_PATH=${HOME} -ENV REPO_PATH ${REPO_PATH} - RUN adduser --disabled-password \ --gecos "Default user" \ --uid ${NB_UID} \ ${NB_USER} -WORKDIR ${REPO_PATH} RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ DISTRO="bionic" && \ @@ -102,6 +97,11 @@ COPY {{ src }} {{ dst }} {{sd}} {% endfor %} +# Allow target path repo is cloned to be configurable +ARG REPO_PATH=${HOME} +ENV REPO_PATH ${REPO_PATH} +WORKDIR ${REPO_PATH} + # Copy and chown stuff. This doubles the size of the repo, because # you can't actually copy as USER, only as root! Thanks, Docker! USER root

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Allow setting REPO_PATH from commandline

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -168,6 +168,11 @@ def get_argparser(): help='Use the local repository in edit mode', ) + argparser.add_argument( + '--repo-path', + help=Repo2Docker.repo_path.help + ) + argparser.add_argument( '--appendix', type=str, @@ -316,6 +321,9 @@ def make_r2d(argv=None): else: r2d.cleanup_checkout = args.clean + if args.repo_path: + r2d.repo_path = args.repo_path + return r2d MODIFY repo2docker/app.py repo2docker/app.py @@ -327,6 +327,16 @@ class Repo2Docker(Application): config=True ) + repo_path = Unicode( + '$HOME', + help=""" + Path inside the image where contents of the repositories are copied to. + + Build arguments in this are expanded. + """, + config=True + ) + def fetch(self, url, ref, checkout_path): """Fetch the contents of `url` and place it in `checkout_path`. @@ -593,7 +603,8 @@ class Repo2Docker(Application): if not self.dry_run: build_args = { 'NB_USER': self.user_name, - 'NB_UID': str(self.user_id) + 'NB_UID': str(self.user_id), + 'REPO_PATH': self.repo_path } self.log.info('Using %s builder\n', bp.__class__.__name__, extra=dict(phase='building'))

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Only set REPO_PATH if explicitly passed in Expanding env vars through ARG and ENV is too confusing to get right.

MODIFY repo2docker/app.py repo2docker/app.py @@ -328,11 +328,11 @@ class Repo2Docker(Application): ) repo_path = Unicode( - '$HOME', + '', help=""" Path inside the image where contents of the repositories are copied to. - Build arguments in this are expanded. + Defaults to ${HOME} if not set """, config=True ) @@ -604,8 +604,9 @@ class Repo2Docker(Application): build_args = { 'NB_USER': self.user_name, 'NB_UID': str(self.user_id), - 'REPO_PATH': self.repo_path } + if self.repo_path: + build_args['REPO_PATH'] = self.repo_path self.log.info('Using %s builder\n', bp.__class__.__name__, extra=dict(phase='building'))

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Explicitly specify log message for docker build failures

MODIFY repo2docker/app.py repo2docker/app.py @@ -617,7 +617,7 @@ class Repo2Docker(Application): extra=dict(phase='building')) elif 'error' in l: self.log.info(l['error'], extra=dict(phase='failure')) - raise docker.errors.BuildError(l['error']) + raise docker.errors.BuildError(l['error'], build_log='') elif 'status' in l: self.log.info('Fetching base image...\r', extra=dict(phase='building'))

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Fix assumption in nix buildpack about workdir

MODIFY repo2docker/buildpacks/nix/install-nix.bash repo2docker/buildpacks/nix/install-nix.bash @@ -5,6 +5,8 @@ set -ex NIX_VERSION="2.1.1" NIX_SHA256="ad10b4da69035a585fe89d7330037c4a5d867a372bb0e52a1542ab95aec67999" +# Do all our operations in /tmp, since we can't rely on current directory being writeable yet. +cd /tmp wget --quiet https://nixos.org/releases/nix/nix-$NIX_VERSION/nix-$NIX_VERSION-x86_64-linux.tar.bz2 echo "$NIX_SHA256 nix-2.1.1-x86_64-linux.tar.bz2" | sha256sum -c tar xjf nix-*-x86_64-linux.tar.bz2

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Add tag command snippet make sure it's an annotated tag

MODIFY docs/source/contributing/tasks.md docs/source/contributing/tasks.md @@ -106,7 +106,12 @@ We try to make a release of repo2docker every few months if possible. We follow semantic versioning. -Check that the Change log is ready and then tag a new release on GitHub. +Check that the Change log is ready and then tag a new release on GitHub: + +```bash +V=0.7.0 git tag -am "release $V" $V +git push origin --tags +``` When the travis run completes check that the new release is available on PyPI. @@ -152,6 +157,7 @@ release for that version (bugfix version 0). ### Keeping the Pipfile and requirements files up to date + We now have both a `dev-requirements.txt` and a `Pifile` for repo2docker, as such it is important to keep these in sync/up-to-date.

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use multi-stage build python 3.7 build wheels in first stage, install in second run with slim image by default instead of full (~200MB vs ~1GB)

MODIFY Dockerfile Dockerfile -FROM python:3.6.3 +ARG PYTHON_VERSION=3.7 +FROM python:${PYTHON_VERSION} + +# build wheels in first image +ADD . /tmp/src +RUN mkdir /tmp/wheelhouse \ + && cd /tmp/wheelhouse \ + && pip3 wheel --no-cache-dir /tmp/src + +# run with slim variant instead of full +# since we won't need compilers and friends +FROM python:${PYTHON_VERSION}-slim + +# we do need git, though +RUN apt-get update \ + && apt-get -y install --no-install-recommends git \ + && rm -rf /var/lib/apt/lists/* + +# install repo2docker +COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse +RUN pip3 install --no-cache-dir /tmp/wheelhouse/*.whl + +# add git-credential helper +COPY ./docker/git-credential-env /usr/local/bin/git-credential-env +RUN git config --system credential.helper env # Used for testing purpose in ports.py EXPOSE 52000 -RUN mkdir /tmp/src -ADD . /tmp/src -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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remove travis docker build no longer needed

MODIFY .travis.yml .travis.yml @@ -29,18 +29,6 @@ script: after_success: - pip install codecov - pushd tests && codecov && popd -jobs: - include: - - stage: deploy - script: skip - if: type = push AND (branch = master OR tag IS present) - env: - - REPO_TYPE= - deploy: - provider: script - script: "./travis/travis-script.bash" - on: - repo: jupyter/repo2docker env: matrix: DELETE travis/travis-script.bash -#!/bin/bash -set -eu -o pipefail - -VERSION=$(git rev-parse --short HEAD) - -IMAGE="jupyter/repo2docker:${VERSION}" -docker build -t ${IMAGE} . - -if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then - docker login -u ${DOCKER_LOGIN} -p "${DOCKER_PASSWORD}" - docker push ${IMAGE} - echo "Pushed new repo2docker image: ${IMAGE}" - if [[ ! -z "${TRAVIS_TAG}" ]]; then - # also push tagged versions - IMAGE_TAG="jupyter/repo2docker:${TRAVIS_TAG/v/}" - docker tag "${IMAGE}" "${IMAGE_TAG}" - docker push "${IMAGE_TAG}" - echo "Pushed new repo2docker image: ${IMAGE_TAG}" - fi -fi

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add dockerhub post_push to publish git-tagged images

ADD hooks/README.md +# Docker build hooks + +These define our [custom hooks for docker automated builds](https://docs.docker.com/docker-hub/builds/advanced/#custom-build-phase-hooks) ADD hooks/post_push +#!/bin/bash + +# when building jupyter/repo2docker:master also push jupyter/repo2docker:abcd1234 + +HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT:8}" +docker tag $DOCKER_REPO:$DOCKER_TAG $HASH_IMAGE +docker push $HASH_IMAGE

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fix commit hash truncation on docker images truncate to 8 characters

MODIFY hooks/post_push hooks/post_push # when building jupyter/repo2docker:master also push jupyter/repo2docker:abcd1234 -HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT:8}" +HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT: -8}" docker tag $DOCKER_REPO:$DOCKER_TAG $HASH_IMAGE docker push $HASH_IMAGE

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Add check for port sepc > 65535

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -90,10 +90,13 @@ def validate_and_generate_port_mapping(port_mappings): """ def check_port(port): try: - int(port) + p = int(port) except ValueError as e: raise ValueError('Port specification "{}" has ' 'an invalid port.'.format(mapping)) + if p > 65535: + raise ValueError('Port specification "{}" specifies ' + 'a port above 65535.'.format(mapping)) return port def check_port_string(p):

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Use a minimal hand-crafted Dockerfile for speed Instead of installing the normal stack just install the notebook server and launch it to check for the launch URL being output correctly.

MODIFY tests/unit/test_connect_url.py tests/unit/test_connect_url.py @@ -5,15 +5,41 @@ import requests import time from repo2docker.app import Repo2Docker + +# Minimal Dockerfile to make build as fast as possible +DOCKER_FILE = """ +FROM python:3.7-slim +# install the notebook package +RUN pip install --no-cache --upgrade pip && \ + pip install --no-cache notebook + +# create user with a home directory +ARG NB_USER +ARG NB_UID +ENV USER ${NB_USER} +ENV HOME /home/${NB_USER} + +RUN adduser --disabled-password \ + --gecos "Default user" \ + --uid ${NB_UID} \ + ${NB_USER} +WORKDIR ${HOME} +USER ${NB_USER} +""" + + def test_connect_url(tmpdir): tmpdir.chdir() - p = tmpdir.join("requirements.txt") - p.write("notebook>=5.6.0") + p = tmpdir.join("Dockerfile") + p.write(DOCKER_FILE) + # we set run=False so that we can start the container ourselves and + # get a handle to the container, used to inspect the logs app = Repo2Docker(repo=str(tmpdir), run=False) app.initialize() - app.start() # This just build the image and does not run it. + app.start() container = app.start_container() + container_url = 'http://{}:{}/api'.format(app.hostname, app.port) expected_url = 'http://{}:{}'.format(app.hostname, app.port)

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Extend doc string for port mapping function

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -70,7 +70,7 @@ def chdir(path): def validate_and_generate_port_mapping(port_mappings): """ - Validate a list of port mappings and return a dictionary of port mappings + Validate a list of port mappings and return a dictionary of port mappings. Args: port_mappings (list): List of strings of format @@ -78,7 +78,8 @@ def validate_and_generate_port_mapping(port_mappings): network interface Returns: - Dictionary of port mappings + Dictionary of port mappings in the format accepted by docker-py's + `containers.run()` method (https://docker-py.readthedocs.io/en/stable/containers.html) Raises: Exception on invalid port mapping

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Moved postBuild comment into the condition.

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -142,8 +142,8 @@ LABEL {{k}}="{{v}}" # We always want containers to run as non-root USER ${NB_USER} -# Make sure that postBuild scripts are marked executable before executing them {% if post_build_scripts -%} +# Make sure that postBuild scripts are marked executable before executing them {% for s in post_build_scripts -%} RUN chmod +x {{ s }} RUN ./{{ s }}

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Adds pytest version to fix travis build errors

MODIFY Pipfile Pipfile # update these accordingly [dev-packages] -pytest="*" +pytest=">=3.6" wheel="*" pytest-cov="*" PyYAML = "*" MODIFY dev-requirements.txt dev-requirements.txt # Note that there is also a Pipfile for this project if you are updating this # file do not forget to update the Pipfile accordingly pyyaml -pytest +pytest>=3.6 wheel pytest-cov

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Fixed sphinx error finding changelog

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -10,7 +10,7 @@ repo2docker merged. community is a great way to save time later. * Make edits in your fork of the repo2docker repository * Submit a pull request (this is how all changes are made) -* Edit [the changelog](./../../changelog.html) +* Edit [the changelog](./../../changelog) by appending your feature / bug fix to the development version. * Wait for a community member to merge your changes * (optional) Deploy a new version of repo2docker to mybinder.org by [following these steps](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html) @@ -31,7 +31,7 @@ to help you make a contribution. * describe why you are proposing the changes you are proposing; * try to not rush changes (the definition of rush depends on how big your changes are); -* Enter your changes into the [changelog](./../../changelog.html) in `docs/source/changelog.rst`; +* Enter your changes into the [changelog](./../../changelog) in `docs/source/changelog.rst`; * someone else has to merge your PR; * new code needs to come with a test; * apply [PEP8](https://www.python.org/dev/peps/pep-0008/) as much

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Updated log info for local content provider

MODIFY repo2docker/contentproviders/base.py repo2docker/contentproviders/base.py @@ -70,4 +70,4 @@ class Local(ContentProvider): msg = "Local content provider assumes {} == {}".format(spec['path'], output_dir) assert output_dir == spec['path'], msg - yield + yield "Using local repo {}.\n".format(spec['path'])

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Set JULIA_DEPOT_PATH Equivalent of JULIA_PKGDIR for Julia 1.0+ Fixes

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -62,6 +62,8 @@ class JuliaBuildPack(CondaBuildPack): will be installed - `JULIA_HOME`: path where all Julia Binaries will be installed - `JULIA_PKGDIR`: path where all Julia libraries will be installed + - `JULIA_DEPOT_PATH`: path where Julia libraries are installed. + Similar to JULIA_PKGDIR, used in 1.0. - `JULIA_VERSION`: default version of julia to be installed - `JUPYTER`: environment variable required by IJulia to point to the `jupyter` executable @@ -74,6 +76,7 @@ class JuliaBuildPack(CondaBuildPack): ('JULIA_HOME', '${JULIA_PATH}/bin'), # julia <= 0.6 ('JULIA_BINDIR', '${JULIA_HOME}'), # julia >= 0.7 ('JULIA_PKGDIR', '${JULIA_PATH}/pkg'), + ('JULIA_DEPOT_PATH', '${JULIA_PKGDIR}'), # julia >= 0.7 ('JULIA_VERSION', self.julia_version), ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter') ]

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Add test for JULIA_DEPOT_PATHt

MODIFY tests/julia/pyplot/verify tests/julia/pyplot/verify @@ -16,3 +16,9 @@ if isfile("graph.png") else exit(1) end + +# We check that PyPlot is installed inside ${JULIA_DEPOT_PATH} +if ! isdir(ENV["JULIA_DEPOT_PATH"] * "/packages/PyPlot") + println("PyPlot not installed under JULIA_DEPOT_PATH") + exit(1) +end \ No newline at end of file

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Remove redundant Julia test This is the equivalent to the pyplot-requirements test, so just do one rather than 2.

DELETE tests/julia/pyplot/README.rst -Julia - REQUIRE ---------------- - -To specify dependencies in Julia, include a REQUIRE file that lists the names -of packages you'd like to be installed. For example: - -``` -PyPlot -IJulia -DataFrames -``` - -Each one will be installed but **not** pre-compiled. If you'd like to -pre-compile your Julia packages, consider using a ``postBuild`` file. - -Note that this example also specifies Python dependencies with an -``environment.yml`` file. DELETE tests/julia/pyplot/REQUIRE -PyPlot DELETE tests/julia/pyplot/environment.yml -dependencies: - - matplotlib - DELETE tests/julia/pyplot/verify -#!/usr/bin/env julia -using PyPlot - -# Make sure we are re-using the same conda python -if ! startswith(PyCall.libpython, ENV["NB_PYTHON_PREFIX"] * "/lib") - println("Not re-using conda python! Using " * PyCall.libpython * " instead") - exit(1) -end - -# We try to plot something, and see if the file saved exists -x = linspace(0,2*pi,1000); y = sin(3*x + 4*cos(2*x)) -plot(x, y, color="red", linewidth=2.0, linestyle="--") -savefig("graph.png") -if isfile("graph.png") - exit(0) -else - exit(1) -end - -# We check that PyPlot is installed inside ${JULIA_DEPOT_PATH} -if ! isdir(ENV["JULIA_DEPOT_PATH"] * "/packages/PyPlot") - println("PyPlot not installed under JULIA_DEPOT_PATH") - exit(1) -end \ No newline at end of file

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fix docker commit tag [ci skip] use the first 8 chars of the commit, not the last

MODIFY hooks/post_push hooks/post_push # when building jupyter/repo2docker:master also push jupyter/repo2docker:abcd1234 -HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT: -8}" +HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT:0:8}" docker tag $DOCKER_REPO:$DOCKER_TAG $HASH_IMAGE docker push $HASH_IMAGE

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Update docs/source/howto/lab_workspaces.rst

MODIFY docs/source/howto/lab_workspaces.rst docs/source/howto/lab_workspaces.rst @@ -14,6 +14,6 @@ another JupyterLab installation in order to share a workspace with someone else. In order to package your workspace with a repository, we recommend -following the steps at the following example repository: +following the steps in this example repository: https://github.com/ian-r-rose/binder-workspace-demo/

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Update conf.py update copyright year in the docs

MODIFY docs/source/conf.py docs/source/conf.py @@ -72,7 +72,7 @@ master_doc = 'index' # General information about the project. project = 'repo2docker' -copyright = '2017, Project Jupyter' +copyright = '2019, Project Jupyter' author = 'Project Jupyter' # The version info for the project you're documenting, acts as replacement for

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missing quotes in GIT_CREDENTIAL_ENV echo without quotes removes newline, echo with quotes preserves it. Previously failing test added

MODIFY docker/git-credential-env docker/git-credential-env #!/bin/bash -echo -e $GIT_CREDENTIAL_ENV +echo -e "$GIT_CREDENTIAL_ENV" ADD tests/unit/test_docker.py +"""Tests for docker bits""" + +import os +from subprocess import check_output + +repo_root = os.path.abspath( + os.path.join(os.path.dirname(__file__), os.pardir, os.pardir) +) + + +def test_git_credential_env(): + credential_env = "username=abc\npassword=def" + out = ( + check_output( + os.path.join(repo_root, "docker", "git-credential-env"), + env={'GIT_CREDENTIAL_ENV': credential_env}, + ) + .decode() + .strip() + ) + assert out == credential_env

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FIX: a temporary workaround for pip-19.0.1 issues

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -63,6 +63,7 @@ class PythonBuildPack(CondaBuildPack): if os.path.exists(requirements_file): assemble_scripts.append(( '${NB_USER}', + 'pip install "pip<19" && ' + \ '{} install --no-cache-dir -r "{}"'.format(pip, requirements_file) ))

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Check if '--debug' is set properly Fixes

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -334,12 +334,12 @@ def main(): r2d.start() except docker.errors.BuildError as e: # This is only raised by us - if r2d.debug: + if r2d.log_level == logging.DEBUG: r2d.log.exception(e) sys.exit(1) except docker.errors.ImageLoadError as e: # This is only raised by us - if r2d.debug: + if r2d.log_level == logging.DEBUG: r2d.log.exception(e) sys.exit(1)

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pin conda during Python-switch step even with auto-update-conda disabled, switching Python version (which reinstalls conda) can end up upgrading to the latest conda Avoid this by adding the conda pinning to that install stage

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -4,7 +4,7 @@ set -ex cd $(dirname $0) MINICONDA_VERSION=4.5.11 -CONDA_VERSION=4.5.11 +CONDA_VERSION=4.5.12 URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -38,7 +38,7 @@ conda install -yq conda==${CONDA_VERSION} # prevent pip installation. # we wouldn't have this issue if we did `conda env create` # instead of `conda env update` in these cases -conda install -y $(cat /tmp/environment.yml | grep -o '\spython=.*') +conda install -y $(cat /tmp/environment.yml | grep -o '\spython=.*') conda==${CONDA_VERSION} # bug in conda 4.3.>15 prevents --set update_dependencies echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc @@ -70,3 +70,5 @@ conda clean -tipsy rm ${INSTALLER_PATH} chown -R $NB_USER:$NB_USER ${CONDA_DIR} + +conda list

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There's a miniconda release for 4.5.12

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -MINICONDA_VERSION=4.5.11 +MINICONDA_VERSION=4.5.12 CONDA_VERSION=4.5.12 URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -13,7 +13,7 @@ chmod +x ${INSTALLER_PATH} # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="e1045ee415162f944b6aebfe560b8fee" +MD5SUM="866ae9dff53ad0874e1d1a60b1ad1ef8" if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"

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empty conda history instead of deleting it conda uses the presence of this file as a magic indicator of conda envs so make it empty, not gone

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -57,12 +57,14 @@ if [[ -f /tmp/kernel-environment.yml ]]; then conda env create -n kernel -f /tmp/kernel-environment.yml ${CONDA_DIR}/envs/kernel/bin/ipython kernel install --prefix "${CONDA_DIR}" - rm -f ${CONDA_DIR}/envs/kernel/conda-meta/history + echo '' > ${CONDA_DIR}/envs/kernel/conda-meta/history fi -# remove conda history file, +# empty conda history file, # which seems to result in some effective pinning of packages in the initial env, -# which we don't intend -rm -f ${CONDA_DIR}/conda-meta/history +# which we don't intend. +# this file must not be *removed*, however +echo '' > ${CONDA_DIR}/envs/kernel/conda-meta/history + # Clean things out! conda clean -tipsy

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Fix path to conda history

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -63,7 +63,7 @@ fi # which seems to result in some effective pinning of packages in the initial env, # which we don't intend. # this file must not be *removed*, however -echo '' > ${CONDA_DIR}/envs/kernel/conda-meta/history +echo '' > ${CONDA_DIR}/conda-meta/history # Clean things out! conda clean -tipsy

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Undo conda update

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -MINICONDA_VERSION=4.5.12 -CONDA_VERSION=4.5.12 +MINICONDA_VERSION=4.5.11 +CONDA_VERSION=4.5.11 URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -13,7 +13,7 @@ chmod +x ${INSTALLER_PATH} # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="866ae9dff53ad0874e1d1a60b1ad1ef8" +MD5SUM="e1045ee415162f944b6aebfe560b8fee" if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"

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Update checked conda version

MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,4 +5,4 @@ assert sys.version_info[:2] == (3, 5), sys.version import numpy import conda -assert conda.__version__ == '4.5.12', conda.__version__ +assert conda.__version__ == '4.5.11', conda.__version__

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Bump tag used to test requirements example

MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml # Test that tags work + ref is added to tag if not present - name: Binder Examples - Requirements url: https://github.com/binder-examples/requirements - ref: test + ref: python-3.7 verify: python -c 'import matplotlib' # Test that custom channels and downgrades don't # get blocked by pinning

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add pip freeze to travis.yml and stop building docs on travis, we are already building them on circle

MODIFY .travis.yml .travis.yml @@ -12,6 +12,7 @@ install: - pip install -r dev-requirements.txt - python setup.py bdist_wheel - pip install dist/*.whl +- pip freeze script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in @@ -22,10 +23,6 @@ script: travis_retry pytest --durations 10 --cov repo2docker -v ${REPO_TYPE} || exit 1; fi; popd; -- pip install -r docs/doc-requirements.txt -- pushd docs; - make html || exit 1; - popd; after_success: - pip install codecov - pushd tests && codecov && popd

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install: one-liner to install most recent upstream code

MODIFY docs/source/install.rst docs/source/install.rst @@ -29,17 +29,21 @@ We recommend installing ``repo2docker`` with the ``pip`` tool:: python3 -m pip install jupyter-repo2docker +for the latest release. To install the most recent code from the upstream repository, run:: + + python3 -m pip install git+https://github.com/jupyter/repo2docker.git + For information on using ``repo2docker``, see :ref:`usage`. Installing from source code --------------------------- -Alternatively, you can install repo2docker from source, -i.e. if you are contributing back to this project:: +Alternatively, you can install repo2docker from a local source tree, +e.g. in case you are contributing back to this project:: git clone https://github.com/jupyter/repo2docker.git cd repo2docker - pip install -e . + python3 -m pip install -e . That's it! For information on using ``repo2docker``, see :ref:`usage`.

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install: don't rely on git, download zip file directly

MODIFY docs/source/install.rst docs/source/install.rst @@ -31,7 +31,7 @@ We recommend installing ``repo2docker`` with the ``pip`` tool:: for the latest release. To install the most recent code from the upstream repository, run:: - python3 -m pip install git+https://github.com/jupyter/repo2docker.git + python3 -m pip install https://github.com/jupyter/repo2docker/archive/master.zip For information on using ``repo2docker``, see :ref:`usage`.

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add default_python replacement to sphinx and get docs version from the package so it doesn't get out of date

MODIFY docs/source/conf.py docs/source/conf.py @@ -80,9 +80,19 @@ author = 'Project Jupyter' # built documents. # # The short X.Y version. -version = '0.1' +import repo2docker +version = repo2docker.__version__ # The full version, including alpha/beta/rc tags. -release = '0.1' +release = version + +from repo2docker.buildpacks.conda import CondaBuildPack + +default_python = CondaBuildPack.major_pythons['3'] + +rst_prolog = """ +.. |default_python| replace:: **Python {default_python}** +.. |default_python_version| replace:: {default_python} +""".format(default_python=default_python) # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages.

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fix "Possible nested set" warning `[:xdigit:]` is not a valid character class in Python regular expressions use explicit hex digit pattern

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -209,7 +209,7 @@ def is_valid_docker_image_name(image_name): (?::([\w][\w.-]{0,127}))? # optional capture <tag-pattern>=':<tag>' # optionally capture <digest-pattern>='@<digest>' - (?:@[A-Za-z][A-Za-z0-9]*(?:[-_+.][A-Za-z][A-Za-z0-9]*)*[:][[:xdigit:]]{32,})? + (?:@[A-Za-z][A-Za-z0-9]*(?:[-_+.][A-Za-z][A-Za-z0-9]*)*[:][A-Fa-f0-9]{32,})? $ """, re.VERBOSE)

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Fix up double label trouble in the config file docs

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -23,6 +23,7 @@ Below is a list of supported configuration files (roughly in the order of build :local: :depth: 1 + .. _environment.yml: ``environment.yml`` - Install a Python environment @@ -49,7 +50,6 @@ though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7. If you include a Python version in a ``runtime.txt`` file in addition to your ``environment.yml``, your ``runtime.txt`` will be ignored. -.. _requirements.txt: .. _requirements.txt: @@ -71,7 +71,6 @@ To install your repository like a Python package, you may include a ``setup.py`` file. repo2docker installs ``setup.py`` files by running ``pip install -e .``. -.. _REQUIRE: .. _REQUIRE: @@ -138,6 +137,7 @@ To see example repositories, visit our `Stencila with R <https://github.com/binder-examples/stencila-r/>`_ and `Stencila with Python <https://github.com/binder-examples/stencila-py>`_ examples. + .. _postBuild: ``postBuild`` - Run code after installing the environment @@ -203,6 +203,7 @@ used for installing libraries. To see an example R repository, visit our `R example in binder-examples <https://github.com/binder-examples/r/blob/master/runtime.txt>`_. + .. _default.nix: ``default.nix`` - the nix package manager

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Add support for julia 1.1, update julia 1.0 version

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -11,10 +11,11 @@ class JuliaBuildPack(PythonBuildPack): minor_julias = { '0.6': '0.6.4', '0.7': '0.7.0', - '1.0': '1.0.0', + '1.0': '1.0.3', + '1.1': '1.1.0', } major_julias = { - '1': '1.0.0', + '1': '1.1.0', } @property @@ -58,7 +59,7 @@ class JuliaBuildPack(PythonBuildPack): - `JULIA_HOME`: path where all Julia Binaries will be installed - `JULIA_PKGDIR`: path where all Julia libraries will be installed - `JULIA_DEPOT_PATH`: path where Julia libraries are installed. - Similar to JULIA_PKGDIR, used in 1.0. + Similar to JULIA_PKGDIR, used in 1.x. - `JULIA_VERSION`: default version of julia to be installed - `JUPYTER`: environment variable required by IJulia to point to the `jupyter` executable

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Update tests for more julia versions

RENAME tests/julia/julia_version/README.rst tests/julia/julia_version-0.6.3/README.rst RENAME tests/julia/julia_version/REQUIRE tests/julia/julia_version-0.6.3/REQUIRE RENAME tests/julia/julia_version/verify tests/julia/julia_version-0.6.3/verify ADD tests/julia/julia_version-1.0/README.rst +Julia - REQUIRE: test version for julia v1.0 +--------------- + +Starting with julia v0.7 and up, the package manager has changed, so this tests +that the julia version can be specified and packages installed correctly. ADD tests/julia/julia_version-1.0/REQUIRE +julia 1.0 + +# Julia packages: +Compat ADD tests/julia/julia_version-1.1/README.rst +Julia - REQUIRE: test version for julia v1.0 +--------------- + +Starting with julia v0.7 and up, the package manager has changed, so this tests +that the julia version can be specified and packages installed correctly. ADD tests/julia/julia_version-1.1/REQUIRE +julia 1.1 + +# Julia packages: +Compat MODIFY tests/julia/julia_version-1/verify tests/julia/julia_version-1/verify #!/usr/bin/env julia # Verify the version: -if VERSION < v"1" +if VERSION < v"1" || VERSION >= v"2" exit(1) end

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Fix typo in julia test README

MODIFY tests/julia/julia_version-1.1/README.rst tests/julia/julia_version-1.1/README.rst -Julia - REQUIRE: test version for julia v1.0 +Julia - REQUIRE: test version for julia v1.1 --------------- Starting with julia v0.7 and up, the package manager has changed, so this tests

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Fix calls to julia_env_exists

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -24,7 +24,7 @@ class JuliaBuildPack(PythonBuildPack): @property def julia_version(self): - if self.julia_env_exists(): + if self.julia_env_exists: # TODO Read version out of the file return self.major_julias['1'] else: @@ -106,7 +106,7 @@ class JuliaBuildPack(PythonBuildPack): (from get_assemble_scripts). """ - if self.julia_env_exists(): + if self.julia_env_exists: return super().get_build_scripts() + [ ( "root", @@ -167,8 +167,7 @@ class JuliaBuildPack(PythonBuildPack): any needed Python packages found in environment.yml. """ - if self.julia_env_exists(): - return super().get_assemble_scripts() + [( + if self.julia_env_exists: "${NB_USER}", # Install and pre-compile all libraries if they've opted into it. # In v0.6, Pkg.resolve() installs all the packages, but in v0.7+, we @@ -216,4 +215,4 @@ class JuliaBuildPack(PythonBuildPack): `JuliaProject.toml` exists """ - return os.path.exists(self.binder_path('REQUIRE')) or self.julia_env_exists() + return os.path.exists(self.binder_path('REQUIRE')) or self.julia_env_exists

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Properly configure Project.toml location for IJulia kernel

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -166,8 +166,8 @@ class JuliaBuildPack(PythonBuildPack): # HACK: Can't seem to tell IJulia to install in sys-prefix # FIXME: Find way to get it to install under /srv and not $HOME? r""" - julia -e 'using Pkg; Pkg.add("IJulia"); using IJulia; installkernel("Julia", "--project={0}");' - """.format('~') + julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" + """ ), ( "${NB_USER}",

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Add comments to julia pack

MODIFY repo2docker/buildpacks/julialegacy/__init__.py repo2docker/buildpacks/julialegacy/__init__.py @@ -157,14 +157,14 @@ class JuliaLegacyBuildPack(PythonBuildPack): def detect(self): """ - Check if current repo should be built with the Julia Build pack + Check if current repo should be built with the Julia Legacy Build pack 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 + Instead we just check if the path to `REQUIRE` exists and that there is + no julia 1.0 style environment """ - # TODO(nhdaly): Add support for Project.toml here as well. return os.path.exists(self.binder_path('REQUIRE')) and not(os.path.exists(self.binder_path('Project.toml')) or os.path.exists(self.binder_path('JuliaProject.toml')))

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Make julia path handling a bit more robust

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py @@ -105,7 +105,7 @@ class JuliaBuildPack(PythonBuildPack): "${NB_USER}", r""" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\", env=Dict(\"JUPYTER_DATA_DIR\"=>\"${NB_PYTHON_PREFIX}/share/jupyter\"));" && \ - julia --project=. -e 'using Pkg; Pkg.instantiate(); pkg"precompile"' + julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); pkg"precompile"' """ ) ]

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Start reading julia version from Project.toml

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py """Generates a Dockerfile based on an input matrix for Julia""" import os +import toml from .python import PythonBuildPack @@ -19,6 +20,11 @@ class JuliaBuildPack(PythonBuildPack): @property def julia_version(self): # TODO Read version out of the file + # TODO Handle JuliaProject.toml + project_toml = toml.load(self.binder_path('Project.toml')) + if 'compat' in project_toml: + if 'julia' in project_toml['compat']: + return project_toml['compat']['julia'] return self.major_julias['1'] def get_build_env(self): MODIFY setup.py setup.py @@ -18,6 +18,7 @@ setup( 'escapism', 'jinja2', 'ruamel.yaml>=0.15', + 'toml', ], python_requires='>=3.4', author='Project Jupyter Contributors',

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Restructure files for julia

MODIFY repo2docker/buildpacks/__init__.py repo2docker/buildpacks/__init__.py @@ -2,7 +2,7 @@ from .base import BuildPack, BaseImage from .python import PythonBuildPack from .conda import CondaBuildPack from .julia import JuliaBuildPack -from .julialegacy import JuliaLegacyBuildPack +from .julia import JuliaLegacyBuildPack from .docker import DockerBuildPack from .legacy import LegacyBinderDockerBuildPack from .r import RBuildPack ADD repo2docker/buildpacks/julia/__init__.py +from .julia_project import JuliaBuildPack +from .julia_require import JuliaLegacyBuildPack \ No newline at end of file RENAME repo2docker/buildpacks/julialegacy/install-repo-dependencies.jl repo2docker/buildpacks/julia/install-repo-dependencies.jl RENAME repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia/julia_project.py RENAME repo2docker/buildpacks/julialegacy/__init__.py repo2docker/buildpacks/julia/julia_require.py

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Fix import bug in julia part of code

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py """Generates a Dockerfile based on an input matrix for Julia""" import os import toml -from .python import PythonBuildPack +from ..python import PythonBuildPack class JuliaProjectTomlBuildPack(PythonBuildPack):

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Fix julia test

MODIFY tests/julia/julia_version-1.1/verify tests/julia/julia_version-1.1/verify -#!/usr/bin/env julia --project=. +#!/usr/bin/env julia # Verify the version: if VERSION < v"1" || VERSION >= v"2" exit(1) end +using Pkg; pkg"activate" + try # Test that the package was installed. using IteratorInterfaceExtensions

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Fix julia test bug

MODIFY repo2docker/buildpacks/julia/julia_require.py repo2docker/buildpacks/julia/julia_require.py @@ -150,7 +150,7 @@ class JuliaRequireBuildPack(PythonBuildPack): def get_build_script_files(self): files = { - 'julialegacy/install-repo-dependencies.jl': '/tmp/install-repo-dependencies.jl', + 'julia/install-repo-dependencies.jl': '/tmp/install-repo-dependencies.jl', } files.update(super().get_build_script_files()) return files

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Fix Python 3.4 compat in julia code

MODIFY repo2docker/buildpacks/julia/julia_semver.py repo2docker/buildpacks/julia/julia_semver.py @@ -94,7 +94,7 @@ def create_semver_matcher(constraint_str): # So we need to handle it separately by bumping the first non-zero number. for i,n in enumerate(constraint): if n != 0 or i == len(constraint)-1: # (using the last existing number handles situations like "^0.0" or "^0") - upper = (*constraint[0:i], n+1) + upper = constraint[0:i] + (n+1,) break return VersionRange(constraint, upper, Exclusivity.EXCLUSIVE) else:

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Handle JuliaProject.toml properly

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -21,6 +21,9 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): @property def julia_version(self): default_julia_version = '1.1.0' + if os.path.exists(self.binder_path('JuliaProject.toml'): + project_toml = toml.load(self.binder_path('JuliaProject.toml')) + else: project_toml = toml.load(self.binder_path('Project.toml')) if 'compat' in project_toml: if 'julia' in project_toml['compat']:

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Fix another python 3.4 issue in julia code

MODIFY repo2docker/buildpacks/julia/julia_semver.py repo2docker/buildpacks/julia/julia_semver.py @@ -102,7 +102,7 @@ def create_semver_matcher(constraint_str): # '~' matching (only allowed to bump the last present number by one) if (comparison_symbol == "~"): - return VersionRange(constraint, (*constraint[:-1], constraint[-1]+1), Exclusivity.INCLUSIVE) + return VersionRange(constraint, constraint[:-1] +(constraint[-1]+1,), Exclusivity.INCLUSIVE) # Use semver package's comparisons for everything else:

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make sure we don't touch user $HOME during install-miniconda.bash which is run as root

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -8,6 +8,10 @@ CONDA_VERSION=4.5.11 URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh +# make sure we don't do anything funky with user's $HOME +# since this is run as root +unset HOME + wget --quiet $URL -O ${INSTALLER_PATH} chmod +x ${INSTALLER_PATH}

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Add test for environment.yml + --target-repo-dir conda sometimes puts stuff in $HOME - specifically under .conda/ - that might cause package installs to fail due to permission mismatches. Ref

RENAME tests/venv/repo-path/README.rst tests/conda/repo-path/README.rst ADD tests/conda/repo-path/environment.yml +dependencies: + - numpy RENAME tests/venv/repo-path/extra-args.yaml tests/conda/repo-path/extra-args.yaml RENAME tests/venv/repo-path/verify tests/conda/repo-path/verify @@ -8,3 +8,6 @@ assert sys.executable == '/srv/conda/bin/python' # Repo should be in /srv/repo assert os.path.exists('/srv/repo/verify') assert os.path.abspath(__file__) == '/srv/repo/verify' + +# We should be able to import the package in environment.yml +import numpy

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Add PR template with links to contrib docs

ADD docs/pull_request_template.md +

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Change contributor guide language to remove the word "code"

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md # Contributing to repo2docker development -## Process for making a code contribution +## Process for making a contribution -This outlines the process for getting changes to the code of -repo2docker merged. +This outlines the process for getting changes to the repo2docker project merged. -* If your change is relatively significant, **open an issue to discuss** - before spending a lot of time writing code. Getting consensus with the +* If your change is a big change, **open an issue to discuss** + before spending a lot of time writing. Getting consensus with the community is a great way to save time later. * Make edits in your fork of the repo2docker repository -* Submit a pull request (this is how all changes are made) +* All changes are made by submitting a pull request. Read the next section for + the guidelines for both reviewers and contributors on merging a PR. * Edit [the changelog](./../../changelog) by appending your feature / bug fix to the development version. -* Wait for a community member to merge your changes +* Wait for a community member to merge your changes. * (optional) Deploy a new version of repo2docker to mybinder.org by [following these steps](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html)

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Update link targets and remove markdown formatting

MODIFY docs/pull_request_template.md docs/pull_request_template.md

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Update docs/source/changelog.rst

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -9,7 +9,8 @@ Release date: TBD New features ------------ -- Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files. +- Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files in :pr:`595` by +:user:`davidanthoff` API changes -----------

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Update repo2docker/buildpacks/julia/julia_semver.py

MODIFY repo2docker/buildpacks/julia/julia_semver.py repo2docker/buildpacks/julia/julia_semver.py # Versioning) strings in .toml files. # # It uses the python "semver" package to do most version string comparisons, but -# the places where julia's SemVer handling differes from the semver package have +# the places where julia's SemVer handling differs from the semver package have # been implemented directly. # # Here, we use tuples to represent a Version, and functors as "matchers". The matcher

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Fix julia detection code

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -21,10 +21,12 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): @property def julia_version(self): default_julia_version = '1.1.0' + if os.path.exists(self.binder_path('JuliaProject.toml')): project_toml = toml.load(self.binder_path('JuliaProject.toml')) else: project_toml = toml.load(self.binder_path('Project.toml')) + if 'compat' in project_toml: if 'julia' in project_toml['compat']: julia_version_str = project_toml['compat']['julia'] @@ -32,8 +34,9 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): # For Project.toml files, install the latest julia version that # satisfies the given semver. julia_version = find_semver_match(julia_version_str, self.all_julias) - if julia_version is None: - return _default_julia_version + if julia_version is not None: + return julia_version + return default_julia_version def get_build_env(self):

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Update julia tests

ADD tests/julia/julia_version-1.0.2/Project.toml +[deps] +IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d" + +[compat] +julia = "1.0.2" ADD tests/julia/julia_version-1.0.2/README.rst +Julia - Project.toml: test version for julia v1.0.3 +--------------- + +Test a Project.toml file for julia. RENAME tests/julia/julia_version-1.1/verify tests/julia/julia_version-1.0.2/verify #!/usr/bin/env julia # Verify the version: -if VERSION < v"1" || VERSION >= v"2" +if VERSION != v"1.0.2" exit(1) end RENAME tests/julia/julia_version-1.1/Project.toml tests/julia/julia_version-default/Project.toml RENAME tests/julia/julia_version-1.1/README.rst tests/julia/julia_version-default/README.rst

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Change type in julia code

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -33,9 +33,9 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): # For Project.toml files, install the latest julia version that # satisfies the given semver. - julia_version = find_semver_match(julia_version_str, self.all_julias) - if julia_version is not None: - return julia_version + _julia_version = find_semver_match(julia_version_str, self.all_julias) + if _julia_version is not None: + return _julia_version return default_julia_version

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Expand environment.yml config notes

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -32,6 +32,8 @@ Below is a list of supported configuration files (roughly in the order of build ``environment.yml`` is the standard configuration file used by `conda <https://conda.io>`_ that lets you install any kind of package, including Python, R, and C/C++ packages. +``repo2docker`` does not use ``environment.yml`` to create and activate a new conda environment. +Rather, it updates a base conda environment with the packages listed in ``environment.yml``. .. note::

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Update julia README files

MODIFY tests/julia/julia_version-1.0.2/README.rst tests/julia/julia_version-1.0.2/README.rst Julia - Project.toml: test version for julia v1.0.3 ---------------- +--------------------------------------------------- Test a Project.toml file for julia. MODIFY tests/julia/julia_version-default/README.rst tests/julia/julia_version-default/README.rst Julia - Project.toml: test version for julia v1.1 ---------------- +------------------------------------------------- Test a Project.toml file for julia.

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Update julia documentation

MODIFY docs/source/howto/languages.rst docs/source/howto/languages.rst @@ -74,6 +74,9 @@ Julia To build an environment with Julia, include a configuration file called ``Project.toml``. The format of this file is documented at `the Julia Pkg.jl documentation <https://julialang.github.io/Pkg.jl/stable/>`_. +To specify a specific version of Julia to install, put a Julia version in the +``Compat`` section of the ``Project.toml`` file, as described +here: https://julialang.github.io/Pkg.jl/stable/compatibility. Languages not covered here ==========================

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Minor rephrasing

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -34,7 +34,7 @@ that lets you install any kind of package, including Python, R, and C/C++ packages. ``repo2docker`` does not use ``environment.yml`` to create and activate a new conda environment. Rather, it updates a base conda environment with the packages listed in ``environment.yml``. -This means that the environment will always have the same name and not follow what is +This means that the environment will always have the same default name, not the name specified in ``environment.yml``. .. note::

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Don't set JULIA_BINDIR env variable

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -49,7 +49,6 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): a string of the environment setting: - `JULIA_PATH`: base path where all Julia Binaries and libraries will be installed - - `JULIA_BINDIR`: path where all Julia Binaries will be installed - `JULIA_DEPOT_PATH`: path where Julia libraries are installed. - `JULIA_VERSION`: default version of julia to be installed - `JUPYTER`: environment variable required by IJulia to point to @@ -60,7 +59,6 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): """ return super().get_build_env() + [ ('JULIA_PATH', '${APP_BASE}/julia'), - ('JULIA_BINDIR', '${JULIA_PATH}/bin'), ('JULIA_DEPOT_PATH', '${JULIA_PATH}/pkg'), ('JULIA_VERSION', self.julia_version), ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter') @@ -80,7 +78,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): executable is added to the list. """ - return super().get_path() + ['${JULIA_BINDIR}'] + return super().get_path() + ['${JULIA_PATH}/bin'] def get_build_scripts(self): """

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Rename semver file and related changes

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py import os import toml from ..python import PythonBuildPack -from .julia_semver import find_semver_match +from .semver import find_semver_match class JuliaProjectTomlBuildPack(PythonBuildPack): """ MODIFY repo2docker/buildpacks/julia/semver.py repo2docker/buildpacks/julia/semver.py @@ -39,6 +39,8 @@ class SemverMatcher(AbstractMatcher): v = v+(0,) v_str = '.'.join(map(str, v)) return semver.match(v_str, self.constraint_str) + def __eq__(self, rhs): + return self.constraint_str == rhs.constraint_str def __repr__(self): return self.constraint_str @@ -60,6 +62,8 @@ class VersionRange(AbstractMatcher): return self.lower <= v < self.upper else: return self.lower <= v <= self.upper + def __eq__(self, rhs): + return self.lower == rhs.lower and self.upper == rhs.upper and self.upper_exclusivity == rhs.upper_exclusivity def __repr__(self): return ("["+".".join(map(str, self.lower)) +"-"+ ".".join(map(str, self.upper)) + (")" if self.upper_exclusivity == Exclusivity.EXCLUSIVE else "]"))

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added some debug for R shiny

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -53,6 +53,8 @@ Only R 3.4.4 is currently supported, which is installed via ``apt`` from the `ubuntu bionic repository <https://packages.ubuntu.com/bionic/r-base>`_. + + Why is my repository is failing to build with ``ResolvePackageNotFound`` ? -------------------------------------------------------------------------- @@ -139,6 +141,18 @@ This allows for easy testing of the container while debugging some items, as well as using a fully customizable container to edit notebooks (among others). + +Why is my R shiny app not launching? +---------------------------------------------------------------------------------- + +If you are trying to run an R shiny app using the ``/shiny/folder_containing_shiny`` +url option, but the launch returns "The application exited during initialization.", +there might be something wrong with the specification of the app. One way of debugging +the app in the container is by running the ``rstudio`` url, open either the ui or +server file for the app, and run the app in the container rstudio. This way you can +see the rstudio logs as it tries to initialise the shiny app. If you a missing a +package or other dependency for the container, this will be obvious at this stage. + .. note:: Editable mode is a convenience option that will bind the

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