narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Set default exclusivity to False meaning inclusive

MODIFY repo2docker/buildpacks/julia/semver.py repo2docker/buildpacks/julia/semver.py @@ -136,7 +136,7 @@ class VersionRange: falls within a `VersionRange` """ - def __init__(self, lower, upper, exclusive): + def __init__(self, lower, upper, exclusive=False): self.lower = lower self.upper = upper self.exclusive = exclusive

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moved the shiny faq below the note

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -141,6 +141,15 @@ 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). +.. note:: + + Editable mode is a convenience option that will bind the + repository to the container working directory (usually + ``$HOME``). If you need to mount to a different location in + the container, use the ``--volumes`` option instead. Similarly, + for a fully customized user Dockerfile, this option is not + guaranteed to work. + Why is my R shiny app not launching? ---------------------------------------------------------------------------------- @@ -153,11 +162,4 @@ server file for the app, and run the app in the container rstudio. This way you see the rstudio logs as it tries to initialise the shiny app. If you a missing a package or other dependency for the container, this will be obvious at this stage. -.. note:: - Editable mode is a convenience option that will bind the - repository to the container working directory (usually - ``$HOME``). 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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Julia: Update links to Pkg.jl documentation and change Compat to [compat] since that is how the section is usually referred to.

MODIFY docs/source/howto/languages.rst docs/source/howto/languages.rst @@ -73,10 +73,10 @@ 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/>`_. +`the Julia Pkg.jl documentation <https://julialang.github.io/Pkg.jl/v1/>`_. 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. +``[compat]`` section of the ``Project.toml`` file, as described +here: https://julialang.github.io/Pkg.jl/v1/compatibility/. Languages not covered here ==========================

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Use different strategy to set JUPYTER dir for IJulia

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -63,7 +63,8 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): ('JULIA_BINDIR', '${JULIA_PATH}/bin'), ('JULIA_DEPOT_PATH', '${JULIA_PATH}/pkg'), ('JULIA_VERSION', self.julia_version), - ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter') + ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter'), + ('JUPYTER_DATA_DIR', '${APP_BASE}/conda/share/jupyter') ] def get_path(self): @@ -118,7 +119,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): ( "${NB_USER}", r""" - julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\", env=Dict(\"JUPYTER_DATA_DIR\"=>\"${APP_BASE}/conda/share/jupyter\"));" && \ + julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && \ julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); pkg"precompile"' """ )

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Add an issue template to direct where things are posted

ADD docs/issue_template.md +

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Add discourse pointer to the README

MODIFY README.md README.md @@ -9,6 +9,8 @@ the configuration files found in the repository. See the [repo2docker documentation](http://repo2docker.readthedocs.io) for more information on using repo2docker. +For support questions please search or post to https://discourse.jupyter.org/c/binder. + See the [contributing guide](CONTRIBUTING.md) for information on contributing to repo2docker.

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Use NB_PYTHON_PREFIX for kernel install path

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -17,7 +17,7 @@ API changes Bug fixes --------- -- Install IJulia kernel into ${APP_BASE}/conda/share/jupyter in :pr:`622` by +- Install IJulia kernel into ${NB_PYTHON_PREFIX}/share/jupyter in :pr:`622` by :user:`davidanthoff`. MODIFY repo2docker/buildpacks/julia/julia_require.py repo2docker/buildpacks/julia/julia_require.py @@ -119,7 +119,7 @@ class JuliaRequireBuildPack(PythonBuildPack): # FIXME: Find way to get it to install under /srv and not $HOME? r""" julia -e 'if (VERSION > v"0.7-") using Pkg; else Pkg.init(); end; Pkg.add("IJulia"); using IJulia;' && \ - mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${APP_BASE}/conda/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} + mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} """ ) ]

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Add some code documentation

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -113,6 +113,10 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): """ Return series of build-steps specific to "this" Julia repository + We make sure that the IJulia package gets installed into the default + environment, and not the project specific one, by running the + IJulia install command with JULIA_PROJECT="". + Instantiate and then precompile all packages in the repos julia environment.

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Update default packages

MODIFY repo2docker/buildpacks/conda/environment.py-3.5.frozen.yml repo2docker/buildpacks/conda/environment.py-3.5.frozen.yml @@ -75,7 +75,7 @@ dependencies: - idna==2.7 - jupyterhub==0.9.4 - mako==1.0.7 - - notebook==5.7.4 + - notebook==5.7.6 - nteract-on-jupyter==1.9.6 - pamela==0.3.0 - python-editor==1.0.3 MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml dependencies: - python=3.7.* - - ipywidgets==7.2.1 - - jupyterlab==0.34.9 - - nbconvert==5.4.0 - - notebook==5.7.4 + - ipywidgets==7.4.2 + - jupyterlab==0.35.4 + - nbconvert==5.4.1 + - notebook==5.7.6 - pip: - nteract_on_jupyter==2.0.0 - jupyterhub==0.9.4

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Update test of editable flag For some reason the notebook server doesn't exit when we send the SIGTERM signal to the container and as a result waiting for the container to shutdown leads to an exit code of 137 (the notebook server gets kill by SIGKILL).

MODIFY tests/unit/test_editable.py tests/unit/test_editable.py @@ -3,10 +3,8 @@ import re import tempfile import time -from repo2docker.app import Repo2Docker from repo2docker.__main__ import make_r2d -from conftest import make_test_func DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'dockerfile', 'editable') @@ -39,19 +37,26 @@ def test_editable_by_host(): app.initialize() app.build() container = app.start_container() + # give the container a chance to start + while container.status != 'running': time.sleep(1) + try: with tempfile.NamedTemporaryFile(dir=DIR, prefix='testfile', suffix='.txt'): status, output = container.exec_run(['sh', '-c', 'ls testfile????????.txt']) assert status == 0 assert re.match(br'^testfile\w{8}\.txt\n$', output) is not None - # File should be removed in the container as well + # After exiting the with block the file should stop existing + # in the container as well as locally status, output = container.exec_run(['sh', '-c', 'ls testfile????????.txt']) - assert status != 1 + assert status == 2 assert re.match(br'^testfile\w{8}\.txt\n$', output) is None finally: - # stop the container - container.stop() - app.wait_for_container(container) + # stop the container, we don't care how it stops or + # what the exit code is. + container.stop(timeout=1) + container.reload() + assert container.status == 'exited', container.status + container.remove()

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Python 3.7 as default in the docs

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -36,7 +36,7 @@ either because the version of the package is too new and your chosen Python is t or vice versa. I 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 +installed with Python 2. The notebook server will run in the default Python 3.7 environment. Julia MODIFY docs/source/usage.rst docs/source/usage.rst @@ -85,7 +85,7 @@ by ``repo2docker`` to see how to configure the build process. .. note:: - ``repo2docker`` builds an environment with Python 3.6 by default. If you'd + ``repo2docker`` builds an environment with Python 3.7 by default. If you'd like a different version, you can specify this in your :ref:`configuration files <config-files>`.

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update checksum for conda installer

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -5,6 +5,10 @@ set -ex cd $(dirname $0) MINICONDA_VERSION=4.5.12 CONDA_VERSION=4.6.11 +# Only MD5 checksums are available for miniconda +# Can be obtained from https://repo.continuum.io/miniconda/ +MD5SUM="4be03f925e992a8eda03758b72a77298" + URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh @@ -15,10 +19,7 @@ unset HOME wget --quiet $URL -O ${INSTALLER_PATH} chmod +x ${INSTALLER_PATH} -# Only MD5 checksums are available for miniconda -# Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="e1045ee415162f944b6aebfe560b8fee" - +# check md5 checksum if ! echo "${MD5SUM} ${INSTALLER_PATH}" | md5sum --quiet -c -; then echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!" exit 1

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changelog addition

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -13,6 +13,8 @@ New features :user:`davidanthoff` - Set JULIA_PROJECT globally, so that every julia instance starts with the julia environment activated in :pr:`612` by :user:`davidanthoff`. +- Update Miniconda version to 4.5.12and Conda version to 4.6.11 in :pr:`637` by + :user:`jhamman` API changes ----------- MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -7,7 +7,7 @@ MINICONDA_VERSION=4.5.12 CONDA_VERSION=4.6.11 # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="4be03f925e992a8eda03758b72a77298" +MD5SUM="866ae9dff53ad0874e1d1a60b1ad1ef8" URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh

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fallback to 4.6.10

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -13,7 +13,7 @@ New features :user:`davidanthoff` - Set JULIA_PROJECT globally, so that every julia instance starts with the julia environment activated in :pr:`612` by :user:`davidanthoff`. -- Update Miniconda version to 4.5.12and Conda version to 4.6.11 in :pr:`637` by +- Update Miniconda version to 4.5.12 and Conda version to 4.6.10 in :pr:`637` by :user:`jhamman` API changes MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -4,7 +4,7 @@ set -ex cd $(dirname $0) MINICONDA_VERSION=4.5.12 -CONDA_VERSION=4.6.11 +CONDA_VERSION=4.6.10 # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ MD5SUM="866ae9dff53ad0874e1d1a60b1ad1ef8"

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Remove conda download cache explicitly

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -181,7 +181,8 @@ class CondaBuildPack(BaseImage): r""" conda env update -n {0} -f "{1}" && \ conda clean -tipsy && \ - conda list -n {0} + conda list -n {0} && \ + rm -rf /srv/conda/pkgs """.format(env_name, environment_yml) )) return super().get_assemble_scripts() + assembly_scripts

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Update recommonmark ocnfiguration In new versions of SPhinx the way we were configuring the recommonmark extension has become deprecated. This switches us to the new way of configuring it.

MODIFY docs/source/conf.py docs/source/conf.py # import sys # sys.path.insert(0, os.path.abspath('.')) -# For conversion from markdown to html -import recommonmark.parser # -- General configuration ------------------------------------------------ @@ -35,6 +33,7 @@ import recommonmark.parser # ones. extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.autoprogram', + 'recommonmark', ] extlinks = { @@ -46,10 +45,6 @@ extlinks = { # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] -# source parser -source_parsers = { - '.md': 'recommonmark.parser.CommonMarkParser', -} from recommonmark.transform import AutoStructify

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ensure git submodules are updated and initialised

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -45,6 +45,12 @@ class Git(ContentProvider): capture=yield_output): yield line + # ensure that git submodules are initialised and updated + for line in execute_cmd(['git', 'submodule', 'update', '--init', '--recursive'], + cwd=output_dir, + capture=yield_output): + yield line + cmd = ['git', 'rev-parse', 'HEAD'] sha1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, cwd=output_dir) self._sha1 = sha1.stdout.read().decode().strip()

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mentioning s2i in faq

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -163,3 +163,15 @@ 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. +Why does repo2docker need to exist? Why not use tool like source2image? +----------------------------------------------------------------------- + +The Jupyter community believes strongly in building on top of pre-existing tools whenever +possible (this is why repo2docker buildpacks largely build off of patterns that already +exist in the data analytics community). We try to perform due-diligence and search for +other communities to leverage and help, but sometimes it makes the most sense to build +our own new tool. In the case of repo2docker, we spent time integrating with a pre-existing +tool called [source2image](https://github.com/openshift/source-to-image). +This is an excellent open tool for containerization, but we +ultimately decided that it did not fit the use-case we wanted to address. For more information, +[here's a short blog post about the decision and the reasoning behind it](https://github.com/yuvipanda/words/blob/fd096dd49d87e624acd8bdf6d13c0cecb930bb3f/content/post/why-not-s2i.md).

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Fix up the server proxy package to get websockets back

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -214,10 +214,11 @@ class RBuildPack(PythonBuildPack): "${NB_USER}", # Install nbrsessionproxy r""" - 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 + pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \ + pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \ + jupyter serverextension enable jupyter_server_proxy --sys-prefix && \ + jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \ + jupyter nbextension enable --py jupyter_server_proxy --sys-prefix """ ), (

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Unpin pip again

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -27,6 +27,9 @@ Bug fixes buildpack in :pr:`633` by :user:`betatim`. - Update to version 5.7.6 of the `notebook` package used in all environments in :pr:`628` by :user:`betatim`. +- Switch to newer version of jupyter-server-proxy to fix websocket handling + in :pr:`646` by :user:`betatim`. +- Update to pip v19.0.3 in :pr:`647` by :user:`betatim`. Version 0.8.0 MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -63,7 +63,6 @@ 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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Document pipfile(.lock) as an option

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -54,6 +54,22 @@ 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. +.. _Pipfile: + +``Pipfile`` and/or ``Pipfile.lock`` - Install a Python environment +================================================================== + +``Pipfile`` and/or ``Pipfile.lock`` specifies a list of Python packages that +should be installed in your environment. ``pipenv install --dev`` will be run to +install the dependencies where the existence of a ``Pipfile.lock`` will make the +``Pipfile`` be ignored. + +.. note:: + + `pipenv <https://github.com/pypa/pipenv/>`_ and `virtualenv + <https://github.com/pypa/virtualenv/>`_ and associated ``requirements.txt`` + files are both managed by the Python Packaging Authority PyPA, where pipenv + and ``Pipfile`` and ``Pipfile.lock`` seem to be the modern solution. .. _requirements.txt:

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Add Pipfile's to PythonBuildPack's detect()

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -78,6 +78,8 @@ class PythonBuildPack(CondaBuildPack): def detect(self): """Check if current repo should be built with the Python buildpack. """ + pipfile = self.binder_path('Pipfile') + pipfile_lock = self.binder_path('Pipfile.lock') requirements_txt = self.binder_path('requirements.txt') runtime_txt = self.binder_path('runtime.txt') setup_py = 'setup.py' @@ -91,4 +93,4 @@ class PythonBuildPack(CondaBuildPack): return False if not os.path.exists('binder') and os.path.exists(setup_py): return True - return os.path.exists(requirements_txt) + return os.path.exists(pipfile) or os.path.exists(pipfile_lock) or os.path.exists(requirements_txt)

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Add Pipfile vs requirements.txt logic

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -58,9 +58,13 @@ class PythonBuildPack(CondaBuildPack): '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format(nb_requirements_file) )) - # install requirements.txt in the kernel env + # install Pipfile.lock, Pipfile, or requirements.txt in the kernel env + pipfile = self.binder_path('Pipfile') + pipfile_lock = self.binder_path('Pipfile.lock') requirements_file = self.binder_path('requirements.txt') - if os.path.exists(requirements_file): + if os.path.exists(pipfile) or os.path.exists(pipfile_lock): + pass + elif os.path.exists(requirements_file): assemble_scripts.append(( '${NB_USER}', 'pip install "pip<19" && ' + \

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Update .gitignore to avoid pytest scrap

MODIFY .gitignore .gitignore @@ -21,6 +21,12 @@ lib64/ share/ include/ +# PyTest remnants +tests/dockerfile/legacy/._binder.Dockerfile +tests/dockerfile/legacy/apt-sources.list +tests/dockerfile/legacy/python3.frozen.yml +tests/dockerfile/legacy/root.frozen.yml + # Docs generated/ test_file_text.txt

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Rethink setup.py with Pipfile As setup.py can be explicitly installed or not from a Pipfile I reasoned that it should not be installed by default after pipenv has used relevant Pipfiles.

RENAME tests/venv/pipfile/setup-py/Pipfile tests/venv/pipfile/setup-py-explicit/Pipfile @@ -4,7 +4,5 @@ verify_ssl = true name = "pypi" [packages] -requests = "*" - -[dev-packages] there = "*" +dummy = {path=".", editable=true} ADD tests/venv/pipfile/setup-py-explicit/README.rst +Python - Pipfile + setup.py +--------------------------- + +The Pipfile asked the local package to be installed with ``setup.py``, was it? RENAME tests/venv/pipfile/setup-py/dummy/__init__.py tests/venv/pipfile/setup-py-explicit/dummy/__init__.py RENAME tests/venv/pipfile/setup-py/setup.py tests/venv/pipfile/setup-py-explicit/setup.py RENAME tests/venv/pipfile/setup-py/verify tests/venv/pipfile/setup-py-explicit/verify #!/usr/bin/env python -import requests import there import dummy DELETE tests/venv/pipfile/setup-py/README.rst -Python - Pipfile(.lock) + setup.py ----------------------------------- - -We should make ``setup.py`` be installed after the ``Pipfile`` or -``Pipfile.lock``.

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Add test for Pipfile + setup.py We want to ignore the setup.py file if it is around along with a Pipfile.

ADD tests/venv/pipfile/setup-py-implicit/Pipfile +[[source]] +url = "https://pypi.python.org/simple" +verify_ssl = true +name = "pypi" + +[packages] +there = "*" ADD tests/venv/pipfile/setup-py-implicit/README.rst +Python - Pipfile + setup.py +--------------------------- + +The Pipfile did not ask for the local package to be installed with ``setup.py``, +so lets ensure it wasn't. ADD tests/venv/pipfile/setup-py-implicit/dummy/__init__.py +def dummy(): + pass ADD tests/venv/pipfile/setup-py-implicit/setup.py +from setuptools import setup, find_packages + +setup( + name='Dummy', + version='1.0.0', + url='https://git-place.org/dummy/dummy.git', + author='Dummy Name', + author_email='dummy@my-email.com', + description='Dummy package for testing purposes only', + packages=find_packages(), + install_requires=['numpy'], +) ADD tests/venv/pipfile/setup-py-implicit/verify +#!/usr/bin/env python +import there + +try: + import dummy +except ImportError: + pass +else: + raise Exception("'dummy' shouldn't have been installed from setup.py when a Pipfile was present")

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Fix the Pipfile + setup.py tests Apparently testing to import the package will work no matter what as we will find it locally so setup.py may not need to run. By adding a small dependency I could check if the dependency is installed and now the tests actually tests what they should.

MODIFY tests/venv/pipfile/setup-py-explicit/setup.py tests/venv/pipfile/setup-py-explicit/setup.py @@ -8,5 +8,5 @@ setup( author_email='dummy@my-email.com', description='Dummy package for testing purposes only', packages=find_packages(), - install_requires=['numpy'], + install_requires=['pypi-pkg-test==0.0.4'], ) MODIFY tests/venv/pipfile/setup-py-explicit/verify tests/venv/pipfile/setup-py-explicit/verify #!/usr/bin/env python import there import dummy + +# This package should be available, as it was a dependency for dummy +import pypi_pkg_test MODIFY tests/venv/pipfile/setup-py-implicit/setup.py tests/venv/pipfile/setup-py-implicit/setup.py @@ -8,5 +8,5 @@ setup( author_email='dummy@my-email.com', description='Dummy package for testing purposes only', packages=find_packages(), - install_requires=['numpy'], + install_requires=['pypi-pkg-test==0.0.4'], ) MODIFY tests/venv/pipfile/setup-py-implicit/verify tests/venv/pipfile/setup-py-implicit/verify @@ -3,7 +3,9 @@ import there try: import dummy + import pypi_pkg_test except ImportError: + # We want an ImportError to be thrown for this test to pass pass else: - raise Exception("'dummy' shouldn't have been installed from setup.py when a Pipfile was present") + raise Exception("'dummy' and its dependency 'pypi_pkg_test' shouldn't have been installed! A Pipfile was present without explicit instructions to install the local package 'dummy'.")

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Improve Pipfile + requirements.txt test Previously we did not check that requirements.txt was ignored properly, now we do.

MODIFY tests/venv/pipfile/requirements-txt/Pipfile tests/venv/pipfile/requirements-txt/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [packages] -requests = "*" +pypi-pkg-test = "*" [dev-packages] there = "*" MODIFY tests/venv/pipfile/requirements-txt/verify tests/venv/pipfile/requirements-txt/verify #!/usr/bin/env python -import requests +import pypi_pkg_test import there + +try: + import numpy +except ImportError: + # We want an ImportError to be thrown for this test to pass + pass +else: + raise Exception("'numpy' shouldn't have been installed! It was listed in requirements.txt but not in the Pipfile that has precedence.")

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Optimize Pipfile + environment.yml test Why install a big package when we can install a trivial one?

MODIFY tests/venv/pipfile/environment-yml/environment.yml tests/venv/pipfile/environment-yml/environment.yml dependencies: - - numpy + - pip: + - pypi-pkg-test MODIFY tests/venv/pipfile/environment-yml/verify tests/venv/pipfile/environment-yml/verify #!/usr/bin/env python -import numpy +import pypi_pkg_test

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Add Pipfile + runtime.txt test

ADD tests/venv/pipfile/py36/Pipfile +[[source]] +url = "https://pypi.python.org/simple" +verify_ssl = true +name = "pypi" + +[packages] +pypi-pkg-test = "*" + +[dev-packages] +there = "*" + +[requires] +python_version = "3.6" ADD tests/venv/pipfile/py36/README.rst +Python - Pipfile with python_version and runtime.txt +---------------------------------------------------- + +We are ignoring the runtime.txt if there is a Pipfile or Pipfile.lock available. +And since `python_version = "3.6"` in the Pipfile, the `python-3.7` in +runtime.txt should be ignored. Is it? ADD tests/venv/pipfile/py36/runtime.txt +python-3.7 \ No newline at end of file ADD tests/venv/pipfile/py36/verify +#!/usr/bin/env python +import sys + +import pypi_pkg_test +import there + +print(sys.version_info) +assert sys.version_info[:2] == (3, 6)

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Add Pipfile.lock to py36 test

ADD tests/venv/pipfile/py36/Pipfile.lock +{ + "_meta": { + "hash": { + "sha256": "6cdb6013c1cba848c7d9070f8cdac089ce88c98f2910dd08ac98acce77811cb7" + }, + "pipfile-spec": 6, + "requires": { + "python_version": "3.6" + }, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.python.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "pypi-pkg-test": { + "hashes": [ + "sha256:3bc6d0d3d671f5da379eb53cc13ecbb97ce66b1d11916ea2035f6f738b963cc3", + "sha256:ae89e01320aa248e9b626218ecc04c0fb4ae0b3b2a7895404277b488961edc25" + ], + "index": "pypi", + "version": "==0.0.4" + } + }, + "develop": { + "there": { + "hashes": [ + "sha256:812638ab3683286bf677f273dd6658de93ebbc99fb74ef2548dc8c045d34e8a6", + "sha256:a65e4b050b14a57ede8bb852c36eb61f0e9d9e1352039d2f9723f8d0601e146a" + ], + "index": "pypi", + "version": "==0.0.9" + } + } +}

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Fix Pipfile + binder-folder support

MODIFY repo2docker/buildpacks/python/__init__.py repo2docker/buildpacks/python/__init__.py @@ -87,6 +87,7 @@ class PythonBuildPack(CondaBuildPack): pipfile = self.binder_path('Pipfile') pipfile_lock = self.binder_path('Pipfile.lock') if os.path.exists(pipfile_lock) or os.path.exists(pipfile): + working_directory = 'binder' if os.path.exists('binder') else '.' assemble_scripts.append(( '${NB_USER}', 'pip install pipenv' @@ -94,11 +95,11 @@ class PythonBuildPack(CondaBuildPack): if not os.path.exists(pipfile_lock): assemble_scripts.append(( '${NB_USER}', - '{} lock --python {}'.format(pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') + '(cd {} && {} lock --python {})'.format(working_directory, pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') )) assemble_scripts.append(( '${NB_USER}', - '{} install --ignore-pipfile --deploy --system --dev --python {}'.format(pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') + '(cd {} && {} install --ignore-pipfile --deploy --system --dev --python {})'.format(working_directory, pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') )) else: # KERNEL_PYTHON_PREFIX is the env with the kernel,

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invoke start script from our entrypoint rather than replacing our entrypoint

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -154,12 +154,12 @@ RUN ./{{ s }} # Add start script {% if start_script is not none -%} -RUN chmod +x "{{ start_script }}" -ENTRYPOINT ["{{ start_script }}"] -{% else %} +ENV R2D_ENTRYPOINT "{{ start_script }}" +{% endif -%} + +# Add entrypoint COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"] -{% endif -%} # Specify the default command to run CMD ["jupyter", "notebook", "--ip", "0.0.0.0"] MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint # lightest possible entrypoint that ensures that # we use a login shell to get a fully configured shell environment # (e.g. sourcing /etc/profile.d, ~/.bashrc, and friends) +if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then + exec "$R2D_ENTRYPOINT" "$@" +else exec "$@" +fi

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env is a prefix now

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -183,7 +183,7 @@ class CondaBuildPack(BaseImage): r""" conda env update -p {0} -f "{1}" && \ conda clean -tipsy && \ - conda list -n {0} && \ + conda list -p {0} && \ rm -rf /srv/conda/pkgs """.format(env_prefix, environment_yml) ))

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verify conda activation (and thereby entrypoint) in tests/conda/simple use pytest for better error reporting

MODIFY tests/conda/simple/environment.yml tests/conda/simple/environment.yml dependencies: - numpy + - pytest MODIFY tests/conda/simple/verify tests/conda/simple/verify -#!/usr/bin/env python -import sys - -assert sys.version_info[:2] == (3, 7), sys.version - -import numpy +#!/bin/sh +pytest -v ./verify.py ADD tests/conda/simple/verify.py +#!/usr/bin/env python +import os +import sys + +def test_sys_version(): + assert sys.version_info[:2] == (3, 7) + +def test_numpy(): + import numpy + +def test_conda_activated(): + assert os.environ.get("CONDA_PREFIX") == os.environ["NB_PYTHON_PREFIX"], dict(os.environ)

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update some tests with new expectations conda is not importable in the frontmost python sys.executable is in $NB_PYTHON_PREFIX (this was true before, but it's value has changed)

MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify #!/usr/bin/env python import sys +from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version +out = check_output(['conda', '--version']).decode('utf8').strip() +assert out == 'conda 4.5.11', out + import numpy -import conda -assert conda.__version__ == '4.5.11', conda.__version__ MODIFY tests/conda/repo-path/verify tests/conda/repo-path/verify @@ -3,7 +3,7 @@ import sys import os # Python should still be in /srv/conda -assert sys.executable == '/srv/conda/bin/python' +assert sys.executable == os.path.join(os.environ['NB_PYTHON_PREFIX'], 'bin', 'python') # Repo should be in /srv/repo assert os.path.exists('/srv/repo/verify') MODIFY tests/conda/simple-py2/verify tests/conda/simple-py2/verify @@ -13,7 +13,7 @@ assert sorted(specs) == ['python2', 'python3'], specs.keys() import json from subprocess import check_output envs = json.loads(check_output(['conda', 'env', 'list', '--json']).decode('utf8')) -assert envs == {'envs': ['/srv/conda', '/srv/conda/envs/kernel']}, envs +assert envs == {'envs': ['/srv/conda', '/srv/conda/envs/kernel', '/srv/conda/envs/notebook']}, envs pkgs = json.loads(check_output(['conda', 'list', '-n', 'kernel', '--json']).decode('utf8')) pkg_names = [pkg['name'] for pkg in pkgs]

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install python2 kernelspec into notebook env like other things, this was always the right thing to do, but more important now that notebook prefix is not the same as CONDA_DIR

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -59,8 +59,8 @@ if [[ -f /tmp/kernel-environment.yml ]]; then cat /tmp/kernel-environment.yml conda env create -p ${KERNEL_PYTHON_PREFIX} -f /tmp/kernel-environment.yml - ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${CONDA_DIR}" - echo '' > ${KERNEL_PYTHON_PREFIX}/envs/kernel/conda-meta/history + ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}" + echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history conda list -p ${KERNEL_PYTHON_PREFIX} fi

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repo-path verifies conda prefix

MODIFY tests/conda/repo-path/verify tests/conda/repo-path/verify import sys import os -# Python should still be in /srv/conda -assert sys.executable == os.path.join(os.environ['NB_PYTHON_PREFIX'], 'bin', 'python') +# conda should still be in /srv/conda +# and Python should still be in $NB_PYTHON_PREFIX +assert sys.executable == os.path.join(os.environ['NB_PYTHON_PREFIX'], 'bin', 'python'), sys.executable +assert sys.executable.startswith("/srv/conda/"), sys.executable # Repo should be in /srv/repo assert os.path.exists('/srv/repo/verify')

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miniconda is 4.6.14

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -13,7 +13,7 @@ New features :user:`davidanthoff` - Set JULIA_PROJECT globally, so that every julia instance starts with the julia environment activated in :pr:`612` by :user:`davidanthoff`. -- Update Miniconda version to 4.5.12 and Conda version to 4.6.14 in :pr:`637` by +- Update Miniconda version to 4.6.14 and Conda version to 4.6.14 in :pr:`637` by :user:`jhamman` - Install notebook into `notebook` env instead of `root`. Activate conda environments and shell integration via ENTRYPOINT MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,6 +5,6 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(['conda', '--version']).decode('utf8').strip() -assert out == 'conda 4.5.11', out +assert out == 'conda 4.6.14', out import numpy

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Fix handling of memory limit command line argument If a string of only numerals is passed as argument we assume it should be converted to an integer and specifies a size in bytes.

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -299,6 +299,11 @@ def make_r2d(argv=None): r2d.user_name = args.user_name if args.build_memory_limit: + # if the string only contains numerals we assume it should be an int + # and specifies a size inn bytes + if args.build_memory_limit.isnumeric(): + r2d.build_memory_limit = int(args.build_memory_limit) + else: r2d.build_memory_limit = args.build_memory_limit if args.environment and not r2d.run:

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fix missing ()

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -84,7 +84,7 @@ class RBuildPack(PythonBuildPack): return True description_R = 'DESCRIPTION' - if (not self.binder_dir and os.path.exists(description_R) + if ((not self.binder_dir and os.path.exists(description_R)) or 'r' in self.stencila_contexts): if not self.checkpoint_date: # no R snapshot date set through runtime.txt

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Add html comments to bug report

MODIFY .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/bug_report.md @@ -6,21 +6,32 @@ labels: '' assignees: '' --- + -**Describe the bug** -A clear and concise description of what the bug is. +### Bug description + + +#### Expected behaviour + + +#### Actual behaviour + + +### How to reproduce + -**To Reproduce** -Steps to reproduce the behaviour: 1. Go to '...' 2. Click on '....' 3. Scroll down to '....' 4. See error -**Expected behaviour** -A clear and concise description of what you expected to happen. +### Your personal set up + -**Versions (please complete the following information):** - OS: [e.g. linux, OSX] - - Docker version: `docker version` - - repo2docker version `repo2docker --version` + - Docker version: `docker version`  + - repo2docker version `repo2docker --version`  +

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Make html comments all on one long line

MODIFY .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/bug_report.md @@ -6,8 +6,7 @@ labels: '' assignees: '' --- - + ### Bug description  @@ -27,9 +26,7 @@ issue, but you can delete them once you've read them if you prefer! --> 4. See error ### Your personal set up - + - OS: [e.g. linux, OSX] - Docker version: `docker version`

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clarify that only one of binder and .binder can be used at once

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -72,14 +72,14 @@ specify the ``branch-name`` or ``commit-hash``. For example:: Where to put configuration files ================================ -``repo2docker`` will look for configuration files in either: +``repo2docker`` will look for configuration files in: * A folder named ``binder/`` in the root of the repository. * A folder named ``.binder/`` in the root of the repository. * The root directory of the repository. -If either the folder ``binder/`` or ``.binder/`` is located at the top level of -the repository, only configuration files in that folder will be considered. +`repo2docker` searches for these folders in order (``binder/``, ``.binder/``, +root). Only configuration files in the first identified folder are considered. Check the complete list of :ref:`configuration files <config-files>` supported by ``repo2docker`` to see how to configure the build process.

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add missing break

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -419,8 +419,9 @@ class BuildPack: def binder_dir(self): if self._binder_dir is None: for dirname in ['binder', '.binder']: - if os.path.exists(dirname): + if os.path.isdir(dirname): self._binder_dir = dirname + break self._binder_dir = '' return self._binder_dir

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error if both binder and .binder dirs exist

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -189,7 +189,6 @@ class BuildPack: self.log = logging.getLogger('repo2docker') self.appendix = '' self.labels = {} - self._binder_dir = None if sys.platform.startswith('win'): self.log.warning("Windows environment detected. Note that Windows " "support is experimental in repo2docker.") @@ -417,13 +416,20 @@ class BuildPack: @property def binder_dir(self): - if self._binder_dir is None: - for dirname in ['binder', '.binder']: - if os.path.isdir(dirname): - self._binder_dir = dirname - break - self._binder_dir = '' - return self._binder_dir + has_binder = os.path.isdir("binder") + has_dotbinder = os.path.isdir(".binder") + + if has_binder and has_dotbinder: + raise RuntimeError( + "The repository contains both a 'binder' and a '.binder' " + "directory. However they are exclusive.") + + if has_dotbinder: + return ".binder" + elif has_binder: + return "binder" + else: + return "" def binder_path(self, path): """Locate a file"""

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fix bash spacing

MODIFY repo2docker/buildpacks/nix/nix-shell-wrapper repo2docker/buildpacks/nix/nix-shell-wrapper @@ -9,7 +9,7 @@ _term() { trap _term SIGTERM # find binder sub-directory (if present) -for dir in "./binder" "./.binder"; do +for dir in "./.binder" "./binder"; do if [ -e $dir ]; then binder_dir=$dir fi

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Reword comment and remove thank you prompt

MODIFY .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/feature_request.md @@ -17,17 +17,13 @@ assignees: '' ### Who would use this feature? - + ### How much effort will adding it take? - + ### Who can do this work?  - -### Thank you maintainers! - -

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fix up nix-shell-wrapper for .binder feature

MODIFY repo2docker/buildpacks/nix/nix-shell-wrapper repo2docker/buildpacks/nix/nix-shell-wrapper @@ -8,16 +8,25 @@ _term() { trap _term SIGTERM +# if there is a binder/ sub-directory it takes precedence +# files outside it are ignored # find binder sub-directory (if present) -for dir in "./.binder" "./binder"; do +binder_dir="./" +for dir in "./binder" "./.binder" ; do if [ -e $dir ]; then binder_dir=$dir + break fi done -# if there is a binder/ sub-directory it takes precedence -# files outside it are ignored -if [ -z $binder_dir ]; then +# raise error if both binder and .binder are found +if [[ -d "./binder" && -d "./.binder" ]]; then + echo "Error: Found both binder and .binder directories." + exit 1 +fi + +echo "binder_dir is: $binder_dir" + nixpath="$binder_dir/default.nix"; if [ -f $binder_dir/start ]; then chmod u+x $binder_dir/start @@ -32,15 +41,6 @@ if [ -z $binder_dir ]; then else nix-shell $nixpath --command "$*" & fi -else - nixpath="./default.nix"; - if [ -f ./start ]; then - chmod u+x ./start - nix-shell $nixpath --command "./start $*" & - else - nix-shell $nixpath --command "$*" & - fi -fi PID=$! wait "$PID"

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Update Julia tests for new conda env path

MODIFY tests/julia/julia_version-1.0.2/verify tests/julia/julia_version-1.0.2/verify @@ -17,7 +17,7 @@ end # Verify that kernels are not installed in home directory (issue #620) try using IJulia - @assert IJulia.kerneldir() == "/srv/conda/share/jupyter/kernels" + @assert IJulia.kerneldir() == ENV["NB_PYTHON_PREFIX"] * "/share/jupyter/kernels" catch exit(1) end MODIFY tests/julia/julia_version-default/verify tests/julia/julia_version-default/verify @@ -17,7 +17,7 @@ end # Verify that kernels are not installed in home directory (issue #620) try using IJulia - @assert IJulia.kerneldir() == "/srv/conda/share/jupyter/kernels" + @assert IJulia.kerneldir() == ENV["NB_PYTHON_PREFIX"] * "/share/jupyter/kernels" catch exit(1) end

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Update docs/source/contributing/contributing.md

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -22,6 +22,12 @@ There are many ways to contribute to repo2docker: We know that there are lots of ways to extend repo2docker! If you're interested in adding a feature then please open a [feature request](https://github.com/jupyter/repo2docker/issues/new?template=feature_request.md). That issue template will ask you a few questions described in detail below. +* **Review someone's Pull Request.** + Whenever somebody proposes changes to the repo2docker codebase, the community reviews + the changes, and provides feedback, edits, and suggestions. Check out the + [open pull requests](https://github.com/jupyter/repo2docker/pulls?q=is%3Apr+is%3Aopen+sort%3Aupdated-desc) + and provide feedback that helps improve the PR and get it merged. Please keep your + feedback positive and constructive! * **Tell people about repo2docker.** As we said above, repo2docker is built by and for its community. If you know anyone who would like to use repo2docker, please tell them about the project!

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add unit tests for binder dir

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -7,6 +7,7 @@ from .app import Repo2Docker from . import __version__ from .utils import validate_and_generate_port_mapping, is_valid_docker_image_name + def validate_image_name(image_name): """ Validate image_name read by argparse ADD tests/unit/test_binder_dir.py +import os + +import pytest + +from repo2docker import buildpacks + + +@pytest.mark.parametrize("binder_dir", ['.binder', 'binder']) +def test_binder_dir_property(tmpdir, binder_dir): + tmpdir.chdir() + os.mkdir(binder_dir) + + bp = buildpacks.BuildPack() + assert binder_dir in bp.binder_dir + assert bp.binder_path('foo.yaml') == os.path.join(binder_dir, 'foo.yaml') + + +def test_root_binder_dir(tmpdir): + tmpdir.chdir() + bp = buildpacks.BuildPack() + assert bp.binder_dir == '' + + +def test_exclusive_binder_dir(tmpdir): + tmpdir.chdir() + os.mkdir('./binder') + os.mkdir('./.binder') + + bp = buildpacks.BuildPack() + with pytest.raises(RuntimeError): + _ = bp.binder_dir

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Add test for integral --build-memory-limit

MODIFY tests/unit/test_args.py tests/unit/test_args.py @@ -40,6 +40,17 @@ def test_dry_run(): assert not r2d.run assert not r2d.push + +def test_mem_limit(): + """ + Test various ways of passing --build-memory-limit + """ + r2d = make_r2d(['--build-memory-limit', '1024', '.']) + assert int(r2d.build_memory_limit) == 1024 + + r2d = make_r2d(['--build-memory-limit', '3K', '.']) + assert int(r2d.build_memory_limit) == 1024 * 3 + def test_run_required(): """ Test all the things that should fail if we pass in --no-run

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Remove the conda package cache as we can't hardlink to it

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -69,6 +69,7 @@ fi # Clean things out! conda clean -tipsy +rm -rf /srv/conda/pkgs # Remove the big installer so we don't increase docker image size too much rm ${INSTALLER_PATH}

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Remove pip cache in root's home directory

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -73,6 +73,8 @@ rm -rf /srv/conda/pkgs # Remove the big installer so we don't increase docker image size too much rm ${INSTALLER_PATH} +# Remove pip cache created as part of installing miniconda +rm -rf /root/.cache chown -R $NB_USER:$NB_USER ${CONDA_DIR}

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Use `-f --all` for conda clean up

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -182,9 +182,8 @@ class CondaBuildPack(BaseImage): '${NB_USER}', r""" conda env update -p {0} -f "{1}" && \ - conda clean -tipsy && \ - conda list -p {0} && \ - rm -rf /srv/conda/pkgs + conda clean --all -f -y && \ + conda list -p {0} """.format(env_prefix, environment_yml) )) return super().get_assemble_scripts() + assembly_scripts MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -68,12 +68,12 @@ if [[ -f /tmp/kernel-environment.yml ]]; then fi # Clean things out! -conda clean -tipsy -rm -rf /srv/conda/pkgs +conda clean --all -f -y # Remove the big installer so we don't increase docker image size too much rm ${INSTALLER_PATH} -# Remove pip cache created as part of installing miniconda + +# Remove the pip cache created as part of installing miniconda rm -rf /root/.cache chown -R $NB_USER:$NB_USER ${CONDA_DIR}

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Update change log in preparation for releasing v0.9.0

MODIFY docs/source/changelog.rst docs/source/changelog.rst Changelog ========= -Version 0.x.x +Version 0.9.0 ============= Release date: TBD @@ -20,6 +20,9 @@ New features in :pr:`651` by :user:`minrk` - Support for `.binder` directory in addition to `binder` directory for location of configuration files, in :pr:`653` by :user:`jhamman`. +- Updated contributor guide and issue templates for bugs, feature requests, + and support questions in :pr:`654` and :pr:`655` by :user:`KirstieJane` and + :user:`betatim`. API changes ----------- @@ -34,9 +37,14 @@ Bug fixes buildpack in :pr:`633` by :user:`betatim`. - Update to version 5.7.6 of the `notebook` package used in all environments in :pr:`628` by :user:`betatim`. +- Update to version 5.7.8 of the `notebook` package and version 2.0.12 of + `nteract-on-jupyter` in :pr:`650` by :user:`betatim`. - Switch to newer version of jupyter-server-proxy to fix websocket handling in :pr:`646` by :user:`betatim`. -- Update to pip v19.0.3 in :pr:`647` by :user:`betatim`. +- Update to pip version 19.0.3 in :pr:`647` by :user:`betatim`. +- Ensure ENTRYPOINT is an absolute path in :pr:`657` by :user:`yuvipanda`. +- Fix handling of `--build-memory-limit` values without a postfix in :pr:`652` + by :user:`betatim`. Version 0.8.0

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Mention the invention of the REES in the change log

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -23,6 +23,9 @@ New features - Updated contributor guide and issue templates for bugs, feature requests, and support questions in :pr:`654` and :pr:`655` by :user:`KirstieJane` and :user:`betatim`. +- Create a page naming and describing the "Reproducible Execution + Environment Specification" (the specification used by repo2docker) + in :pr:`662` by :user:`choldgraf`. API changes -----------

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bumping release date

MODIFY docs/source/changelog.rst docs/source/changelog.rst Changelog ========= -Version 0.9.0 + +Version x.x.x ============= Release date: TBD +New features +------------ + +API changes +----------- + +Bug fixes +--------- + + +Version 0.9.0 +============= + +Release date: 2019-05-05 + New features ------------ - Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files in :pr:`595` by

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Fix memory limits set for container image builds

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -523,13 +523,17 @@ class BuildPack: tar.close() tarf.seek(0) + # If you work on this bit of code check the corresponding code in + # buildpacks/docker.py where it is duplicated + limits = {} + if memory_limit: + # We'd like to always disable swap but all we can do is set the + # total amount. This means we only limit it when the caller set + # a memory limit limits = { - # Always disable memory swap for building, since mostly - # nothing good can come of that. - 'memswap': -1 + 'memory': memory_limit, + 'memswap': memory_limit + 1 } - if memory_limit: - limits['memory'] = memory_limit build_kwargs = dict( fileobj=tarf, MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py @@ -21,13 +21,17 @@ class DockerBuildPack(BuildPack): def build(self, client, image_spec, memory_limit, build_args, cache_from, extra_build_kwargs): """Build a Docker image based on the Dockerfile in the source repo.""" + # If you work on this bit of code check the corresponding code in + # buildpacks/base.py where it is duplicated + limits = {} + if memory_limit: + # We'd like to always disable swap but all we can do is set the + # total amount. This means we onnly limit it when the caller set + # a memory limit limits = { - # Always disable memory swap for building, since mostly - # nothing good can come of that. - 'memswap': -1 + 'memory': memory_limit, + 'memswap': memory_limit + 1 } - if memory_limit: - limits['memory'] = memory_limit build_kwargs = dict( path=os.getcwd(),

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Swap limit doesn't have to be bigger than memory limit

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -535,7 +535,7 @@ class BuildPack: # a memory limit limits = { 'memory': memory_limit, - 'memswap': memory_limit + 1 + 'memswap': memory_limit } build_kwargs = dict( MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py @@ -33,7 +33,7 @@ class DockerBuildPack(BuildPack): # a memory limit limits = { 'memory': memory_limit, - 'memswap': memory_limit + 1 + 'memswap': memory_limit, } build_kwargs = dict(

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Clarify comment around memswap & memory

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -530,9 +530,10 @@ class BuildPack: "integer but is '{}'".format(type(memory_limit))) limits = {} if memory_limit: - # We'd like to always disable swap but all we can do is set the - # total amount. This means we only limit it when the caller set - # a memory limit + # We want to always disable swap. Docker expects `memswap` to + # be total allowable memory, *including* swap - while `memory` + # points to non-swap memory. We set both values to the same so + # we use no swap. limits = { 'memory': memory_limit, 'memswap': memory_limit MODIFY repo2docker/buildpacks/docker.py repo2docker/buildpacks/docker.py @@ -28,9 +28,10 @@ class DockerBuildPack(BuildPack): "integer but is '{}'".format(type(memory_limit))) limits = {} if memory_limit: - # We'd like to always disable swap but all we can do is set the - # total amount. This means we onnly limit it when the caller set - # a memory limit + # We want to always disable swap. Docker expects `memswap` to + # be total allowable memory, *including* swap - while `memory` + # points to non-swap memory. We set both values to the same so + # we use no swap. limits = { 'memory': memory_limit, 'memswap': memory_limit,

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extract pipfile: add to ordered list

MODIFY repo2docker/app.py repo2docker/app.py @@ -30,8 +30,15 @@ from traitlets.config import Application from . import __version__ from .buildpacks import ( - PythonBuildPack, DockerBuildPack, LegacyBinderDockerBuildPack, - CondaBuildPack, JuliaProjectTomlBuildPack, JuliaRequireBuildPack, RBuildPack, NixBuildPack + CondaBuildPack, + DockerBuildPack, + JuliaProjectTomlBuildPack, + JuliaRequireBuildPack, + LegacyBinderDockerBuildPack, + NixBuildPack, + PipfileBuildPack, + PythonBuildPack, + RBuildPack, ) from . import contentproviders from .utils import ByteSpecification, chdir @@ -91,6 +98,7 @@ class Repo2Docker(Application): NixBuildPack, RBuildPack, CondaBuildPack, + PipfileBuildPack, PythonBuildPack, ], config=True, MODIFY repo2docker/buildpacks/__init__.py repo2docker/buildpacks/__init__.py from .base import BuildPack, BaseImage from .python import PythonBuildPack +from .pipfile import PipfileBuildPack from .conda import CondaBuildPack from .julia import JuliaProjectTomlBuildPack from .julia import JuliaRequireBuildPack

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extract pipfile: get binder_dir right finally While trying to update the buildpack for changes in the PR that added support for using a .binder directory I regressed to faulty logic. This PR fixes that, adds some comments to avoid it, and get's things right enough to manage to get the tests to succeed.

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -84,25 +84,25 @@ class PipfileBuildPack(CondaBuildPack): # install Pipfile.lock or fallback to installing Pipfile pipenv = '${KERNEL_PYTHON_PREFIX}/bin/pipenv' + python = '${KERNEL_PYTHON_PREFIX}/bin/python' pipfile = self.binder_path('Pipfile') pipfile_lock = self.binder_path('Pipfile.lock') - working_directory = 'binder' if os.path.exists('binder') else '.' + working_directory = self.binder_dir or '.' assemble_scripts.append(( '${NB_USER}', 'pip install pipenv' )) - if os.path.exists(pipfile_lock): + # if Pipfile.lock isn't found, Pipfile is used to create one + if not os.path.exists(pipfile_lock): assemble_scripts.append(( '${NB_USER}', - '(cd {} && {} install --ignore-pipfile --deploy --system --dev --python {})'.format(working_directory, pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') + '(cd {} && {} lock --python {})'.format(working_directory, pipenv, python) )) - elif os.path.exists(pipfile): + # install Pipfile.lock assemble_scripts.append(( '${NB_USER}', - '(cd {} && {} lock --python {})'.format(working_directory, pipenv, '${KERNEL_PYTHON_PREFIX}/bin/python') + '(cd {} && {} install --ignore-pipfile --deploy --system --dev --python {})'.format(working_directory, pipenv, python) )) - else: - raise Exception("Neither Pipfile.lock or Pipfile was found but assumed to be available.") return assemble_scripts

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Test Pipfile in binder-dir with Setup.py

ADD tests/pipfile/setup-py-explicit-in-binder-dir/.binder/Pipfile +[[source]] +url = "https://pypi.python.org/simple" +verify_ssl = true +name = "pypi" + +[packages] +there = "*" +dummy = {path="..", editable=true} ADD tests/pipfile/setup-py-explicit-in-binder-dir/README.rst +Python - Pipfile + setup.py +--------------------------- + +The Pipfile asked the local package in the parent directory to be installed with +``setup.py``, was it? ADD tests/pipfile/setup-py-explicit-in-binder-dir/dummy/__init__.py +def dummy(): + pass ADD tests/pipfile/setup-py-explicit-in-binder-dir/setup.py +from setuptools import setup, find_packages + +setup( + name='Dummy', + version='1.0.0', + url='https://git-place.org/dummy/dummy.git', + author='Dummy Name', + author_email='dummy@my-email.com', + description='Dummy package for testing purposes only', + packages=find_packages(), + install_requires=['pypi-pkg-test==0.0.4'], +) ADD tests/pipfile/setup-py-explicit-in-binder-dir/verify +#!/usr/bin/env python +import there +import dummy + +# This package should be available, as it was a dependency for dummy +import pypi_pkg_test

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Use getpass instead of pwd to fetch username getpass is available onn windows as well as unix, whereas pwd is not available on windows.

MODIFY repo2docker/app.py repo2docker/app.py @@ -7,13 +7,12 @@ Usage: python -m repo2docker https://github.com/you/your-repo """ -import argparse import errno import json import sys import logging import os -import pwd +import getpass import shutil import tempfile import time @@ -213,7 +212,7 @@ class Repo2Docker(Application): """ Default user_name to current running user. """ - return pwd.getpwuid(os.getuid()).pw_name + return getpass.getuser() appendix = Unicode( config=True,

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Add test that default username is picked

MODIFY repo2docker/__init__.py repo2docker/__init__.py from ._version import get_versions __version__ = get_versions()['version'] del get_versions + +from .app import Repo2Docker MODIFY tests/unit/test_users.py tests/unit/test_users.py @@ -5,6 +5,20 @@ import os import subprocess import tempfile import time +from unittest import mock + +from repo2docker import Repo2Docker + + +def test_automatic_username_deduction(): + # check we pickup the right username + with mock.patch('os.environ') as mock_env: + expected = 'someusername' + mock_env.get.return_value = expected + + r2d = Repo2Docker() + assert r2d.user_name == expected + def test_user(): """

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set CONDA_DEFAULT_ENV so that `conda install` commands affect the kernel environment instead of the base env This should preserve `conda install` behavior for Dockerfiles that inherit from r2d images. This behavior is already managed by the ENTRYPOINT which properly activates the env.

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -36,6 +36,13 @@ class CondaBuildPack(BaseImage): env.append(('KERNEL_PYTHON_PREFIX', '${NB_PYTHON_PREFIX}')) return env + def get_env(self): + """Make kernel env the default for `conda install`""" + env = super().get_env() + [ + ('CONDA_DEFAULT_ENV', '${KERNEL_PYTHON_PREFIX}'), + ] + return env + def get_path(self): """Return paths (including conda environment path) to be added to the PATH environment variable.

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test `conda install` in the default env in postBuild

ADD tests/conda/default-env/postBuild +#!/bin/bash +# install pytest with conda in the default env (should be $KERNEL_PYTHON_PREFIX) +conda install -yq pytest +# install there with pip (should be the same) +pip install there ADD tests/conda/default-env/verify +#!/bin/sh +pytest -v ./verify.py ADD tests/conda/default-env/verify.py +#!/usr/bin/env python +import os +import sys + + +def test_sys_prefix(): + # verify that pytest was installed in the notebook env + assert sys.prefix == os.environ["KERNEL_PYTHON_PREFIX"] + + +def test_there(): + # verify that there was installed in the notebook env + import there

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set CONDA_DEFAULT_ENV in activate script as well

MODIFY repo2docker/buildpacks/conda/activate-conda.sh repo2docker/buildpacks/conda/activate-conda.sh @@ -3,9 +3,16 @@ CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/conda.sh" test -f $CONDA_PROFILE && . $CONDA_PROFILE if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then # if the kernel is a separate env, stack them - # so both are on PATH + # so both are on PATH, notebook first conda activate ${KERNEL_PYTHON_PREFIX} conda activate --stack ${NB_PYTHON_PREFIX} + + # even though it's second on $PATH + # make sure CONDA_DEFAULT_ENV is the *kernel* env + # so that `!conda install PKG` installs in the kernel env + # where user packages are installed, not the notebook env + # which only contains UI when the two are different + export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}" else conda activate ${NB_PYTHON_PREFIX} fi

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Update docstrings in Zenodo provider

MODIFY repo2docker/contentproviders/zenodo.py repo2docker/contentproviders/zenodo.py @@ -15,6 +15,7 @@ class Zenodo(ContentProvider): """Provide contents of a Zenodo deposit.""" def detect(self, doi, ref=None, extra_args=None): + """Trigger this provider for things that resolve to a Zenodo record""" doi = doi.lower() # 10.5281 is the Zenodo DOI prefix if doi.startswith("10.5281/"): @@ -36,6 +37,7 @@ class Zenodo(ContentProvider): return {"record": self.record_id} def fetch(self, spec, output_dir, yield_output=False): + """Fetch and unpack a Zenodo record""" record_id = spec["record"] yield "Fetching Zenodo record {}.\n".format(record_id) @@ -93,7 +95,5 @@ class Zenodo(ContentProvider): @property def content_id(self): - """A unique ID to represent the version of the content. - Uses the first seven characters of the git commit ID of the repository. - """ + """The Zenodo record ID as the content of a record is immutable""" return self.record_id

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Add comment about supporting Zenodo instances not at zenodo.org

MODIFY repo2docker/contentproviders/zenodo.py repo2docker/contentproviders/zenodo.py @@ -16,6 +16,10 @@ class Zenodo(ContentProvider): def detect(self, doi, ref=None, extra_args=None): """Trigger this provider for things that resolve to a Zenodo record""" + # To support Zenodo instances not hosted at zenodo.org we need to + # start maintaining a list of known DOI prefixes and their hostname. + # We should also change to returning a complete `record_url` that + # fetch() can use instead of constructing a URL there doi = doi.lower() # 10.5281 is the Zenodo DOI prefix if doi.startswith("10.5281/"):

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Add external test for Zennodo provider

MODIFY tests/conftest.py tests/conftest.py @@ -213,11 +213,13 @@ class RemoteRepoList(pytest.File): with self.fspath.open() as f: repos = yaml.safe_load(f) for repo in repos: + args = [] + if "ref" in repo: + args += ['--ref', repo['ref']] + args += [repo['url'], + '--', + ] + shlex.split(repo['verify']) yield Repo2DockerTest( repo['name'], self, - args=[ - '--ref', repo['ref'], - repo['url'], - '--', - ] + shlex.split(repo['verify']), + args=args, ) 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 +# Zenodo record of https://github.com/mbcxqcw2/EEModel/tree/v1.03 +- name: 10.5281/zenodo.1211089 + url: 10.5281/zenodo.1211089 + verify: python2 -c 'import matplotlib'

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Run pre-commit hooks on travis

MODIFY .travis.yml .travis.yml @@ -15,21 +15,44 @@ install: - pip install dist/*.whl - pip freeze script: +- | + # run autoformat + if [[ "$REPO_TYPE" == "lint" ]]; then + pre-commit run --all-files + fi +- | + # run any of the other tests + if [[ "$REPO_TYPE" != "lint" ]]; then # cd into tests so CWD being repo2docker does not hide # possible issues with MANIFEST.in -- pushd tests; + pushd tests; if [ ${REPO_TYPE} == "r" ] || [ ${REPO_TYPE} == "stencila-r" ] || [ ${REPO_TYPE} == "stencila-py" ]; then travis_wait 30 pytest --durations 10 --cov repo2docker -v ${REPO_TYPE} || exit 1; else travis_retry pytest --durations 10 --cov repo2docker -v ${REPO_TYPE} || exit 1; fi; popd; + fi after_success: - pip install codecov - pushd tests && codecov && popd +after_failure: +- | + # point to auto-lint-fix + if [[ "$REPO_TYPE" == "lint" ]]; then + echo "You can install pre-commit hooks to automatically run formatting" + echo "on each commit with:" + echo " pre-commit install" + echo "or you can run by hand on staged files with" + echo " pre-commit run" + echo "or after-the-fact on already committed files with" + echo " pre-commit run --all-files" + fi + env: matrix: + - REPO_TYPE=lint - REPO_TYPE=unit - REPO_TYPE=base - REPO_TYPE=conda

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Add documentation for installing and using black

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -116,7 +116,7 @@ make that your current directory with `cd repo2docker`. ### Set up a local virtual environment -After cloning the repository (or your fork of the repository), you should set up an +After cloning the repository, you should set up an isolated environment to install libraries required for running / developing repo2docker. @@ -130,6 +130,7 @@ source bin/activate pip3 install -e . pip3 install -r dev-requirements.txt pip3 install -r docs/doc-requirements.txt +pip3 install black ``` This should install all the libraries required for testing & running repo2docker! @@ -145,7 +146,22 @@ pipenv install --dev This should install both the dev and docs requirements at once! -### Set up + +### Code formatting + +We use [`black`](https://black.readthedocs.io/en/stable/) as code formatter to +get a consistent layout for all the code in this project. This makes reading +the code easier. + +To format your code run `black .` in the top-level directory of this repository. +Many editors have plugins that will automatically apply black as you edit files. + +We also have a pre-commit hook setup that will check that code is formatted +according to black's style guide. You can activate it with `pre-commit install`. + +As part of our continuous integration tests we will check that code is +formatted properly and the tests will fail if this is not the case. + ### Verify that docker is installed and running

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add git-lfs needed for cloning repos with files stored in LFS

MODIFY Dockerfile Dockerfile @@ -12,8 +12,11 @@ RUN mkdir /tmp/wheelhouse \ FROM python:${PYTHON_VERSION}-slim # we do need git, though -RUN apt-get update \ - && apt-get -y install --no-install-recommends git \ +# git-lfs is in backports +ARG DEB_RELEASE=stretch +RUN echo "deb http://deb.debian.org/debian ${DEB_RELEASE}-backports main" > /etc/apt/sources.list.d/backports.list \ + && apt-get update \ + && apt-get -t ${DEB_RELEASE}-backports -y install --no-install-recommends git git-lfs \ && rm -rf /var/lib/apt/lists/* # install repo2docker

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verify lfs files

MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml - name: 10.5281/zenodo.1211089 url: 10.5281/zenodo.1211089 verify: python2 -c 'import matplotlib' +# Test that files in git-lfs are properly cloned +- name: LFS + url: https://github.com/binderhub-ci-repos/lfs + ref: 9abf54a + verify: grep "I am stored in git lfs" in-lfs.dat

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More general doi to url

MODIFY repo2docker/contentproviders/zenodo.py repo2docker/contentproviders/zenodo.py @@ -33,20 +33,10 @@ class Zenodo(ContentProvider): # Transform a DOI to a URL # If not a doi, assume we have a URL and return if is_doi(doi): - # Zenodo instances will most likely use DataCite DOIs - # Could also resolve the DOI to get the url - # Get url from DataCite doi = normalize_doi(doi) - req = Request( - "https://api.datacite.org/dois/{}".format(doi), - headers={"accept": "application/json"}, - ) - resp = self._urlopen(req) - - record = json.loads(resp.read().decode("utf-8")) - url = record["data"]["attributes"]["url"] - return url + resp = self._urlopen("https://doi.org/{}".format(doi)) + return resp.url else: return doi @@ -78,11 +68,10 @@ class Zenodo(ContentProvider): ] url = self._process_doi(doi) - resp = self._urlopen(url) - self.record_id = resp.url.rsplit("/", maxsplit=1)[1] for host in hosts: if any([url.startswith(s) for s in host["hostname"]]): + self.record_id = url.rsplit("/", maxsplit=1)[1] return {"record": self.record_id, "host": host} def fetch(self, spec, output_dir, yield_output=False):

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base docker image on alpine much lighter image

MODIFY Dockerfile Dockerfile -ARG PYTHON_VERSION=3.7 -FROM python:${PYTHON_VERSION} +ARG ALPINE_VERSION=3.9.4 +FROM alpine:${ALPINE_VERSION} + +RUN apk add --no-cache git python3 python3-dev # build wheels in first image ADD . /tmp/src RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ + && pip3 install wheel \ && pip3 wheel --no-cache-dir /tmp/src -# run with slim variant instead of full -# since we won't need compilers and friends -FROM python:${PYTHON_VERSION}-slim +FROM alpine:${ALPINE_VERSION} -# we do need git, though -# git-lfs is in backports -ARG DEB_RELEASE=stretch -RUN echo "deb http://deb.debian.org/debian ${DEB_RELEASE}-backports main" > /etc/apt/sources.list.d/backports.list \ - && apt-get update \ - && apt-get -t ${DEB_RELEASE}-backports -y install --no-install-recommends git git-lfs \ - && rm -rf /var/lib/apt/lists/* +# install python, git +RUN apk add --no-cache git git-lfs python3 # install repo2docker COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse

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Autoformatting applied

MODIFY tests/pipfile/pipfile-lock/verify tests/pipfile/pipfile-lock/verify @@ -8,4 +8,6 @@ except ImportError: # We want an ImportError to be thrown for this test to pass pass else: - raise Exception("'numpy' shouldn't have been installed! It was listed in Pipfile but not in the Pipfile.lock.") + raise Exception( + "'numpy' shouldn't have been installed! It was listed in Pipfile but not in the Pipfile.lock." + ) MODIFY tests/pipfile/requirements-txt/verify tests/pipfile/requirements-txt/verify @@ -8,4 +8,6 @@ except ImportError: # We want an ImportError to be thrown for this test to pass pass else: - raise Exception("'numpy' shouldn't have been installed! It was listed in requirements.txt but not in the Pipfile that has precedence.") + raise Exception( + "'numpy' shouldn't have been installed! It was listed in requirements.txt but not in the Pipfile that has precedence." + ) MODIFY tests/pipfile/setup-py-implicit/verify tests/pipfile/setup-py-implicit/verify @@ -8,4 +8,6 @@ except ImportError: # We want an ImportError to be thrown for this test to pass pass else: - raise Exception("'dummy' and its dependency 'pypi_pkg_test' shouldn't have been installed! A Pipfile was present without explicit instructions to install the local package 'dummy'.") + raise Exception( + "'dummy' and its dependency 'pypi_pkg_test' shouldn't have been installed! A Pipfile was present without explicit instructions to install the local package 'dummy'." + )

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Add support for julia 1.0.4 and 1.1.1

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -13,7 +13,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): # ALL EXISTING JULIA VERSIONS # Note that these must remain ordered, in order for the find_semver_match() # function to behave correctly. - all_julias = ["0.7.0", "1.0.0", "1.0.1", "1.0.2", "1.0.3", "1.1.0"] + all_julias = ["0.7.0", "1.0.0", "1.0.1", "1.0.2", "1.0.3", "1.0.4", "1.1.0", "1.1.1"] @property def julia_version(self): MODIFY repo2docker/buildpacks/julia/julia_require.py repo2docker/buildpacks/julia/julia_require.py @@ -8,8 +8,8 @@ class JuliaRequireBuildPack(PythonBuildPack): Julia build pack which uses conda and REQUIRE. """ - minor_julias = {"0.6": "0.6.4", "0.7": "0.7.0", "1.0": "1.0.3", "1.1": "1.1.0"} - major_julias = {"1": "1.1.0"} + minor_julias = {"0.6": "0.6.4", "0.7": "0.7.0", "1.0": "1.0.4", "1.1": "1.1.1"} + major_julias = {"1": "1.1.1"} @property def julia_version(self):

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Remove more files during the image build to slimdown the image

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -191,6 +191,9 @@ class CondaBuildPack(BaseImage): r""" conda env update -p {0} -f "{1}" && \ conda clean --all -f -y && \ + find ${{CONDA_DIR}} -follow -type f -name '*.a' -delete && \ + find ${{CONDA_DIR}} -follow -type f -name '*.pyc' -delete && \ + find ${{CONDA_DIR}} -follow -type f -name '*.js.map' -delete && \ conda list -p {0} """.format( env_prefix, environment_yml MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -70,6 +70,11 @@ fi # Clean things out! conda clean --all -f -y +# Remove static libaries, compiled Python byte code, JS map files +find ${CONDA_DIR} -follow -type f -name '*.a' -delete +find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete +find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete + # Remove the big installer so we don't increase docker image size too much rm ${INSTALLER_PATH}

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Switch to using -L for `find` instead of -follow

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -191,9 +191,9 @@ class CondaBuildPack(BaseImage): r""" conda env update -p {0} -f "{1}" && \ conda clean --all -f -y && \ - find ${{CONDA_DIR}} -follow -type f -name '*.a' -delete && \ - find ${{CONDA_DIR}} -follow -type f -name '*.pyc' -delete && \ - find ${{CONDA_DIR}} -follow -type f -name '*.js.map' -delete && \ + find -L ${{CONDA_DIR}} -type f -name '*.a' -delete && \ + find -L ${{CONDA_DIR}} -type f -name '*.pyc' -delete && \ + find -L ${{CONDA_DIR}} -type f -name '*.js.map' -delete && \ conda list -p {0} """.format( env_prefix, environment_yml MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -71,9 +71,9 @@ fi conda clean --all -f -y # Remove static libaries, compiled Python byte code, JS map files -find ${CONDA_DIR} -follow -type f -name '*.a' -delete -find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete -find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete +find -L ${CONDA_DIR} -type f -name '*.a' -delete +find -L ${CONDA_DIR} -type f -name '*.pyc' -delete +find -L ${CONDA_DIR} -type f -name '*.js.map' -delete # Remove the big installer so we don't increase docker image size too much rm ${INSTALLER_PATH}

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Adjust copied notes to the Pipfile buildpack

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -65,10 +65,14 @@ class PipfileBuildPack(CondaBuildPack): def get_assemble_scripts(self): """Return series of build-steps specific to this repository. """ - # If we have a runtime.txt & that's set to python-2.7, - # requirements.txt will be installed in the *kernel* env - # and requirements3.txt (if it exists) - # will be installed in the python 3 notebook server env. + # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the + # use of Python 2, Python 2.7 will be made available in the *kernel* + # environment. The notebook servers environment on the other hand + # requires Python 3 but may require something additional installed in it + # still such as `nbgitpuller`. For this purpose, a "requirements3.txt" + # file will be used to install dependencies for the notebook servers + # environment, if Python 2 had been specified for the kernel + # environment. assemble_scripts = super().get_assemble_scripts() if self.py2:

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Clarify Pipfile's use of relative paths

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -96,6 +96,9 @@ class PipfileBuildPack(CondaBuildPack): python = "${KERNEL_PYTHON_PREFIX}/bin/python" pipfile = self.binder_path("Pipfile") pipfile_lock = self.binder_path("Pipfile.lock") + # let pipenv work relative to the dir that has the Pipfile that can + # contain relative references such as: + # my_package = {path=".", editable=true} working_directory = self.binder_dir or "." assemble_scripts.append(("${NB_USER}", "pip install pipenv")) # if Pipfile.lock isn't found, Pipfile is used to create one

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Fix Pipfile buildpack's docstring

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py -"""Generates Dockerfiles based on an input matrix based on Python.""" +"""Buildpack for git repos with Pipfile.lock or Pipfile within them. `pipenv` +will be used to install the dependencies but we will manually install declared +Python versions instead of using PyEnv.""" + import os import re @@ -96,8 +99,8 @@ class PipfileBuildPack(CondaBuildPack): python = "${KERNEL_PYTHON_PREFIX}/bin/python" pipfile = self.binder_path("Pipfile") pipfile_lock = self.binder_path("Pipfile.lock") - # let pipenv work relative to the dir that has the Pipfile that can - # contain relative references such as: + # let pipenv work relative to the dir that has the Pipfile, it is + # important as they can contain relative references such as: # my_package = {path=".", editable=true} working_directory = self.binder_dir or "." assemble_scripts.append(("${NB_USER}", "pip install pipenv"))

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Fix Pipfile buildpacks python version detection

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -25,11 +25,11 @@ class PipfileBuildPack(CondaBuildPack): files_to_search_in_order = [ { "path": self.binder_path("Pipfile.lock"), - "pattern": r"\s*\"python_(?:full_)?version\": \"?([0-9a-z\.]*)\"?", # ' "python_version": "3.6"' + "pattern": r"\s*[\",\']python_(?:full_)?version[\",\']: [\",\']?([0-9a-z\.]*)[\",\']?", # ' "python_version": "3.6"' }, { "path": self.binder_path("Pipfile"), - "pattern": r"python_(?:full_)?version\s*=+\s*\"?([0-9a-z\.]*)\"?", # 'python_version = "3.6"' + "pattern": r"python_(?:full_)?version\s*=+\s*[\",\']?([0-9a-z\.]*)[\",\']?", # 'python_version = "3.6"' }, { "path": self.binder_path("runtime.txt"),

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Iterate on Pipfile documentation

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -59,17 +59,16 @@ though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7. ``Pipfile`` and/or ``Pipfile.lock`` - Install a Python environment ================================================================== -``Pipfile`` and/or ``Pipfile.lock`` specifies a list of Python packages that -should be installed in your environment. ``pipenv install --dev`` will be run to -install the dependencies where the existence of a ``Pipfile.lock`` will make the -``Pipfile`` be ignored. - -.. note:: - - `pipenv <https://github.com/pypa/pipenv/>`_ and `virtualenv - <https://github.com/pypa/virtualenv/>`_ and associated ``requirements.txt`` - files are both managed by the Python Packaging Authority PyPA, where pipenv - and ``Pipfile`` and ``Pipfile.lock`` seem to be the modern solution. +`pipenv <https://github.com/pypa/pipenv/>`_ allows you to manage a virtual +environment Python dependencies. When using ``pipenv``, you end up with +``Pipfile`` and ``Pipfile.lock`` files. The lock file contains explicit details +about the packages that has been installed that met the criteria within the +``Pipfile``. + +If both ``Pipfile`` and ``Pipfile.lock`` are found by repo2docker, the former +will be ignored in favor of the lock file. Also note that these files +distinguish packages and development packages and that repo2docker will install +both kinds. .. _requirements.txt:

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Pipfile changelog entry

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -12,6 +12,8 @@ New features ------------ - Increased minimum Python version supported for running `repo2docker` itself to Python 3.5 in :pr:`684` by :user:`betatim`. +- Support for `Pipfile` and `Pipfile.lock` implemented in :pr:`649` by + :user:`consideratio`. API changes -----------

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updated link for the community edition of docker

MODIFY docs/source/install.rst docs/source/install.rst @@ -11,7 +11,7 @@ Prerequisite: Docker Install `Docker <https://www.docker.com>`_ as it is required to build Docker images. The -`Community Edition <https://www.docker.com/community-edition>`_, +`Community Edition <https://docs.docker.com/install/>`_, is available for free. Recent versions of Docker are recommended.

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Make the python environment explicit during pip install

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -88,7 +88,7 @@ class PipfileBuildPack(CondaBuildPack): assemble_scripts.append( ( "${NB_USER}", - 'pip install --no-cache-dir -r "{}"'.format( + '${{NB_PYTHON_PREFIX}}/pip install --no-cache-dir -r "{}"'.format( nb_requirements_file ), )

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Install pipenv in the kernel environ

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -105,7 +105,7 @@ class PipfileBuildPack(CondaBuildPack): working_directory = self.binder_dir or "." # install pipenv to install dependencies within Pipfile.lock or Pipfile - assemble_scripts.append(("${NB_USER}", "pip install pipenv")) + assemble_scripts.append(("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv")) # NOTES: # - Without prioritizing the PATH to KERNEL_PYTHON_PREFIX over

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Pin pipenv utilized to version: 2018.11.26

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -105,7 +105,7 @@ class PipfileBuildPack(CondaBuildPack): working_directory = self.binder_dir or "." # install pipenv to install dependencies within Pipfile.lock or Pipfile - assemble_scripts.append(("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv")) + assemble_scripts.append(("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv=2018.11.26")) # NOTES: # - Without prioritizing the PATH to KERNEL_PYTHON_PREFIX over

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Syntax typo fix

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -106,7 +106,7 @@ class PipfileBuildPack(CondaBuildPack): # install pipenv to install dependencies within Pipfile.lock or Pipfile assemble_scripts.append( - ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv=2018.11.26") + ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv==2018.11.26") ) # NOTES:

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Correct path typo and add note about '//'

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -88,7 +88,7 @@ class PipfileBuildPack(CondaBuildPack): assemble_scripts.append( ( "${NB_USER}", - '${{NB_PYTHON_PREFIX}}/pip install --no-cache-dir -r "{}"'.format( + '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format( nb_requirements_file ), ) @@ -106,7 +106,7 @@ class PipfileBuildPack(CondaBuildPack): # install pipenv to install dependencies within Pipfile.lock or Pipfile assemble_scripts.append( - ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/pip install pipenv==2018.11.26") + ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26") ) # NOTES:

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Add inline comment about '\'

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -124,6 +124,10 @@ class PipfileBuildPack(CondaBuildPack): # reproducibility. # - The `--ignore-pipfile` requires a .lock file to be around as if # there isn't, no other option remain. + # - The '\\' will is within a Python """ """ string render to a '\'. A + # Dockerfile where this later is read within, will thanks to the '\' + # let the RUN command continue on the next line. So it is only added + # to avoid forcing us to write it all on a single line. assemble_scripts.append( ( "${NB_USER}",

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Update target_repo_dir docstring See

MODIFY repo2docker/app.py repo2docker/app.py @@ -354,7 +354,8 @@ class Repo2Docker(Application): target_repo_dir = Unicode( "", help=""" - Path inside the image where contents of the repositories are copied to. + Path inside the image where contents of the repositories are copied to, + and where all the build operations (such as postBuild) happen. Defaults to ${HOME} if not set """,

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Install R packages before copying repo contents

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -291,15 +291,38 @@ class RBuildPack(PythonBuildPack): return super().get_build_scripts() + scripts - def get_assemble_scripts(self): - """ - Return series of build-steps specific to this repository. - """ - assemble_scripts = super().get_assemble_scripts() + def get_preassemble_scripts(self): + """Install contents of install.R""" + scripts = [] installR_path = self.binder_path("install.R") if os.path.exists(installR_path): - assemble_scripts += [("${NB_USER}", "Rscript %s" % installR_path)] + packages = [] + with open(installR_path) as f: + for line in f: + line = line.strip() + # skip commented out lines + if line.startswith("#"): + continue + else: + # XXX This needs a better solution for detecting which + # XXX kind of string quoting the user used/how to + # XXX escape quotes... + # using " as quote + if '"' in line: + packages.append("-e '{}'".format(line)) + # using ' as quote or no quotes + else: + packages.append('-e "{}"'.format(line)) + + package_expressions = " \\ \n".join(sorted(packages)) + scripts += [("${NB_USER}", "R --quiet %s" % package_expressions)] + + return super().get_preassemble_scripts() + scripts + + def get_assemble_scripts(self): + """Install the repository itself as a R package""" + assemble_scripts = super().get_assemble_scripts() description_R = "DESCRIPTION" if not self.binder_dir and os.path.exists(description_R):

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Remove print statement and unused import

MODIFY repo2docker/contentproviders/zenodo.py repo2docker/contentproviders/zenodo.py @@ -4,7 +4,7 @@ import shutil from os import makedirs from os import path -from urllib.request import build_opener, urlopen, Request +from urllib.request import urlopen, Request from urllib.error import HTTPError from zipfile import ZipFile, is_zipfile MODIFY repo2docker/utils.py repo2docker/utils.py @@ -422,8 +422,6 @@ doi_regexp = re.compile( def is_doi(val): """Returns None if val doesn't match pattern of a DOI. http://en.wikipedia.org/wiki/Digital_object_identifier.""" - print(type(val)) - print(val) return doi_regexp.match(val)

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Switch to binder-examples/requirements for our tests

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 -# Zenodo record of https://github.com/mbcxqcw2/EEModel/tree/v1.03 -- name: 10.5281/zenodo.1211089 - url: 10.5281/zenodo.1211089 - verify: python2 -c 'import matplotlib' +# Zenodo record of https://github.com/binder-examples/requirements +- name: 10.5281/zenodo.3242074 + url: 10.5281/zenodo.3242074 + verify: python -c 'import matplotlib' # Test that files in git-lfs are properly cloned - name: LFS url: https://github.com/binderhub-ci-repos/lfs

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