Merge branch 'opencoarrays-teams' of https://github.com/sourceryinstitute/OpenCoarrays into opencoarrays-teams

Author: Alessandro Fanfarillo

.Dockerfiles/master-jupyter-inherit/.dockerignore

@@ -0,0 +1,10 @@
+*.log
+log.*
+.git
+.gitignore
+hooks
+*~
+Untitled*.ipynb
+Makefile
+#*#
+\#*\#

.Dockerfiles/master-jupyter-inherit/Dockerfile

@@ -0,0 +1,79 @@
+FROM jupyter/minimal-notebook:da2c5a4d00fa
+
+MAINTAINER Izaak Beekman <[email protected]>
+
+USER root
+ENV GCC_VERSION 7.2.0
+
+ENV NB_USER jovyan
+ENV NB_UID 1000
+ENV HOME /home/${NB_USER}
+
+RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="file" \
+    && set -v \
+    && cat /etc/issue \
+    && uname -a \
+    && echo "${DEBIAN_FRONTEND}" \
+    && apt-get update -y \
+    && apt-get install -y \
+    software-properties-common \
+    && add-apt-repository ppa:ubuntu-toolchain-r/test -y \
+    && apt-get update -y \
+    && apt-get install -y \
+    build-essential \
+    gcc-7=${GCC_VERSION}-1ubuntu1~16.04 \
+    gfortran-7=${GCC_VERSION}-1ubuntu1~16.04 \
+    g++-7=${GCC_VERSION}-1ubuntu1~16.04 \
+    mpich \
+    ${transientBuildDeps} \
+    && update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-7 \
+    && update-alternatives --set gcc "/usr/bin/gcc-7" \
+    && gcc --version \
+    && gfortran --version \
+    && mpiexec --version \
+    && mpifort --version \
+    && mpicc --version \
+    && apt-get clean \
+    && apt-get purge -y --auto-remove ${transientBuildDeps} \
+    && rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*
+
+# Build-time metadata as defined at http://label-schema.org
+    ARG BUILD_DATE
+    ARG VCS_REF
+    ARG VCS_URL
+    ARG VCS_VERSION=latest
+    LABEL org.label-schema.schema-version="1.0" \
+          org.label-schema.build-date="${BUILD_DATE}" \
+          org.label-schema.name="" \
+          org.label-schema.description="Coarray Fortran compiler with GFortran ${GCC_VERSION}, OpenCoarrays and MPICH backend" \
+          org.label-schema.url="https://github.com/sourceryinstitute/OpenCoarrays#readme/" \
+          org.label-schema.vcs-ref="${VCS_REF}" \
+          org.label-schema.vcs-url="${VCS_URL}" \
+          org.label-schema.version="${VCS_VERSION}" \
+          org.label-schema.vendor="SourceryInstitute" \
+          org.label-schema.license="BSD" \
+          org.label-schema.docker.cmd="docker run -i -t -p 8888:8888 sourceryinstitute/opencoarrays-notebook"
+
+ARG RUN_TESTS=false
+
+RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="cmake git" \
+    && set -v \
+    && echo "${DEBIAN_FRONTEND}" \
+    && apt-get update && apt-get install -y \
+    ${transientBuildDeps} \
+    && cmake --version \
+    && gcc --version \
+    && gfortran --version \
+    && git clone --single-branch https://github.com/sourceryinstitute/OpenCoarrays \
+    && mkdir OpenCoarrays/build \
+    && cd OpenCoarrays/build \
+    && FC="$(which gfortran)" CC="$(which gcc)" cmake -DCMAKE_BUILD_TYPE=Release .. \
+    && make -j "$(nproc)" install \
+    && if [ "${RUN_TESTS}" = "true" ] ; then ctest --output-on-failure ; fi \
+    && cd ../.. \
+    && caf --version \
+    && cafrun --version \
+    && rm -rf OpenCoarrays \
+    && apt-get clean \
+    && apt-get purge -y --auto-remove ${transientBuildDeps} \
+    && rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*

.Dockerfiles/master-jupyter-inherit/Makefile

@@ -0,0 +1,38 @@
+SHELL := /usr/local/bin/bash -o pipefail
+NAME = sourceryinstitute/opencoarrays-notebook
+#UBADGER_ENDPOINT = "https://hooks.microbadger.com/images/sourceryinstitute/jupyter-caf-kernel/CEL6DIVw-OVbUIXieZhZwvDXl3I="
+GIT_MASTER_HEAD_SHA:=$(shell git rev-parse --short=12 --verify HEAD)
+
+.PHONY: help build push run runclean clean
+.DEFAULT_GOAL := help
+
+# Add the following 'help' target to your Makefile
+# And add help text after each target name starting with '\#\#'
+
+help: ## This help message
+	@echo -e "$$(grep -hE '^\S+:.*##' $(MAKEFILE_LIST) | sed -e 's/:.*##\s*/:/' -e 's/^\(.\+\):\(.*\)/\\x1b[36m\1\\x1b[m:\2/' | column -c2 -t -s :)"
+
+build: $(subst /,_,$(NAME))-build.stamp ## Build docker file. Depending on which packages are rebuilt this may take a long time
+
+$(subst /,_,$(NAME))-build.stamp: Dockerfile .dockerignore hooks/build ## Target for doing & timestamping the build
+	touch $@
+	hooks/build 2>&1 | tee $(subst stamp,log,$@) || rm -rf $@
+	docker tag $(NAME):latest $(NAME):$(GIT_MASTER_HEAD_SHA)
+
+push: $(subst /,_,$(NAME))-push.stamp ## Push prebuild docker image up to hub.docker.com
+
+$(subst /,_,$(NAME))-push.stamp: $(subst /,_,$(NAME))-build.stamp Dockerfile .dockerignore hooks/build ## Target for doing & timestamping the push
+	touch $@
+	docker push $(NAME):latest | tee $(subst stamp,log,$@) || rm -rf $@
+	docker push $(NAME):$(GIT_MASTER_HEAD_SHA) | tee -a $(subst stamp,log,$@) || rm -rf $@
+	-curl -X POST "$(UBADGER_ENDPOINT)"
+
+run: ## Target to run jupyter-hub docker server
+	docker run -i -t -p 8888:8888 $(NAME) | tee $(subst /,_,$(NAME))-run.log
+
+runclean: ## Target to run jupyter-hub docker server, discarding changes
+	docker run --rm -i -t -p 8888:8888 $(NAME) | tee $(subst /,_,$(NAME))-runclean.log
+
+clean:
+	-rm -rf $(subst /,_,$(NAME))*.stamp
+	-find . -name 'Untitled*.ipynd' -exec rm -f {} \;

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

@@ -0,0 +1,62 @@
+#!/bin/bash
+# See https://github.com/rossf7/label-schema-automated-build
+#     or https://medium.com/microscaling-systems/labelling-automated-builds-on-docker-hub-f3d073fb8e1#.wgkzfdnfr
+#     for more details.
+
+# $IMAGE_NAME var is injected into the build so the tag is correct.
+
+set -o verbose
+set -o pipefail
+set -o errexit
+set -x
+
+git fetch -v --all --tags
+git fetch -v --all --depth=9999999 --update-shallow
+git tag --list
+git branch
+
+d_repo='sourceryinstitute/OpenCoarrays'
+d_git_remotes=($(git remote show))
+echo "${#d_git_remotes[@]} git remotes found."
+n_remotes=${#d_git_remotes[@]}
+if (( n_remotes > 0 )) ; then
+    echo "Using remote: ${d_git_remotes[0]}"
+    d_vcs_url="$(git remote -v | awk 'FNR == 1 {print $2}')"
+fi
+
+if [[ -z "${d_vcs_url:-}" ]]; then
+    d_vcs_url="https://github.com/${DOCKER_REPO:-${d_repo}}"
+fi
+
+branch_name="$(git symbolic-ref -q HEAD)" || true
+branch_name="${branch_name##refs/heads/}"
+branch_name="${branch_name:-DETACHED-HEAD}"
+
+d_vcs_describe="$(git describe --tags --always || true)"
+d_tag="${IMAGE_NAME##*:}"
+d_tag="${d_tag:-${branch_name}-$(date +%s)}"
+d_vcs_tag="$(git rev-parse --short=12 --verify HEAD)"
+
+if [[ ${IMAGE_NAME:-} ]]; then
+  export RUN_TESTS=false
+else
+  export RUN_TESTS=${RUN_TESTS:-false}
+fi
+
+
+opencoarrays_version="${d_vcs_describe}"
+if [[ -n "${open_coarrays_version:-}" ]]; then
+  opencoarrays_version=1.9.2
+fi
+
+echo "Build hook running"
+docker build --build-arg OPENCOARRAYS_VERSION="${opencoarrays_version}" \
+             --build-arg RUN_TESTS=${RUN_TESTS} \
+             --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
+             --build-arg VCS_REF="${SOURCE_COMMIT:-$(git rev-parse --short HEAD)}" \
+             --build-arg VCS_URL="${d_vcs_url}" \
+	     --build-arg VCS_VERSION="${d_vcs_describe:-${d_tag}}" \
+	     --rm \
+	     --pull \
+             -t "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:latest")}" .
+docker tag "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:latest")}" "${IMAGE_NAME:-$(tr '[:upper:]' '[:lower:]' <<< "${d_repo}:${d_vcs_tag}")}"

.VERSION

@@ -1,6 +1,6 @@
 $Format:%d%n%n$
 # Fall back version, probably last release:
-1.9.0
+1.9.3
 
 # OpenCoarrays version file. This project uses semantic
 # versioning. For details see http://semver.org

.gitattributes

@@ -32,6 +32,14 @@ developer-scripts export-ignore
 codecov.yml export-ignore
 *.enc export-ignore
 .github export-ignore
+makefile export-ignore
+Makefile export-ignore
+make.inc* export-ignore
+.Dockerfiles export-ignore
+
+# Experimental conduits/backends
+src/gasnet export-ignore
+src/openshmem export-ignore
 
 # Perform substitutions when `git export`ing these files
 .VERSION export-subst

.github/PULL_REQUEST_TEMPLATE.md

@@ -36,18 +36,18 @@ This pull request (PR) is a:
 
 ### I certify that ###
 
-- [ ] I have reviewed the [contributing guidelines] and followed the
-      policies on:
-      - Pull request (PR) naming to indicate work in progress (WIP),
-        and to attach the PR to the appropriate bug report, or feature
-        request [issue]
+- [ ] I reviewed and followed the [contributing guidelines], including
+      - Increasing test coverage for all feature-addition PRs
+      - Increasing test coverage for all bug-fix PRs for which there
+        does not already exist a related test that failed before the PR
+      - At least maintaining test coverage for all other PRs
+      - Ensuring that all tests pass when run locally 
+      - Naming PR  to indicate work in progress (WIP) and to attach the PR
+        to the appropriate bug report or feature request [issue]
       - White space (no trailing white space or white space errors may
         be introduced)
       - Commenting code where it is non-obvious and non-trivial
-      - Running tests locally, to ensure all of them pass
-      - Maintaining or increasing test coverage
       - Logically atomic, self consistent and coherent commits
       - Commit message content
-      - Waiting 24 hours before self-approving the pull request to
-        give another OpenCoarrays developer a chance to review my
-        proposed code
+      - Waiting 24 hours before self-approving the PR to give another
+        OpenCoarrays developer a chance to review my proposed code