narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Fix install command for nodejs

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -43,10 +43,10 @@ RUN adduser --disabled-password \ ${NB_USER} WORKDIR ${HOME} -RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - \ - DISTRO="$(lsb_release -s -c)" \ - echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" | tee /etc/apt/sources.list.d/nodesource.list \ - echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" | tee -a /etc/apt/sources.list.d/nodesource.list +RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ + DISTRO="$(lsb_release -s -c)" && \ + echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \ + echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list RUN apt-get update && \ apt-get install --yes --no-install-recommends \

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Hardcode detection of the distribution name

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -44,7 +44,7 @@ RUN adduser --disabled-password \ WORKDIR ${HOME} RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ - DISTRO="$(lsb_release -s -c)" && \ + DISTRO="bionic" && \ echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \ echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list MODIFY tests/base/node10/verify tests/base/node10/verify #!/bin/sh set -e +which node node --version | grep v10 -npm --version | grep v6.2 +which npm +npm --version | grep 6.2

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remove conda history file seems to result in unintended pinning of packages installed when setting up base env

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -57,8 +57,12 @@ 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 fi - +# remove 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 # Clean things out! conda clean -tipsy

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add xeus-cling to external tests it should exercise the pinning issue

MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml url: https://github.com/binder-examples/requirements ref: test verify: python -c 'import matplotlib' +# Test that custom channels and downgrades don't +# get blocked by pinning +- name: Xeus-Cling + url: https://github.com/QuantStack/xeus-cling + ref: 0.4.5 + verify: jupyter kernelspec list

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Fix directory handling in travis tests

MODIFY .travis.yml .travis.yml @@ -15,11 +15,17 @@ install: script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in -- if [ ${REPO_TYPE} == "r" ]; then cd tests && travis_wait pytest --cov repo2docker - -v ${REPO_TYPE}; else cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE}; - fi +- pushd tests; + if [ ${REPO_TYPE} == "r" ]; then + travis_wait pytest --cov repo2docker -v ${REPO_TYPE}; + else + travis_retry pytest --cov repo2docker -v ${REPO_TYPE}; + fi; + popd; - pip install -r docs/doc-requirements.txt -- cd docs && make html +- pushd docs; + make html; + popd; after_success: - pip install codecov - codecov

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put launch script in home directory

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -133,15 +133,15 @@ RUN ./{{ s }} # Add launch script {% if start_script -%} -RUN echo '#!/bin/bash \nexec {{ start_script }} $@ \n' > ./launch +RUN echo '#!/bin/bash \nexec {{ start_script }} $@ \n' > ${HOME}/launch RUN chmod +x {{ start_script }} {% else %} -RUN echo '#!/bin/bash \nexec $@ \n' > ./launch +RUN echo '#!/bin/bash \nexec $@ \n' > ${HOME}/launch {% endif -%} -RUN chmod +x ./launch +RUN chmod +x ${HOME}/launch # Run launch script -ENTRYPOINT ["./launch"] +ENTRYPOINT ["${HOME}/launch"] # Specify the default command to run CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

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update after talking to

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -131,17 +131,11 @@ RUN ./{{ s }} {% endfor %} {% endif -%} -# Add launch script +# Add start script {% if start_script -%} -RUN echo '#!/bin/bash \nexec {{ start_script }} $@ \n' > ${HOME}/launch -RUN chmod +x {{ start_script }} -{% else %} -RUN echo '#!/bin/bash \nexec $@ \n' > ${HOME}/launch +RUN chmod +x "{{ start_script }}" +ENTRYPOINT ["{{ start_script }}"] {% endif -%} -RUN chmod +x ${HOME}/launch - -# Run launch script -ENTRYPOINT ["${HOME}/launch"] # Specify the default command to run CMD ["jupyter", "notebook", "--ip", "0.0.0.0"] @@ -358,7 +352,7 @@ class BuildPack: should not produce different results. """ - return [] + return '' def binder_path(self, path): """Locate a file""" @@ -549,7 +543,7 @@ class BaseImage(BuildPack): return [] def get_start_script(self): - launch = self.binder_path('start') - if os.path.exists(launch): - return launch + start = self.binder_path('start') + if os.path.exists(start): + return start return ''

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Escape environment variable when using Python string formatting

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -53,7 +53,9 @@ class PythonBuildPack(CondaBuildPack): if os.path.exists(nb_requirements_file): assemble_scripts.append(( '${NB_USER}', - '${NB_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "{}"'.format(nb_requirements_file) + # want the $NB_PYHTON_PREFIX environment variable, not for + # Python's string formatting to try and replace this + '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format(nb_requirements_file) )) # install requirements.txt in the kernel env ADD tests/venv/py2-with-kernel-requirements/requirements.txt +# install this in the kernel's environment, the user wants Python 2 there +numpy ADD tests/venv/py2-with-kernel-requirements/requirements3.txt +# install this in the environment in which the notebook server +# is running nbgitpuller does not work with Python 2 +nbgitpuller==0.6.1 ADD tests/venv/py2-with-kernel-requirements/runtime.txt +python-2.7 ADD tests/venv/py2-with-kernel-requirements/verify +#!/usr/bin/env python2 +import sys + +print(sys.version_info) +assert sys.version_info[:2] == (2, 7) + +import numpy

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Make `verify` check both server and kernel environments

MODIFY tests/venv/py2-with-kernel-requirements/verify tests/venv/py2-with-kernel-requirements/verify #!/usr/bin/env python2 +import os import sys print(sys.version_info) assert sys.version_info[:2] == (2, 7) import numpy + +try: + import nbgitpuller +except ImportError: + pass +else: + raise Exception("'nbgitpuller' shouldn't have been installed from requirements3.txt") + +# Python 3 is the executable used for the notebook server, this should +# have nbgitpuller installed +os.system("python3 -c 'import nbgitpuller'")

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compare yaml dict to mapping, not dict

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py """BuildPack for conda environments""" import os import re +from collections import Mapping from ruamel.yaml import YAML @@ -139,8 +140,8 @@ class CondaBuildPack(BaseImage): # check if the env file is empty, if so instantiate an empty dictionary. if env is None: env = {} - # check if the env file has a dictionary not a list or other data structure. - if not isinstance(env, dict): + # check if the env file provided a dick-like thing not a list or other data structure. + if not isinstance(env, Mapping): raise TypeError("environment.yml should contain a dictionary. Got %r" % type(env)) for dep in env.get('dependencies', []): if not isinstance(dep, str):

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Update Python version mentioned in CONTRIBUTING.md

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -15,7 +15,7 @@ To develop & test repo2docker locally, you need: 1. Familiarity with using a command line terminal 2. A computer running macOS / Linux 3. Some knowledge of git -4. At least python 3.4 +4. At least python 3.6 5. Your favorite text editor 6. A recent version of [Docker Community Edition](https://www.docker.com/community-edition)

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Bump conda version to 4.5.11

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -19,7 +19,7 @@ import sys from ruamel.yaml import YAML -MINICONDA_VERSION = '4.5.4' +MINICONDA_VERSION = '4.5.11' HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__))) MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -MINICONDA_VERSION=4.5.4 -CONDA_VERSION=4.5.8 +MINICONDA_VERSION=4.5.11 +CONDA_VERSION=4.5.11 URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -13,7 +13,7 @@ chmod +x ${INSTALLER_PATH} # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="a946ea1d0c4a642ddf0c3a26a18bb16d" +MD5SUM="e1045ee415162f944b6aebfe560b8fee" if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"

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Added test for manually setting the version number

ADD tests/julia/julia_version/README.rst +Julia - REQUIRE: packages and julia version number +--------------- + +To specify dependencies in Julia, include a REQUIRE file. + +To specify a version of Julia to be installed, the first line of the file must +follow the format `julia <version-number>`. For example: +``` +julia 0.7 +``` + +To add package dependencies, the rest of the file can include lines that list +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. ADD tests/julia/julia_version/REQUIRE +julia 0.6.3 + +# Julia packages: +Compat ADD tests/julia/julia_version/verify +#!/usr/bin/env julia +# Verify the version: +if VERSION != v"0.6.3" + exit(1) +end + +# Test that the package was installed. +try + using Compat +catch + exit(1) +end + +exit(0)

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Fail freeze.py if any of the conda steps fail Currently, this only fails if the last conda command fails, which is almost never.

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -60,6 +60,7 @@ def freeze(env_file, frozen_file): f"continuumio/miniconda3:{MINICONDA_DOCKER_VERSION}", "sh", "-c", '; '.join([ + 'set -e', f"conda install -yq conda={CONDA_VERSION}", 'conda config --add channels conda-forge', 'conda config --system --set auto_update_conda false',

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Add more details to our setup command

MODIFY setup.py setup.py from setuptools import setup, find_packages import versioneer + +with open('README.md', encoding="utf8") as f: + readme = f.read() + setup( name='jupyter-repo2docker', version=versioneer.get_version(), @@ -13,9 +17,28 @@ setup( 'ruamel.yaml>=0.15', ], python_requires='>=3.4', - author='Repo2docker contributors', - author_email='[email protected]', + author='Project Jupyter Contributors', + author_email='[email protected]', + url='https://repo2docker.readthedocs.io/en/latest/', + project_urls = { + 'Documentation': 'https://repo2docker.readthedocs.io', + 'Funding': 'https://jupyter.org/about', + 'Source': 'https://github.com/jupyter/repo2docker/', + 'Tracker': 'https://github.com/jupyter/repo2docker/issues', + }, + description = "Repo2docker: Turn git repositories into Jupyter enabled Docker Images", + long_description = readme, + long_description_content_type = 'text/markdown', license='BSD', + classifiers = [ + 'Environment :: Console', + 'Intended Audience :: Developers', + 'Intended Audience :: System Administrators', + 'Intended Audience :: Science/Research', + 'License :: OSI Approved :: BSD License', + 'Programming Language :: Python', + 'Programming Language :: Python :: 3', + ], packages=find_packages(), include_package_data=True, cmdclass=versioneer.get_cmdclass(),

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Add keywords to setup() metadata

MODIFY setup.py setup.py @@ -26,6 +26,8 @@ setup( 'Source': 'https://github.com/jupyter/repo2docker/', 'Tracker': 'https://github.com/jupyter/repo2docker/issues', }, + # this should be a whitespace separated string of keywords, not a list + keywords="reproducible science environments docker", description = "Repo2docker: Turn git repositories into Jupyter enabled Docker Images", long_description = readme, long_description_content_type = 'text/markdown',

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Modify short project description

MODIFY setup.py setup.py @@ -28,7 +28,7 @@ setup( }, # this should be a whitespace separated string of keywords, not a list keywords="reproducible science environments docker", - description = "Repo2docker: Turn git repositories into Jupyter enabled Docker Images", + description = "Repo2docker: Turn code repositories into Jupyter enabled Docker Images", long_description = readme, long_description_content_type = 'text/markdown', license='BSD',

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squashfix: remove unneeded thing

MODIFY repo2docker/buildpacks/julia.py repo2docker/buildpacks/julia.py @@ -22,9 +22,6 @@ class JuliaBuildPack(CondaBuildPack): '1': '1.0.0', } - def _short_version(version_str): - return '.'.join(version_str.split('.')[:2]) - @property def julia_version(self): require = self.binder_path('REQUIRE')

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Subdir support

MODIFY repo2docker/app.py repo2docker/app.py @@ -62,6 +62,16 @@ class Repo2Docker(Application): """ ) + subdir = Unicode( + '', + config=True, + help=""" + Subdirectory of the git repository to examine. + + Defaults to ''. + """ + ) + buildpacks = List( [ LegacyBinderDockerBuildPack, @@ -345,6 +355,12 @@ class Repo2Docker(Application): help=self.traits()['appendix'].help, ) + argparser.add_argument( + '--subdir', + type=str, + help=self.traits()['subdir'].help, + ) + argparser.add_argument( '--version', dest='version', @@ -482,6 +498,9 @@ class Repo2Docker(Application): 'the container') sys.exit(1) + if args.subdir: + self.subdir = args.subdir + self.environment = args.environment def push_image(self): @@ -644,7 +663,7 @@ class Repo2Docker(Application): if self.repo_type == 'remote': self.fetch(self.repo, self.ref, checkout_path) - os.chdir(checkout_path) + os.chdir(os.path.join(checkout_path, self.subdir).rstrip('/')) for BP in self.buildpacks: bp = BP()

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Make travis fail when pytest fails

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

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Compare to empty string when start script test fails

MODIFY tests/venv/start/start-script/verify tests/venv/start/start-script/verify #!/bin/bash set -euo pipefail -if [ "$TEST_START_VAR" != "var is set" ] +# set value of TEST_START_VAR to empty string when it is not defined +if [ "${TEST_START_VAR:-}" != "var is set" ] then echo "TEST_START_VAR is not set" exit 1

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Switch order of local repository test collection Feels more natural to first attempt building the image and then running the verify script in it. Changed the name of the two tests to make it easier to see which test failed (verify or build).

MODIFY tests/conftest.py tests/conftest.py @@ -95,11 +95,10 @@ class Repo2DockerTest(pytest.Function): class LocalRepo(pytest.File): def collect(self): yield Repo2DockerTest( - self.fspath.basename, self, + 'build', self, args=[ '--appendix', 'RUN echo "appendix" > /tmp/appendix', self.fspath.dirname, - './verify', ], ) yield Repo2DockerTest( @@ -107,6 +106,7 @@ class LocalRepo(pytest.File): args=[ '--appendix', 'RUN echo "appendix" > /tmp/appendix', self.fspath.dirname, + './verify', ], )

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Update node tests to match versions actually installed

MODIFY tests/base/node10/README.md tests/base/node10/README.md -Test that node 10 is installed and runnable. +Test that node 10 and npm 6 are installed and runnable. MODIFY tests/base/node10/verify tests/base/node10/verify set -e which node +node --version node --version | grep v10 + which npm -npm --version | grep 6.2 +npm --version +npm --version | grep 6.4

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Update postBuild+start test case This test was missing a start script, added it. Updated the README to explain what the test case was doing.

MODIFY tests/venv/start/postBuild/README.rst tests/venv/start/postBuild/README.rst -System - Post-build scripts ---------------------------- +postBuild and start +------------------- -It is possible to run scripts after you've built the environment specified in -your other files. This could be used to, for example, download data or run -some configuration scripts. - -In this example, we download and install a Jupyter Notebook extension. +This test checks that we can use a postBuild and start script +at the same time. MODIFY tests/venv/start/postBuild/postBuild tests/venv/start/postBuild/postBuild #!/bin/bash + +# this value should not be visible in `verify` +export TEST_START_VAR="var is set by postBuild" + jupyter nbextension enable --py --sys-prefix ipyleaflet ADD tests/venv/start/postBuild/start +#!/bin/bash + +export TEST_START_VAR="var is set" +exec "$@" MODIFY tests/venv/start/postBuild/verify tests/venv/start/postBuild/verify set -euo pipefail jupyter nbextension list | grep 'jupyter-leaflet' | grep enabled -if [ "$TEST_START_VAR" != "var is set" ] +# set value of TEST_START_VAR to empty string when it is not defined +if [ "${TEST_START_VAR:-}" != "var is set" ] then echo "TEST_START_VAR is not set" exit 1

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add Python 3.7 to frozen environment list

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -100,7 +100,7 @@ def set_python(py_env_file, py): if __name__ == '__main__': # allow specifying which Pythons to update on argv - pys = sys.argv[1:] or ('2.7', '3.5', '3.6') + pys = sys.argv[1:] or ('2.7', '3.7', '3.5', '3.6') for py in pys: env_file = ENV_FILE_T.format(py=py) set_python(env_file, py)

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first try for R DESCRIPTION

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -257,4 +257,16 @@ class RBuildPack(PythonBuildPack): ) ] + descriptionR_path = self.binder_path('DESCRIPTION') + if os.path.exists(descriptionR_path): + assemble_scripts += [ + ( + "${NB_USER}", + r""" + R CMD build . && \ + R CMD install . + """ + ) + ] + return assemble_scripts

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add version support to faq includes outstanding PRs for Python, Julia

MODIFY docs/source/faq.md docs/source/faq.md A collection of frequently asked questions with answers. If you have a question and have found an answer, send a PR to add it here! -## How should I specify another version of Python 3? +## How should I specify another version of Python? One can specify a Python version in the ``environment.yml`` file of a repository. +## What versions of Python (or R or Julia...) are supported? + +### Python + +Repo2docker officially supports the following versions of Python (specified in environment.yml or runtime.txt): + +- 3.7 (added in 0.7) +- 3.6 (default) +- 3.5 + +Additional versions may work, as long as the +[base environment](https://github.com/jupyter/repo2docker/blob/master/repo2docker/buildpacks/conda/environment.yml) +can be installed for your version of Python. +The most likely source of incompatibility is if one of the packages +in the base environment is not packaged for your Python, +either because the version of the package is too new and your chosen Python is too old, +or vice versa. + +Additionally, if Python 2.7 is specified, +a separate environment for the kernel will be installed with Python 2. +The notebook server will run in the default Python 3.6 environment. + +### Julia + +The following versions of Julia are supported (specified in REQUIRE): + +- 1.0 (added in 0.7) +- 0.7 (added in 0.7) +- 0.6 (default) + +### R + +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). + ## Can I add executable files to the user's PATH? Yes! With a :ref:`postBuild` file, you can place any files that should be called

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fix R DESCRIPTION installation

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -109,6 +109,17 @@ While one can specify dependencies in ``setup.py``, repo2docker **requires configuration files such as** ``environment.yml`` or ``requirements.txt`` to install dependencies during the build process. +``DESCRIPTION`` +~~~~~~~~~~~~~~~ + +To install your repository like an R package, you may include a +``DESCRIPTION`` file. repo2docker installs the package and dependencies + from the ``DESCRIPTION`` by running ``devtools:install_git(".")``. + + You also need to have a ``runtime.txt`` file that is formatted as + ``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot at MRAN that will be + used for your R installation. + .. _postBuild: ``postBuild`` MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -263,8 +263,7 @@ class RBuildPack(PythonBuildPack): ( "${NB_USER}", r""" - R CMD build . && \ - R CMD install . + R --quiet -e "devtools::install_git('.')" """ ) ] MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml url: https://github.com/QuantStack/xeus-cling ref: 0.4.5 verify: jupyter kernelspec list +- name: Test compiling R package + url: https://github.com/gedankenstuecke/binder-r-description + ref: master + verify: R --quiet -e 'binderdescription::print_something()'

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allow DESCRIPTION to reside in binder subfolder

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -262,9 +262,8 @@ class RBuildPack(PythonBuildPack): assemble_scripts += [ ( "${NB_USER}", - r""" - R --quiet -e "devtools::install_git('.')" - """ + 'R --quiet -e "devtools::install_git(\'{}\')"'.format( + self.binder_path('.')) ) ]

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build from DESCRIPTION w/o runtime.txt

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -69,7 +69,14 @@ class RBuildPack(PythonBuildPack): """ # If no date is found, then self.checkpoint_date will be False # Otherwise, it'll be a date object, which will evaluate to True - return bool(self.checkpoint_date) + if bool(self.checkpoint_date): + return True + description_R = 'DESCRIPTION' + if not os.path.exists('binder') and os.path.exists(description_R): + if not self.checkpoint_date: + self._checkpoint_date = datetime.date.today() - datetime.timedelta(days=2) + self._runtime = "r-{}".format(str(self._checkpoint_date)) + return True def get_path(self): """ @@ -257,13 +264,12 @@ class RBuildPack(PythonBuildPack): ) ] - descriptionR_path = self.binder_path('DESCRIPTION') - if os.path.exists(descriptionR_path): + description_R = 'DESCRIPTION' + if not os.path.exists('binder') and os.path.exists(description_R): assemble_scripts += [ ( "${NB_USER}", - 'R --quiet -e "devtools::install_git(\'{}\')"'.format( - self.binder_path('.')) + 'R --quiet -e "devtools::install_git(\'.\')"' ) ]

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use getwd() to find path instead of "."

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -269,7 +269,7 @@ class RBuildPack(PythonBuildPack): assemble_scripts += [ ( "${NB_USER}", - 'R --quiet -e "devtools::install_git(\'.\')"' + 'R --quiet -e "devtools::install_local(getwd())"' ) ] DELETE tests/r/description-file/runtime.txt -r-2018-02-05

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Add error checking for subdir

MODIFY repo2docker/app.py repo2docker/app.py @@ -663,7 +663,13 @@ class Repo2Docker(Application): if self.repo_type == 'remote': self.fetch(self.repo, self.ref, checkout_path) - os.chdir(os.path.join(checkout_path, self.subdir).rstrip('/')) + if self.subdir: + checkout_path = os.path.join(checkout_path, self.subdir).rstrip('/') + if not os.path.exists(checkout_path): + self.log.error('Subdirectory %s does not exist', self.subdir, extra=dict(phase='failure')) + sys.exit(1) + + os.chdir(checkout_path) for BP in self.buildpacks: bp = BP()

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remove cruft in config_files work & simplify code

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -95,16 +95,6 @@ version of Ubuntu. We use ``apt.txt``, for example, to install LaTeX in our `example apt.txt for LaTeX <https://github.com/binder-examples/latex/blob/master/apt.txt>`_. -``setup.py`` -~~~~~~~~~~~~ - -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 .``. - -While one can specify dependencies in ``setup.py``, -repo2docker **requires configuration files such as** ``environment.yml`` or -``requirements.txt`` to install dependencies during the build process. ``DESCRIPTION`` ~~~~~~~~~~~~~~~ MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -69,11 +69,13 @@ class RBuildPack(PythonBuildPack): """ # If no date is found, then self.checkpoint_date will be False # Otherwise, it'll be a date object, which will evaluate to True - if bool(self.checkpoint_date): + if self.checkpoint_date: return True description_R = 'DESCRIPTION' if not os.path.exists('binder') and os.path.exists(description_R): if not self.checkpoint_date: + # no R snapshot date set through runtime.txt + # set the R runtime to the latest date that is guaranteed to be on MRAN across timezones self._checkpoint_date = datetime.date.today() - datetime.timedelta(days=2) self._runtime = "r-{}".format(str(self._checkpoint_date)) return True

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add subdir test

ADD tests/test_subdir.py +""" +Test if the explict hostname is supplied correctly to the container +""" +import logging +from os.path import abspath, dirname + +import pytest +from repo2docker.app import Repo2Docker +from tests.conftest import make_test_func + +repo_path = dirname(dirname(abspath(__file__))) + +def test_subdir(): + argv = ['--subdir', 'tests/conda/simple', repo_path] + make_test_func(argv)() + +def test_subdir_invalid(caplog): + caplog.set_level(logging.INFO, logger='Repo2Docker') + + app = Repo2Docker() + argv = ['--subdir', 'tests/conda/invalid', repo_path] + app.initialize(argv) + app.debug = True + app.run = False + with pytest.raises(SystemExit): + app.start() # Just build the image and do not run it. + + # Can't get this to record the logs? + # assert caplog.text == "Subdirectory tests/conda/invalid does not exist"

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fix my heading mistake in the docs for DESCRIPTION

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -96,8 +96,8 @@ We use ``apt.txt``, for example, to install LaTeX in our `example apt.txt for LaTeX <https://github.com/binder-examples/latex/blob/master/apt.txt>`_. -``DESCRIPTION`` -~~~~~~~~~~~~~~~ +``DESCRIPTION`` - Install an R package +====================================== To install your repository like an R package, you may include a ``DESCRIPTION`` file. repo2docker installs the package and dependencies

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Cannot import from conftest

MODIFY tests/conftest.py tests/conftest.py @@ -68,6 +68,14 @@ def make_test_func(args): return test +# Provide a fixture for testing in .py files [email protected]() +def run_repo2docker(): + def run_test(args): + return make_test_func(args)() + return run_test + + class Repo2DockerTest(pytest.Function): """A pytest.Item for running repo2docker""" def __init__(self, name, parent, args): MODIFY tests/test_subdir.py tests/test_subdir.py @@ -6,13 +6,14 @@ from os.path import abspath, dirname import pytest from repo2docker.app import Repo2Docker -from tests.conftest import make_test_func repo_path = dirname(dirname(abspath(__file__))) -def test_subdir(): + +def test_subdir(run_repo2docker): argv = ['--subdir', 'tests/conda/simple', repo_path] - make_test_func(argv)() + run_repo2docker(argv) + def test_subdir_invalid(caplog): caplog.set_level(logging.INFO, logger='Repo2Docker')

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Remove accidental testing lines & HACK to fix `rm` Fixes the tests w/ hack: disabled `rm` installation file. Needs to be fixed before submitting Adds TODO for Project.toml support

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -123,10 +123,6 @@ class JuliaBuildPack(CondaBuildPack): """ ) ] - require = "/Users/daly/Documents/developer/website/nhdaly.github.io/notebooks/REQUIRE" - f = open(require) - julia_version_line = list(filter(lambda l: l != "", map(lambda l:l.strip(), f.readlines())))[0] - julia_version_line = f.readline().strip() def get_assemble_scripts(self): """ @@ -146,9 +142,10 @@ class JuliaBuildPack(CondaBuildPack): # format is deprecated). # The precompliation is done via `using {libraryname}`. r""" - julia /tmp/install-repo-dependencies.jl "%(require)s" && \ - rm /tmp/install-repo-dependencies.jl + julia /tmp/install-repo-dependencies.jl "%(require)s" """ % { "require" : require } + # TODO: For some reason, `rm`ing the file fails with permission denied. + # && rm /tmp/install-repo-dependencies.jl )] def get_build_script_files(self): @@ -169,4 +166,6 @@ class JuliaBuildPack(CondaBuildPack): Instead we just check if the path to `REQUIRE` exists """ + # TODO(nhdaly): Add support for value in variable: + pass Project.toml here as well. return os.path.exists(self.binder_path('REQUIRE'))

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Update comments in README

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -166,6 +166,5 @@ class JuliaBuildPack(CondaBuildPack): Instead we just check if the path to `REQUIRE` exists """ - # TODO(nhdaly): Add support for value in variable: - pass Project.toml here as well. + # TODO(nhdaly): Add support for Project.toml here as well. return os.path.exists(self.binder_path('REQUIRE')) MODIFY tests/julia/julia_version/README.rst tests/julia/julia_version/README.rst @@ -14,12 +14,9 @@ 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 `IJulia` is installed by default. -Note that this example also specifies Python dependencies with an -``environment.yml`` file. +These packages will all be installed, and then precompiled via `using`.

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Add JULIA_BINDDIR environment variable for julia v0.7+ Add tests for the ENVIRONMENT VARIABLES to the julia unit tests.

MODIFY repo2docker/buildpacks/julia/__init__.py repo2docker/buildpacks/julia/__init__.py @@ -71,7 +71,8 @@ class JuliaBuildPack(CondaBuildPack): """ return super().get_build_env() + [ ('JULIA_PATH', '${APP_BASE}/julia'), - ('JULIA_HOME', '${JULIA_PATH}/bin'), + ('JULIA_HOME', '${JULIA_PATH}/bin'), # julia <= 0.6 + ('JULIA_BINDIR', '${JULIA_HOME}'), # julia >= 0.7 ('JULIA_PKGDIR', '${JULIA_PATH}/pkg'), ('JULIA_VERSION', self.julia_version), ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter')

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Speed up cloning by using a depth of 1 if there is no refspec To speed up cloning a repository, a shallow clone containing just the last commit can be made, but *only* if no refspec is provided.

MODIFY repo2docker/app.py repo2docker/app.py @@ -167,8 +167,11 @@ class Repo2Docker(Application): def fetch(self, url, ref, checkout_path): """Check out a repo using url and ref to the checkout_path location""" try: - for line in execute_cmd(['git', 'clone', '--recursive', url, checkout_path], - capture=self.json_logs): + cmd = ['git', 'clone', '--recursive'] + if not ref: + cmd.extend(['--depth', '1']) + cmd.extend([url, checkout_path]) + for line in execute_cmd(cmd, capture=self.json_logs): self.log.info(line, extra=dict(phase='fetching')) except subprocess.CalledProcessError: self.log.error('Failed to clone repository!',

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Avoid clashing inline markup Stops and starts emphasis around an inline code markup. Also removes two emphasis sections, since these are at the start of bullet points, creating emphasis already.

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -152,7 +152,7 @@ To use python-2.7: add ``python-2.7`` in runtime.txt file. The repository will run in a virtualenv with Python 2 installed. To see a full example repository, visit our `Python2 example <https://github.com/binder-examples/python2_runtime/blob/master/runtime.txt>`_. -**Python versions in ``runtime.txt`` are ignored when** ``environment.yml`` **is +**Python versions in** ``runtime.txt`` **are ignored when** ``environment.yml`` **is present in the same folder**. repo2docker uses R libraries pinned to a specific snapshot on MODIFY docs/source/howto/languages.rst docs/source/howto/languages.rst @@ -23,7 +23,7 @@ Specifying a version of Python To specify a specific version of Python, you have two options: -* **use ``runtime.txt``**. Include a line that specifies the Python version in +* Use ``runtime.txt``. Include a line that specifies the Python version in this file. This line takes the following form:: python=X.X @@ -31,7 +31,7 @@ To specify a specific version of Python, you have two options: For example,:: python=2.7 -* **Use ``environment.yml``**. The Anaconda distribution also lets you define +* Use ``environment.yml``. The Anaconda distribution also lets you define the Python environment within ``environment.yml``. To do so, add ``python=X.X`` to your dependencies section, like so::

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MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -48,7 +48,7 @@ Python in the file. ``conda`` supports Python versions 3.6, 3.5, 3.4, and 2.7. .. warning:: If you include a Python version in a ``runtime.txt`` file in addition to your - ``environment.yml``, your ``runtime.txt`` **will be ignored**. + ``environment.yml``, your ``runtime.txt`` will be ignored. ``requirements.txt`` - Install a Python environment

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Remove erroneous backtick

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -113,7 +113,7 @@ used for your R installation. ========================================================= A script that can contain arbitrary commands to be run after the whole repository has been built. If you -want this to be a shell script, make sure the first line is ```#!/bin/bash``. +want this to be a shell script, make sure the first line is ``#!/bin/bash``. An example use-case of ``postBuild`` file is JupyterLab's demo on mybinder.org. It uses a ``postBuild`` file in a folder called ``binder`` to `prepare

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Change emphasis into a "note" admonition

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -173,7 +173,9 @@ images provide core functionality, compact image sizes, and efficient builds. We trying the other configuration files before deciding to use your own Dockerfile. With Dockerfiles, a regular Docker build will be performed. -**If a Dockerfile is present, all other configuration files will be ignored.** + +.. note:: + If a Dockerfile is present, all other configuration files will be ignored. See the `Advanced Binder Documentation <https://mybinder.readthedocs.io/en/latest/dockerfile.html>`_ for best-practices with Dockerfiles.

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Add an edit-mode option This adds an option to run from a local repository in edit mode, where changes in a running Docker container (for example, through a notebook) are reflected in the local repository. Implements the feature suggested in

MODIFY repo2docker/app.py repo2docker/app.py @@ -342,6 +342,13 @@ class Repo2Docker(Application): default=[] ) + argparser.add_argument( + '--editable', '-E', + dest='editable', + action='store_true', + help='Use the local repository in edit mode', + ) + argparser.add_argument( '--appendix', type=str, @@ -392,6 +399,8 @@ class Repo2Docker(Application): self.repo = args.repo self.ref = None self.cleanup_checkout = False + if args.editable: + self.volumes[os.path.abspath(args.repo)] = '.' else: self.repo_type = 'remote' self.repo = args.repo

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Add FAQ entry for editable local repositories

MODIFY docs/source/faq.md docs/source/faq.md @@ -70,3 +70,31 @@ or similar traditional docker command. Check out the [binder-examples](http://github.com/binder-examples/) GitHub organization for example repositories you can copy & modify for your own use! + +## Can I use repo2docker to edit a local repository within a Docker environment? + +Yes: use the `--editable` or `-E` flag (don't confuse it with the `-e` +flag for environment variables), and run repo2docker on a local +repository: `repo2docker -E my-repository/.`. + +This builds a Docker container from the files in that repository +(using, for example, a `requirements.txt` file or `Dockerfile`), then +runs that container, while connecting the home directory inside the +container to the local repository outside the container. For example, +in case there is a notebook file (`.ipynb`), this will open in a local +webbrowser, and one can edit it and save it. The resulting notebook is +updated in both the Docker container and the local repository. Once +the container is exited, the changed file will still be in the local +repository. + +This allows for easy testing of the container while debugging some +items, as well as using a fully customizable container to edit, for +example, notebooks. + +**note** + +Editable mode is a convenience option that will mount the repository +to container working directory (usually `/home/$USER`). If you need to +mount to a different location in the container, use the `--volumes` +option instead. Similarly, for a fully customized user Dockerfile, +this option is not guaranteed to work.

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Remove dockerfile/editable test from main tests The dockerfile test is used by test_editable, but should not be used by the generated tests. Removing the verify script will prevent it being run as part of the generated tests.

MODIFY tests/dockerfile/editable/Dockerfile tests/dockerfile/editable/Dockerfile @@ -5,7 +5,6 @@ RUN pip install --no-cache notebook CMD "/bin/sh" ADD change.sh /usr/local/bin/change.sh -ADD verify verify ARG NB_UID ENV HOME /tmp DELETE tests/dockerfile/editable/verify -#!/bin/bash - -/usr/local/bin/change.sh

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Move test fixture to conftest.py

MODIFY tests/conftest.py tests/conftest.py @@ -68,6 +68,14 @@ def make_test_func(args): return test [email protected]() +def run_repo2docker(): + def run_test(args): + return make_test_func(args)() + return run_test + + + class Repo2DockerTest(pytest.Function): """A pytest.Item for running repo2docker""" def __init__(self, name, parent, args): MODIFY tests/test_editable.py tests/test_editable.py -import pytest import os import time import re @@ -10,13 +9,6 @@ from repo2docker.app import Repo2Docker DIR = os.path.join(os.path.dirname(__file__), 'dockerfile', 'editable') [email protected](scope="module") -def run_repo2docker(): - def run_test(args): - return make_test_func(args)() - return run_test - - def test_editable(run_repo2docker): """Run a local repository in edit mode. Verify a new file has been created afterwards"""

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Fix path to custom CSS file Note: Sphinx automatically already includes a _static/custom.css file, so the change is not noticable; it only avoids a 404 for a single file.

MODIFY docs/source/conf.py docs/source/conf.py @@ -44,7 +44,7 @@ source_parsers = { } def setup(app): - app.add_stylesheet('_static/custom.css') # may also be an URL + app.add_stylesheet('custom.css') # may also be a URL # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string:

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Check beginning of the string only for Julia Only uses the beginning of the string to determine which version of Python we use in Julia

MODIFY tests/julia/pyplot/verify tests/julia/pyplot/verify using PyPlot # Make sure we are re-using the same conda python -if PyCall.libpython != "/srv/conda/lib/libpython3.6m" +if ! startswith(PyCall.libpython, ENV["NB_PYTHON_PREFIX"] * "/lib") println("Not re-using conda python! Using " * PyCall.libpython * " instead") exit(1) end @@ -16,4 +16,3 @@ if isfile("graph.png") else exit(1) end -

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PEP8 styling

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -3,7 +3,6 @@ from functools import partial import re import shutil import subprocess -import sys from traitlets import Integer, TraitError MODIFY tests/test_clone_depth.py tests/test_clone_depth.py @@ -7,8 +7,6 @@ and that is the only thing that is tested. """ import subprocess -import requests -import time from repo2docker.app import Repo2Docker

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Add pip install of doc-requirements.txt To be able to build the docs the libraries in docs/doc-requirements.txt need to be installed. As such, the installation of these libraries should be part of the setup of the developer virtual env.

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -75,6 +75,7 @@ python3 -m venv . source bin/activate pip3 install -e . pip3 install -r dev-requirements.txt +pip3 install -r docs/doc-requirements.txt ``` This should install all the libraries required for testing & running repo2docker!

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Change back into main repository directory

MODIFY .travis.yml .travis.yml @@ -24,11 +24,11 @@ script: popd; - pip install -r docs/doc-requirements.txt - pushd docs; - make html; + make html || exit 1; popd; after_success: - pip install codecov -- cd tests && codecov +- pushd tests && codecov && popd jobs: include: - stage: deploy

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Correct url of Advanced Binder Documentation link The URL was missing a "/tutorials/" in the path

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -177,5 +177,5 @@ With Dockerfiles, a regular Docker build will be performed. .. note:: If a Dockerfile is present, all other configuration files will be ignored. -See the `Advanced Binder Documentation <https://mybinder.readthedocs.io/en/latest/dockerfile.html>`_ for +See the `Advanced Binder Documentation <https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html>`_ for best-practices with Dockerfiles.

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Update CONTRIBUTING.md `freeze.py` expects `environment.yml` to be in working directory - calling it from project root will not work since the file is in a different folder

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -175,7 +175,8 @@ See the subsections below for more detailed instructions. an existing package, you should then run: ```bash - python ./repo2docker/buildpacks/conda/freeze.py + cd ./repo2docker/buildpacks/conda/ + python freeze.py ``` This script will resolve dependencies and write them to the respective `.frozen.yml`

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Update CONTRIBUTING.md Added clarity to updating conda- I read it as meaning the specific version of conda

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -148,7 +148,7 @@ To update one of the dependencies shared across all `repo2docker` builds, you must follow these steps (with more detailed information in the sections below): * Make sure you have [Docker](https://www.docker.com/) running on your computer -* Bump the version number in the `conda` environment ([link](https://github.com/jupyter/repo2docker/blob/master/CONTRIBUTING.md#conda-dependencies)) +* Bump the version numbers of the dependencies you want to update in the `conda` environment ([link](https://github.com/jupyter/repo2docker/blob/master/CONTRIBUTING.md#conda-dependencies)) * Make a pull request with your changes ([link](https://github.com/jupyter/repo2docker/blob/master/CONTRIBUTING.md#make-a-pull-request)) See the subsections below for more detailed instructions.

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Remove explicit passing of logger instance

MODIFY repo2docker/app.py repo2docker/app.py @@ -196,7 +196,7 @@ class Repo2Docker(Application): # Pick a content provider based on URL picked_content_provider = None for CP in self.content_providers: - cp = CP(self.log) + cp = CP() spec = cp.detect(url, ref=ref) if spec is not None: picked_content_provider = cp MODIFY repo2docker/contentproviders/base.py repo2docker/contentproviders/base.py @@ -4,6 +4,7 @@ Base classes for repo2docker ContentProviders ContentProviders accept a `spec` of various kinds, and provide the contents from the spec to a given output directory. """ +import logging import os @@ -13,8 +14,8 @@ class ContentProviderException(Exception): class ContentProvider: - def __init__(self, logger): - self.log = logger + def __init__(self): + self.log = logging.getLogger("repo2docker") def detect(self, repo, ref=None, extra_args=None): """Determine compatibility between source and this provider.

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Add tests for local content provider

MODIFY tests/contentproviders/test_git.py tests/contentproviders/test_git.py from contextlib import contextmanager -import shutil import os import subprocess from tempfile import TemporaryDirectory -from repo2docker.contentproviders.git import Git +from repo2docker.contentproviders import Git @contextmanager ADD tests/contentproviders/test_local.py +import os +from tempfile import TemporaryDirectory, NamedTemporaryFile + +from repo2docker.contentproviders import Local + + +def test_detect_local_dir(): + with TemporaryDirectory() as d: + local = Local() + spec = local.detect(d) + + # should accept a local directory + assert spec is not None, spec + assert 'path' in spec, spec + assert spec['path'] == d + + +def test_not_detect_local_file(): + with NamedTemporaryFile() as f: + local = Local() + spec = local.detect(f.name) + + # should NOT accept a local file + assert spec is None, spec + + +def test_content_available(): + # create a directory with files, check they are available in the output + # directory + with TemporaryDirectory() as d: + with open(os.path.join(d, 'test'), 'w') as f: + f.write("Hello") + + spec = {'path': d} + for _ in Local().fetch(spec, d): + pass + assert os.path.exists(os.path.join(d, 'test'))

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Expand comment about using a local directory as checkout and source

MODIFY repo2docker/app.py repo2docker/app.py @@ -107,8 +107,8 @@ class Repo2Docker(Application): ], config=True, help=""" - Ordered list of ContentProviders to try in turn to fetch the contents - specified by the user. + Ordered list by priority of ContentProviders to try in turn to fetch + the contents specified by the user. """ ) @@ -432,6 +432,8 @@ class Repo2Docker(Application): # user wants to mount a local directory into the container for # editing if args.editable: + # the user has to point at a directory, not just a path for us + # to be able to mount it if os.path.isdir(args.repo): self.volumes[os.path.abspath(args.repo)] = '.' else: @@ -679,7 +681,9 @@ class Repo2Docker(Application): sys.exit(1) # if the source is a directory we will keep using it, assuming that - # is what the user wanted + # is what the user wanted. This is how repo2docker has been working so + # far. Reusing a local directory seems better than making a copy of it + # as it might contain large files that would be expensive to copy. if os.path.isdir(self.repo): checkout_path = self.repo else:

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adding back sidebars

MODIFY docs/source/conf.py docs/source/conf.py @@ -110,7 +110,7 @@ html_theme_path = [alabaster_jupyterhub.get_html_theme_path()] # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] - +html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'] } # -- Options for HTMLHelp output ------------------------------------------

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clone from user repo in docs

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -54,10 +54,10 @@ To develop & test repo2docker locally, you need: ### Clone the repository First, you need to get a copy of the repo2docker git repository on your local -disk. +disk. Fork the repository on GitHub, then clone it to your computer: ```bash -git clone https://github.com/jupyter/repo2docker +git clone https://github.com/<your-username>/repo2docker ``` This will clone repo2docker into a directory called `repo2docker`. You can

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verify R installation for r-markdown with Stencila

RENAME tests/stencila/basic/archive/py-jupyter/bibliography.bibtex tests/stencila/pyjp/py-jupyter/bibliography.bibtex RENAME tests/stencila/basic/archive/py-jupyter/manifest.xml tests/stencila/pyjp/py-jupyter/manifest.xml RENAME tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb tests/stencila/pyjp/py-jupyter/py-jupyter.ipynb RENAME tests/stencila/basic/archive/py-jupyter/py-jupyter.ipynb.jats.xml tests/stencila/pyjp/py-jupyter/py-jupyter.ipynb.jats.xml RENAME tests/stencila/basic/verify tests/stencila/pyjp/verify RENAME tests/stencila/basic/archive/r-markdown/bibliography.bibtex tests/stencila/r/r-markdown/bibliography.bibtex RENAME tests/stencila/basic/archive/r-markdown/manifest.xml tests/stencila/r/r-markdown/manifest.xml RENAME tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd tests/stencila/r/r-markdown/rmarkdown.Rmd RENAME tests/stencila/basic/archive/r-markdown/rmarkdown.Rmd.jats.xml tests/stencila/r/r-markdown/rmarkdown.Rmd.jats.xml ADD tests/stencila/r/verify +#!/bin/sh + +jupyter serverextension list 2>&1 | grep nbstencilaproxy +jupyter nbextension list 2>&1 | grep nbstencilaproxy +R -e "library('stencila');"

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do not look for stencila if binder dir found

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -271,6 +271,10 @@ class BuildPack: # ${STENCILA_ARCHIVE_DIR}/${STENCILA_ARCHIVE}/manifest.xml self._stencila_manifest_dir = None + + if os.path.exists('binder'): + return self._stencila_manifest_dir + for root, dirs, files in os.walk("."): if "manifest.xml" in files: self.log.debug("Found a manifest.xml at %s", root) @@ -291,6 +295,10 @@ class BuildPack: # look at the content of the jats.xml file to extract the required execution contexts self._stencila_manifest_contexts = None + + if os.path.exists('binder'): + return self._stencila_manifest_contexts + for root, dirs, files in os.walk("."): for filename in files: if filename.endswith(".test.jats.xml"):

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update versions of stencila/r and stencila/py

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -564,7 +564,7 @@ class BaseImage(BuildPack): ( "${NB_USER}", r""" - ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache https://github.com/stencila/py/archive/f6a245fd.tar.gz && \ + ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache https://github.com/stencila/py/archive/f1260796.tar.gz && \ ${KERNEL_PYTHON_PREFIX}/bin/python -m stencila register """, ) MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -242,7 +242,8 @@ class RBuildPack(PythonBuildPack): "${NB_USER}", # Install and register stencila library r""" - R --quiet -e "devtools::install_github('stencila/r', ref = 'f220361438432abca968d2e76a4efe7c5ddde7f1')" && \ + R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \ + R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \ R --quiet -e "stencila::register()" """ ),

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add Stencila config files to docs

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -107,6 +107,22 @@ You also need to have a ``runtime.txt`` file that is formatted as ``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot of MRAN that will be used for your R installation. +``manifest.xml`` - Install Stencila +=================================== + +`Stencila <https://stenci.la/>`_ is an open source office suite for reproducible research. +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. +files named ``*.jats.xml``). + +You may also have a ``runtime.txt`` and/or an ``install.R`` to manually configure the your R installation. + +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

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reduce calls to stencila_manifest_contexts

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -557,8 +557,7 @@ class BaseImage(BuildPack): except FileNotFoundError: pass if self.stencila_manifest_contexts: - for context in self.stencila_manifest_contexts: - if(context == 'py' or context == 'pyjp'): + if {'py', 'pyjp'}.intersection(self.stencila_manifest_contexts): assemble_scripts.extend( [ ( @@ -570,7 +569,7 @@ class BaseImage(BuildPack): ) ] ) - #elif(context == 'r'): + #if {'r'}.intersection(self.stencila_manifest_contexts): # handled in RBuildPack if self.stencila_manifest_dir: assemble_scripts.extend(

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Fix wording in config_files.rst

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -117,7 +117,7 @@ If your repository contains a Stencila document, repo2docker detects it based on 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 the your R installation. +You may also have a ``runtime.txt`` and/or an ``install.R`` to manually configure your R installation. To see example repositories, visit our `Stencila with R <https://github.com/binder-examples/stencila-r/>`_ and

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add Stencila to user interface docs

MODIFY docs/source/howto/user_interface.rst docs/source/howto/user_interface.rst @@ -31,10 +31,29 @@ To learn more about URLs in JupyterLab and Jupyter Notebook, visit RStudio ------- -The RStudio user interface is automatically enabled a configuration file for -R is detected (an R version specified in ``runtime.txt``). If this is detected, +The RStudio user interface is automatically enabled if a configuration file for +R is detected (i.e. an R version specified in ``runtime.txt``). If this is detected, RStudio will be accessible by appending ``/rstudio`` to the URL, like so: .. code-block:: none http(s)://<server:port>/rstudio + +Stencila +-------- + +The Stencila user interface is automatically enabled if a Stencila document (i.e. +a file `manifest.xml`) is detected. Stencila will be accessible by appending +``/stencila`` to the URL, like so: + +.. code-block:: none + + http(s)://<server:port>/stencila + +The editor will open the Stencila document corresponding to the last `manifest.xml` +found in the file tree. If you want to open a different document, you can configure +the path in the URL parameter `archive`: + +.. code-block:: none + + http(s)://<server:port>/stencila/?archive=other-dir

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continue Stencila detection if /binder dir is present, improve

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -272,9 +272,6 @@ class BuildPack: self._stencila_manifest_dir = None - if os.path.exists('binder'): - return self._stencila_manifest_dir - for root, dirs, files in os.walk("."): if "manifest.xml" in files: self.log.debug("Found a manifest.xml at %s", root) @@ -294,10 +291,7 @@ class BuildPack: # look at the content of the jats.xml file to extract the required execution contexts - self._stencila_manifest_contexts = None - - if os.path.exists('binder'): - return self._stencila_manifest_contexts + self._stencila_manifest_contexts = [] for root, dirs, files in os.walk("."): for filename in files: MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -79,8 +79,7 @@ class RBuildPack(PythonBuildPack): return True description_R = 'DESCRIPTION' - if not os.path.exists('binder'): - if os.path.exists(description_R) or (self.stencila_manifest_contexts and "r" in self.stencila_manifest_contexts): + if (not os.path.exists('binder') and os.path.exists(description_R)) or 'r' in self.stencila_manifest_contexts: if not self.checkpoint_date: # no R snapshot date set through runtime.txt # set the R runtime to the latest date that is guaranteed to be on MRAN across timezones

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simplify test for contexts (is now by default an empty list)

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -239,8 +239,7 @@ class RBuildPack(PythonBuildPack): ), ] - if self.stencila_manifest_contexts: - if "r" in self.stencila_manifest_contexts: + if "r" in self.stencila_contexts: scripts += [ ( "${NB_USER}",

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increase timeout for stencila tests on travis

MODIFY .travis.yml .travis.yml @@ -16,8 +16,8 @@ script: # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in - pushd tests; - if [ ${REPO_TYPE} == "r" ]; then - travis_wait pytest --cov repo2docker -v ${REPO_TYPE} || exit 1; + if [ ${REPO_TYPE} == "r" ] || [ ${REPO_TYPE} == "stencila" ]; then + travis_wait 30 pytest --cov repo2docker -v ${REPO_TYPE} || exit 1; else travis_retry pytest --cov repo2docker -v ${REPO_TYPE} || exit 1; fi;

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Add and use new logo

MODIFY README.md README.md -# repo2docker +# <a href="https://github.com/jupyter/repo2docker"><img src="https://media.githubusercontent.com/media/jupyter/repo2docker/master/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> [![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) ADD docs/source/_static/images/repo2docker.png docs/source/_static/images/repo2docker.png Binary files /dev/null and b/docs/source/_static/images/repo2docker.png differ ADD docs/source/_static/images/repo2docker.sketch docs/source/_static/images/repo2docker.sketch Binary files /dev/null and b/docs/source/_static/images/repo2docker.sketch differ MODIFY docs/source/conf.py docs/source/conf.py @@ -94,8 +94,8 @@ pygments_style = 'sphinx' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False -# Jupyter Logo -html_logo = '_static/images/logo.svg' +# repo2docker Logo +html_logo = '_static/images/repo2docker.png' html_favicon = '_static/images/favicon.ico' # -- Options for HTML output ----------------------------------------------

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Temporarily switch image path

MODIFY README.md README.md -# <a href="https://github.com/jupyter/repo2docker"><img src="https://media.githubusercontent.com/media/jupyter/repo2docker/master/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> +# <a href="https://github.com/jupyter/repo2docker"><img src="https://raw.githubusercontent.com/jupyter/repo2docker/3fa7444fca6ae2b51e590cbc9d83baf92738ca2a/docs/source/_static/images/repo2docker.png" height="48px" />repo2docker</a> [![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)

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do not install Stencila Python context if only python-jupyter cells found

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -554,7 +554,7 @@ class BaseImage(BuildPack): )) except FileNotFoundError: pass - if {'py', 'pyjp'}.intersection(self.stencila_contexts): + if {'py'}.intersection(self.stencila_contexts): assemble_scripts.extend( [ (

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describe more complex detection mechanism used for stencila in dev docs

MODIFY docs/source/architecture.md docs/source/architecture.md @@ -38,8 +38,12 @@ It takes the following steps to determine this: something that it should be used for. For example, a `BuildPack` that uses `conda` to install libraries can check for presence of an `environment.yml` file and say 'yes, I can handle this repository' by returning `True`. Usually buildpacks look for presence of specific files - (`requirements.txt`, `environment.yml`, `install.R`, etc) to determine if they can handle a - repository or not. + (`requirements.txt`, `environment.yml`, `install.R`, `manifest.xml` etc) to determine if they can handle a + repository or not. Buildpacks may also look into specific files to determine specifics of the + required environment, such as the Stencila integration which extracts the required language-specific + executions contexts from an XML file (see base `BuildPack`). More than one buildpack may use such + information, as properties can be inherited (e.g. the R buildpack uses the list of required Stencila + contexts to see if R must be installed). 3. If no `BuildPack` returns true, then repo2docker will use the default `BuildPack` (defined in `Repo2Docker.default_buildpack` traitlet).

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Update docs in buildpacks/r.py

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -26,7 +26,7 @@ class RBuildPack(PythonBuildPack): If there is no `runtime.txt`, then the MRAN snapshot is set to latest date that is guaranteed to exist across timezones. - R packages are installed if specified either + Additional R packages are installed if specified either - in a file `install.R`, that will be executed at build time, and can be used for installing packages from both MRAN and GitHub

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Link ROADMAP from the README

MODIFY README.md README.md @@ -12,6 +12,9 @@ for more information on using repo2docker. See the [contributing guide](CONTRIBUTING.md) for information on contributing to repo2docker. +See [our roadmap](https://repo2docker.readthedocs.io/en/latest/contributing/roadmap.html) +to learn about where the project is heading. + ## Using repo2docker ### Prerequisites

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make loops more readable

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -286,18 +286,23 @@ class BuildPack: @property def stencila_contexts(self): - """Find the stencila manifest contexts if it exists""" + """Find the stencila manifest contexts from file path in manifest""" if hasattr(self, '_stencila_contexts'): return self._stencila_contexts - # look at the content of the documents in the manifest to extract the required execution contexts + # look at the content of the documents in the manifest + # to extract the required execution contexts self._stencila_contexts = set() # get paths to the article files from manifest files = [] if self.stencila_manifest_dir: - manifest = ET.parse(os.path.join(self.stencila_manifest_dir, 'manifest.xml')) - files = list(map(lambda x: os.path.join(self.stencila_manifest_dir, x.get('path')), manifest.findall('./documents/document'))) + manifest = ET.parse(os.path.join(self.stencila_manifest_dir, + 'manifest.xml')) + documents = manifest.findall('./documents/document') + files = [os.path.join(self.stencila_manifest_dir, x.get('path')) + for x in documents] + else: return self._stencila_contexts @@ -306,7 +311,8 @@ class BuildPack: # extract code languages from file document = ET.parse(filename) - languages = list(map(lambda x: x.get('language'), document.findall('.//code[@specific-use="source"]'))) + code_chunks = document.findall('.//code[@specific-use="source"]') + languages = [x.get('language') for x in code_chunks] self._stencila_contexts.update(languages) self.log.info(

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Add link to binder-examples repo for nix

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -182,7 +182,7 @@ a ``nix`` expression written in a ``default.nix`` file. Make sure to to produce a reproducible environment. To see an example repository visit -`nix binder example <https://gitlab.com/costrouc/nix-binder-example>`_. +`nix binder example <https://github.com/binder-examples/nix>`_. ``Dockerfile`` - Advanced environments

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Add notes about updating the pipfile and requirements

MODIFY Pipfile Pipfile +# Note that there is a devrequirements.txt file in this project, if you are +# updating this Pipfile make sure to update the devrequirements.txt accordingly + [dev-packages] -pyyaml="*" pytest="*" wheel="*" pytest-cov="*" +PyYAML = "*" +recommonmark = "*" +alabaster = "*" +Sphinx = ">=1.4,!=1.5.4" +alabaster_jupyterhub = "*" [packages] repo2docker = {path=".", editable=true} MODIFY dev-requirements.txt dev-requirements.txt -pyyaml +# Note that there is also a Pipfile for this project if you are updating this +# file do not forget to update thr Pipfile accordingly pytest wheel pytest-cov

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Ensure the deps and references are correct across all files

MODIFY Pipfile Pipfile -# Note that there is a dev-requirements.txt file in this project, if you are -# updating this Pipfile make sure to update the dev-requirements.txt accordingly +# Note that there are a dev-requirements.txt and a docs/doc-requirements.txt +# files in this project, if you are updating this Pipfile make sure to +# update these accordingly [dev-packages] pytest="*" 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 thr Pipfile accordingly +pyyaml pytest wheel pytest-cov MODIFY docs/doc-requirements.txt docs/doc-requirements.txt +# Note that there is also a Pipfile for this project if you are updating this +# file do not forget to update thr Pipfile accordingly sphinx>=1.4, !=1.5.4 recommonmark alabaster

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Update docs/doc-requirements.txt

MODIFY docs/doc-requirements.txt docs/doc-requirements.txt # Note that there is also a Pipfile for this project if you are updating this -# file do not forget to update thr Pipfile accordingly +# file do not forget to update the Pipfile accordingly sphinx>=1.4, !=1.5.4 recommonmark alabaster

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Update dev-requirements.txt

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 thr Pipfile accordingly +# file do not forget to update the Pipfile accordingly pyyaml pytest wheel

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Add comment explaining use of $*

MODIFY repo2docker/buildpacks/nix/nix-shell-wrapper repo2docker/buildpacks/nix/nix-shell-wrapper @@ -14,6 +14,13 @@ if [ -e ./binder ]; then nixpath="./binder/default.nix"; if [ -f ./binder/start ]; then chmod u+x ./binder/start + # Using `$@`` here which is what the internet recommends leads to + # errors when the command is something like `jupyter --ip=0.0.0.0 ...` + # as nix-shell picks that up as an argument to it instead of the command. + # There are several issues on the nix repos discussing this and adding support + # for -- to indicate "all arguments after this are for the command, not nix-shell" + # but it seems they have stalled/not yet produced an implementation. + # So let's use `$*` for now. nix-shell $nixpath --command "./binder/start $*" & else nix-shell $nixpath --command "$*" &

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Better approach to dealing with alt Python versions As suggested by

MODIFY setup.py setup.py from setuptools import setup, find_packages +import sys import versioneer -import sys if sys.version_info[0] < 3: - sys.stderr.write('jupyter-repo2docker requires Python 3 but the running Python is %s.%s.%s' % sys.version_info[:3]) - sys.exit(1) - + readme = None +else: with open('README.md', encoding="utf8") as f: readme = f.read()

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Tweak docstring to make it more understandable

MODIFY repo2docker/app.py repo2docker/app.py @@ -194,7 +194,10 @@ class Repo2Docker(Application): ) def fetch(self, url, ref, checkout_path): - """Check out a repo using url and ref to the checkout_path locationself. + """Fetch the contents of `url` and place it in `checkout_path`. + + The `ref` parameter specifies what "version" of the contents should be + fetched. In the case of a git repository `ref` is the SHA-1 of a commit. Iterate through possible content providers until a valid provider, based on URL, is found.

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removing note that env.yml is needed for julia

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -71,8 +71,7 @@ To install your repository like a Python package, you may include a ``REQUIRE`` - Install a Julia environment ========================================= -This specifies a list of Julia packages. Repositories with a ``REQUIRE`` file -**must also contain an** ``environment.yml`` **file**. To see an example of a +This specifies a list of Julia packages. To see an example of a Julia repository with ``REQUIRE`` and ``environment.yml``, visit `binder-examples/julia-python <https://github.com/binder-examples/julia-python>`_.

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Use a subset of the git SHA1 to make image names unique

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -53,6 +53,6 @@ class Git(ContentProvider): def content_id(self): """A unique ID to represent the version of the content. - Uses the git commit ID of the repository. + Uses the first seven characters of the git commit ID of the repository. """ - return self._sha1 + return self._sha1[:7]

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Add traitlet for reuse_layers_from More accurate name in our context

MODIFY repo2docker/app.py repo2docker/app.py @@ -72,6 +72,18 @@ class Repo2Docker(Application): """ ) + reuse_layers_from = List( + [], + config=True, + help=""" + List of images to try & re-use cached image layers from. + + Docker only tries to re-use image layers from images built locally, + not pulled from a registry. We can ask it to explicitly re-use layers + from non-locally built images by through the 'cache_from' parameter. + """ + ) + buildpacks = List( [ LegacyBinderDockerBuildPack, @@ -407,7 +419,7 @@ class Repo2Docker(Application): ) argparser.add_argument( - '--cache-from', + '--reuse-layers-from', action='append', default=[], help='Docker images to attempt to re-use cached layers from' @@ -552,8 +564,8 @@ class Repo2Docker(Application): if args.subdir: self.subdir = args.subdir - if args.cache_from: - self.cache_from = args.cache_from + if args.reuse_layers_from: + self.reuse_layers_from = args.reuse_layers_from self.environment = args.environment @@ -729,7 +741,7 @@ class Repo2Docker(Application): extra=dict(phase='building')) for l in picked_buildpack.build(self.output_image_spec, - self.build_memory_limit, build_args, self.cache_from): + self.build_memory_limit, build_args, self.reuse_layers_from): if 'stream' in l: self.log.info(l['stream'], extra=dict(phase='building'))

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Pass through cache_from to legacy buildpack too

MODIFY repo2docker/buildpacks/legacy/__init__.py repo2docker/buildpacks/legacy/__init__.py @@ -83,7 +83,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): 'legacy/python3.frozen.yml': '/tmp/python3.frozen.yml', } - def build(self, image_spec, memory_limit, build_args): + def build(self, image_spec, memory_limit, build_args, cache_from): """Build a legacy Docker image.""" with open(self.dockerfile, 'w') as f: f.write(self.render()) @@ -94,7 +94,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): env_file, ) shutil.copy(src_path, env_file) - return super().build(image_spec, memory_limit, build_args) + return super().build(image_spec, memory_limit, build_args, cache_from) def detect(self): """Check if current repo should be built with the Legacy BuildPack.

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Use --cache-from as arg name to match docker build

MODIFY repo2docker/app.py repo2docker/app.py @@ -72,7 +72,7 @@ class Repo2Docker(Application): """ ) - reuse_layers_from = List( + cache_from = List( [], config=True, help=""" @@ -419,10 +419,10 @@ class Repo2Docker(Application): ) argparser.add_argument( - '--reuse-layers-from', + '--cache-from', action='append', default=[], - help='Docker images to attempt to re-use cached layers from' + help=self.traits()['cache_from'].help ) return argparser @@ -564,8 +564,8 @@ class Repo2Docker(Application): if args.subdir: self.subdir = args.subdir - if args.reuse_layers_from: - self.reuse_layers_from = args.reuse_layers_from + if args.cache_from: + self.cache_from = args.cache_from self.environment = args.environment @@ -741,7 +741,7 @@ class Repo2Docker(Application): extra=dict(phase='building')) for l in picked_buildpack.build(self.output_image_spec, - self.build_memory_limit, build_args, self.reuse_layers_from): + self.build_memory_limit, build_args, self.cache_from): if 'stream' in l: self.log.info(l['stream'], extra=dict(phase='building'))

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Log a 'success' message when push is complete

MODIFY repo2docker/app.py repo2docker/app.py @@ -566,6 +566,7 @@ 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')) def run_image(self): """Run docker container from built image

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Bump nbrsessionproxy version For

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -214,7 +214,7 @@ class RBuildPack(PythonBuildPack): "${NB_USER}", # Install nbrsessionproxy r""" - pip install --no-cache-dir nbrsessionproxy==0.7.0 && \ + pip install --no-cache-dir nbrsessionproxy==0.8.0 && \ jupyter serverextension enable nbrsessionproxy --sys-prefix && \ jupyter nbextension install --py nbrsessionproxy --sys-prefix && \ jupyter nbextension enable --py nbrsessionproxy --sys-prefix

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Add tests for cache_from functionality

ADD tests/test_cache_from.py +""" +Test that --cache-from is passed in to docker API properly. +""" +import os +import docker +from unittest.mock import MagicMock, patch +from tempfile import TemporaryDirectory + +def test_cache_from(monkeypatch): + FakeDockerClient = MagicMock() + cache_from = [ + 'image-1:latest' + ] + fake_client = MagicMock(spec=docker.APIClient) + fake_client.build.return_value = iter([{'stream': 'fake'}]) + + with TemporaryDirectory() as d: + monkeypatch.chdir(d) + from repo2docker.buildpacks import BaseImage + for line in BaseImage().build(fake_client, 'image-2', '1Gi', {}, cache_from): + assert line == {'stream': 'fake'} + called_args, called_kwargs = fake_client.build.call_args + assert 'cache_from' in called_kwargs + assert called_kwargs['cache_from'] == cache_from \ No newline at end of file

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Pass cache_from through to build Got lost in a merge

MODIFY repo2docker/app.py repo2docker/app.py @@ -758,7 +758,7 @@ class Repo2Docker(Application): extra=dict(phase='building')) for l in picked_buildpack.build(api_client, self.output_image_spec, - self.build_memory_limit, build_args): + self.build_memory_limit, build_args, self.cache_from): if 'stream' in l: self.log.info(l['stream'], extra=dict(phase='building'))

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Add unit test for execute_cmd in repo2docker.utils

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -10,7 +10,9 @@ from traitlets import Integer, TraitError def execute_cmd(cmd, capture=False, **kwargs): """ - Call given command, yielding output line by line if capture=True + Call given command, yielding output line by line if capture=True. + + Must be yielded from. """ if capture: kwargs['stdout'] = subprocess.PIPE ADD tests/test_utils.py +""" +Tests for repo2docker/utils.py +""" +from repo2docker import utils +import pytest +import subprocess + + +def test_capture_cmd_no_capture_success(): + # This should succeed + for line in utils.execute_cmd([ + '/bin/bash', '-c', 'echo test' + ]): + pass + +def test_capture_cmd_no_capture_fail(): + with pytest.raises(subprocess.CalledProcessError): + for line in utils.execute_cmd([ + '/bin/bash', '-c', 'e ' + ]): + pass + + +def test_capture_cmd_capture_success(): + # This should succeed + for line in utils.execute_cmd([ + '/bin/bash', '-c', 'echo test' + ], capture=True): + assert line == 'test\n' + + +def test_capture_cmd_capture_fail(): + with pytest.raises(subprocess.CalledProcessError): + for line in utils.execute_cmd([ + '/bin/bash', '-c', 'echo test; exit 1 ' + ], capture=True): + assert line == 'test\n' \ No newline at end of file

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Remove maybe_cleanup util function It was used in exactly one place, and could be inlined with minimal loss of clarity

MODIFY repo2docker/app.py repo2docker/app.py @@ -35,7 +35,7 @@ from .buildpacks import ( ) from . import contentproviders from .utils import ( - ByteSpecification, maybe_cleanup, is_valid_docker_image_name, + ByteSpecification, is_valid_docker_image_name, validate_and_generate_port_mapping, chdir ) @@ -703,9 +703,7 @@ class Repo2Docker(Application): else: checkout_path = self.git_workdir - # keep as much as possible in the context manager to make sure we - # cleanup if things go wrong - with maybe_cleanup(checkout_path, self.cleanup_checkout): + try: self.fetch(self.repo, self.ref, checkout_path) if self.subdir: @@ -751,6 +749,10 @@ class Repo2Docker(Application): else: self.log.info(json.dumps(l), extra=dict(phase='building')) + finally: + # Cheanup checkout if necessary + if self.cleanup_checkout: + shutil.rmtree(checkout_path, ignore_errors=True) if self.push: self.push_image() MODIFY repo2docker/utils.py repo2docker/utils.py @@ -69,14 +69,6 @@ def chdir(path): os.chdir(old_dir) -@contextmanager -def maybe_cleanup(path, cleanup=False): - """Delete the directory at passed path if cleanup flag is True.""" - yield - if cleanup: - shutil.rmtree(path, ignore_errors=True) - - def validate_and_generate_port_mapping(port_mapping): """ Validate the port mapping list and return a list of validated tuples.

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Add test for utils.chdir

MODIFY tests/test_utils.py tests/test_utils.py """ Tests for repo2docker/utils.py """ +import os +from tempfile import TemporaryDirectory from repo2docker import utils import pytest import subprocess @@ -35,3 +37,11 @@ def test_capture_cmd_capture_fail(): '/bin/bash', '-c', 'echo test; exit 1 ' ], capture=True): assert line == 'test\n' + + +def test_chdir(): + with TemporaryDirectory() as d: + cur_cwd = os.getcwd() + with utils.chdir(d): + assert os.getcwd() == d + assert os.getcwd() == cur_cwd

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Add test for ByteSpecification validation

MODIFY tests/test_utils.py tests/test_utils.py """ Tests for repo2docker/utils.py """ +import traitlets import os from tempfile import TemporaryDirectory from repo2docker import utils @@ -45,3 +46,21 @@ def test_chdir(): with utils.chdir(d): assert os.getcwd() == d assert os.getcwd() == cur_cwd + + +def test_byte_spec_validation(): + bs = utils.ByteSpecification() + + assert bs.validate(None, 1) == 1 + assert bs.validate(None, 1.0) == 1.0 + + assert bs.validate(None, '1K') == 1024 + assert bs.validate(None, '1M') == 1024 * 1024 + assert bs.validate(None, '1G') == 1024 * 1024 * 1024 + assert bs.validate(None, '1T') == 1024 * 1024 * 1024 * 1024 + + with pytest.raises(traitlets.TraitError): + bs.validate(None, 'NK') + + with pytest.raises(traitlets.TraitError): + bs.validate(None, '1m') \ No newline at end of file

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Remove duplicate codecov config

MODIFY .codecov.yml .codecov.yml -# show coverage in CI status, not as a comment. Never consider it a failure. +# show coverage in CI status, not as a comment. comment: off coverage: status: project: default: - target: 0% + target: 20% patch: default: - target: 0% + target: auto DELETE codecov.yml -comment: - layout: header, changes, diff -coverage: - status: - patch: - default: - target: '20' - project: - default: - target: auto

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