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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 ${NPM_DIR}
+
# empty conda history file,
# which seems to result in some effective pinning of packages in the initial env,
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Pin doc-requirements.txt versions
Hopefully dependabot can take care of them | MODIFY
docs/doc-requirements.txt
docs/doc-requirements.txt
# Note that there is also a Pipfile for this project if you are updating this
# file do not forget to update the Pipfile accordingly
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fix side-effect method name and add fixme note | MODIFY
repo2docker/buildpacks/conda/__init__.py
repo2docker/buildpacks/conda/__init__.py
@@ -43,8 +43,10 @@ class CondaBuildPack(BaseImage):
"""
if not self._nb_environment_file:
- # get_build_scripts locates requirements/environment files
- self.get_build_scripts()
+ # get_build_script_files locates requirements/environment files,
+ # populating the _nb_environment_file attribute and others.
+ # FIXME: move file detection and initialization of those attributes to its own step?
+ self.get_build_script_files()
env = super().get_build_env() + [
("CONDA_DIR", "${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
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- jupyter-offlinenotebook==0.2.1
- - jupyter-resource-usage==0.5.1
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- - 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
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- - 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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.github/workflows/release.yml
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uses: docker/build-push-action@e1b7f96249f2e4c8e4ac1519b9608c0d48944a1f
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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
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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}
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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
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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):
),
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)
- scripts += rstudio_base_scripts()
+ scripts += rstudio_base_scripts(self.r_version)
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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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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",
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+ "3.6.1": "3.6.1-3bionic",
"4.0": "4.0.5-1.1804.0",
"4.0.2": "4.0.2-1.1804.0",
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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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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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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")
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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:
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for d in log_dirs:
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+ log_path = os.path.join(d, ".jupyter-server-log.txt")
try:
log_file = open(log_path, "ab")
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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
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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
- ),
+ """,
),
(
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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 && \
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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 \
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+ wget --quiet -O /tmp/r-{self.r_version}.deb \
+ https://cdn.rstudio.com/r/ubuntu-$(source /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-{self.r_version}_1_amd64.deb && \
apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb > /dev/null && \
rm /tmp/r-{self.r_version}.deb && \
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Use . instead of source
As Dockerfile executes with /bin/sh, not /bin/bash | MODIFY
repo2docker/buildpacks/r.py
repo2docker/buildpacks/r.py
@@ -263,7 +263,7 @@ class RBuildPack(PythonBuildPack):
libclang-dev \
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+ https://cdn.rstudio.com/r/ubuntu-$(. /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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