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docker.py: remove workaround for old black
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -61,10 +61,7 @@ class DockerEngine(ContainerEngine): dockerfile="", fileobj=None, path="", - # fmt: off - # black adds a trailing , but this is invalid in Python 3.5 **kwargs - # fmt: on ): return self._apiclient.build( buildargs=buildargs, @@ -102,10 +99,7 @@ class DockerEngine(ContainerEngine): publish_all_ports=False, remove=False, volumes=None, - # fmt: off - # black adds a trailing , but this is invalid in Python 3.5 **kwargs - # fmt: on ): client = docker.from_env(version="auto") container = client.containers.run(
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Add Container.wait()
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -25,6 +25,9 @@ class DockerContainer(Container): def stop(self, *, timeout=10): return self._c.stop(timeout=timeout) + def wait(self): + return self._c.wait() + @property def exitcode(self): return self._c.attrs["State"]["ExitCode"] @@ -61,7 +64,7 @@ class DockerEngine(ContainerEngine): dockerfile="", fileobj=None, path="", - **kwargs + **kwargs, ): return self._apiclient.build( buildargs=buildargs, @@ -99,7 +102,7 @@ class DockerEngine(ContainerEngine): publish_all_ports=False, remove=False, volumes=None, - **kwargs + **kwargs, ): client = docker.from_env(version="auto") container = client.containers.run( MODIFY repo2docker/engine.py repo2docker/engine.py @@ -62,6 +62,12 @@ class Container(ABC): timeout : If the container doesn't gracefully stop after this timeout kill it """ + @abstractmethod + def wait(self): + """ + Wait for the container to stop + """ + @property @abstractmethod def exitcode(self): @@ -161,7 +167,7 @@ class ContainerEngine(LoggingConfigurable): dockerfile="", fileobj=None, path="", - **kwargs + **kwargs, ): """ Build a container @@ -255,7 +261,7 @@ class ContainerEngine(LoggingConfigurable): publish_all_ports=False, remove=False, volumes={}, - **kwargs + **kwargs, ): """ Run a container
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Remove nodesource' nodejs We get node from the default JupyterLab install, since that comes from conda-forge. This was not the case when we started - we installed JupyterLab with pip. We no longer need the nodesource node. All the env vars, etc should still work!
MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -52,11 +52,6 @@ RUN groupadd \ --uid ${NB_UID} \ ${NB_USER} -RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ - DISTRO="bionic" && \ - echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \ - echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list - # Base package installs are not super interesting to users, so hide their outputs # If install fails for some reason, errors will still be printed RUN apt-get -qq update && \ @@ -247,7 +242,6 @@ class BuildPack: return { # Utils! "less", - "nodejs", "unzip", }
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Explicitly specify where npm is PATH doesn't seem to be set at this point to include the conda environment we just installed?
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -99,7 +99,7 @@ class CondaBuildPack(BaseImage): ( "${NB_USER}", r""" - npm config --global set prefix ${NPM_DIR} + ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR} """, ), ]
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Move where npm config is set
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -96,12 +96,6 @@ class CondaBuildPack(BaseImage): chown -R ${NB_USER}:${NB_USER} ${NPM_DIR} """, ), - ( - "${NB_USER}", - r""" - ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR} - """, - ), ] major_pythons = {"2": "2.7", "3": "3.7"} MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -48,6 +48,9 @@ echo "installing notebook env:" cat /tmp/environment.yml time mamba env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml +# Set NPM config +${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR} + # empty conda history file, # which seems to result in some effective pinning of packages in the initial env, # which we don't intend.
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Pin doc-requirements.txt versions Hopefully dependabot can take care of them
MODIFY docs/doc-requirements.txt docs/doc-requirements.txt # Note that there is also a Pipfile for this project if you are updating this # file do not forget to update the Pipfile accordingly -sphinx>=1.4, !=1.5.4 -recommonmark -sphinxcontrib-autoprogram -pydata-sphinx-theme +sphinx==4.0.2 +recommonmark==0.7.1 +sphinxcontrib-autoprogram==0.1.7 +pydata-sphinx-theme==0.6.3
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Remove CircleCI docs build Same as our RTD build, and the previews there are nicer
DELETE .circleci/config.yml -version: 2 -jobs: - # Define a "build_docs" job to be run with Circle - build_docs: - # This is the base environment that Circle will use - docker: - - image: circleci/python:3.8-buster - steps: - # Get our data and merge with upstream - - run: sudo apt-get update - - checkout - # Update our path - - run: echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV - # Restore cached files to speed things up - - restore_cache: - keys: - - cache-pip - - run: pip install --user -e . - # Install the packages needed to build our documentation - # This will depend on your particular package! - - run: pip install --user -r docs/doc-requirements.txt - # Cache some files for a speedup in subsequent builds - - save_cache: - key: cache-pip - paths: - - ~/.cache/pip - # Build the docs - - run: - name: Build docs to store - command: | - cd docs - make html - # Tell Circle to store the documentation output in a folder that we can access later - - store_artifacts: - path: docs/build/html/ - destination: html - -# Tell CircleCI to use this workflow when it builds the site -workflows: - version: 2 - default: - jobs: - - build_docs
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fix side-effect method name and add fixme note
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -43,8 +43,10 @@ class CondaBuildPack(BaseImage): """ if not self._nb_environment_file: - # get_build_scripts locates requirements/environment files - self.get_build_scripts() + # get_build_script_files locates requirements/environment files, + # populating the _nb_environment_file attribute and others. + # FIXME: move file detection and initialization of those attributes to its own step? + self.get_build_script_files() env = super().get_build_env() + [ ("CONDA_DIR", "${APP_BASE}/conda"),
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always unpack a single zenodo zip
MODIFY repo2docker/contentproviders/zenodo.py repo2docker/contentproviders/zenodo.py @@ -63,12 +63,11 @@ class Zenodo(DoiProvider): record = resp.json() - is_software = deep_get(record, host["type"]).lower() == "software" files = deep_get(record, host["filepath"]) only_one_file = len(files) == 1 for file_ref in files: for line in self.fetch_file( - file_ref, host, output_dir, is_software and only_one_file + file_ref, host, output_dir, unzip=only_one_file ): yield line MODIFY tests/unit/contentproviders/test_zenodo.py tests/unit/contentproviders/test_zenodo.py @@ -99,7 +99,7 @@ def test_fetch_software_from_github_archive(requests_mock): "links": {"download": "file://{}".format(zen_path)}, } ], - "metadata": {"upload_type": "software"}, + "metadata": {"upload_type": "other"}, } requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response) requests_mock.get(
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Expose `timestamps`, `since` args in Container.logs Behavior is defined as what docker does needed for avoiding duplicate log statements
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -13,8 +13,8 @@ class DockerContainer(Container): def reload(self): return self._c.reload() - def logs(self, *, stream=False): - return self._c.logs(stream=stream) + def logs(self, *, stream=False, timestamps=False, since=None): + return self._c.logs(stream=stream, timestamps=timestamps, since=since) def kill(self, *, signal="KILL"): return self._c.kill(signal=signal) MODIFY repo2docker/engine.py repo2docker/engine.py @@ -21,7 +21,7 @@ class Container(ABC): """ @abstractmethod - def logs(self, *, stream=False): + def logs(self, *, stream=False, timestamps=False, since=None): """ Get the container logs. @@ -29,6 +29,13 @@ class Container(ABC): ---------- stream : bool If `True` return an iterator over the log lines, otherwise return all logs + timestamps : bool + If `True` log lines will be prefixed with iso8601 timestamps followed by space + since : int + An integer timestamp. + Can be constructed by parsing timestamps in prefixed lines issued when `timestamps=True`. + If given, start logs from this point, + instead of from container start. Returns -------
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Rename requirements.py-3.5.txt to requirements.py-3.5.pip This is an attempt to have this file ignored by dependabot since it contains frozen dependencies
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -163,7 +163,7 @@ class CondaBuildPack(BaseImage): py_frozen_name = f"environment.py-{py_version}.lock" if os.path.exists(os.path.join(HERE, py_frozen_name)): frozen_name = py_frozen_name - pip_frozen_name = f"requirements.py-{py_version}.txt" + pip_frozen_name = f"requirements.py-{py_version}.pip" if not frozen_name: self.log.warning(f"No frozen env for {py_version}") files[ RENAME repo2docker/buildpacks/conda/requirements.py-3.5.txt repo2docker/buildpacks/conda/requirements.py-3.5.pip
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fix: workaround docker==5.0.0 not importing its dependencies
MODIFY Dockerfile Dockerfile @@ -11,6 +11,7 @@ RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ && pip3 wheel --no-cache-dir /tmp/src \ + && rm /tmp/wheelhouse/six*.whl \ && ls -l /tmp/wheelhouse FROM alpine:${ALPINE_VERSION} MODIFY setup.py setup.py @@ -57,6 +57,9 @@ setup( "requests", "ruamel.yaml>=0.15", "semver", + # six installation is a workaround of https://github.com/docker/docker-py/pull/2844. + # When removing this, also remove the "rm /tmp/wheelhouse/six*.whl" line in ./Dockerfile + "six", "toml", "traitlets", ],
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fix: avoid docker 5.0.0
MODIFY Dockerfile Dockerfile @@ -11,7 +11,6 @@ RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ && pip3 wheel --no-cache-dir /tmp/src \ - && rm /tmp/wheelhouse/six*.whl \ && ls -l /tmp/wheelhouse FROM alpine:${ALPINE_VERSION} MODIFY setup.py setup.py @@ -48,7 +48,7 @@ setup( version=versioneer.get_version(), install_requires=[ "chardet", - "docker", + "docker!=5.0.0", "entrypoints", "escapism", "iso8601", @@ -57,9 +57,6 @@ setup( "requests", "ruamel.yaml>=0.15", "semver", - # six installation is a workaround of https://github.com/docker/docker-py/pull/2844. - # When removing this, also remove the "rm /tmp/wheelhouse/six*.whl" line in ./Dockerfile - "six", "toml", "traitlets", ],
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fix: Dockerfile issue regarding six
MODIFY Dockerfile Dockerfile @@ -11,6 +11,7 @@ RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ && pip3 wheel --no-cache-dir /tmp/src \ + && rm /tmp/wheelhouse/six*.whl \ && ls -l /tmp/wheelhouse FROM alpine:${ALPINE_VERSION}
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bump environment.yml jupyter-resource-usage==0.6.0 jupyterlab==3.1.0 jupyterhub-singleuser==1.4.2 nbconvert==6.1.0 notebook==6.4.0
MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -5,9 +5,9 @@ dependencies: - pip - ipywidgets==7.6.3 - jupyter-offlinenotebook==0.2.1 - - jupyter-resource-usage==0.5.1 - - jupyterlab==3.0.7 - - jupyterhub-singleuser==1.3.0 - - nbconvert==6.0.7 - - notebook==6.2.0 + - jupyter-resource-usage==0.6.0 + - jupyterlab==3.1.0 + - jupyterhub-singleuser==1.4.2 + - nbconvert==6.1.0 + - notebook==6.4.0 - nteract_on_jupyter==2.1.3
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environment.yml: packages must support py3.6
MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -8,6 +8,8 @@ dependencies: - jupyter-resource-usage==0.6.0 - jupyterlab==3.1.0 - jupyterhub-singleuser==1.4.2 - - nbconvert==6.1.0 - - notebook==6.4.0 + # Newer versions require python 3.7 + - nbconvert==6.0.7 + # 6.4.0 conda package requires python 3.7 + - notebook==6.3.0 - nteract_on_jupyter==2.1.3
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sphinx conf.py: root_doc
MODIFY docs/source/conf.py docs/source/conf.py @@ -60,8 +60,8 @@ def setup(app): # source_suffix = ['.rst', '.md'] source_suffix = [".rst", ".md"] -# The master toctree document. -master_doc = "index" +# The root toctree document. +root_doc = master_doc = "index" # General information about the project. project = "repo2docker"
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Remove automated docker cloud hooks
MODIFY Dockerfile Dockerfile @@ -5,8 +5,7 @@ RUN apk add --no-cache git python3 python3-dev py-pip build-base # build wheels in first image ADD . /tmp/src -# restore the hooks directory so that the repository isn't marked as dirty -RUN cd /tmp/src && git clean -xfd && git checkout -- hooks && git status +RUN cd /tmp/src && git clean -xfd && git status RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ DELETE hooks/README.md -# Docker build hooks - -These define our [custom hooks for docker automated builds](https://docs.docker.com/docker-hub/builds/advanced/#custom-build-phase-hooks) DELETE hooks/post_push -#!/bin/bash - -# when building jupyter/repo2docker:main -# also push jupyter/repo2docker:1.2.3-3.abcd1234 (replace + with -) -version=$(docker run $DOCKER_REPO:$DOCKER_TAG jupyter-repo2docker --version | sed s@+@-@) -VERSION_IMAGE="$DOCKER_REPO:$version" -docker tag $DOCKER_REPO:$DOCKER_TAG "$VERSION_IMAGE" -docker push "$VERSION_IMAGE"
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Remove arm64 for now
MODIFY .github/workflows/release.yml .github/workflows/release.yml @@ -92,6 +92,6 @@ jobs: uses: docker/build-push-action@e1b7f96249f2e4c8e4ac1519b9608c0d48944a1f with: context: . - platforms: linux/amd64,linux/arm64 + platforms: linux/amd64 push: true tags: ${{ env.TAGS }}
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Switch to main
MODIFY .github/workflows/release.yml .github/workflows/release.yml @@ -46,7 +46,7 @@ jobs: steps: - name: Should we push this image to a public registry? run: | - if [ "${{ startsWith(github.ref, 'refs/tags/') || (github.ref == 'refs/heads/master') }}" = "true" ]; then + if [ "${{ startsWith(github.ref, 'refs/tags/') || (github.ref == 'refs/heads/main') }}" = "true" ]; then # Empty => Docker Hub echo "REGISTRY=" >> $GITHUB_ENV else @@ -82,8 +82,8 @@ jobs: run: | VERSION=$(python3 -c 'import versioneer; print(versioneer.get_version().replace("+", "-"))') TAGS="${{ env.REGISTRY }}jupyter/repo2docker:$VERSION" - if [ "${{ github.ref }}" == "refs/heads/master" ]; then - TAGS="$TAGS,${{ env.REGISTRY }}jupyter/repo2docker:master" + if [ "${{ github.ref }}" == "refs/heads/main" ]; then + TAGS="$TAGS,${{ env.REGISTRY }}jupyter/repo2docker:main" fi echo "TAGS=$TAGS" echo "TAGS=$TAGS" >> $GITHUB_ENV
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Typo fix utils docstring
MODIFY repo2docker/utils.py repo2docker/utils.py @@ -62,7 +62,7 @@ def execute_cmd(cmd, capture=False, **kwargs): def chdir(path): """Change working directory to `path` and restore it again - This context maanger is useful if `path` stops existing during your + This context manager is useful if `path` stops existing during your operations. """ old_dir = os.getcwd()
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__init__.py: r_version: fixed description
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -258,9 +258,9 @@ class CondaBuildPack(BaseImage): @property def r_version(self): - """Detect the Python version for a given `environment.yml` + """Detect the R version for a given `environment.yml` - Will return 'x.y' if version is found (e.g '3.6'), + Will return 'x.y.z' if version is found (e.g '4.1.1'), or a Falsy empty string '' if not found. """
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Add Docker image quay.io to README
MODIFY README.md README.md [![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](https://github.com/jupyterhub/repo2docker/actions) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) [![Contribute](https://img.shields.io/badge/I_want_to_contribute!-grey?logo=jupyter)](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html) +[![Docker Repository on Quay](https://quay.io/repository/jupyterhub/repo2docker/status "Docker Repository on Quay")](https://quay.io/repository/jupyterhub/repo2docker) `repo2docker` fetches a git repository and builds a container image based on the configuration files found in the repository. @@ -95,3 +96,8 @@ files that ``repo2docker`` can use, see the The philosophy of repo2docker is inspired by [Heroku Build Packs](https://devcenter.heroku.com/articles/buildpacks). + + +## Docker Image + +Repo2Docker can be run inside a Docker container if access to the Docker Daemon is provided, for example see [BinderHub](https://github.com/jupyterhub/binderhub). Docker images are [published to quay.io](https://quay.io/repository/jupyterhub/repo2docker). The old [Docker Hub image](https://hub.docker.com/r/jupyter/repo2docker) is no longer supported.
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Remove environment requirement from docker publish workflow This seems to prevent the workflow running in PRs
MODIFY .github/workflows/release.yml .github/workflows/release.yml @@ -38,8 +38,6 @@ jobs: env: DEFAULT_REGISTRY: quay.io IMAGE_NAME: jupyterhub/repo2docker - # Secrets are in a separate GitHub environment so only this job and branch has access - environment: quay.io services: # So that we can test this in PRs/branches
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docker workflow: Ensure $REGISTRY is printed GITHUB_ENV only takes effect on following actions
MODIFY .github/workflows/release.yml .github/workflows/release.yml @@ -50,10 +50,11 @@ jobs: - name: Should we push this image to a public registry? run: | if [ "${{ startsWith(github.ref, 'refs/tags/') || (github.ref == 'refs/heads/main') }}" = "true" ]; then - echo "REGISTRY=$DEFAULT_REGISTRY" >> $GITHUB_ENV + REGISTRY=$DEFAULT_REGISTRY else - echo "REGISTRY=localhost:5000" >> $GITHUB_ENV + REGISTRY=localhost:5000 fi + echo "REGISTRY=$REGISTRY" >> $GITHUB_ENV echo "Publishing to $REGISTRY" # versioneer requires the full git history for non-tags
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Add docker latest tag for tagged releases
MODIFY .github/workflows/release.yml .github/workflows/release.yml @@ -75,7 +75,7 @@ jobs: # Allows pushing to registry on localhost:5000 driver-opts: network=host - - name: Setup push rights to Docker Hub + - name: Setup push rights to Docker registry if: env.REGISTRY != 'localhost:5000' run: | docker login -u "${{ secrets.DOCKER_REGISTRY_USERNAME }}" -p "${{ secrets.DOCKER_REGISTRY_TOKEN }}" "${{ env.REGISTRY }}" @@ -89,6 +89,10 @@ jobs: if [ "${{ github.ref }}" == "refs/heads/main" ]; then TAGS="$TAGS,${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:main" fi + if [ "${{ startsWith(github.ref, 'refs/tags/') }}" = "true" ]; then + TAGS="$TAGS,${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest" + fi + echo "TAGS=$TAGS" echo "TAGS=$TAGS" >> $GITHUB_ENV
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Use static badge for quay.io container
MODIFY README.md README.md [![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](https://github.com/jupyterhub/repo2docker/actions) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) [![Contribute](https://img.shields.io/badge/I_want_to_contribute!-grey?logo=jupyter)](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html) -[![Docker Repository on Quay](https://quay.io/repository/jupyterhub/repo2docker/status "Docker Repository on Quay")](https://quay.io/repository/jupyterhub/repo2docker?tab=tags) +[![Docker Repository on Quay](https://img.shields.io/badge/quay.io-container-green "Docker Repository on Quay")](https://quay.io/repository/jupyterhub/repo2docker?tab=tags) `repo2docker` fetches a git repository and builds a container image based on the configuration files found in the repository.
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Container registry PRs (quay.io)
MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -8,6 +8,8 @@ Version 2021.08.0 `Full changelog <https://github.com/jupyterhub/repo2docker/compare/2021.03.0...2021.08.0>`_ +The repo2docker container image has moved to `quay.io/jupyterhub/repo2docker <https://quay.io/repository/jupyterhub/repo2docker?tab=tags>`_ + New features ------------ @@ -32,6 +34,8 @@ Bug fixes Other merged PRs ---------------- +- Update README quay.io URL, Add docker latest tag :pr:`1075` by :user:`manics` +- GitHub workflow build and push to Docker hub :pr:`1071` by :user:`manics` - Rename master branch to main :pr:`1068` by :user:`manics` - Remove Pipfile & Pipfile.lock :pr:`1054` by :user:`yuvipanda` - Remove CircleCI docs build :pr:`1053` by :user:`yuvipanda`
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Default to JupyterLab
MODIFY repo2docker/app.py repo2docker/app.py @@ -582,6 +582,7 @@ class Repo2Docker(Application): "--port", port, "--NotebookApp.custom_display_url=http://{}:{}".format(host_name, port), + "--NotebookApp.default_url=/lab", ] ports = {"%s/tcp" % port: port} else:
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Bump JupyterLab to 3.1.11
MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -6,7 +6,7 @@ dependencies: - ipywidgets==7.6.3 - jupyter-offlinenotebook==0.2.1 - jupyter-resource-usage==0.6.0 - - jupyterlab==3.1.1 + - jupyterlab==3.1.11 - jupyterhub-singleuser==1.4.2 # Newer versions require python 3.7 - nbconvert==6.0.7
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classic notebook interface
MODIFY docs/source/howto/user_interface.rst docs/source/howto/user_interface.rst @@ -25,8 +25,8 @@ or folder. To learn more about URLs in JupyterLab and Jupyter Notebook, visit `starting JupyterLab <http://jupyterlab.readthedocs.io/en/latest/getting_started/starting.html>`_. -Classic Notebook -================ +Classic Notebook Interface +========================== The classic notebook is also available without any configuration. To switch to the classic notebook,
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bump jupyterlab to 3.1.17
MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -6,7 +6,7 @@ dependencies: - ipywidgets==7.6.3 - jupyter-offlinenotebook==0.2.1 - jupyter-resource-usage==0.6.0 - - jupyterlab==3.1.11 + - jupyterlab==3.1.17 - jupyterhub-singleuser==1.4.2 # Newer versions require python 3.7 - nbconvert==6.0.7
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Add explicit support for labels build parameter
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -73,6 +73,7 @@ class DockerEngine(ContainerEngine): dockerfile="", fileobj=None, path="", + labels=None, **kwargs, ): return self._apiclient.build( @@ -87,6 +88,7 @@ class DockerEngine(ContainerEngine): dockerfile=dockerfile, fileobj=fileobj, path=path, + labels=labels, **kwargs, ) MODIFY repo2docker/engine.py repo2docker/engine.py @@ -176,6 +176,7 @@ class ContainerEngine(LoggingConfigurable): dockerfile="", fileobj=None, path="", + labels=None, **kwargs, ): """ @@ -204,6 +205,8 @@ class ContainerEngine(LoggingConfigurable): A tar file-like object containing the build context path : str path to the Dockerfile + labels : dict + Dictionary of labels to set on the image Returns -------
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Add --label command line option
MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -204,6 +204,14 @@ def get_argparser(): argparser.add_argument("--appendix", type=str, help=Repo2Docker.appendix.help) + argparser.add_argument( + "--label", + dest="labels", + action="append", + help="Extra label to set on the image, in form name=value", + default=[], + ) + argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help) argparser.add_argument( @@ -246,6 +254,13 @@ def make_r2d(argv=None): if args.appendix: r2d.appendix = args.appendix + for l in args.labels: + if "=" in l: + key, val = l.split("=", 1) + r2d.labels[key] = val + else: + r2d.labels[l] = "" + r2d.repo = args.repo r2d.ref = args.ref MODIFY repo2docker/app.py repo2docker/app.py @@ -237,6 +237,17 @@ class Repo2Docker(Application): """, ) + labels = Dict( + {}, + help=""" + Extra labels to set on the final image. + + Each Label is a key-value pair, with the key being the name of the label + and the value its value. + """, + config=True, + ) + json_logs = Bool( False, help=""" @@ -747,6 +758,8 @@ class Repo2Docker(Application): picked_buildpack.labels["repo2docker.repo"] = repo_label picked_buildpack.labels["repo2docker.ref"] = self.ref + picked_buildpack.labels.update(self.labels) + if self.dry_run: print(picked_buildpack.render()) else:
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Support R 4.1
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -77,6 +77,7 @@ class RBuildPack(PythonBuildPack): "3.6.1": "3.6.1-3bionic", "4.0": "4.0.2-1.1804.0", "4.0.2": "4.0.2-1.1804.0", + "4.1": "4.1.2-1.1804.0", } # the default if nothing is specified r_version = "3.6" MODIFY tests/r/r4/runtime.txt tests/r/r4/runtime.txt -r-4.0-2020-07-07 +r-4.1-2021-07-07 MODIFY tests/r/r4/verify tests/r/r4/verify library('ggplot2') print(version) -if (version$major != "4") { +if (version$major != "4" and as.double(version$minor) >= 1) { quit("yes", 1) }
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Quieter R builds We redirect stdout (not stderr) of apt-get update and install in most other places (check out base.py) to not clutter the output
MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -29,8 +29,8 @@ def rstudio_base_scripts(): r""" curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \ echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \ - apt-get update && \ - apt install -y /tmp/rstudio.deb && \ + apt-get update > /dev/null && \ + apt install -y /tmp/rstudio.deb > /dev/null && \ rm /tmp/rstudio.deb && \ apt-get -qq purge && \ apt-get -qq clean && \ @@ -45,7 +45,7 @@ def rstudio_base_scripts(): r""" curl --silent --location --fail {url} > {deb} && \ echo '{checksum} {deb}' | md5sum -c - && \ - dpkg -i {deb} && \ + dpkg -i {deb} > /dev/null && \ rm {deb} """.format( url=SHINY_URL, checksum=SHINY_CHECKSUM, deb="/tmp/shiny.deb" MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -258,11 +258,11 @@ class RBuildPack(PythonBuildPack): ( "root", r""" - apt-get update && \ + apt-get update > /dev/null && \ apt-get install --yes r-base={R_version} \ r-base-dev={R_version} \ r-recommended={R_version} \ - libclang-dev && \ + libclang-dev > /dev/null && \ apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/*
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Clarify what version of R we are testing for
MODIFY tests/r/r4/verify tests/r/r4/verify library('ggplot2') print(version) -if (version$major != "4" && as.double(version$minor) >= 1) { +# Fail if version is not 4.1 +if (!(version$major == "4" && as.double(version$minor) >= 1 && as.double(version$minor) < 2)) { quit("yes", 1) }
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Add command line option to pass extra build args
MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -212,6 +212,14 @@ def get_argparser(): default=[], ) + argparser.add_argument( + "--build-arg", + dest="build_args", + action="append", + help="Extra build arg to pass to the build process, in form name=value", + default=[], + ) + argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help) argparser.add_argument( @@ -261,6 +269,10 @@ def make_r2d(argv=None): else: r2d.labels[l] = "" + for a in args.build_args: + key, _, val = a.partition("=") + r2d.extra_build_args[key] = val + r2d.repo = args.repo r2d.ref = args.ref MODIFY repo2docker/app.py repo2docker/app.py @@ -248,6 +248,15 @@ class Repo2Docker(Application): config=True, ) + extra_build_args = Dict( + {}, + help=""" + Extra build args to pass to the image build process. + This is pretty much only useful for custom Dockerfile based builds. + """, + config=True, + ) + json_logs = Bool( False, help=""" @@ -777,6 +786,8 @@ class Repo2Docker(Application): } if self.target_repo_dir: build_args["REPO_DIR"] = self.target_repo_dir + build_args.update(self.extra_build_args) + self.log.info( "Using %s builder\n", bp.__class__.__name__,
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Use str.partition() for --label argument parsing
MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -263,11 +263,8 @@ def make_r2d(argv=None): r2d.appendix = args.appendix for l in args.labels: - if "=" in l: - key, val = l.split("=", 1) + key, _, val = l.partition("=") r2d.labels[key] = val - else: - r2d.labels[l] = "" for a in args.build_args: key, _, val = a.partition("=")
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Fix some code comment references to MRAN
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -20,18 +20,19 @@ class RBuildPack(PythonBuildPack): r-<year>-<month>-<date> Where 'year', 'month' and 'date' refer to a specific - date snapshot of https://mran.microsoft.com/timemachine - from which libraries are to be installed. + date whose CRAN snapshot we will use to fetch packages. + Uses https://packagemanager.rstudio.com, or MRAN if no snapshot + is found on packagemanager.rstudio.com 2. A `DESCRIPTION` file signaling an R package - If there is no `runtime.txt`, then the MRAN snapshot is set to latest + If there is no `runtime.txt`, then the CRAN snapshot is set to latest date that is guaranteed to exist across timezones. 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 + and can be used for installing packages from both CRAN and GitHub - as dependencies in a `DESCRIPTION` file @@ -99,7 +100,7 @@ class RBuildPack(PythonBuildPack): @property def checkpoint_date(self): """ - Return the date of MRAN checkpoint to use for this repo + Return the date of CRAN checkpoint to use for this repo Returns '' if no date is specified """ @@ -220,7 +221,7 @@ class RBuildPack(PythonBuildPack): for installing R packages into - RStudio - R's devtools package, at a particular frozen version - (determined by MRAN) + (determined by CRAN) - IRKernel - nbrsessionproxy (to access RStudio via Jupyter Notebook)
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Add test for r3.6
ADD tests/r/r3.6/install.R +install.packages("ggplot2") ADD tests/r/r3.6/runtime.txt +r-3.6-2018-07-07 ADD tests/r/r3.6/verify +#!/usr/bin/env Rscript +library('ggplot2') + +print(version) +# Fail if version is not 3.6 +if (!(version$major == "3" && as.double(version$minor) >= 6 && as.double(version$minor) < 7)) { + quit("yes", 1) +}
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Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1
MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -6,8 +6,9 @@ dependencies: - pip - ipywidgets==7.6.3 - jupyter-offlinenotebook==0.2.1 - - jupyter-resource-usage==0.6.0 - - jupyterlab==3.1.17 + - jupyter-resource-usage==0.6.1 + - jupyterlab==3.2.5 + # jupyterhub-singleuser==1.5.0 won't install with python 3.6 (but 2.0.1 does!) - jupyterhub-singleuser==1.4.2 # Newer versions require python 3.7 - nbconvert==6.0.7
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Add help message to freeze.py
MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -9,6 +9,7 @@ Usage: python freeze.py [3.8] """ +from argparse import ArgumentParser from datetime import datetime import os import pathlib @@ -106,10 +107,21 @@ 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", "3.6", "3.7", "3.8", "3.9") + parser = ArgumentParser( + description=( + "Refreeze conda environments. See " + "https://repo2docker.readthedocs.io/en/latest/contributing/tasks.html#update-and-freeze-buildpack-dependencies" + ) + ) + parser.add_argument( + "py", + nargs="*", + help="Python version(s) to update and freeze", + default=("2.7", "3.6", "3.7", "3.8", "3.9"), + ) + args = parser.parse_args() default_py = "3.7" - for py in pys: + for py in args.py: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) set_python(env_file, py) frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + ".lock")
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Fix call to rstudio_base_scripts
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -364,7 +364,7 @@ class CondaBuildPack(BaseImage): ), ) ) - scripts += rstudio_base_scripts() + scripts += rstudio_base_scripts(self.r_version) scripts += [ ( "root",
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Test that older r snapshots get MRAN
MODIFY tests/r/r4.0/verify tests/r/r4.0/verify @@ -6,3 +6,8 @@ print(version) if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version$minor) < 1)) { quit("yes", 1) } + +# The date we have chosen should give us an MRAN mirror +if (!grepl("https://mran.microsoft.com", options()$CRAN, fixed=TRUE)) { + quit("yes", 1) +}
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Check for MRAN differently
MODIFY tests/r/mran/verify tests/r/mran/verify @@ -4,6 +4,6 @@ library('ggplot2') print(version) # Fail if MRAN isn't the configured CRAN mirror -if (!grepl("https://mran.microsoft.com", options()$CRAN, fixed=TRUE)) { +if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) { quit("yes", 1) } MODIFY tests/r/r4.0/verify tests/r/r4.0/verify @@ -8,6 +8,6 @@ if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version } # The date we have chosen should give us an MRAN mirror -if (!grepl("https://mran.microsoft.com", options()$CRAN, fixed=TRUE)) { +if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) { quit("yes", 1) } \ No newline at end of file
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Explicitly install r-base-core Otherwise latest version was being installed, giving us R 4.1 even when we ask for 4.0
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -76,7 +76,7 @@ class RBuildPack(PythonBuildPack): "3.6": "3.6.1-3bionic", "3.6.0": "3.6.0-2bionic", "3.6.1": "3.6.1-3bionic", - "4.0": "4.0.2-1.1804.0", + "4.0": "4.0.5-1.1804.0", "4.0.2": "4.0.2-1.1804.0", "4.1": "4.1.2-1.1804.0", } @@ -294,7 +294,7 @@ class RBuildPack(PythonBuildPack): "root", r""" apt-get update > /dev/null && \ - apt-get install --yes r-base={R_version} \ + apt-get install --yes r-base={R_version} r-base-core={R_version} \ r-base-dev={R_version} \ r-recommended={R_version} \ libclang-dev \
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Update r 3.6 package version pins Based on output of apt-cache madison r-base-core
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -73,9 +73,9 @@ class RBuildPack(PythonBuildPack): "3.5.1": "3.5.1-2bionic", "3.5.2": "3.5.2-1bionic", "3.5.3": "3.5.3-1bionic", - "3.6": "3.6.1-3bionic", + "3.6": "3.6.3-1bionic", "3.6.0": "3.6.0-2bionic", - "3.6.1": "3.6.1-3bionic", + "3.6.1": "3.6.1-1bionic", "4.0": "4.0.5-1.1804.0", "4.0.2": "4.0.2-1.1804.0", "4.1": "4.1.2-1.1804.0",
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Fix test for particular version of R 3.6
MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -43,7 +43,7 @@ def test_version_completion(tmpdir): f.write(f"r-3.6-2019-01-01") r = buildpacks.RBuildPack() - assert r.r_version == "3.6.1-3bionic" + assert r.r_version == "3.6.3-1bionic" @pytest.mark.parametrize(
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Clarify when mran raises valueerror
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -217,7 +217,6 @@ class RBuildPack(PythonBuildPack): r = requests.head(url) if r.ok: return url - else: raise ValueError( "No snapshot found for {} or {} days prior in mran.microsoft.com".format( snapshot_date.strftime("%Y-%m-%d"), max_days_prior
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Bump default R version to 4.1 3.6 is almost 4 years old now.
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -80,7 +80,7 @@ class RBuildPack(PythonBuildPack): "4.1": "4.1.2-1.1804.0", } # the default if nothing is specified - r_version = "3.6" + r_version = "4.1" if not hasattr(self, "_r_version"): parts = self.runtime.split("-") MODIFY tests/r/simple/verify tests/r/simple/verify #!/usr/bin/env Rscript library('ggplot2') + +# Fail if version is not 4.1 +if (!(version$major == "4" && as.double(version$minor) >= 1 && as.double(version$minor) < 2)) { + quit("yes", 1) +} \ No newline at end of file
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Update test to match new default R version
MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -22,7 +22,7 @@ def test_unsupported_version(tmpdir): @pytest.mark.parametrize( - "runtime_version, expected", [("", "3.6"), ("3.6", "3.6"), ("3.5.1", "3.5")] + "runtime_version, expected", [("", "4.1"), ("3.6", "3.6"), ("3.5.1", "3.5")] ) def test_version_specification(tmpdir, runtime_version, expected): tmpdir.chdir()
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Hardcode rspm URL as snapshot for IRKernel
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -239,10 +239,11 @@ class RBuildPack(PythonBuildPack): devtools is part of our 'core' base install, so we should have some control over what version we install here. """ - # IRKernel gets into CRAN on Nov 16 2018 (https://packagemanager.rstudio.com/client/#/repos/1/packages/IRkernel), - # so we try snapshot to just after that. We use rspm as we want binary packages all the time - # FIXME: Hardcode this to prevent an extra call to the rspm API - return self.get_rspm_snapshot_url(datetime.date(2021, 12, 16)) + # Picked from https://packagemanager.rstudio.com/client/#/repos/1/overview + # Hardcoded rather than dynamically determined from a date to avoid extra API calls + # Plus, we can always use packagemanager.rstudio.com here as we always install the + # necessary apt packages. + return "https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" def get_build_scripts(self): """
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Remove unnecessary print()
MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -78,7 +78,6 @@ def test_snapshot_rspm_date(): r = buildpacks.RBuildPack() for requested, expected in test_dates.items(): snapshot_url = r.get_rspm_snapshot_url(requested) - print(snapshot_url) assert snapshot_url.startswith( "https://packagemanager.rstudio.com/all/__linux__/bionic/" + expected.strftime("%Y-%m-%d")
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Move 3.6.1 back to 3.6.1-3bionic Was accidentally included along with the 3.6.3-1biocnic upgrade for 3.6
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -75,7 +75,7 @@ class RBuildPack(PythonBuildPack): "3.5.3": "3.5.3-1bionic", "3.6": "3.6.3-1bionic", "3.6.0": "3.6.0-2bionic", - "3.6.1": "3.6.1-1bionic", + "3.6.1": "3.6.1-3bionic", "4.0": "4.0.5-1.1804.0", "4.0.2": "4.0.2-1.1804.0", "4.1": "4.1.2-1.1804.0",
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Say 'apt repository' rather than PPA PPA is a specific kind of apt repository, hosted on launchpad.net. We use which is just a regular apt repository. The PPA terminology always confused me, so this just clears that up
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -177,7 +177,7 @@ class RBuildPack(PythonBuildPack): "lsb-release", ] # For R 3.4 we use the default Ubuntu package, for other versions we - # install from a different PPA + # install from a different apt repository if V(self.r_version) < V("3.5"): packages.append("r-base") packages.append("r-base-dev") MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -117,7 +117,7 @@ def test_install_from_base(tmpdir): assert "r-base" in r.get_packages() -def test_install_from_ppa(tmpdir): +def test_install_from_cran_apt_repo(tmpdir): # check that for R>3.4 we don't install r-base from Ubuntu tmpdir.chdir() @@ -128,7 +128,7 @@ def test_install_from_ppa(tmpdir): assert "r-base" not in r.get_packages() -def test_custom_ppa(tmpdir): +def test_custom_cran_apt_repo(tmpdir): tmpdir.chdir() with open("runtime.txt", "w") as f: @@ -138,12 +138,12 @@ def test_custom_ppa(tmpdir): scripts = r.get_build_scripts() - # check that at least one of the build scripts adds this new PPA + # check that at least one of the build scripts adds this new apt repository for user, script in scripts: if "https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" in script: break else: - assert False, "Should have added a new PPA" + assert False, "Should have added a new apt repository" # check that we install the right package for user, script in scripts:
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adhere to lint
MODIFY tests/conda/simple-py2/verify tests/conda/simple-py2/verify @@ -14,13 +14,17 @@ assert sorted(specs) == ["python2", "python3"], specs.keys() import json from subprocess import check_output -envs = json.loads(check_output(["/tmp/bin/micromamba", "env", "list", "--json"]).decode("utf8")) +envs = json.loads( + check_output(["/tmp/bin/micromamba", "env", "list", "--json"]).decode("utf8") +) assert envs == { "envs": ["/srv/conda", "/srv/conda/envs/kernel", "/srv/conda/envs/notebook"] }, envs pkgs = json.loads( - check_output(["/tmp/bin/micromamba", "list", "-n", "kernel", "--json"]).decode("utf8") + check_output(["/tmp/bin/micromamba", "list", "-n", "kernel", "--json"]).decode( + "utf8" + ) ) pkg_names = [pkg["name"] for pkg in pkgs] assert "ipykernel" in pkg_names, pkg_names
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use latest micromamba
MODIFY repo2docker/buildpacks/conda/activate-conda.sh repo2docker/buildpacks/conda/activate-conda.sh @@ -7,7 +7,7 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then # if the kernel is a separate env, stack them # so both are on PATH, notebook first micromamba activate ${KERNEL_PYTHON_PREFIX} - micromamba activate ${NB_PYTHON_PREFIX} --stack + micromamba activate --stack ${NB_PYTHON_PREFIX} # even though it's second on $PATH # make sure CONDA_DEFAULT_ENV is the *kernel* env MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,6 +5,6 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip() -assert out == "0.12.0", out +assert out == "0.12.1", out import numpy
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fix tests + change name of script
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -115,8 +115,8 @@ class CondaBuildPack(BaseImage): "root", r""" TIMEFORMAT='time: %3R' \ - bash -c 'time /tmp/install-miniforge.bash' && \ - rm -rf /tmp/install-miniforge.bash /tmp/env + bash -c 'time /tmp/install-micromamba.bash' && \ + rm /tmp/install-micromamba.bash /tmp/environment.yml """, ), ( @@ -146,7 +146,7 @@ class CondaBuildPack(BaseImage): """ files = { - "conda/install-miniforge.bash": "/tmp/install-miniforge.bash", + "conda/install-micromamba.bash": "/tmp/install-micromamba.bash", "conda/activate-conda.sh": "/etc/profile.d/activate-conda.sh", } py_version = self.python_version MODIFY tests/pipfile/environment-yml/environment.yml tests/pipfile/environment-yml/environment.yml dependencies: + - pip - pip: - pypi-pkg-test
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use latest micromamba and fix MAMBA_ROOT_PREFIX
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -55,6 +55,7 @@ class CondaBuildPack(BaseImage): ("NPM_DIR", "${APP_BASE}/npm"), ("NPM_CONFIG_GLOBALCONFIG", "${NPM_DIR}/npmrc"), ("NB_ENVIRONMENT_FILE", self._nb_environment_file), + ("MAMBA_ROOT_PREFIX", "${CONDA_DIR}"), ] if self._nb_requirements_file: env.append(("NB_REQUIREMENTS_FILE", self._nb_requirements_file)) MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -6,7 +6,7 @@ set -ex cd $(dirname $0) -URL="https://micro.mamba.pm/api/micromamba/linux-64/latest" +URL="https://anaconda.org/conda-forge/micromamba/0.13.1/download/linux-64/micromamba-0.13.1-0.tar.bz2" # make sure we don't do anything funky with user's $HOME # since this is run as root MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,6 +5,6 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip() -assert out == "0.13.0", out +assert out == "0.13.1", out import numpy
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add MAMBA_EXE environment variable
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -56,6 +56,7 @@ class CondaBuildPack(BaseImage): ("NPM_CONFIG_GLOBALCONFIG", "${NPM_DIR}/npmrc"), ("NB_ENVIRONMENT_FILE", self._nb_environment_file), ("MAMBA_ROOT_PREFIX", "${CONDA_DIR}"), + ("MAMBA_EXE", "/tmp/bin/micromamba"), ] if self._nb_requirements_file: env.append(("NB_REQUIREMENTS_FILE", self._nb_requirements_file))
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use env update instead of install
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -339,7 +339,7 @@ class CondaBuildPack(BaseImage): "${NB_USER}", r""" TIMEFORMAT='time: %3R' \ - bash -c 'time /tmp/bin/micromamba install -p {0} -f "{1}" && \ + bash -c 'time /tmp/bin/micromamba env update -p {0} -f "{1}" && \ # time /tmp/bin/micromamba clean --all -y && \ /tmp/bin/micromamba list -p {0} \ '
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revert back to using install
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -339,7 +339,7 @@ class CondaBuildPack(BaseImage): "${NB_USER}", r""" TIMEFORMAT='time: %3R' \ - bash -c 'time /tmp/bin/micromamba update -p {0} -f "{1}" && \ + bash -c 'time /tmp/bin/micromamba install -p {0} -f "{1}" && \ # time /tmp/bin/micromamba clean --all -y && \ /tmp/bin/micromamba list -p {0} \ '
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use strict channel priority
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -33,7 +33,7 @@ channels: auto_update_conda: false show_channel_urls: true update_dependencies: false -channel_priority: flexible +channel_priority: strict EOT echo "installing notebook env:"
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fix rm targets
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -118,7 +118,7 @@ class CondaBuildPack(BaseImage): r""" TIMEFORMAT='time: %3R' \ bash -c 'time /tmp/install-base-env.bash' && \ - rm /tmp/install-base-env.bash /tmp/environment.yml + rm -rf /tmp/install-base-env.bash /tmp/env """, ), (
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Use micromamba 0.15.2
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -6,7 +6,7 @@ set -ex cd $(dirname $0) -URL="https://anaconda.org/conda-forge/micromamba/0.15.0/download/linux-64/micromamba-0.15.0-1.tar.bz2" +URL="https://anaconda.org/conda-forge/micromamba/0.15.2/download/linux-64/micromamba-0.15.2-1.tar.bz2" # make sure we don't do anything funky with user's $HOME # since this is run as root 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(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip() -assert out == "0.15.0", out +assert out == "0.15.2", out import numpy
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use wget better
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -14,7 +14,7 @@ URL="https://github.com/mamba-org/boa-forge/releases/download/micromamba-nightly unset HOME mkdir -p ${CONDA_DIR} -time wget -qO- ${URL} # | tar -xvj bin/micromamba +time wget ${URL} mkdir -p /tmp/bin mv micromamba-nightly-linux-64 /tmp/bin/micromamba chmod 0755 /tmp/bin/micromamba
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[ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
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use mamba with fixed zstd linkage
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -7,7 +7,7 @@ set -ex cd $(dirname $0) # URL="https://anaconda.org/conda-forge/micromamba/0.16.0/download/linux-64/micromamba-0.16.0-0.tar.bz2" -URL="https://github.com/mamba-org/boa-forge/releases/download/micromamba-nightly-21.10.8.959/micromamba-nightly-linux-64" +URL="https://github.com/mamba-org/boa-forge/releases/download/micromamba-nightly-21.10.12.1026/micromamba-nightly-linux-64" # make sure we don't do anything funky with user's $HOME # since this is run as root @@ -36,7 +36,7 @@ channels: auto_update_conda: false show_channel_urls: true update_dependencies: false -channel_priority: strict +# channel_priority: flexible EOT echo "installing notebook env:"
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[ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
[ 1, 1202, 312, 2536, 69, 598, 5499, 998, 5084, 1692, 410, 2, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100, -100 ]
Use micromamba 0.17 and install conda & mamba into base env
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -6,8 +6,7 @@ set -ex cd $(dirname $0) -# URL="https://anaconda.org/conda-forge/micromamba/0.16.0/download/linux-64/micromamba-0.16.0-0.tar.bz2" -URL="https://github.com/mamba-org/boa-forge/releases/download/micromamba-nightly-21.10.12.1026/micromamba-nightly-linux-64" +URL="https://anaconda.org/conda-forge/micromamba/0.17.0/download/linux-64/micromamba-0.17.0-0.tar.bz2" # make sure we don't do anything funky with user's $HOME # since this is run as root @@ -39,6 +38,8 @@ update_dependencies: false # channel_priority: flexible EOT +micromamba install conda mamba -y + echo "installing notebook env:" cat "${NB_ENVIRONMENT_FILE}"
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Update micromamba installation
MODIFY repo2docker/buildpacks/conda/install-base-env.bash repo2docker/buildpacks/conda/install-base-env.bash @@ -13,16 +13,13 @@ URL="https://anaconda.org/conda-forge/micromamba/0.17.0/download/linux-64/microm unset HOME mkdir -p ${CONDA_DIR} -time wget ${URL} -mkdir -p /tmp/bin -mv micromamba-nightly-linux-64 /tmp/bin/micromamba +time wget -qO- ${URL} | tar -xvj bin/micromamba chmod 0755 /tmp/bin/micromamba export MAMBA_ROOT_PREFIX=${CONDA_DIR} export MAMBA_EXE="/tmp/bin/micromamba" -eval "$(./bin/micromamba shell hook -p ${CONDA_DIR} -s posix)" -./bin/micromamba shell init -s bash -p ${CONDA_DIR} +eval "$(/tmp/bin/micromamba shell hook -p ${CONDA_DIR} -s posix)" micromamba activate 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(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip() -assert out == "0.16.0", out +assert out == "0.17.0", out import numpy
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Fix CI by calling shell init
MODIFY repo2docker/buildpacks/conda/activate-conda.sh repo2docker/buildpacks/conda/activate-conda.sh # enable conda and activate the notebook environment -export MAMBA_EXE="/tmp/bin/micromamba" +/tmp/bin/micromamba shell init -s bash -p ${CONDA_DIR} export MAMBA_ROOT_PREFIX="/srv/conda" CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/mamba.sh" test -f $CONDA_PROFILE && . $CONDA_PROFILE
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note why --no-install-recommends is important for r packages
MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -31,6 +31,9 @@ def rstudio_base_scripts(r_version): return [ ( "root", + # we should have --no-install-recommends on all our apt-get install commands, + # but here it's important because these recommend r-base, + # which will upgrade the installed version of R, undoing our pinned version r""" curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \ curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \ MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -292,6 +292,9 @@ class RBuildPack(PythonBuildPack): ), ( "root", + # we should have --no-install-recommends on all our apt-get install commands, + # but here it's important because it will pull in CRAN packages + # via r-recommends, which is only guaranteed to be compatible with the latest r-base-core r""" apt-get update > /dev/null && \ apt-get install --yes --no-install-recommends \
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set USER root after each directive block matches expectations in the directive sequences not strictly required after preassemble because we have no root steps between preassemble and assemble, so we could remove the `last_user = "root"` there instead includes regression test
MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -100,6 +100,8 @@ COPY --chown={{ user }}:{{ user }} {{ src }} {{ dst }} {% for sd in build_script_directives -%} {{ sd }} {% endfor %} +# ensure root user after build scripts +USER root # Allow target path repo is cloned to be configurable ARG REPO_DIR=${HOME} @@ -138,6 +140,8 @@ COPY --chown={{ user }}:{{ user }} src/{{ src }} ${REPO_DIR}/{{ dst }} {% for sd in preassemble_script_directives -%} {{ sd }} {% endfor %} +# ensure root user after preassemble scripts +USER root # Copy stuff. COPY --chown={{ user }}:{{ user }} src/ ${REPO_DIR} ADD tests/r/apt/apt.txt +libsodium-dev ADD tests/r/apt/install.R +install.packages("viridisLite") ADD tests/r/apt/runtime.txt +r-4.1-2021-10-22 ADD tests/r/apt/verify +#!/usr/bin/env bash +set -euo pipefail +apt list +apt list | grep libsodium-dev +# make sure we got R +which R
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Delete /tmp/downloaded_packages after running install.R This can often leave ~100-200MB in /tmp that isn't re-used after the image is set up.
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -387,7 +387,10 @@ class RBuildPack(PythonBuildPack): scripts += [ ( "${NB_USER}", - "Rscript %s && touch /tmp/.preassembled || true" % installR_path, + # Delete /tmp/downloaded_packages only if install.R fails, as the second + # invocation of install.R might be able to reuse them + "Rscript %s && touch /tmp/.preassembled || true && rm -rf /tmp/downloaded_packages" + % installR_path, ) ] @@ -403,7 +406,8 @@ class RBuildPack(PythonBuildPack): ( "${NB_USER}", # only run install.R if the pre-assembly failed - "if [ ! -f /tmp/.preassembled ]; then Rscript {}; fi".format( + # Delete any downloaded packages in /tmp, as they aren't reused by R + """if [ ! -f /tmp/.preassembled ]; then Rscript {}; rm -rf /tmp/downloaded_packages; fi""".format( installR_path ), )
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Re-add call to clean
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -340,7 +340,7 @@ class CondaBuildPack(BaseImage): r""" TIMEFORMAT='time: %3R' \ bash -c 'time ${{MAMBA_EXE}} install -p {0} -f "{1}" && \ - # time ${{MAMBA_EXE}} clean --all -y && \ + time ${{MAMBA_EXE}} clean --all -y && \ ${{MAMBA_EXE}} list -p {0} \ ' """.format( @@ -359,7 +359,7 @@ class CondaBuildPack(BaseImage): "${NB_USER}", r""" ${{MAMBA_EXE}} install -p {0} r-base{1} r-irkernel=1.2 r-devtools -y && \ - # ${{MAMBA_EXE}} clean --all -f -y && \ + ${{MAMBA_EXE}} clean --all -f -y && \ ${{MAMBA_EXE}} list -p {0} """.format( env_prefix, r_pin
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remove deprecated call to distutils strtobool
MODIFY tests/unit/contentproviders/test_mercurial.py tests/unit/contentproviders/test_mercurial.py -from pathlib import Path +import os import subprocess +from pathlib import Path from tempfile import TemporaryDirectory -import os -from distutils.util import strtobool import pytest from repo2docker.contentproviders import Mercurial from repo2docker.contentproviders.mercurial import args_enabling_topic -SKIP_HG = strtobool(os.environ.get("REPO2DOCKER_SKIP_HG_TESTS", "False")) + +SKIP_HG = os.environ.get("REPO2DOCKER_SKIP_HG_TESTS", "").lower() not in { + "", + "0", + "false", + "no", +} skip_if_no_hg_tests = pytest.mark.skipif( SKIP_HG,
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Allow passing in traitlets via commandline Without this, you *always* needed a repo2docker_config.py file to configure anything. This PR makes r2d match the behavior of most traitlets based applications (like jupyter_server, jupyterhub, nbconvert, etc) Fixes
MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -251,9 +251,10 @@ def make_r2d(argv=None): print(__version__) sys.exit(0) - args = get_argparser().parse_args(argv) + args, traitlet_args = get_argparser().parse_known_args(argv) r2d = Repo2Docker() + r2d.parse_command_line(traitlet_args) if args.debug: r2d.log_level = logging.DEBUG MODIFY repo2docker/app.py repo2docker/app.py @@ -490,7 +490,7 @@ class Repo2Docker(Application): extra=dict(phase="failed"), ) - def initialize(self): + def initialize(self, *args, **kwargs): """Init repo2docker configuration before start""" # FIXME: Remove this function, move it to setters / traitlet reactors if self.json_logs:
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Allow passing in extra args to Docker initialization Puts it in the ContainerEngine interface specific to Docker, so PodMan can implement its own when necessary. Fixes
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -3,6 +3,7 @@ Docker container engine for repo2docker """ import docker +from traitlets import Dict from iso8601 import parse_date from .engine import Container, ContainerEngine, ContainerEngineException, Image @@ -53,12 +54,26 @@ class DockerEngine(ContainerEngine): string_output = False + extra_init_args = Dict( + {}, + help=""" + Extra kwargs to pass to docker client when initializing it. + + Dictionary that allows users to specify extra parameters to pass + to APIClient, parameters listed in https://docker-py.readthedocs.io/en/stable/api.html#docker.api.client.APIClient. + + Parameters here are merged with whatever is picked up from the + environment. + """, + config=True, + ) + def __init__(self, *, parent): super().__init__(parent=parent) try: - self._apiclient = docker.APIClient( - version="auto", **docker.utils.kwargs_from_env() - ) + kwargs = docker.utils.kwargs_from_env() + kwargs.update(self.extra_init_args) + self._apiclient = docker.APIClient(version="auto", **kwargs) except docker.errors.DockerException as e: raise ContainerEngineException("Check if docker is running on the host.", e)
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Clarify how kwargs is set
MODIFY repo2docker/docker.py repo2docker/docker.py @@ -73,7 +73,8 @@ class DockerEngine(ContainerEngine): try: kwargs = docker.utils.kwargs_from_env() kwargs.update(self.extra_init_args) - self._apiclient = docker.APIClient(version="auto", **kwargs) + kwargs.setdefault("version", "auto") + self._apiclient = docker.APIClient(**kwargs) except docker.errors.DockerException as e: raise ContainerEngineException("Check if docker is running on the host.", e)
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Remove -f command-line argument
MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -359,7 +359,7 @@ class CondaBuildPack(BaseImage): "${NB_USER}", r""" ${{MAMBA_EXE}} install -p {0} r-base{1} r-irkernel=1.2 r-devtools -y && \ - ${{MAMBA_EXE}} clean --all -f -y && \ + ${{MAMBA_EXE}} clean --all -y && \ ${{MAMBA_EXE}} list -p {0} """.format( env_prefix, r_pin
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update Python in dockerfile tests installing with Python 3.5 is starting to fail
MODIFY tests/dockerfile/binder-dir/binder/Dockerfile tests/dockerfile/binder-dir/binder/Dockerfile -FROM python:3.5 +FROM python:3.10 RUN pip install --no-cache notebook MODIFY tests/dockerfile/simple/Dockerfile tests/dockerfile/simple/Dockerfile -FROM python:3.5 +FROM python:3.10 RUN pip install --no-cache notebook
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Pass build_args to `render()` during `--no-build` for consistency with regular builds
MODIFY repo2docker/app.py repo2docker/app.py @@ -773,25 +773,26 @@ class Repo2Docker(Application): picked_buildpack.labels.update(self.labels) + build_args = { + "NB_USER": self.user_name, + "NB_UID": str(self.user_id), + } + if self.target_repo_dir: + build_args["REPO_DIR"] = self.target_repo_dir + build_args.update(self.extra_build_args) + if self.dry_run: - print(picked_buildpack.render()) + print(picked_buildpack.render(build_args)) else: self.log.debug( - picked_buildpack.render(), extra=dict(phase="building") + picked_buildpack.render(build_args), + extra=dict(phase="building"), ) if self.user_id == 0: raise ValueError( "Root as the primary user in the image is not permitted." ) - build_args = { - "NB_USER": self.user_name, - "NB_UID": str(self.user_id), - } - if self.target_repo_dir: - build_args["REPO_DIR"] = self.target_repo_dir - build_args.update(self.extra_build_args) - self.log.info( "Using %s builder\n", bp.__class__.__name__,
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handle r version unspecified in environment.yml
MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -14,7 +14,7 @@ def rstudio_base_scripts(r_version): shiny_proxy_version = "1.1" shiny_sha256sum = "80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee" - if V(r_version) <= V("4.1"): + if r_version and V(r_version) <= V("4.1"): # Older RStudio and jupyter-rsession-proxy for v4.1 and below rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb" rstudio_sha256sum = ( ADD tests/conda/r-unspecified/environment.yml +dependencies: + - r-base + - r-ggplot2 ADD tests/conda/r-unspecified/verify +#!/bin/sh + +jupyter serverextension list 2>&1 | grep jupyter_server_proxy +jupyter nbextension list 2>&1 | grep jupyter_server_proxy +R -e "library('ggplot2')" +# Fail if version is not at least 4.1 +R -e 'if (!(version$major == "4" && as.double(version$minor) >= 1)) quit("yes", 1)'
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upgrade RStudio Server to v2022.02.1
MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -14,17 +14,9 @@ def rstudio_base_scripts(r_version): shiny_proxy_version = "1.1" shiny_sha256sum = "80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee" - if r_version and V(r_version) <= V("4.1"): - # Older RStudio and jupyter-rsession-proxy for v4.1 and below - rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb" + rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.02.1-461-amd64.deb" rstudio_sha256sum = ( - "187af05cab1221282487fdc33f4b161484c3228eaade3d6697b1d41c206ee6d9" - ) - rsession_proxy_version = "1.4" - else: - rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb" - rstudio_sha256sum = ( - "c58df09468870b89f1796445853dce2dacaa0fc5b7bb1f92b036fa8da1d1f8a3" + "239e8d93e103872e7c6d827113d88871965f82ffb0397f5638025100520d8a54" ) rsession_proxy_version = "2.0.1"
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handle permission issue
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -23,11 +23,13 @@ SIGNALS = set(signal.Signals) - {signal.SIGKILL, signal.SIGSTOP, signal.SIGCHLD} def main(): - # open log file to send output - log_file = open( - os.path.join(os.environ.get("REPO_DIR", "."), ".jupyter-server-log.txt"), - "ab", - ) + # open log file to send output; fall back to writing it in + # the current working directory + if "REPO_DIR" in os.environ and os.access(os.environ["REPO_DIR"], 7): + log_path = os.path.join(os.environ["REPO_DIR"], ".jupyter-server-log.txt") + else: + log_path = os.path.join(".", ".jupyter-server-log.txt") + log_file = open(log_path, "ab") # build the command # like `exec "$@"`
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iterate through different log locations
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -12,6 +12,7 @@ import select import signal import subprocess import sys +import tempfile # output chunk size to read CHUNK_SIZE = 1024 @@ -23,13 +24,20 @@ SIGNALS = set(signal.Signals) - {signal.SIGKILL, signal.SIGSTOP, signal.SIGCHLD} def main(): - # open log file to send output; fall back to writing it in - # the current working directory - if "REPO_DIR" in os.environ and os.access(os.environ["REPO_DIR"], 7): - log_path = os.path.join(os.environ["REPO_DIR"], ".jupyter-server-log.txt") - else: - log_path = os.path.join(".", ".jupyter-server-log.txt") + # open log file to send output; iterate through different + # base locations + log_dirs = [".", tempfile.gettempdir()] + if "REPO_DIR" in os.environ: + log_dirs.insert(os.environ["REPO_DIR"], 0) + for d in log_dirs: + log_path = join(d, 'log.txt') + try: log_file = open(log_path, "ab") + except PermissionError: + continue + else: + # success + break # build the command # like `exec "$@"`
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fix insert call
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -28,7 +28,7 @@ def main(): # base locations log_dirs = [".", tempfile.gettempdir()] if "REPO_DIR" in os.environ: - log_dirs.insert(os.environ["REPO_DIR"], 0) + log_dirs.insert(0, os.environ["REPO_DIR"]) for d in log_dirs: log_path = join(d, 'log.txt') try:
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fix join() call
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -30,7 +30,7 @@ def main(): if "REPO_DIR" in os.environ: log_dirs.insert(0, os.environ["REPO_DIR"]) for d in log_dirs: - log_path = join(d, 'log.txt') + log_path = os.path.join(d, 'log.txt') try: log_file = open(log_path, "ab") except PermissionError:
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keep server log name
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -33,7 +33,7 @@ def main(): if "REPO_DIR" in os.environ: log_dirs.insert(0, os.environ["REPO_DIR"]) for d in log_dirs: - log_path = os.path.join(d, 'log.txt') + log_path = os.path.join(d, ".jupyter-server-log.txt") try: log_file = open(log_path, "ab") except PermissionError:
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Fix Read-Only filesystem permission issue for log file
MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -30,17 +30,21 @@ def main(): # 2. current working directory: "." # 3. default temp directory for the OS (e.g. /tmp for linux) log_dirs = [".", tempfile.gettempdir()] + log_file = None if "REPO_DIR" in os.environ: log_dirs.insert(0, os.environ["REPO_DIR"]) for d in log_dirs: log_path = os.path.join(d, ".jupyter-server-log.txt") try: log_file = open(log_path, "ab") - except PermissionError: + except Exception: continue else: # success break + # raise Exception if log_file could not be set + if log_file is None: + raise Exception("Could not open '.jupyter-server-log.txt' log file " ) # build the command # like `exec "$@"`
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Shallow clone HEAD Previously repo2docker only performed shallow clones when refspec was not provided. We now also perform shallow clones if refspec is explicitly set to HEAD. Binder always specifies a refspec, often HEAD, so this should improve some build times.
MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -17,12 +17,12 @@ class Git(ContentProvider): def fetch(self, spec, output_dir, yield_output=False): repo = spec["repo"] - ref = spec.get("ref", None) + ref = spec.get("ref") or "HEAD" # make a, possibly shallow, clone of the remote repository try: cmd = ["git", "clone"] - if ref is None: + if ref == "HEAD": # check out of HEAD is performed after the clone is complete cmd.extend(["--depth", "1"]) else: @@ -35,13 +35,13 @@ class Git(ContentProvider): except subprocess.CalledProcessError as e: msg = "Failed to clone repository from {repo}".format(repo=repo) - if ref is not None: + if ref != "HEAD": msg += " (ref {ref})".format(ref=ref) msg += "." raise ContentProviderException(msg) from e # check out the specific ref given by the user - if ref is not None: + if ref != "HEAD": hash = check_ref(ref, output_dir) if hash is None: self.log.error(
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Actually install the downloaded deb
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -255,7 +255,8 @@ class RBuildPack(PythonBuildPack): ( "root", rf""" - wget --quiet -o /tmp/r-{self.r_version} https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-{self.r_version}_1_amd64.deb + wget --quiet -o /tmp/r-{self.r_version}.deb https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-{self.r_version}_1_amd64.deb && \ + dpkg -i /tmp/r-{self.r_version}.deb """, ), (
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Always provide full semver for R version Other wise our semver package cries
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -67,6 +67,16 @@ class RBuildPack(PythonBuildPack): Will return the version specified by the user or the current default version. """ + version_map = { + "4.2": "4.2.0", + "4.1": "4.1.3", + "4.0": "4.0.5", + "3.6": "3.6.3", + "3.5": "3.5.3", + "3.4": "3.4.0", + "3.3": "3.3.3", + } + # the default if nothing is specified r_version = "4.1.0" @@ -74,6 +84,10 @@ class RBuildPack(PythonBuildPack): parts = self.runtime.split("-") if len(parts) == 5: r_version = parts[1] + # For versions of form x.y, we want to explicitly provide x.y.z - latest patchlevel + # available. Users can howver explicitly specify the full version to get something specific + if r_version in version_map: + r_version = version_map[r_version] # translate to the full version string self._r_version = r_version
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Use new path for Renviron
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -302,9 +302,9 @@ class RBuildPack(PythonBuildPack): # Set paths so that RStudio shares libraries with base R # install. This first comments out any R_LIBS_USER that # might be set in /etc/R/Renviron and then sets it. - r""" - sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \ - echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron + rf""" + sed -i -e '/^R_LIBS_USER=/s/^/#/' /opt/R/{self.r_version}/lib/R/etc/Renviron && \ + echo "R_LIBS_USER=${{R_LIBS_USER}}" >> /opt/R/{self.r_version}/lib/R/etc/Renviron """, ), ( @@ -317,8 +317,6 @@ class RBuildPack(PythonBuildPack): r""" R RHOME && \ mkdir -p /usr/lib/R/etc /etc/rstudio && \ - echo 'options(repos = c(CRAN = "{cran_mirror_url}"))' > /usr/lib/R/etc/Rprofile.site && \ - echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))' >> /usr/lib/R/etc/Rprofile.site && \ echo 'r-cran-repos={cran_mirror_url}' > /etc/rstudio/rsession.conf """.format( cran_mirror_url=cran_mirror_url
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Set CRAN mirror URL for R
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -314,13 +314,12 @@ class RBuildPack(PythonBuildPack): # Quite hilarious, IMO. # See https://docs.rstudio.com/rspm/1.0.12/admin/binaries.html # Set mirror for RStudio too, by modifying rsession.conf - r""" + rf""" R RHOME && \ - mkdir -p /usr/lib/R/etc /etc/rstudio && \ + mkdir -p /etc/rstudio && \ + echo 'options(repos = c(CRAN = "{cran_mirror_url}"))' > /opt/R/{self.r_version}/lib/R/etc/Rprofile.site && \ echo 'r-cran-repos={cran_mirror_url}' > /etc/rstudio/rsession.conf - """.format( - cran_mirror_url=cran_mirror_url - ), + """, ), ( "${NB_USER}",
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Use apt rather than debi to install packages apt also seems to fetch dependencies when needed
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -261,13 +261,10 @@ class RBuildPack(PythonBuildPack): scripts = [ ( "root", - # gdebi is required to install dependencies of the deb packages from rstudio - # dpkg is built in, but doesn't allow us to fetch & install dependencies in one go r""" apt-get update > /dev/null && \ apt-get install --yes --no-install-recommends \ libclang-dev \ - gdebi \ libzmq3-dev > /dev/null """, # apt-get -qq purge && \ @@ -278,7 +275,7 @@ class RBuildPack(PythonBuildPack): "root", rf""" wget --quiet -O /tmp/r-{self.r_version}.deb https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-{self.r_version}_1_amd64.deb && \ - gdebi --quiet --non-interactive /tmp/r-{self.r_version}.deb && \ + apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb && \ rm /tmp/r-{self.r_version}.deb && \ ln -s /opt/R/{self.r_version}/bin/R /usr/local/bin/R && \ ln -s /opt/R/{self.r_version}/bin/Rscript /usr/local/bin/Rscript && \
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Cleanup apt-update files after installation
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -257,22 +257,17 @@ class RBuildPack(PythonBuildPack): scripts = [ ( "root", - r""" + rf""" apt-get update > /dev/null && \ apt-get install --yes --no-install-recommends \ libclang-dev \ - libzmq3-dev > /dev/null - """, - # apt-get -qq purge && \ - # apt-get -qq clean && \ - # rm -rf /var/lib/apt/lists/* - ), - ( - "root", - rf""" + libzmq3-dev > /dev/null && \ wget --quiet -O /tmp/r-{self.r_version}.deb https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-{self.r_version}_1_amd64.deb && \ - apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb && \ + apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb > /dev/null && \ rm /tmp/r-{self.r_version}.deb && \ + apt-get -qq purge && \ + apt-get -qq clean && \ + rm -rf /var/lib/apt/lists/* && \ ln -s /opt/R/{self.r_version}/bin/R /usr/local/bin/R && \ ln -s /opt/R/{self.r_version}/bin/Rscript /usr/local/bin/Rscript && \ R --version
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Don't specify distro specific build number
MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -29,7 +29,7 @@ def test_version_completion(tmpdir): f.write(f"r-3.6-2019-01-01") r = buildpacks.RBuildPack() - assert r.r_version == "3.6.3-1bionic" + assert r.r_version == "3.6.3" @pytest.mark.parametrize(
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Don't hardcode Ubuntu version when fetching R This allows us to dynamically change the base image without having to manually change the version string here
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -262,7 +262,8 @@ class RBuildPack(PythonBuildPack): apt-get install --yes --no-install-recommends \ libclang-dev \ libzmq3-dev > /dev/null && \ - wget --quiet -O /tmp/r-{self.r_version}.deb https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-{self.r_version}_1_amd64.deb && \ + wget --quiet -O /tmp/r-{self.r_version}.deb \ + https://cdn.rstudio.com/r/ubuntu-$(source /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-{self.r_version}_1_amd64.deb && \ apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb > /dev/null && \ rm /tmp/r-{self.r_version}.deb && \ apt-get -qq purge && \
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Use . instead of source As Dockerfile executes with /bin/sh, not /bin/bash
MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -263,7 +263,7 @@ class RBuildPack(PythonBuildPack): libclang-dev \ libzmq3-dev > /dev/null && \ wget --quiet -O /tmp/r-{self.r_version}.deb \ - https://cdn.rstudio.com/r/ubuntu-$(source /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-{self.r_version}_1_amd64.deb && \ + https://cdn.rstudio.com/r/ubuntu-$(. /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-{self.r_version}_1_amd64.deb && \ apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb > /dev/null && \ rm /tmp/r-{self.r_version}.deb && \ apt-get -qq purge && \
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