Merge pull request #282 from ctr26/binder

Binder

.binder/Dockerfile

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+
+# FROM buildpack-deps:bionic
+# FROM nvidia/container-toolkit:1.6.0-ubuntu18.04
+# FROM datmo/buildpack-deps:gpu
+FROM floydhub/buildpack-deps:cuda10.0-cudnn7-1.0
+# packaging dependencies
+# ENV DEBIAN_FRONTEND=noninteractive
+# RUN apt-get update && apt-get install -y --no-install-recommends \
+#         dh-make \
+#         fakeroot \
+#         build-essential \
+#         devscripts \
+#         lsb-release && \
+#     rm -rf /var/lib/apt/lists/*
+
+# # packaging
+# ARG PKG_VERS
+# ARG PKG_REV
+# ARG RUNTIME_VERSION
+# ARG DOCKER_VERSION
+
+# ENV DEBFULLNAME "NVIDIA CORPORATION"
+# ENV DEBEMAIL "[email protected]"
+# ENV REVISION "$PKG_VERS-$PKG_REV"
+# ENV DOCKER_VERSION $DOCKER_VERSION
+# ENV RUNTIME_VERSION $RUNTIME_VERSION
+# ENV SECTION ""
+
+# # output directory
+# ENV DIST_DIR=/tmp/nvidia-docker2-$PKG_VERS
+# RUN mkdir -p $DIST_DIR /dist
+
+# # nvidia-docker 2.0
+# COPY .binder/nvidia-docker $DIST_DIR/nvidia-docker
+# COPY .binder/daemon.json $DIST_DIR/daemon.json
+
+# WORKDIR $DIST_DIR
+# COPY .binder/debian ./debian
+
+# # RUN sed -i "s;@VERSION@;${REVISION};" debian/changelog && \
+# #     sed -i "s;@VERSION@;${PKG_VERS};" $DIST_DIR/nvidia-docker && \
+# #     if [ "$REVISION" != "$(dpkg-parsechangelog --show-field=Version)" ]; then echo "$(dpkg-parsechangelog --show-field=Version)" && exit 1; fi
+
+# # CMD export DISTRIB="$(lsb_release -cs)" && \
+# #     debuild --preserve-env --dpkg-buildpackage-hook='sh debian/prepare' -i -us -uc -b && \
+# #     mv /tmp/*.deb /dist
+
+# RUN set -eux; \
+# 	apt-get update; \
+# 	apt-get install -y --no-install-recommends \
+# 		ca-certificates \
+# 		curl \
+# 		netbase \
+# 		wget \
+# # https://bugs.debian.org/929417
+# 		tzdata \
+# 	; \
+# 	rm -rf /var/lib/apt/lists/*
+
+# RUN set -ex; \
+# 	if ! command -v gpg > /dev/null; then \
+# 		apt-get update; \
+# 		apt-get install -y --no-install-recommends \
+# 			gnupg \
+# 			dirmngr \
+# 		; \
+# 		rm -rf /var/lib/apt/lists/*; \
+# 	fi
+
+# # procps is very common in build systems, and is a reasonably small package
+# RUN apt-get update && apt-get install -y --no-install-recommends \
+# 		bzr \
+# 		git \
+# 		mercurial \
+# 		openssh-client \
+# 		subversion \
+# 		\
+# 		procps \
+# 	&& rm -rf /var/lib/apt/lists/*
+
+
+# RUN set -ex; \
+# 	apt-get update; \
+# 	apt-get install -y --no-install-recommends \
+# 		autoconf \
+# 		automake \
+# 		bzip2 \
+# 		dpkg-dev \
+# 		file \
+# 		g++ \
+# 		gcc \
+# 		imagemagick \
+# 		libbz2-dev \
+# 		libc6-dev \
+# 		libcurl4-openssl-dev \
+# 		libdb-dev \
+# 		libevent-dev \
+# 		libffi-dev \
+# 		libgdbm-dev \
+# 		libglib2.0-dev \
+# 		libgmp-dev \
+# 		libjpeg-dev \
+# 		libkrb5-dev \
+# 		liblzma-dev \
+# 		libmagickcore-dev \
+# 		libmagickwand-dev \
+# 		libmaxminddb-dev \
+# 		libncurses5-dev \
+# 		libncursesw5-dev \
+# 		libpng-dev \
+# 		libpq-dev \
+# 		libreadline-dev \
+# 		libsqlite3-dev \
+# 		libssl-dev \
+# 		libtool \
+# 		libwebp-dev \
+# 		libxml2-dev \
+# 		libxslt-dev \
+# 		libyaml-dev \
+# 		make \
+# 		patch \
+# 		unzip \
+# 		xz-utils \
+# 		zlib1g-dev \
+# 		\
+# # https://lists.debian.org/debian-devel-announce/2016/09/msg00000.html
+# 		$( \
+# # if we use just "apt-cache show" here, it returns zero because "Can't select versions from package 'libmysqlclient-dev' as it is purely virtual", hence the pipe to grep
+# 			if apt-cache show 'default-libmysqlclient-dev' 2>/dev/null | grep -q '^Version:'; then \
+# 				echo 'default-libmysqlclient-dev'; \
+# 			else \
+# 				echo 'libmysqlclient-dev'; \
+# 			fi \
+# 		) \
+# 	; \
+# 	rm -rf /var/lib/apt/lists/*
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
+
+RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
+
+ENV LC_ALL en_US.UTF-8
+
+ENV LANG en_US.UTF-8
+
+ENV LANGUAGE en_US.UTF-8
+
+ENV SHELL /bin/bash
+
+ARG NB_USER
+
+ARG NB_UID
+
+ENV USER ${NB_USER}
+
+ENV HOME /home/${NB_USER}
+
+RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --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
+
+RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
+
+
+EXPOSE 8888
+
+ENV APP_BASE /srv
+
+ENV NPM_DIR ${APP_BASE}/npm
+
+ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
+
+ENV CONDA_DIR ${APP_BASE}/conda
+
+ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
+
+ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
+
+ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
+
+ENV NB_ENVIRONMENT_FILE="/tmp/environment.py-3.7.lock"
+
+COPY --chown=${NB_USER}:${NB_USER} .binder/environment.py-3.7.lock ${NB_ENVIRONMENT_FILE}
+
+COPY --chown=${NB_USER}:${NB_USER} .binder/activate_conda.sh /etc/profile.d/activate-conda.sh
+
+RUN chmod +x /etc/profile.d/activate-conda.sh
+
+COPY --chown=${NB_USER}:${NB_USER} .binder/environment.yml /tmp/environment.yml
+
+COPY --chown=${NB_USER}:${NB_USER} .binder/install_miniforge.sh /tmp/install-miniforge.bash
+
+RUN chmod +x /tmp/install-miniforge.bash
+
+RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
+
+USER ${NB_USER}
+
+RUN npm config --global set prefix ${NPM_DIR}
+
+USER root
+
+RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm /tmp/install-miniforge.bash ${NB_ENVIRONMENT_FILE}
+
+ARG REPO_DIR=${HOME}
+
+ENV REPO_DIR ${REPO_DIR}
+
+
+WORKDIR ${REPO_DIR}
+
+RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
+
+
+ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
+
+
+ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
+
+
+COPY --chown=${USER}:${USER} .binder/environment.yml ${REPO_DIR}/.binder/environment.yml
+
+COPY --chown=${USER}:${USER} . ${REPO_DIR}
+
+RUN chmod +x "${REPO_DIR}/.binder/postBuildAdmin" && "${REPO_DIR}/.binder/postBuildAdmin"
+
+USER ${NB_USER}
+
+
+RUN TIMEFORMAT='time: %3R' bash -c 'time mamba env update -p ${NB_PYTHON_PREFIX} -f ".binder/environment.yml" && time mamba clean --all -f -y && mamba list -p ${NB_PYTHON_PREFIX} '
+
+
+LABEL repo2docker.ref="None"
+
+LABEL repo2docker.repo="local"
+
+LABEL repo2docker.version="2021.01.0"
+
+
+# COPY --chown=${USER}:${USER} . {REPO_DIR}
+
+USER ${NB_USER}
+
+RUN chmod +x .binder/postBuild && "${REPO_DIR}/.binder/postBuild"
+
+RUN chmod +x "${REPO_DIR}/.binder/start"
+ENV R2D_ENTRYPOINT "${REPO_DIR}/.binder/start"
+# COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
+# ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
+CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

.binder/activate_conda.sh

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

.binder/daemon.json

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+{
+    "runtimes": {
+        "nvidia": {
+            "path": "nvidia-container-runtime",
+            "runtimeArgs": []
+        }
+    }
+}

.binder/debian/changelog

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+nvidia-docker2 (2.6.0-1) UNRELEASED; urgency=medium
+
+  * Add dependence on nvidia-container-runtime >= 3.5.0
+  * Add Jenkinsfile for building packages
+
+ -- NVIDIA CORPORATION <[email protected]>  Thu, 29 Apr 2021 05:25:25 +0000
+
+nvidia-docker2 (2.5.0-1) UNRELEASED; urgency=medium
+
+  * Bump version to v2.5.0
+  * Add dependence on nvidia-container-runtime >= 3.4.0
+  * Update readme to point to the official documentatio
+  * Add %config directive to daemon.json for RPM installations
+
+ -- NVIDIA CORPORATION <[email protected]>  Wed, 16 Sep 2020 13:55:52 +0000
+
+nvidia-docker2 (2.4.0-1) UNRELEASED; urgency=medium
+
+  * 09a01276 Update package license to match source license
+  * b9c70155 Update dependence on nvidia-container-runtime to 3.3.0
+
+ -- NVIDIA CORPORATION <[email protected]>  Wed, 08 Jul 2020 20:33:10 +0000
+
+nvidia-docker2 (2.3.0-1) UNRELEASED; urgency=medium
+
+  * 0d3b049a Update build system to support multi-arch builds
+  * 8557216d Require new MIG changes
+
+ -- NVIDIA CORPORATION <[email protected]>  Fri, 15 May 2020 12:04:57 +0000
+
+nvidia-docker2 (2.2.2-1) UNRELEASED; urgency=medium
+
+  * 2e9f20b Improve pass-through of docker arguments
+  * 4edca2f Pave the way for a hypothetical transitional package from v1
+
+ -- NVIDIA CORPORATION <[email protected]>  Wed, 07 Mar 2018 04:06:38 +0000

.binder/debian/compat

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+9

.binder/debian/control

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+Source: nvidia-docker2
+Section: @SECTION@utils
+Priority: optional
+Maintainer: NVIDIA CORPORATION <[email protected]>
+Standards-Version: 3.9.8
+Homepage: https://github.com/NVIDIA/nvidia-docker/wiki
+Vcs-Git: https://github.com/NVIDIA/nvidia-docker
+Vcs-Browser: https://github.com/NVIDIA/nvidia-docker
+Build-Depends: debhelper (>= 9)
+
+Package: nvidia-docker2
+Architecture: all
+Breaks: nvidia-docker (<< 2.0.0)
+Replaces: nvidia-docker (<< 2.0.0)
+Depends: ${misc:Depends}, nvidia-container-runtime (>= @RUNTIME_VERSION@), @DOCKER_VERSION@
+Description: nvidia-docker CLI wrapper
+ Replaces nvidia-docker with a new implementation based on
+ nvidia-container-runtime