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Merge pull request #464 from sourceryinstitute/Docker-from-master
Dockerfile to in cloud with jupyter-CAF-kernel
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‎.Dockerfiles/master-jupyter-inherit/.dockerignore

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*.log
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log.*
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.git
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.gitignore
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hooks
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*~
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Untitled*.ipynb
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Makefile
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#*#
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\#*\#

‎.Dockerfiles/master-jupyter-inherit/Dockerfile

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FROM jupyter/minimal-notebook:da2c5a4d00fa
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MAINTAINER Izaak Beekman <[email protected]>
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USER root
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ENV GCC_VERSION 7.2.0
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ENV NB_USER jovyan
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ENV NB_UID 1000
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ENV HOME /home/${NB_USER}
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RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="file" \
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&& set -v \
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&& cat /etc/issue \
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&& uname -a \
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&& echo "${DEBIAN_FRONTEND}" \
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&& apt-get update -y \
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&& apt-get install -y \
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software-properties-common \
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&& add-apt-repository ppa:ubuntu-toolchain-r/test -y \
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&& apt-get update -y \
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&& apt-get install -y \
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build-essential \
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gcc-7=${GCC_VERSION}-1ubuntu1~16.04 \
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gfortran-7=${GCC_VERSION}-1ubuntu1~16.04 \
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g++-7=${GCC_VERSION}-1ubuntu1~16.04 \
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mpich \
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${transientBuildDeps} \
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&& update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-7 \
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&& update-alternatives --set gcc "/usr/bin/gcc-7" \
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&& gcc --version \
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&& gfortran --version \
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&& mpiexec --version \
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&& mpifort --version \
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&& mpicc --version \
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&& apt-get clean \
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&& apt-get purge -y --auto-remove ${transientBuildDeps} \
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&& rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*
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# Build-time metadata as defined at http://label-schema.org
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ARG BUILD_DATE
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ARG VCS_REF
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ARG VCS_URL
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ARG VCS_VERSION=latest
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LABEL org.label-schema.schema-version="1.0" \
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org.label-schema.build-date="${BUILD_DATE}" \
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org.label-schema.name="" \
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org.label-schema.description="Coarray Fortran compiler with GFortran ${GCC_VERSION}, OpenCoarrays and MPICH backend" \
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org.label-schema.url="https://github.com/sourceryinstitute/OpenCoarrays#readme/" \
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org.label-schema.vcs-ref="${VCS_REF}" \
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org.label-schema.vcs-url="${VCS_URL}" \
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org.label-schema.version="${VCS_VERSION}" \
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org.label-schema.vendor="SourceryInstitute" \
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org.label-schema.license="BSD" \
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org.label-schema.docker.cmd="docker run -i -t -p 8888:8888 sourceryinstitute/opencoarrays-notebook"
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ARG RUN_TESTS=false
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RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="cmake git" \
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&& set -v \
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&& echo "${DEBIAN_FRONTEND}" \
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&& apt-get update && apt-get install -y \
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${transientBuildDeps} \
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&& cmake --version \
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&& gcc --version \
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&& gfortran --version \
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&& git clone --single-branch https://github.com/sourceryinstitute/OpenCoarrays \
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&& mkdir OpenCoarrays/build \
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&& cd OpenCoarrays/build \
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&& FC="$(which gfortran)" CC="$(which gcc)" cmake -DCMAKE_BUILD_TYPE=Release .. \
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&& make -j "$(nproc)" install \
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&& if [ "${RUN_TESTS}" = "true" ] ; then ctest --output-on-failure ; fi \
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&& cd ../.. \
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&& caf --version \
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&& cafrun --version \
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&& rm -rf OpenCoarrays \
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&& apt-get clean \
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&& apt-get purge -y --auto-remove ${transientBuildDeps} \
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&& rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*

‎.Dockerfiles/master-jupyter-inherit/Makefile

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SHELL := /usr/local/bin/bash -o pipefail
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NAME = sourceryinstitute/opencoarrays-notebook
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#UBADGER_ENDPOINT = "https://hooks.microbadger.com/images/sourceryinstitute/jupyter-caf-kernel/CEL6DIVw-OVbUIXieZhZwvDXl3I="
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GIT_MASTER_HEAD_SHA:=$(shell git rev-parse --short=12 --verify HEAD)
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.PHONY: help build push run runclean clean
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.DEFAULT_GOAL := help
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# Add the following 'help' target to your Makefile
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# And add help text after each target name starting with '\#\#'
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help: ## This help message
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@echo -e "$$(grep -hE '^\S+:.*##' $(MAKEFILE_LIST) | sed -e 's/:.*##\s*/:/' -e 's/^\(.\+\):\(.*\)/\\x1b[36m\1\\x1b[m:\2/' | column -c2 -t -s :)"
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build: $(subst /,_,$(NAME))-build.stamp ## Build docker file. Depending on which packages are rebuilt this may take a long time
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$(subst /,_,$(NAME))-build.stamp: Dockerfile .dockerignore hooks/build ## Target for doing & timestamping the build
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touch $@
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hooks/build 2>&1 | tee $(subst stamp,log,$@) || rm -rf $@
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docker tag $(NAME):latest $(NAME):$(GIT_MASTER_HEAD_SHA)
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push: $(subst /,_,$(NAME))-push.stamp ## Push prebuild docker image up to hub.docker.com
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$(subst /,_,$(NAME))-push.stamp: $(subst /,_,$(NAME))-build.stamp Dockerfile .dockerignore hooks/build ## Target for doing & timestamping the push
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touch $@
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docker push $(NAME):latest | tee $(subst stamp,log,$@) || rm -rf $@
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docker push $(NAME):$(GIT_MASTER_HEAD_SHA) | tee -a $(subst stamp,log,$@) || rm -rf $@
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-curl -X POST "$(UBADGER_ENDPOINT)"
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run: ## Target to run jupyter-hub docker server
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docker run -i -t -p 8888:8888 $(NAME) | tee $(subst /,_,$(NAME))-run.log
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runclean: ## Target to run jupyter-hub docker server, discarding changes
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docker run --rm -i -t -p 8888:8888 $(NAME) | tee $(subst /,_,$(NAME))-runclean.log
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clean:
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-rm -rf $(subst /,_,$(NAME))*.stamp
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-find . -name 'Untitled*.ipynd' -exec rm -f {} \;

‎.Dockerfiles/master-jupyter-inherit/hooks/build

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#!/bin/bash
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# See https://github.com/rossf7/label-schema-automated-build
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# or https://medium.com/microscaling-systems/labelling-automated-builds-on-docker-hub-f3d073fb8e1#.wgkzfdnfr
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# for more details.
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# $IMAGE_NAME var is injected into the build so the tag is correct.
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set -o verbose
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set -o pipefail
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set -o errexit
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set -x
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git fetch -v --all --tags
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git fetch -v --all --depth=9999999 --update-shallow
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git tag --list
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git branch
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d_repo='sourceryinstitute/OpenCoarrays'
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d_git_remotes=($(git remote show))
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echo "${#d_git_remotes[@]} git remotes found."
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n_remotes=${#d_git_remotes[@]}
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if (( n_remotes > 0 )) ; then
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echo "Using remote: ${d_git_remotes[0]}"
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d_vcs_url="$(git remote -v | awk 'FNR == 1 {print $2}')"
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fi
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if [[ -z "${d_vcs_url:-}" ]]; then
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d_vcs_url="https://github.com/${DOCKER_REPO:-${d_repo}}"
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fi
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branch_name="$(git symbolic-ref -q HEAD)" || true
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branch_name="${branch_name##refs/heads/}"
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branch_name="${branch_name:-DETACHED-HEAD}"
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d_vcs_describe="$(git describe --tags --always || true)"
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d_tag="${IMAGE_NAME##*:}"
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d_tag="${d_tag:-${branch_name}-$(date +%s)}"
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d_vcs_tag="$(git rev-parse --short=12 --verify HEAD)"
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if [[ ${IMAGE_NAME:-} ]]; then
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export RUN_TESTS=false
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else
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export RUN_TESTS=${RUN_TESTS:-false}
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fi
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opencoarrays_version="${d_vcs_describe}"
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if [[ -n "${open_coarrays_version:-}" ]]; then
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opencoarrays_version=1.9.2
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fi
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echo "Build hook running"
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docker build --build-arg OPENCOARRAYS_VERSION="${opencoarrays_version}" \
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--build-arg RUN_TESTS=${RUN_TESTS} \
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--build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
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--build-arg VCS_REF="${SOURCE_COMMIT:-$(git rev-parse --short HEAD)}" \
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--build-arg VCS_URL="${d_vcs_url}" \
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--build-arg VCS_VERSION="${d_vcs_describe:-${d_tag}}" \
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--rm \
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--pull \
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-t "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:latest")}" .
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docker tag "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:latest")}" "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:${d_vcs_tag}")}"

‎.gitattributes

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makefile export-ignore
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Makefile export-ignore
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make.inc* export-ignore
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.Dockerfiles export-ignore
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# Experimental conduits/backends
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src/gasnet export-ignore

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