narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Succeed even if no requirements.txt is present Will just get default jupyter installation + venv

MODIFY ubuntu1610-python35-venv/s2i/bin/assemble ubuntu1610-python35-venv/s2i/bin/assemble @@ -23,4 +23,6 @@ echo "---> Installing application source..." cp -Rf /tmp/src/. ./ echo "---> Building application from source..." +if [ -f requirements.txt ]; then ${APP_DIR}/venv/bin/pip install --no-cache-dir -r requirements.txt +fi

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Install git into base image

MODIFY ubuntu1610-python35-venv/Dockerfile ubuntu1610-python35-venv/Dockerfile @@ -7,7 +7,7 @@ LABEL io.openshift.s2i.scripts-url=image:///usr/libexec/s2i ENV APP_DIR /srv/app RUN apt-get update -RUN apt-get install --yes python3 python3-venv tar +RUN apt-get install --yes python3 python3-venv tar git RUN adduser --disabled-password --gecos "Default Jupyter user" jovyan

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Cleanup apt after installing things we want

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -6,9 +6,13 @@ LABEL io.openshift.s2i.scripts-url=image:///usr/libexec/s2i ENV APP_DIR /srv/app -RUN apt-get update -RUN apt-get install --yes python3 python3-venv tar git - +RUN apt-get update && \ + apt-get install --yes --no-install-recommends \ + python3 \ + python3-venv \ + tar \ + git && \ + apt-get purge && apt-get clean RUN adduser --disabled-password --gecos "Default Jupyter user" jovyan

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Set PATH to include the venv's bin

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -5,6 +5,7 @@ MAINTAINER Yuvi Panda <yuvipanda@gmail.com> LABEL io.openshift.s2i.scripts-url=image:///usr/libexec/s2i ENV APP_DIR /srv/app +ENV PATH ${APP_DIR}/venv/bin:$PATH RUN apt-get update && \ apt-get install --yes --no-install-recommends \

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Pin versions of notebook & jupyterhub being installed

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -25,7 +25,7 @@ USER jovyan RUN python3 -m venv venv # FIXME: Specify actual versions here -RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir jupyter jupyterhub +RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 COPY ./s2i/bin/ /usr/libexec/s2i

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Cleanup the singleuser builder image

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -17,14 +17,13 @@ RUN apt-get update && \ RUN adduser --disabled-password --gecos "Default Jupyter user" jovyan -RUN mkdir -p ${APP_DIR} && chown -R jovyan:jovyan /srv/app +RUN mkdir -p ${APP_DIR} && chown -R jovyan:jovyan ${APP_DIR} -WORKDIR ${APP_DIR} +WORKDIR /home/jovyan USER jovyan -RUN python3 -m venv venv +RUN python3 -m venv ${APP_DIR}/venv -# FIXME: Specify actual versions here RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 COPY ./s2i/bin/ /usr/libexec/s2i

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Make the makefile versioned + more useful

MODIFY singleuser-builder/Makefile singleuser-builder/Makefile -IMAGE_NAME = ubuntu1610-python35-venv +IMAGE_NAME = jupyterhub/singleuser-builder +VERSION = $(shell cat version) .PHONY: build build: - docker build -t $(IMAGE_NAME) . + docker build -t $(IMAGE_NAME):$(VERSION) . .PHONY: test test: - docker build -t $(IMAGE_NAME)-candidate . - IMAGE_NAME=$(IMAGE_NAME)-candidate test/run + docker build -t $(IMAGE_NAME)-candidate:$(VERSION) . + IMAGE_NAME=$(IMAGE_NAME)-candidate:$(VERSION) test/run MODIFY singleuser-builder/s2i/bin/assemble singleuser-builder/s2i/bin/assemble #!/bin/bash -e # -# S2I assemble script for the 'ubuntu1610-python35-venv' image. +# S2I assemble script for the jupyterhub/singleuser-builder image. # The 'assemble' script builds your application source so that it is ready to run. # # For more information refer to the documentation: # https://github.com/openshift/source-to-image/blob/master/docs/builder_image.md # -# If the 'ubuntu1610-python35-venv' assemble script is executed with the '-h' flag, print the usage. if [[ "$1" == "-h" ]]; then exec /usr/libexec/s2i/usage fi ADD singleuser-builder/version +v0.1

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Install ipywidgets in base I consider it part of base notebook install :)

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -24,7 +24,7 @@ WORKDIR /home/jovyan USER jovyan RUN python3 -m venv ${APP_DIR}/venv -RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 +RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 ipywidgets==5.2.3 COPY ./s2i/bin/ /usr/libexec/s2i

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Cleanup assemble script to keep workspace clean

MODIFY singleuser-builder/s2i/bin/assemble singleuser-builder/s2i/bin/assemble @@ -13,15 +13,11 @@ fi # Restore artifacts from the previous build (if they exist). # -if [ "$(ls /tmp/artifacts/ 2>/dev/null)" ]; then - echo "---> Restoring build artifacts..." - mv /tmp/artifacts/. ./ -fi - echo "---> Installing application source..." -cp -Rf /tmp/src/. ./ +mkdir -p ${APP_DIR}/src +cp -Rf /tmp/src/. ${APP_DIR}/src echo "---> Building application from source..." -if [ -f requirements.txt ]; then - ${APP_DIR}/venv/bin/pip install --no-cache-dir -r requirements.txt +if [ -f ${APP_DIR}/src/requirements.txt ]; then + ${APP_DIR}/venv/bin/pip install --no-cache-dir -r ${APP_DIR}/src/requirements.txt fi

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Properly install ipywidgets in base image

MODIFY singleuser-builder/Dockerfile singleuser-builder/Dockerfile @@ -24,7 +24,8 @@ WORKDIR /home/jovyan USER jovyan RUN python3 -m venv ${APP_DIR}/venv -RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 ipywidgets==5.2.3 +RUN ${APP_DIR}/venv/bin/pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 ipywidgets==5.2.3 && \ + ${APP_DIR}/venv/bin/jupyter nbextension enable --py widgetsnbextension COPY ./s2i/bin/ /usr/libexec/s2i

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Copy github source into to working directory too This is a hack to make sure that binder-like workflows work ok

MODIFY singleuser-builder/s2i/bin/assemble singleuser-builder/s2i/bin/assemble @@ -17,6 +17,10 @@ echo "---> Installing application source..." mkdir -p ${APP_DIR}/src cp -Rf /tmp/src/. ${APP_DIR}/src +# HACK: We copy it to current directory too, since people wanna see the +# notebooks and stuff in there. Figure out a way to tweak this? +cp -Rf /tmp/src/. . + echo "---> Building application from source..." if [ -f ${APP_DIR}/src/requirements.txt ]; then ${APP_DIR}/venv/bin/pip install --no-cache-dir -r ${APP_DIR}/src/requirements.txt

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try, fail and give up on getting miniconda to work Someone else should do this :)

MODIFY singleuser-builder-conda/Dockerfile singleuser-builder-conda/Dockerfile @@ -25,8 +25,9 @@ ADD install-miniconda.bash /usr/local/bin/install-miniconda.bash RUN /usr/local/bin/install-miniconda.bash USER $NB_USER -RUN pip install --no-cache-dir notebook==5.0.0 jupyterhub==0.7.2 ipywidgets==5.2.3 && \ - jupyter nbextension enable --py widgetsnbextension +ADD environment.yml . +RUN conda env create --quiet -n base +RUN rm environment.yml COPY ./s2i/bin/ /usr/libexec/s2i ADD singleuser-builder-conda/environment.yml +name: base +dependencies: +- notebook==5.0.0 +- ipykernel==4.6.0 +- ipywidgets==6.0.0 +- pip: + jupyterhub==0.7.2 MODIFY singleuser-builder-conda/s2i/bin/assemble singleuser-builder-conda/s2i/bin/assemble @@ -19,7 +19,7 @@ cp -Rf /tmp/src/. . echo "---> Building application from source..." if [ -f environment.yml ]; then - conda env update -f environment.yml + conda env update -n base -f environment.yml elif [ -f requirements.txt ]; then pip install -r requirements.txt fi MODIFY singleuser-builder-conda/s2i/bin/run singleuser-builder-conda/s2i/bin/run # https://github.com/openshift/source-to-image/blob/master/docs/builder_image.md # +source activate base exec jupyter notebook --ip=0.0.0.0 MODIFY singleuser-builder-conda/version singleuser-builder-conda/version -v0.1.1 +v0.1.3

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Fail and give up at getting miniconda working again

MODIFY singleuser-builder-conda/Dockerfile singleuser-builder-conda/Dockerfile @@ -14,7 +14,7 @@ RUN apt-get update && \ apt-get purge && apt-get clean ENV CONDA_DIR /opt/conda -ENV PATH $CONDA_DIR/bin:$PATH +ENV PATH $CONDA_DIR/envs/base/bin:$CONDA_DIR/bin/:$PATH ENV NB_USER jovyan RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER} @@ -26,7 +26,7 @@ RUN /usr/local/bin/install-miniconda.bash USER $NB_USER ADD environment.yml . -RUN conda env create --quiet -n base +RUN conda env create --quiet -n base && conda clean -tipsy RUN rm environment.yml COPY ./s2i/bin/ /usr/libexec/s2i MODIFY singleuser-builder-conda/environment.yml singleuser-builder-conda/environment.yml @@ -4,4 +4,4 @@ dependencies: - ipykernel==4.6.0 - ipywidgets==6.0.0 - pip: - jupyterhub==0.7.2 + - jupyterhub==0.7.2 MODIFY singleuser-builder-conda/version singleuser-builder-conda/version -v0.1.3 +v0.1.4

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Switch to an even older docker API version This works with GKE which has Docker 1.11

MODIFY builder/app.py builder/app.py @@ -78,7 +78,7 @@ class Builder(Application): if bp.detect(output_path): bp.build(output_path, self.output_image_spec) - client = docker.from_env(version='1.24') + client = docker.from_env(version='1.23') for line in client.images.push(self.output_image_spec, stream=True): progress = json.loads(line.decode('utf-8')) print(progress['status'])

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Bump s2i builder images

MODIFY builder/detectors.py builder/detectors.py @@ -22,8 +22,8 @@ class BuildPack(LoggingConfigurable): class PythonBuildPack(BuildPack): runtime_builder_map = Dict({ - 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.2', - 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.2', + 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.3', + 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.3', }) runtime = Unicode(

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Print entire progress object Should be moved into structlog soon

MODIFY builder/app.py builder/app.py @@ -81,7 +81,7 @@ class Builder(Application): client = docker.from_env(version='1.23') for line in client.images.push(self.output_image_spec, stream=True): progress = json.loads(line.decode('utf-8')) - print(progress['status']) + print(progress) if __name__ == '__main__': f = Builder()

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Update venv image version again Should move these out to config soon

MODIFY builder/detectors.py builder/detectors.py @@ -22,8 +22,8 @@ class BuildPack(LoggingConfigurable): class PythonBuildPack(BuildPack): runtime_builder_map = Dict({ - 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.3', - 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.3', + 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.4', + 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.4', }) runtime = Unicode(

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Add a simple but fully functional Dockerfile

ADD Dockerfile +FROM ubuntu:16.10 + +RUN apt-get update && \ + apt-get install --yes --no-install-recommends \ + curl \ + python3 \ + python3-pip \ + python3-setuptools \ + git && \ + apt-get clean && apt-get purge + +COPY install-s2i.bash /usr/local/bin/install-s2i.bash +RUN /usr/local/bin/install-s2i.bash + +RUN pip3 install --no-cache-dir git+https://github.com/yuvipanda/builder@e7d51c3 + ADD install-s2i.bash +#!/bin/bash +set -e + +cd /usr/local/bin/ && curl -L https://github.com/openshift/source-to-image/releases/download/v1.1.5/source-to-image-v1.1.5-4dd7721-linux-amd64.tar.gz | tar xvz +

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Add a dockerfile based BuildPack Great escape hatch

MODIFY builder/app.py builder/app.py @@ -9,7 +9,7 @@ import docker import subprocess -from .detectors import BuildPack, PythonBuildPack +from .detectors import BuildPack, PythonBuildPack, DockerBuildPack class Builder(Application): config_file = Unicode( @@ -42,7 +42,7 @@ class Builder(Application): buildpacks = List( None, - [PythonBuildPack], + [DockerBuildPack, PythonBuildPack], config=True ) @@ -77,6 +77,10 @@ class Builder(Application): bp = bp_class() if bp.detect(output_path): bp.build(output_path, self.output_image_spec) + break + else: + raise Exception("No compatible builders found") + client = docker.from_env(version='1.23') for line in client.images.push(self.output_image_spec, stream=True): MODIFY builder/detectors.py builder/detectors.py import os import subprocess +import docker + from traitlets import Unicode, Dict from traitlets.config import LoggingConfigurable @@ -20,6 +22,21 @@ class BuildPack(LoggingConfigurable): +class DockerBuildPack(BuildPack): + def detect(self, workdir): + return os.path.exists(os.path.join(workdir, 'Dockerfile')) + + def build(self, workdir, output_image_spec): + client = docker.APIClient(base_url='unix://var/run/docker.sock', version='auto') + for progress in client.build( + path=workdir, + tag=output_image_spec, + decode=True + ): + # FIXME: Properly stream back useful information only + pass + + class PythonBuildPack(BuildPack): runtime_builder_map = Dict({ 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.4',

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Have Dockerfile build off current dir Makes it much easier to test!

MODIFY Dockerfile Dockerfile @@ -12,5 +12,7 @@ RUN apt-get update && \ COPY install-s2i.bash /usr/local/bin/install-s2i.bash RUN /usr/local/bin/install-s2i.bash -RUN pip3 install --no-cache-dir git+https://github.com/yuvipanda/builder@e7d51c3 +RUN mkdir /tmp/src +ADD . /tmp/src +RUN pip3 install /tmp/src

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Bump version of venv builders

MODIFY builder/detectors.py builder/detectors.py @@ -39,8 +39,8 @@ class DockerBuildPack(BuildPack): class PythonBuildPack(BuildPack): runtime_builder_map = Dict({ - 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.4', - 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.4', + 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.5', + 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.5', }) runtime = Unicode(

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Do a hacky attempt at not rebuilding already-built images This is such a complete and utter hack, and I should be somewhat ashamed of myself. *However*, the docker registry API seems to be a piece of poop, and there seem to be absolutely no client libraries for it in python :(

MODIFY builder/app.py builder/app.py @@ -67,6 +67,23 @@ class Builder(Application): self.load_config_file(self.config_file) def run(self): + # HACK: Try to just pull this and see if that works. + # if it does, then just bail. + # WHAT WE REALLY WANT IS TO NOT DO ANY WORK IF THE IMAGE EXISTS + client = docker.APIClient(base_url='unix://var/run/docker.sock', version='auto') + + try: + repo, tag = self.output_image_spec.split(':') + for line in client.pull( + repository=repo, + tag=tag, + stream=True, + ): + print(json.loads(line.decode('utf-8'))) + return + except docker.errors.ImageNotFound: + pass + output_path = os.path.join(self.git_workdir, self.build_name) self.fetch( self.source_url, @@ -82,8 +99,7 @@ class Builder(Application): raise Exception("No compatible builders found") - client = docker.from_env(version='1.23') - for line in client.images.push(self.output_image_spec, stream=True): + for line in client.push(self.output_image_spec, stream=True): progress = json.loads(line.decode('utf-8')) print(progress)

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Actually check out the ref that is passed to builder We weren't actually doing this earlier. boo

MODIFY builder/app.py builder/app.py @@ -75,7 +75,7 @@ class Builder(Application): sys.exit(1) try: - for line in execute_cmd(['git', '--git-dir', os.path.join(output_path, '.git'), 'checkout', ref]): + for line in execute_cmd(['git', '--git-dir', os.path.join(output_path, '.git'), 'reset', '--hard', ref]): self.log.info(line, extra=dict(phase='fetching')) except subprocess.CalledProcessError: self.log.error('Failed to check out ref %s', ref, extra=dict(phase='failed')) @@ -113,7 +113,7 @@ class Builder(Application): output_path = os.path.join(self.git_workdir, self.build_name) self.fetch( self.source_url, - 'master', + self.source_ref, output_path ) for bp_class in self.buildpacks:

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cleanup after installing in assemble step

MODIFY singleuser-builder-conda/s2i/bin/assemble singleuser-builder-conda/s2i/bin/assemble @@ -20,6 +20,7 @@ cp -Rf /tmp/src/. . echo "---> Building application from source..." if [ -f environment.yml ]; then conda env update -n root -f environment.yml + conda clean -tipsy elif [ -f requirements.txt ]; then pip install -r requirements.txt fi

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launch docker with kwargs_from_env respects DOCKER_HOST, etc.

MODIFY builder/app.py builder/app.py @@ -9,6 +9,7 @@ from pythonjsonlogger import jsonlogger from traitlets.config import Application, LoggingConfigurable, Unicode, Dict, List from traitlets import Type import docker +from docker.utils import kwargs_from_env import subprocess @@ -96,7 +97,7 @@ class Builder(Application): # HACK: Try to just pull this and see if that works. # if it does, then just bail. # WHAT WE REALLY WANT IS TO NOT DO ANY WORK IF THE IMAGE EXISTS - client = docker.APIClient(base_url='unix://var/run/docker.sock', version='auto') + client = docker.APIClient(version='auto', **kwargs_from_env()) repo, tag = self.output_image_spec.split(':') for line in client.pull(

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[ 1, 20738, 6267, 598, 1205, 67, 2080, 67, 3074, 203, 455, 1181, 87, 5467, 3507, 654, 67, 8908, 16, 5527, 18, 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 ]

catch ImageNotFound on initial pull

MODIFY builder/app.py builder/app.py @@ -100,6 +100,7 @@ class Builder(Application): client = docker.APIClient(version='auto', **kwargs_from_env()) repo, tag = self.output_image_spec.split(':') + try: for line in client.pull( repository=repo, tag=tag, @@ -110,6 +111,8 @@ class Builder(Application): break else: return + except docker.errors.ImageNotFound: + pass output_path = os.path.join(self.git_workdir, self.build_name) self.fetch(

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comments for pull cases

MODIFY builder/app.py builder/app.py @@ -108,10 +108,13 @@ class Builder(Application): ): progress = json.loads(line.decode('utf-8')) if 'error' in progress: + # pull failed, proceed to build break else: + # image exists, nothing to build return except docker.errors.ImageNotFound: + # image not found, proceed to build pass output_path = os.path.join(self.git_workdir, self.build_name)

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Make sure that the cleanup is actually conditional

MODIFY builder/app.py builder/app.py @@ -69,6 +69,7 @@ class Builder(Application): 'source': 'Builder.source_url', 'ref': 'Builder.source_ref', 'output': 'Builder.output_image_spec', + 'clean': 'Builder.cleanup_checkout', 'f': 'Builder.config_file', }) @@ -155,6 +156,7 @@ class Builder(Application): self.log.info('Pushing image', extra=dict(progress=layers, phase='pushing')) last_emit_time = time.time() + if self.cleanup_checkout: shutil.rmtree(output_path)

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Use cwd switching to do git operations Setting just --git-dir is not enough, you also need to set work-dir. Just setting cwd is better

MODIFY builder/app.py builder/app.py @@ -83,7 +83,7 @@ class Builder(Application): sys.exit(1) try: - for line in execute_cmd(['git', '--git-dir', os.path.join(output_path, '.git'), 'reset', '--hard', ref]): + for line in execute_cmd(['git', 'reset', '--hard', ref], output_path): self.log.info(line, extra=dict(phase='fetching')) except subprocess.CalledProcessError: self.log.error('Failed to check out ref %s', ref, extra=dict(phase='failed')) MODIFY builder/detectors.py builder/detectors.py @@ -65,12 +65,12 @@ class S2IBuildPack(BuildPack): 'build', '--exclude', '""', '--ref', ref, - workdir, + '.', build_image, output_image_spec, ] try: - for line in execute_cmd(cmd): + for line in execute_cmd(cmd, cwd=workdir): self.log.info(line, extra=dict(phase='building', builder=self.name)) except subprocess.CalledProcessError: self.log.error('Failed to build image!', extra=dict(phase='failed')) MODIFY builder/utils.py builder/utils.py import subprocess -def execute_cmd(cmd): +def execute_cmd(cmd, cwd=None): """ Call given command, yielding output line by line """ - proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) + proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True, cwd=cwd) try: for line in iter(proc.stdout.readline, ''):

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Upgrade version of s2i

MODIFY install-s2i.bash install-s2i.bash #!/bin/bash set -e -cd /usr/local/bin/ && curl -L https://github.com/openshift/source-to-image/releases/download/v1.1.5/source-to-image-v1.1.5-4dd7721-linux-amd64.tar.gz | tar xvz +cd /usr/local/bin/ && curl -L https://github.com/openshift/source-to-image/releases/download/v1.1.6/source-to-image-v1.1.6-f519129-linux-amd64.tar.gz | tar xvz

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Add a simple README

ADD README.md +## Builder + +**Note*: The project will probably be renamed soon! + +A simple commandline tool that builds a docker image off a git repository & pushes it to a repo. + +It mostly relies on other tools ([Source to Image](https://github.com/openshift/source-to-image) or just docker) +for doing the actual building. It is a simple wrapper that does detection to figure out which +build method to use, and how to invoke that build method.

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Remove .gitignore in anticipation of merging with s2i

DELETE .gitignore -node_modules -*.py[co] -*~ -.cache -.DS_Store -build -dist -docs/_build -docs/source/_static/rest-api -.ipynb_checkpoints -# ignore config file at the top-level of the repo -# but not sub-dirs -/jupyterhub_config.py -jupyterhub_cookie_secret -jupyterhub.sqlite -share/jupyter/hub/static/components -share/jupyter/hub/static/css/style.min.css -share/jupyter/hub/static/css/style.min.css.map -*.egg-info -MANIFEST -.coverage -htmlcov -bin/ -lib/ -include/ -share/

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Rename builder to repo2docker Package name is jupyter-repo2docker

RENAME builder/__init__.py repo2docker/__init__.py RENAME builder/app.py repo2docker/app.py @@ -19,9 +19,9 @@ from .detectors import BuildPack, PythonBuildPack, DockerBuildPack, CondaBuildPa from .utils import execute_cmd -class Builder(Application): +class Repo2Docker(Application): config_file = Unicode( - 'builder_config.py', + 'repo2docker_config.py', config=True ) @@ -66,11 +66,11 @@ class Builder(Application): ) aliases = Dict({ - 'source': 'Builder.source_url', - 'ref': 'Builder.source_ref', - 'output': 'Builder.output_image_spec', - 'clean': 'Builder.cleanup_checkout', - 'f': 'Builder.config_file', + 'source': 'Repo2Docker.source_url', + 'ref': 'Repo2Docker.source_ref', + 'output': 'Repo2Docker.output_image_spec', + 'clean': 'Repo2Docker.cleanup_checkout', + 'f': 'Repo2Docker.config_file', }) @@ -161,6 +161,6 @@ class Builder(Application): if __name__ == '__main__': - f = Builder() + f = Repo2Docker() f.initialize() f.run() RENAME builder/detectors.py repo2docker/detectors.py RENAME builder/utils.py repo2docker/utils.py MODIFY setup.py setup.py from setuptools import setup, find_packages setup( - name='builder', + name='jupyter-repo2docker', version='0.1', install_requires=[ 'docker',

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Rename alias for output image Makes more sense

MODIFY repo2docker/app.py repo2docker/app.py @@ -89,7 +89,7 @@ class Repo2Docker(Application): aliases = Dict({ 'source': 'Repo2Docker.source_url', 'ref': 'Repo2Docker.source_ref', - 'output': 'Repo2Docker.output_image_spec', + 'image': 'Repo2Docker.output_image_spec', 'clean': 'Repo2Docker.cleanup_checkout', 'f': 'Repo2Docker.config_file', })

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Specify the type of buildpack list elements

MODIFY repo2docker/app.py repo2docker/app.py @@ -67,7 +67,7 @@ class Repo2Docker(Application): ) buildpacks = List( - None, + Type(BuildPack), [DockerBuildPack, CondaBuildPack, PythonBuildPack], config=True, help="""

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Add a little more bit of documentation

MODIFY repo2docker/app.py repo2docker/app.py @@ -22,7 +22,10 @@ from .utils import execute_cmd class Repo2Docker(Application): config_file = Unicode( 'repo2docker_config.py', - config=True + config=True, + help=""" + Path to read traitlets configuration file from. + """ ) source_url = Unicode(

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Rename source_url and source_ref to repo and ref Makes more sense, and also now consistent with the repository name

MODIFY repo2docker/app.py repo2docker/app.py @@ -28,16 +28,18 @@ class Repo2Docker(Application): """ ) - source_url = Unicode( - None, + repo = Unicode( + '.', allow_none=True, config=True, help=""" - URL to the git repository to clone. + The git repository to clone. + + Could be a https URL, or a file path. """ ) - source_ref = Unicode( + ref = Unicode( 'master', allow_none=True, config=True, @@ -90,8 +92,8 @@ class Repo2Docker(Application): ) aliases = Dict({ - 'source': 'Repo2Docker.source_url', - 'ref': 'Repo2Docker.source_ref', + 'repo': 'Repo2Docker.repo', + 'ref': 'Repo2Docker.ref', 'image': 'Repo2Docker.output_image_spec', 'clean': 'Repo2Docker.cleanup_checkout', 'f': 'Repo2Docker.config_file', @@ -151,15 +153,15 @@ class Repo2Docker(Application): checkout_path = os.path.join(self.git_workdir, str(uuid.uuid4())) self.fetch( - self.source_url, - self.source_ref, + self.repo, + self.ref, checkout_path ) for bp_class in self.buildpacks: bp = bp_class() if bp.detect(checkout_path): self.log.info('Using %s builder', bp.name, extra=dict(phase='building')) - bp.build(checkout_path, self.source_ref, self.output_image_spec) + bp.build(checkout_path, self.ref, self.output_image_spec) break else: self.log.error('Could not figure out how to build this repository! Tell us?', extra=dict(phase='failed'))

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Add a __main__ and an entrypoint

ADD repo2docker/__main__.py +from .app import Repo2Docker + +if __name__ == '__main__': + f = Repo2Docker() + f.run() MODIFY repo2docker/app.py repo2docker/app.py @@ -186,7 +186,3 @@ class Repo2Docker(Application): shutil.rmtree(checkout_path) -if __name__ == '__main__': - f = Repo2Docker() - f.initialize() - f.run() MODIFY setup.py setup.py @@ -12,4 +12,9 @@ setup( author_email='yuvipanda@gmail.com', license='BSD', packages=find_packages(), + entry_points={ + 'console_scripts': [ + 'jupyter-repo2docker = repo2docker.__main__:main' + ] + }, )

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Set a default image name if none is provided It's kind of shitty but better than just erroring.

MODIFY repo2docker/app.py repo2docker/app.py @@ -6,6 +6,7 @@ import logging import uuid import shutil from pythonjsonlogger import jsonlogger +import escapism from traitlets.config import Application, LoggingConfigurable @@ -126,6 +127,12 @@ class Repo2Docker(Application): self.log.setLevel(logging.INFO) self.load_config_file(self.config_file) + if self.output_image_spec is None: + # Attempt to set a sane default! + # HACK: Provide something more descriptive? + self.output_image_spec = escapism.escape(self.repo).lower() + ':' + self.ref.lower() + + def run(self): # HACK: Try to just pull this and see if that works. # if it does, then just bail.

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Make push optional and default to False Let's optimize the defaults for good commandline usage rather than for binderhub usage

MODIFY repo2docker/app.py repo2docker/app.py @@ -92,11 +92,20 @@ class Repo2Docker(Application): """ ) + push = Bool( + False, + config=True, + help=""" + If the image should be pushed after it is built. + """ + ) + aliases = Dict({ 'repo': 'Repo2Docker.repo', 'ref': 'Repo2Docker.ref', 'image': 'Repo2Docker.output_image_spec', 'clean': 'Repo2Docker.cleanup_checkout', + 'push': 'Repo2Docker.push', 'f': 'Repo2Docker.config_file', }) @@ -174,11 +183,15 @@ class Repo2Docker(Application): self.log.error('Could not figure out how to build this repository! Tell us?', extra=dict(phase='failed')) sys.exit(1) + if self.push: # Build a progress setup for each layer, and only emit per-layer info every 1.5s layers = {} last_emit_time = time.time() for line in client.push(self.output_image_spec, stream=True): progress = json.loads(line.decode('utf-8')) + if 'error' in progress: + self.log.error(progress['error'], extra=dict(phase='failed')) + sys.exit(1) if 'id' not in progress: continue if 'progressDetail' in progress and progress['progressDetail']: @@ -189,6 +202,7 @@ class Repo2Docker(Application): self.log.info('Pushing image', extra=dict(progress=layers, phase='pushing')) last_emit_time = time.time() + if self.cleanup_checkout: shutil.rmtree(checkout_path)

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Kill the container when our program exits

MODIFY repo2docker/app.py repo2docker/app.py @@ -180,8 +180,13 @@ class Repo2Docker(Application): ports={'8888/tcp': 8888}, detach=True ) + try: for line in container.logs(stream=True): self.log.info(line.decode('utf-8').rstrip(), extra=dict(phase='running')) + finally: + self.log.info('Stopping container...', extra=dict(phase='running')) + container.kill() + container.remove() def start(self): # HACK: Try to just pull this and see if that works.

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Don't use host network for running containers Doesn't really work on OS X. BOO!

MODIFY repo2docker/app.py repo2docker/app.py @@ -179,7 +179,7 @@ class Repo2Docker(Application): client = docker.from_env(version='auto') container = client.containers.run( self.output_image_spec, - network_mode='host', + ports={'8888/tcp': None}, detach=True ) try:

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Print out the host port number in a log message Eventually, we should actually be passing the port number inside the docker container, after verifying that it is available on the host. We can deal with races by doing the same thing that ipython notebook does.

MODIFY repo2docker/app.py repo2docker/app.py @@ -182,6 +182,12 @@ class Repo2Docker(Application): ports={'8888/tcp': None}, detach=True ) + while container.status == 'created': + time.sleep(0.5) + container.reload() + + host_port = container.attrs['NetworkSettings']['Ports']['8888/tcp'][0]['HostPort'] + self.log.info('Port 8888 mapped to port %s on the machine docker is running on', host_port, extra=dict(phase='running')) try: for line in container.logs(stream=True): self.log.info(line.decode('utf-8').rstrip(), extra=dict(phase='running'))

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support repo as positional arg and flesh out some Application basics: version, name, docstring

MODIFY repo2docker/__init__.py repo2docker/__init__.py +__version__ = '0.1.0' MODIFY repo2docker/app.py repo2docker/app.py +"""repo2docker: convert git repositories into jupyter-suitable docker images + +Images produced by repo2docker can be used with Jupyter notebooks standalone or via JupyterHub. + +Usage: + + python -m repo2docker https://github.com/you/your-repo +""" import sys import json import os @@ -18,9 +26,13 @@ import subprocess from .detectors import BuildPack, PythonBuildPack, DockerBuildPack, CondaBuildPack from .utils import execute_cmd - +from . import __version__ class Repo2Docker(Application): + name = 'jupyter-repo2docker' + version = __version__ + description = __doc__ + config_file = Unicode( 'repo2docker_config.py', config=True, @@ -36,7 +48,7 @@ class Repo2Docker(Application): help=""" The git repository to clone. - Could be a https URL, or a file path. + Could be a git URL or a file path. """ ) @@ -149,6 +161,14 @@ class Repo2Docker(Application): self.log.setLevel(logging.INFO) self.load_config_file(self.config_file) + if len(self.extra_args) == 1: + # accept repo as a positional arg + self.repo = self.extra_args[0] + elif len(self.extra_args) > 1: + print("%s accepts at most one positional argument." % self.name, file=sys.stderr) + print("See python -m repo2docker --help for usage", file=sys.stderr) + self.exit(1) + if self.output_image_spec is None: # Attempt to set a sane default! # HACK: Provide something more descriptive?

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Move image existence check to a separate repo

MODIFY repo2docker/app.py repo2docker/app.py @@ -216,31 +216,19 @@ class Repo2Docker(Application): container.kill() container.remove() - def start(self): + def image_exists(self): + client = docker.from_env(version='auto') # HACK: Try to just pull this and see if that works. # if it does, then just bail. # WHAT WE REALLY WANT IS TO NOT DO ANY WORK IF THE IMAGE EXISTS - client = docker.APIClient(version='auto', **kwargs_from_env()) - - repo, tag = self.output_image_spec.split(':') try: - for line in client.pull( - repository=repo, - tag=tag, - stream=True, - ): - progress = json.loads(line.decode('utf-8')) - if 'error' in progress: - # pull failed, proceed to build - break - else: - # image exists, nothing to build - return + image = client.images.pull(self.output_image_spec) + return True except docker.errors.ImageNotFound: - # image not found, proceed to build - pass - + return False + def start(self): + if not self.image_exists(): checkout_path = os.path.join(self.git_workdir, str(uuid.uuid4())) self.fetch( self.repo,

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Use same port in host and docker container Makes it work on Linux and the default OS X install I think

MODIFY repo2docker/app.py repo2docker/app.py @@ -197,17 +197,17 @@ class Repo2Docker(Application): def run_image(self): client = docker.from_env(version='auto') + port = self._get_free_port() container = client.containers.run( self.output_image_spec, - ports={'8888/tcp': None}, - detach=True + ports={'%s/tcp' % port: port}, + detach=True, + command=['jupyter', 'notebook', '--ip', '0.0.0.0', '--port', str(port)], ) while container.status == 'created': time.sleep(0.5) container.reload() - host_port = container.attrs['NetworkSettings']['Ports']['8888/tcp'][0]['HostPort'] - self.log.info('Port 8888 mapped to port %s on the machine docker is running on', host_port, extra=dict(phase='running')) try: for line in container.logs(stream=True): self.log.info(line.decode('utf-8').rstrip(), extra=dict(phase='running')) @@ -216,6 +216,17 @@ class Repo2Docker(Application): container.kill() container.remove() + def _get_free_port(self): + """ + Hacky method to get a free random port on local host + """ + import socket + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + s.bind(("",0)) + port = s.getsockname()[1] + s.close() + return port + def image_exists(self): client = docker.from_env(version='auto') # HACK: Try to just pull this and see if that works.

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Fix format of command

MODIFY builder.md builder.md @@ -79,4 +79,6 @@ repos. 3. Once everything above is done, you should be able to build a repo by specifying a source repo URL with this command: + ```bash python -m repo2docker https://github.com/yourname/your-repo + ```

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apply platform tag to wheels

ADD setup.cfg +[wheel] +universal=1 \ No newline at end of file MODIFY setup.py setup.py @@ -72,6 +72,24 @@ if sys.platform in checksums: else: print("I don't know how to bundle s2i for %s" % sys.platform) +cmdclass = {} +try: + from wheel.bdist_wheel import bdist_wheel + from wheel.pep425tags import get_platform +except ImportError: + # no wheel + pass +else: + # apply current platform tag + # because we bundle platform-specific s2i binaries + class PlatformBDistWheel(bdist_wheel): + def initialize_options(self): + super(PlatformBDistWheel, self).initialize_options() + if self.plat_name is None: + self.plat_name = get_platform() + + cmdclass['bdist_wheel'] = PlatformBDistWheel + setup( name='jupyter-repo2docker', version='0.1', @@ -84,6 +102,7 @@ setup( author='Yuvi Panda', author_email='yuvipanda@gmail.com', license='BSD', + cmdclass=cmdclass, package_data={ 'repo2docker': ['s2i'], },

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flush lines with carriage returns for terminal progress bars

MODIFY repo2docker/utils.py repo2docker/utils.py +from functools import partial import subprocess def execute_cmd(cmd, capture=False, **kwargs): @@ -16,9 +17,21 @@ def execute_cmd(cmd, capture=False, **kwargs): raise subprocess.CalledProcessError(ret, cmd) return + buf = [] + def flush(): + line = b''.join(buf).decode('utf8', 'replace') + buf[:] = [] + return line + + c_last = '' try: - for line in iter(proc.stdout.readline, b''): - yield line.decode('utf8', 'replace') + for c in iter(partial(proc.stdout.read, 1), b''): + if c_last == b'\r' and buf and c != b'\n': + yield flush() + buf.append(c) + if c == b'\n': + yield flush() + c_last = c finally: ret = proc.wait() if ret != 0:

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comment about output capturing

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -12,11 +12,16 @@ def execute_cmd(cmd, capture=False, **kwargs): proc = subprocess.Popen(cmd, **kwargs) if not capture: + # not capturing output, let the subprocesses talk directly to the terminal ret = proc.wait() if ret != 0: raise subprocess.CalledProcessError(ret, cmd) return + # Capture output for logging. + # Each line will be yielded as text. + # This should behave the same as .readline(), but splits on `\r` OR `\n`, + # not just `\n`. buf = [] def flush(): line = b''.join(buf).decode('utf8', 'replace')

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update manifest for sdist

MODIFY .gitignore .gitignore @@ -5,5 +5,6 @@ build *.egg-info *.py[co] __pycache__ +MANIFEST repo2docker/s2i ADD MANIFEST.in +exclude repo2docker/s2i +include Dockerfile +include *.md +include LICENSE +include setup.cfg + +graft s2i-builders

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Add link to builder doc

MODIFY README.md README.md @@ -37,3 +37,7 @@ method to use, and how to invoke that build method. The `s2i-builders` directory contains builder images which can be used to provide custom `conda` and `venv` environments suitable for running **JupyterHub**. + +## Documentation + +[Creating a new builder](builder.md)

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respect docker env in docker buildpack

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -3,6 +3,7 @@ import sys import subprocess import docker +from docker.utils import kwargs_from_env from traitlets import Unicode, Dict, Bool from traitlets.config import LoggingConfigurable @@ -37,7 +38,7 @@ class DockerBuildPack(BuildPack): return os.path.exists(os.path.join(workdir, 'Dockerfile')) def build(self, workdir, ref, output_image_spec): - client = docker.APIClient(base_url='unix://var/run/docker.sock', version='auto') + client = docker.APIClient(version='auto', **kwargs_from_env()) for progress in client.build( path=workdir, tag=output_image_spec,

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only log build output if capture=true use stdout.write otherwise

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -45,7 +45,12 @@ class DockerBuildPack(BuildPack): decode=True ): if 'stream' in progress: + if self.capture: self.log.info(progress['stream'], extra=dict(phase='building')) + else: + sys.stdout.write(progress['stream']) + +_legacybinder_docker_appendix = """ class S2IBuildPack(BuildPack):

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move dockerfile appendix into LegacyBinderDockerBuildPack.dockerfile_appendix and make it overrideable

MODIFY repo2docker/detectors.py repo2docker/detectors.py import os import sys import subprocess +from textwrap import dedent import docker from docker.utils import kwargs_from_env @@ -50,7 +51,11 @@ class DockerBuildPack(BuildPack): else: sys.stdout.write(progress['stream']) -_legacy_binder_docker_appendix = """ + +class LegacyBinderDockerBuildPack(DockerBuildPack): + + name = Unicode('Legacy Binder Dockerfile') + dockerfile_appendix = Unicode(dedent(r""" USER root COPY . /home/main/notebooks RUN chown -R main:main /home/main/notebooks @@ -65,11 +70,8 @@ RUN conda install -n python3 notebook==5.0.0 ipykernel==4.6.0 && \ /home/main/anaconda2/bin/ipython kernel install --prefix=/home/main/anaconda2/envs/python3 ENV JUPYTER_PATH /home/main/anaconda2/share/jupyter:$JUPYTER_PATH CMD jupyter notebook --ip 0.0.0.0 -""" - -class LegacyBinderDockerBuildPack(DockerBuildPack): + """), config=True) - name = Unicode('Legacy Binder Dockerfile') def detect(self, workdir): dockerfile = os.path.join(workdir, 'Dockerfile') if not os.path.exists(dockerfile): @@ -86,8 +88,9 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): return False def amend_dockerfile(self, dockerfile): + print(self.dockerfile_appendix) with open(dockerfile, 'a') as f: - f.write(_legacy_binder_docker_appendix) + f.write(self.dockerfile_appendix) class S2IBuildPack(BuildPack):

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Don't print appendix on each run for legacy dockerfile

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -55,6 +55,7 @@ class DockerBuildPack(BuildPack): class LegacyBinderDockerBuildPack(DockerBuildPack): name = Unicode('Legacy Binder Dockerfile') + dockerfile_appendix = Unicode(dedent(r""" USER root COPY . /home/main/notebooks @@ -88,7 +89,6 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): return False def amend_dockerfile(self, dockerfile): - print(self.dockerfile_appendix) with open(dockerfile, 'a') as f: f.write(self.dockerfile_appendix)

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Add makefile for building and pushing image

ADD Makefile +VERSION=$(shell git rev-parse --short HEAD) +IMAGE_PREFIX=jupyter/ + +build-image: + docker build -t $(IMAGE_PREFIX)repo2docker:v$(VERSION) . + +push-image: + docker push $(IMAGE_PREFIX)repo2docker:v$(VERSION) + +.all: + build-image push-image

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Add makefile targets to push docker images

MODIFY s2i-builders/conda/Makefile s2i-builders/conda/Makefile @@ -6,7 +6,5 @@ VERSION = $(shell cat version) build: docker build -t $(IMAGE_NAME):$(VERSION) . -.PHONY: test -test: - docker build -t $(IMAGE_NAME)-candidate:$(VERSION) . - IMAGE_NAME=$(IMAGE_NAME)-candidate:$(VERSION) test/run +push: + docker push "$(IMAGE_NAME):$(VERSION)" MODIFY s2i-builders/venv/Makefile s2i-builders/venv/Makefile @@ -5,3 +5,7 @@ VERSION = $(shell cat version) build: docker build -t $(IMAGE_PREFIX)3.5:$(VERSION) . -f Dockerfile docker build -t $(IMAGE_PREFIX)2.7:$(VERSION) . -f Dockerfile.py2 + +push: + docker push "$(IMAGE_PREFIX)3.5:$(VERSION)" + docker push "$(IMAGE_PREFIX)2.7:$(VERSION)"

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Use never versions of s2i builder images in detectors

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -130,7 +130,7 @@ class CondaBuildPack(S2IBuildPack): """Build Pack for installing from a conda environment.yml using S2I""" name = Unicode('conda') - build_image = Unicode('jupyterhub/singleuser-builder-conda:v0.1.5', config=True) + build_image = Unicode('jupyterhub/singleuser-builder-conda:v0.2.0', config=True) def detect(self, workdir): return os.path.exists(os.path.join(workdir, 'environment.yml')) @@ -140,8 +140,8 @@ class PythonBuildPack(S2IBuildPack): """Build Pack for installing from a pip requirements.txt using S2I""" name = Unicode('python-pip') runtime_builder_map = Dict({ - 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.1.5', - 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.1.5', + 'python-2.7': 'jupyterhub/singleuser-builder-venv-2.7:v0.2.0', + 'python-3.5': 'jupyterhub/singleuser-builder-venv-3.5:v0.2.0', }) runtime = Unicode(

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Add a default build pack Gives you a blank python3 environment

MODIFY repo2docker/app.py repo2docker/app.py @@ -26,7 +26,7 @@ import subprocess from .detectors import ( BuildPack, PythonBuildPack, DockerBuildPack, LegacyBinderDockerBuildPack, - CondaBuildPack, + CondaBuildPack, DefaultBuildPack ) from .utils import execute_cmd from . import __version__ @@ -93,7 +93,7 @@ class Repo2Docker(Application): buildpacks = List( Type(BuildPack), - [LegacyBinderDockerBuildPack, DockerBuildPack, CondaBuildPack, PythonBuildPack], + [LegacyBinderDockerBuildPack, DockerBuildPack, CondaBuildPack, PythonBuildPack, DefaultBuildPack], config=True, help=""" Ordered list of BuildPacks to try to use to build a git repository. MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -158,3 +158,10 @@ class PythonBuildPack(S2IBuildPack): pass self.build_image = self.runtime_builder_map[self.runtime] return True + +class DefaultBuildPack(S2IBuildPack): + build_image = Unicode('jupyterhub/singleuser-builder-venv-3.5:v0.2.0') + name = Unicode('default') + def detect(self, workdir): + return True +

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Remove docker-pull hack No longer check if image exists by doing a docker-pull - binderhub will no longer start a build if it knows that the image already exists

MODIFY repo2docker/app.py repo2docker/app.py @@ -251,25 +251,14 @@ class Repo2Docker(Application): s.close() return port - def image_exists(self): - client = docker.from_env(version='auto') - # HACK: Try to just pull this and see if that works. - # if it does, then just bail. - # WHAT WE REALLY WANT IS TO NOT DO ANY WORK IF THE IMAGE EXISTS - try: - image = client.images.pull(self.output_image_spec) - return True - except docker.errors.ImageNotFound: - return False - def start(self): - if not self.image_exists(): checkout_path = os.path.join(self.git_workdir, str(uuid.uuid4())) self.fetch( self.repo, self.ref, checkout_path ) + for bp_class in self.buildpacks: bp = bp_class(parent=self, log=self.log, capture=self.json_logs) if bp.detect(checkout_path): @@ -288,6 +277,3 @@ class Repo2Docker(Application): if self.run: self.run_image() - - -

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Add jupyterlab by default to the conda builder

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -130,7 +130,7 @@ class CondaBuildPack(S2IBuildPack): """Build Pack for installing from a conda environment.yml using S2I""" name = Unicode('conda') - build_image = Unicode('jupyterhub/singleuser-builder-conda:v0.2.0', config=True) + build_image = Unicode('jupyterhub/singleuser-builder-conda:v0.2.1', config=True) def detect(self, workdir): return os.path.exists(os.path.join(workdir, 'environment.yml')) MODIFY s2i-builders/conda/environment.yml s2i-builders/conda/environment.yml @@ -4,5 +4,6 @@ dependencies: - ipython==6.0.0 - ipykernel==4.6.0 - ipywidgets==6.0.0 + - jupyterlab==0.22.1 - pip: - jupyterhub==0.7.2 MODIFY s2i-builders/conda/version s2i-builders/conda/version -v0.2.0 +v0.2.1

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Bump version of image for default builder

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -160,7 +160,7 @@ class PythonBuildPack(S2IBuildPack): return True class DefaultBuildPack(S2IBuildPack): - build_image = Unicode('jupyterhub/singleuser-builder-venv-3.5:v0.2.0') + build_image = Unicode('jupyterhub/singleuser-builder-venv-3.5:v0.2.1') name = Unicode('default') def detect(self, workdir): return True

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s2i/venv: Don't have hacky numpy hack build a wheel

MODIFY s2i-builders/venv/s2i/bin/assemble s2i-builders/venv/s2i/bin/assemble @@ -27,7 +27,7 @@ if [ -f ${APP_DIR}/src/requirements.txt ]; then # This is because some packages (tiffiles *cough*) need numpy to be fully installed # for their setup.py to work, and this... causes all sorts of problems. if grep --quiet numpy ${APP_DIR}/src/requirements.txt; then - ${APP_DIR}/venv/bin/pip install $(grep numpy ${APP_DIR}/src/requirements.txt) + ${APP_DIR}/venv/bin/pip install --no-cache-dir $(grep numpy ${APP_DIR}/src/requirements.txt) fi ${APP_DIR}/venv/bin/pip install --no-cache-dir -r ${APP_DIR}/src/requirements.txt fi

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julia version bump

MODIFY s2i-builders/julia/Dockerfile s2i-builders/julia/Dockerfile @@ -36,7 +36,7 @@ RUN mkdir -p ${APP_DIR} && chown -R jovyan:jovyan ${APP_DIR} # Install Julia ENV JULIA_PATH /usr/local/julia -ENV JULIA_VERSION 0.5.2 +ENV JULIA_VERSION 0.6.0 RUN mkdir $JULIA_PATH && \ curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1 @@ -55,7 +55,7 @@ ENV PATH ${APP_DIR}/venv/bin:$PATH:${JULIA_PATH}/bin ENV JULIA_PKGDIR ${APP_DIR}/.julia RUN julia -e 'Pkg.init(); Pkg.add("IJulia")' && \ - mv ${HOME}/.local/share/jupyter/kernels/julia-0.5/ ${APP_DIR}/venv/share/jupyter/kernels/julia-0.5 + mv ${HOME}/.local/share/jupyter/kernels/julia-0.6/ ${APP_DIR}/venv/share/jupyter/kernels/julia-0.6 COPY ./s2i/bin/ /usr/libexec/s2i

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tweak how the python2 kerenl is installed install in its own prefix as well

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -68,7 +68,8 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): conda remove -n python3 nb_conda_kernels && \ conda install -n root ipykernel==4.6.0 && \ /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \ - /home/main/anaconda2/bin/ipython kernel install --prefix=/home/main/anaconda2/envs/python3 + /home/main/anaconda2/bin/ipython kernel install --prefix=/home/main/anaconda2/envs/python3 && \ + /home/main/anaconda2/bin/ipython kernel install --sys-prefix ENV JUPYTER_PATH /home/main/anaconda2/share/jupyter:$JUPYTER_PATH CMD jupyter notebook --ip 0.0.0.0 """), config=True)

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Fix legacy dockerfile buildpack to work properly

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -4,6 +4,7 @@ Generates a variety of Dockerfiles based on an input matrix import textwrap from traitlets.config import LoggingConfigurable from traitlets import Unicode, Set, List, Dict, Tuple, Bool, default +from textwrap import dedent import jinja2 import tarfile import io @@ -637,7 +638,7 @@ class DockerBuildPack(BuildPack): with open('Dockerfile') as f: return f.read() -class LegacyBinderDockerBuildPack(DockerBuildPack): +class LegacyBinderDockerBuildPack(BuildPack): name = 'Legacy Binder Dockerfile' @@ -663,7 +664,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack): with open('Dockerfile') as f: return f.read() + self.dockerfile_appendix - def detect(self, workdir): + def detect(self): try: with open('Dockerfile', 'r') as f: for line in f:

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Pre-compile Julia libraries when possible

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -600,7 +600,7 @@ class JuliaBuildPack(BuildPack): # HACK: Can't seem to tell IJulia to install in sys-prefix # FIXME: Find way to get it to install under /srv and not $HOME? r""" - julia -e 'Pkg.init(); Pkg.add("IJulia")' && \ + julia -e 'Pkg.init(); Pkg.add("IJulia"); using IJulia;' && \ mv ${HOME}/.local/share/jupyter/kernels/julia-0.6 ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-0.6 """ ) @@ -610,9 +610,16 @@ class JuliaBuildPack(BuildPack): def setup_assembly(self): return [( "${NB_USER}", + # Pre-compile all libraries if they've opted into it. `using {libraryname}` does the + # right thing r""" cat REQUIRE >> ${JULIA_PKGDIR}/v0.6/REQUIRE && \ - julia -e "Pkg.resolve()" + julia -e ' \ + Pkg.resolve(); \ + for pkg in keys(Pkg.Reqs.parse("REQUIRE")) \ + eval(:(using $(Symbol(pkg)))) \ + end \ + ' """ )]

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Break properly when no builders are found

MODIFY repo2docker/app.py repo2docker/app.py @@ -292,9 +292,10 @@ class Repo2Docker(Application): self.log.info(l['error'], extra=dict(phase='failure')) sys.exit(1) else: - self.log.info(json.dumps(l), extra=dict(phase='failure')) - sys.exit(1) + self.log.info(json.dumps(l), extra=dict(phase='building')) break + else: + raise Exception("No builder found!") if self.cleanup_checkout: shutil.rmtree(checkout_path)

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Try to make Dockerfiles ordering more deterministic

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -349,7 +349,7 @@ class BuildPack(LoggingConfigurable): last_user = 'root' for user, script in self.assemble_scripts: if last_user != user: - build_script_directives.append("USER {}".format(user)) + assemble_script_directives.append("USER {}".format(user)) last_user = user assemble_script_directives.append("RUN {}".format( textwrap.dedent(script.strip('\n')) @@ -363,7 +363,7 @@ class BuildPack(LoggingConfigurable): build_script_directives=build_script_directives, assemble_script_directives=assemble_script_directives, build_script_files=self.build_script_files, - base_packages=self.base_packages + base_packages=sorted(self.base_packages) ) def build(self, image_spec): @@ -378,7 +378,7 @@ class BuildPack(LoggingConfigurable): io.BytesIO(dockerfile) ) - for src in self.build_script_files: + for src in sorted(self.build_script_files): tar.add(src) tar.add('.', 'src/')

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Don't install GA! At best, this will be for binder only, and we should figure out other ways of turning this one on.

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -476,13 +476,9 @@ class PythonBuildPack(BuildPack): notebook==5.0.0 \ jupyterhub==0.7.2 \ ipywidgets==6.0.0 \ - jupyterlab==0.24.1 \ - nbgoogleanalytics==0.1.0 && \ + jupyterlab==0.24.1 && \ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ - jupyter serverextension enable --py jupyterlab --sys-prefix && \ - jupyter nbextension install --py nbgoogleanalytics --sys-prefix && \ - jupyter nbextension enable --py nbgoogleanalytics --sys-prefix && \ - jupyter serverextension enable --py nbgoogleanalytics --sys-prefix + jupyter serverextension enable --py jupyterlab --sys-prefix """ ) ]

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Cleanup default logging for interactive use

MODIFY repo2docker/app.py repo2docker/app.py @@ -205,6 +205,8 @@ class Repo2Docker(Application): # our log messages include carriage returns, newlines, etc. # remove the additional newline from the stream handler self.log.handlers[0].terminator = '' + # We don't want a [Repo2Docker] on all messages + self.log.handlers[0].formatter = logging.Formatter(fmt='%(message)s') if len(self.extra_args) == 1: # accept repo as a positional arg

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Pass exit code of container back

MODIFY repo2docker/app.py repo2docker/app.py @@ -269,11 +269,12 @@ class Repo2Docker(Application): for line in container.logs(stream=True): self.log.info(line.decode('utf-8'), extra=dict(phase='running')) finally: - # FIXME: We should pass the container's exit code back out! self.log.info('Stopping container...\n', extra=dict(phase='running')) if container.status == 'running': container.kill() + exit_code = container.attrs['State']['ExitCode'] container.remove() + sys.exit(exit_code) def _get_free_port(self): """

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Add integration tests! We run jupyter-repo2docker and verify that the things we expect to be installed are installed.

ADD tests/conftest.py +""" +Custom test collector for our integration tests. + +Each directory that has a script named 'verify' is considered +a test. jupyter-repo2docker is run on that directory, +and then ./verify is run inside the built container. It should +return a non-zero exit code for the test to be considered a +success. +""" +import pytest +import subprocess + +def pytest_collect_file(parent, path): + if path.basename == 'verify': + return Repo(path, parent) + +class Repo(pytest.File): + def collect(self): + yield RepoTest(self.fspath.basename, self, self.fspath) + + +class RepoTest(pytest.Item): + def __init__(self, name, parent, path): + super().__init__(name, parent) + self.path = path + + def runtest(self): + subprocess.check_call([ + 'jupyter-repo2docker', + str(self.path.dirname), + './verify' + ]) ADD tests/venv/numpy/requirements.txt +numpy ADD tests/venv/numpy/verify +#!/usr/bin/env python +import sys + +assert sys.version_info[:2] == (3, 5) + +import numpy ADD tests/venv/py2/requirements.txt +numpy ADD tests/venv/py2/runtime.txt +python-2.7 ADD tests/venv/py2/verify +#!/usr/bin/env python2 +import sys + +print(sys.version_info) +assert sys.version_info[:2] == (2, 7) + +import numpy

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Clean out README

MODIFY README.md README.md # jupyter-repo2docker -**jupyter-repo2docker**, a command line tool, builds a docker image from a git -repository and can push the image to a docker registry. + +[![Build Status](https://travis-ci.org/jupyter/repo2docker.svg?branch=master)](https://travis-ci.org/jupyter/repo2docker) + +**jupyter-repo2docker** is a tool to build, run and push docker images from source code repositories. ## Installation To install from pypi, the python packaging index: ```bash -python3 -m pip install jupyter-repo2docker +pip install jupyter-repo2docker ``` To install from source: ```bash -git clone https://github.com/jupyterhub/jupyter-repo2docker.git -cd jupyter-repo2docker +git clone https://github.com/jupyter/repo2docker.git +cd repo2docker python3 -m pip install . ``` - -## Usage - -To access help for the application: - - jupyter-repo2docker -h - -## Technical Overview for Contributors - -**jupyter-repo2docker** uses other tools -([Source to Image](https://github.com/openshift/source-to-image) or just docker) -for doing the actual building of the image. - -The `repo2docker` directory contains the application which detects which build -method to use, and how to invoke that build method. - -The `s2i-builders` directory contains builder images which can be used to -provide custom `conda` and `venv` environments suitable for running -**JupyterHub**. - -## Documentation - -[Creating a new builder](docs/source/builder.md)

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Cleanup Dockerfile + Manifest

MODIFY Dockerfile Dockerfile @@ -2,17 +2,12 @@ FROM ubuntu:17.04 RUN apt-get update && \ apt-get install --yes --no-install-recommends \ - curl \ python3 \ python3-pip \ python3-setuptools \ git && \ apt-get clean && apt-get purge -# FIXME: Remove this if pip install with setup.py can do it instead? -COPY install-s2i.bash /usr/local/bin/install-s2i.bash -RUN /usr/local/bin/install-s2i.bash - RUN mkdir /tmp/src ADD . /tmp/src RUN pip3 install --no-cache-dir /tmp/src MODIFY MANIFEST.in MANIFEST.in -exclude repo2docker/s2i -include Dockerfile include *.md include LICENSE include setup.cfg \ No newline at end of file - -graft s2i-builders

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Refresh container state before trying to kill it Stops racy tests where sometimes the container is already dead before we try to kill it

MODIFY repo2docker/app.py repo2docker/app.py @@ -278,8 +278,9 @@ class Repo2Docker(Application): for line in container.logs(stream=True): self.log.info(line.decode('utf-8'), extra=dict(phase='running')) finally: - self.log.info('Stopping container...\n', extra=dict(phase='running')) + container.reload() if container.status == 'running': + self.log.info('Stopping container...\n', extra=dict(phase='running')) container.kill() exit_code = container.attrs['State']['ExitCode'] container.remove()

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Add test for postBuild script

ADD tests/venv/postBuild/postBuild +#!/bin/bash +jupyter nbextension enable --py --sys-prefix ipyleaflet ADD tests/venv/postBuild/requirements.txt +ipyleaflet ADD tests/venv/postBuild/verify +#!/bin/bash +set -e +jupyter nbextension list | grep 'jupyter-leaflet' | grep enabled

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Switch to buildpack-deps as base image We were just slowly recreating this anyway

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -15,7 +15,7 @@ import json import docker TEMPLATE = r""" -FROM ubuntu:17.04 +FROM buildpack-deps:zesty # Set up locales properly RUN apt-get update && \ @@ -147,49 +147,10 @@ class BuildPack(LoggingConfigurable): base_packages = Set( { # Utils! - "git", "tar", "curl", "wget", "less", - "ca-certificates", - # Include everything from the popular buildpack-deps docker image - "autoconf", - "automake", - "bzip2", - "file", - "g++", - "gcc", - "imagemagick", - "libbz2-dev", - "libc6-dev", - "libcurl4-openssl-dev", - "libdb-dev", - "libevent-dev", - "libffi-dev", - "libgdbm-dev", - "libgeoip-dev", - "libglib2.0-dev", - "libjpeg-dev", - "libkrb5-dev", - "liblzma-dev", - "libmagickcore-dev", - "libmagickwand-dev", - "libncurses-dev", - "libpng-dev", - "libpq-dev", - "libreadline-dev", - "libsqlite3-dev", - "libssl-dev", - "libtool", - "libwebp-dev", - "libxml2-dev", - "libxslt-dev", - "libyaml-dev", - "make", - "patch", - "xz-utils", - "zlib1g-dev", }, help=""" Base set of apt packages that are installed for all images.

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Actually tell docker to bind ports

MODIFY repo2docker/app.py repo2docker/app.py @@ -266,7 +266,7 @@ class Repo2Docker(Application): ports = {} container = client.containers.run( self.output_image_spec, - ports={}, + ports=ports, detach=True, command=run_cmd )

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Add a pyplot based julia test case

ADD tests/julia/pyplot/REQUIRE +PyPlot ADD tests/julia/pyplot/environment.yml +dependencies: + - matplotlib + ADD tests/julia/pyplot/verify +#!/usr/bin/env julia +# We try to plot something, and see if the file saved exists +using PyPlot +x = linspace(0,2*pi,1000); y = sin(3*x + 4*cos(2*x)) +plot(x, y, color="red", linewidth=2.0, linestyle="--") +savefig("graph.png") +if isfile("graph.png") + exit(0) +else + exit(1) +end +

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Use travis matrixes to speed up tests

MODIFY .travis.yml .travis.yml @@ -12,4 +12,9 @@ install: script: # Run at least 4 tests in parallel. These tests are all fully # parallelizable - - pytest -v -n4 tests/* + - pytest -v -n4 tests/${REPO_TYPE} + +env: + - REPO_TYPE=conda + - REPO_TYPE=venv + - REPO_TYPE=julia RENAME tests/default/verify tests/venv/default/verify

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Fix dockerfile builds and add tests for them

MODIFY .travis.yml .travis.yml @@ -18,3 +18,4 @@ env: - REPO_TYPE=conda - REPO_TYPE=venv - REPO_TYPE=julia + - REPO_TYPE=dockerfile MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -677,6 +677,15 @@ class DockerBuildPack(BuildPack): with open('Dockerfile') as f: return f.read() + def build(self, image_spec): + client = docker.APIClient(version='auto', **docker.utils.kwargs_from_env()) + for line in client.build( + path=os.getcwd(), + tag=image_spec, + decode=True + ): + yield line + class LegacyBinderDockerBuildPack(BuildPack): name = 'Legacy Binder Dockerfile' ADD tests/dockerfile/jupyter-stack/Dockerfile +FROM jupyter/base-notebook:b4dd11e16ae4 + +RUN pip install there +ADD verify verify ADD tests/dockerfile/jupyter-stack/verify +#!/usr/bin/env python +import sys + +assert sys.version_info[:2] == (3, 6) + +import jupyter +import there ADD tests/dockerfile/simple/Dockerfile +FROM alpine:3.5 + +ENTRYPOINT "/bin/sh" + +ADD sayhi.sh /usr/local/bin/sayhi.sh +ADD verify verify ADD tests/dockerfile/simple/sayhi.sh +#!/bin/bash +echo hi +exit 0 ADD tests/dockerfile/simple/verify +#!/bin/sh +set -e +/usr/local/bin/sayhi.sh

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Fix legacy dockerfile buildpack and add tests

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -686,7 +686,7 @@ class DockerBuildPack(BuildPack): ): yield line -class LegacyBinderDockerBuildPack(BuildPack): +class LegacyBinderDockerBuildPack(DockerBuildPack): name = 'Legacy Binder Dockerfile' ADD tests/dockerfile/legacy/Dockerfile +FROM andrewosh/binder-base + +USER root + +# Add Julia dependencies +RUN apt-get update +RUN apt-get install -y julia libnettle4 && apt-get clean + +USER main + +# Install Julia kernel +RUN julia -e 'Pkg.add("IJulia")' +RUN julia -e 'Pkg.add("Gadfly")' && julia -e 'Pkg.add("RDatasets")' + +ADD verify verify ADD tests/dockerfile/legacy/verify +#!/usr/bin/env python +import sys + +assert sys.version_info[:2] == (2, 7) + +import jupyter

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Silence massive unreadable error messages when fetching base images

MODIFY repo2docker/app.py repo2docker/app.py @@ -324,6 +324,8 @@ class Repo2Docker(Application): elif 'error' in l: self.log.info(l['error'], extra=dict(phase='failure')) sys.exit(1) + elif 'status' in l: + self.log.info('Fetching base image...\r', extra=dict(phase='building')) else: self.log.info(json.dumps(l), extra=dict(phase='building'))

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Mark repo2docker as requiring at least Python 3.4 And test with 3.4 on Travis.

MODIFY .travis.yml .travis.yml @@ -3,7 +3,7 @@ sudo: required services: - docker python: - - 3.5 + - 3.4 install: - pip install -e . MODIFY setup.py setup.py @@ -4,7 +4,7 @@ from setuptools import setup, find_packages setup( name='jupyter-repo2docker', - version='0.2.10', + version='0.3', install_requires=[ 'docker', 'traitlets', @@ -12,13 +12,14 @@ setup( 'escapism', 'jinja2' ], + python_requires='>=3.4', author='Yuvi Panda', author_email='yuvipanda@gmail.com', license='BSD', packages=find_packages(), entry_points={ 'console_scripts': [ - 'jupyter-repo2docker = repo2docker.__main__:main' + 'jupyter-repo2docker = repo2docker.__main__:main', ] }, )

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Fix tarfile mode parameter that doesn't work in 3.4

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -352,7 +352,7 @@ class BuildPack(LoggingConfigurable): def build(self, image_spec): tarf = io.BytesIO() - tar = tarfile.open(fileobj=tarf, mode='x') + tar = tarfile.open(fileobj=tarf, mode='w') dockerfile_tarinfo = tarfile.TarInfo("Dockerfile") dockerfile = self.render().encode('utf-8') dockerfile_tarinfo.size = len(dockerfile)

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Print stdout for all the tests! Makes it easier to verify what is going on.

MODIFY .travis.yml .travis.yml @@ -12,7 +12,7 @@ install: script: # Run at least 4 tests in parallel. These tests are all fully # parallelizable - - pytest -v -n4 tests/${REPO_TYPE} + - pytest -s -v -n4 tests/${REPO_TYPE} env: - REPO_TYPE=conda

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Make sure that build_script_files don't bust cache This slowed down everything!

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -362,8 +362,21 @@ class BuildPack(LoggingConfigurable): io.BytesIO(dockerfile) ) + def _filter_tar(tar): + # We need to unset these for build_script_files we copy into tar + # Otherwise they seem to vary each time, preventing effective use + # of the cache! + # https://github.com/docker/docker-py/pull/1582 is related + tar.uname = '' + tar.gname = '' + tar.uid = 1000 + tar.gid = 1000 + return tar + for src in sorted(self.build_script_files): - tar.add(src) + src_parts = src.split('/') + src_path = os.path.join(os.path.dirname(__file__), 'files', *src_parts) + tar.add(src_path, src, filter=_filter_tar) tar.add('.', 'src/') @@ -512,8 +525,8 @@ class CondaBuildPack(BuildPack): path = ['${CONDA_DIR}/bin'] build_script_files = { - os.path.join(os.path.dirname(__file__), 'files', 'conda', 'install-miniconda.bash'): '/tmp/install-miniconda.bash', - os.path.join(os.path.dirname(__file__), 'files', 'conda', 'environment.yml'): '/tmp/environment.yml', + 'conda/install-miniconda.bash': '/tmp/install-miniconda.bash', + 'conda/environment.yml': '/tmp/environment.yml' } build_scripts = [

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Don't add packages list if there are no packages

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -54,6 +54,7 @@ RUN apt-get update && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* +{% if packages -%} RUN apt-get update && \ apt-get install --yes \ {% for package in packages -%} @@ -62,6 +63,7 @@ RUN apt-get update && \ && apt-get purge && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* +{% endif -%} EXPOSE 8888

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Allow specifying requirements.txt with environment.yml They both get installed.

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -552,6 +552,11 @@ class CondaBuildPack(BuildPack): conda clean -tipsy """ )) + if os.path.exists('requirements.txt'): + assembly_scripts.append(( + '${NB_USER}', + 'pip install --no-cache-dir -r requirements.txt' + )) return assembly_scripts def detect(self): ADD tests/conda/requirements/environment.yml +dependencies: + - numpy ADD tests/conda/requirements/requirements.txt +there ADD tests/conda/requirements/verify +#!/usr/bin/env python +import sys + +assert sys.version_info[:2] == (3, 6) + +import numpy +import there

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Validate that Julia is using our pre-installed conda

MODIFY tests/julia/pyplot/verify tests/julia/pyplot/verify #!/usr/bin/env julia -# We try to plot something, and see if the file saved exists using PyPlot + +# Make sure we are re-using the same conda python +if PyCall.python != "/srv/conda/bin/python" + exit(1) +end + +# We try to plot something, and see if the file saved exists x = linspace(0,2*pi,1000); y = sin(3*x + 4*cos(2*x)) plot(x, y, color="red", linewidth=2.0, linestyle="--") savefig("graph.png")

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Filter all of src too when adding to tar This also seems to be required to more consistently use the Docker build cache.

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -380,7 +380,7 @@ class BuildPack(LoggingConfigurable): src_path = os.path.join(os.path.dirname(__file__), 'files', *src_parts) tar.add(src_path, src, filter=_filter_tar) - tar.add('.', 'src/') + tar.add('.', 'src/', filter=_filter_tar) tar.close() tarf.seek(0)

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Make julia verify check for libpython path PyCall.python just seems to say 'python'

MODIFY tests/julia/pyplot/verify tests/julia/pyplot/verify using PyPlot # Make sure we are re-using the same conda python -if PyCall.python != "/srv/conda/bin/python" +if PyCall.libpython != "/srv/conda/lib/libpython3.6m" + println("Not re-using conda python! Using " * PyCall.libpython * " instead") exit(1) end

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fixing RTD build

MODIFY .gitignore .gitignore @@ -13,3 +13,7 @@ repo2docker/s2i lib/ share/ include/ + +# Docs +generated/ +test_file_text.txt MODIFY docs/source/conf.py docs/source/conf.py @@ -215,5 +215,5 @@ for folder, _, files in os.walk(os.path.join('..', '..', 'tests')): for key in FILE_ORDER_PREFERENCE: for istring in FILES_DICT[key]: s += istring -with open('./generated/test_file_text.txt', 'w') as ff: +with open('./test_file_text.txt', 'w') as ff: ff.write(s) MODIFY docs/source/samples.rst docs/source/samples.rst @@ -4,4 +4,4 @@ Sample build files There are many options for specifying your environment with ``repo2docker``. The following sections describe a few samples to get you started. -.. include:: generated/test_file_text.txt +.. include:: test_file_text.txt

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fixing conf import

MODIFY docs/source/conf.py docs/source/conf.py @@ -185,8 +185,6 @@ epub_copyright = copyright epub_exclude_files = ['search.html'] # Build the repo2docker test syntax -from glob import glob -import numpy as np import os s = '' FILE_ORDER_PREFERENCE = ['System', 'Python', 'Julia', 'Docker', 'Misc']

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config file for RTD

MODIFY docs/doc-requirements.txt docs/doc-requirements.txt -mne -graphviz -pygraphviz sphinx>=1.4, !=1.5.4 jupyter_alabaster_theme recommonmark ADD readthedocs.yml +name: repo2docker +type: sphinx +python: + version: 3 +requirements_file: doc/doc-requirements.txt

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Add npm to base image Too many things require npm to build now

MODIFY repo2docker/detectors.py repo2docker/detectors.py @@ -149,10 +149,12 @@ class BuildPack(LoggingConfigurable): base_packages = Set( { # Utils! - "tar", - "curl", - "wget", "less", + + # FIXME: Use npm from nodesource! + # Everything seems to depend on npm these days, unfortunately. + "npm", + "nodejs-legacy" }, help=""" Base set of apt packages that are installed for all images.

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Add --print-dockerfile & --no-build options

MODIFY repo2docker/app.py repo2docker/app.py @@ -144,6 +144,12 @@ class Repo2Docker(Application): help='Push docker image to repository' ) + argparser.add_argument( + '--print-dockerfile', + help="Print dockerfile contents to stdout", + action='store_true', + ) + argparser.add_argument( '--no-run', dest='run', @@ -158,6 +164,13 @@ class Repo2Docker(Application): help="Don't clean up remote checkouts after we are done" ) + argparser.add_argument( + '--no-build', + dest='build', + action='store_false', + help="Do not actually build the image. Useful in conjugation with --print-dockerfile." + ) + argparser.add_argument( 'cmd', nargs='*', @@ -210,6 +223,13 @@ class Repo2Docker(Application): self.run = args.run self.json_logs = args.json_logs + self.print_dockerfile = args.print_dockerfile + self.build = args.build + if not self.build: + # Can't push nor run if we aren't building + self.run = False + self.push = False + self.run_cmd = args.cmd @@ -296,6 +316,10 @@ class Repo2Docker(Application): picked_buildpack = bp break + if self.print_dockerfile: + self.log.info(picked_buildpack.render(), extra=dict(phase='building')) + + if self.build: self.log.info('Using %s builder\n', bp.name, extra=dict(phase='building')) for l in picked_buildpack.build(self.output_image_spec): if 'stream' in l:

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Output Dockerfile contents if set to --debug The Dockerfile we generate won't really work at all outside of repo2docker. This makes it very clear that these are purely for debugging purposes.

MODIFY repo2docker/app.py repo2docker/app.py @@ -145,8 +145,8 @@ class Repo2Docker(Application): ) argparser.add_argument( - '--print-dockerfile', - help="Print dockerfile contents to stdout", + '--debug', + help="Turn on debug logging", action='store_true', ) @@ -182,6 +182,9 @@ class Repo2Docker(Application): def initialize(self): args = self.get_argparser().parse_args() + if args.debug: + self.log_level = logging.DEBUG + self.load_config_file(args.config) if os.path.exists(args.repo): @@ -223,7 +226,6 @@ class Repo2Docker(Application): self.run = args.run self.json_logs = args.json_logs - self.print_dockerfile = args.print_dockerfile self.build = args.build if not self.build: # Can't push nor run if we aren't building @@ -316,8 +318,7 @@ class Repo2Docker(Application): picked_buildpack = bp break - if self.print_dockerfile: - self.log.info(picked_buildpack.render(), extra=dict(phase='building')) + self.log.debug(picked_buildpack.render(), extra=dict(phase='building')) if self.build: self.log.info('Using %s builder\n', bp.name, extra=dict(phase='building'))

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