Merge branch 'master' into co_broadcast-derived-type

Author: Damian Rouson

.VERSION

@@ -1,6 +1,6 @@
 $Format:%d%n%n$
 # Fall back version, probably last release:
-2.7.0
+2.7.1
 
 # OpenCoarrays version file. This project uses semantic
 # versioning. For details see http://semver.org

.github/FUNDING.yml

@@ -0,0 +1,8 @@
+# These are supported funding model platforms
+
+github: [zbeekman, rouson, afanfa]
+# patreon: # Replace with a single Patreon username
+# open_collective: # Replace with a single Open Collective username
+# ko_fi: # Replace with a single Ko-fi username
+# tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+custom: http://www.sourceryinstitute.org/store/p5/Donation.html

.travis.yml

@@ -1,45 +1,67 @@
 ---
-language: c
+language: minimal
 
 os: osx
 
 env:
   global:
-#    - ZERO_AR_DATE=1
+    - ZERO_AR_DATE=1
     - TZ=UTC
     - CACHE="${HOME}/.local"
-    - MPICH_VER="3.2.1"
+    - MPICH_VER="3.3"
     - MPICH_URL_HEAD="https://www.mpich.org/static/downloads/${MPICH_VER}"
     - MPICH_URL_TAIL="mpich-${MPICH_VER}.tar.gz"
-    - MPICH_GCC6_BOT_URL_HEAD="https://github.com/sourceryinstitute/OpenCoarrays/files/1956499/"
-    - MPICH_GCC7_BOT_URL_HEAD="https://github.com/sourceryinstitute/OpenCoarrays/files/1956441/"
-    - MPICH_BOT_URL_TAIL="mpich-3.2.1_1.high_sierra.bottle.1.tar.gz"
     - BUILD_TYPES="Debug RelWithDebInfo Release CodeCoverage"
     - PATH="${HOME}/.local/bin:$PATH"
-  # matrix:
-  #   - GCC="6 7" OSX_PACKAGES="gcc@7 gcc@6 cmake shellcheck" BUILD_TYPE="cmake"
 
 matrix:
   fast_finish: true
   include:
     - &macOS
       os: osx
+      osx_image: xcode10.2
       env:
         - BUILD_TYPE="InstallScript"
           GCC=9
-          OSX_PACKAGES="gcc shellcheck cmake mpich"
-          # cmake should be removed, but we should be installing binaries
-          # because building from source takes forever
-    # -
-    #   <<: *macOS
-    #   env:
-    #     - GCC=8
-    #       BUILD_TYPES="debug RelWithDebInfo Release"
-    #       OSX_PACKAGES="gcc openmpi shellcheck cmake"
+          CC=gcc-9
+          CXX=g++-9
+          FC=gfortran-9
+      addons:
+        homebrew:
+          packages:
+            - gcc
+            - mpich
+            - shellcheck
+          update: true
+    - &macOS_allowed_failure
+      <<: *macOS
+      env:
+        - GCC=9
+          FC=gfortran-${GCC}
+          BUILD_TYPES="Release CodeCoverage"
+      addons:
+        homebrew:
+          packages:
+            - cmake
+            - gcc
+            - openmpi
+            - shellcheck
+          update: true
+    -
+      <<: *macOS
+      env:
+        - GCC=9
+          FC=gcc-${GCC}
+          CC=gcc-${GCC}
+          CXX=g++-${GCC}
+      addons:
+        homebrew:
+          brewfile: true
+          update: true
     - &ubuntu
       os: linux
       sudo: false
-      dist: trusty
+      dist: xenial
       env:
         - GCC=8
       cache:
@@ -50,7 +72,8 @@ matrix:
         apt:
           sources: &linuxsrcs
             - ubuntu-toolchain-r-test
-            - george-edison55-precise-backports
+            - sourceline: 'deb https://apt.kitware.com/ubuntu/ xenial main'
+              key_url: 'https://apt.kitware.com/keys/kitware-archive-latest.asc'
           packages: &gcc8pkgs
             - gcc-8
             - gfortran-8
@@ -92,11 +115,12 @@ matrix:
 
   allow_failures:
     - *linux_allowed_failure
-    - osx
+    - *macOS_allowed_failure
+
+    # macOS allowed failure due to random test timeouts w/ clang & OpenMPI
 
 before_install:
   - source developer-scripts/travis/before_install.all.sh
-  - developer-scripts/travis/before_install.${TRAVIS_OS_NAME}.sh
 
 install:
   - pwd
@@ -105,6 +129,9 @@ install:
 script:
   - pwd
   - export SOURCE_DATE_EPOCH=$(git show -s --format=%ct $TRAVIS_COMMIT)
+  - export LC_ALL=C
+  - export TZ=UTC
+  - export ZERO_AR_DATE=1
   - echo "SOURCE_DATE_EPOCH = ${SOURCE_DATE_EPOCH}"
   - ./developer-scripts/travis/test-script.${BUILD_TYPE:-cmake}.sh
 
@@ -113,56 +140,6 @@ after_script:
   - for version in ${GCC}; do bash <(curl -s https://codecov.io/bash) -x $(type -P gcov-${GCC}) >> coverage.log 2>> coverage.err || true ; done
   - tail coverage.log || true
   - tail coverage.err || true
-  - |
-    if [[ "${TRAVIS_TAG}" ]]; then
-      if [[ "v${TRAVIS_TAG}" != "v$(sed -n '/[0-9]\{1,\}\(\.[0-9]\{1,\}\)\{1,\}/{s/^\([^.]*\)\([0-9]\{1,\}\(\.[0-9]\{1,\}\)\{1,\}\)\(.*\)/\2/p;q;}' .VERSION)" ]]; then
-        echo "ERROR: You are trying to tag a new release but have a version missmatch in \`.VERSION\`"
-        false # throw an error
-      fi
-    fi
-
-# before_deploy:
-#   - git archive -v --prefix "OpenCoarrays-${TRAVIS_TAG}/" -o "OpenCoarrays-${TRAVIS_TAG}.tar.gz" ${TRAVIS_TAG}
-#   - |
-#     echo '# To verify cryptographic checksums `shasum -c opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Mac OS X,' > "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-#     echo '# `sha256sum -c  opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Linux.' >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-#     if [[ $(uname -s) == Darwin ]]; then
-#       shasum -a 256 "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-#     else
-#       sha256sum  "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-#     fi
-#   - |
-#     openssl aes-256-cbc -K ${encrypted_ef4535c39461_key} -iv ${encrypted_ef4535c39461_iv} -in subkey-328B3A0E-secret.asc.enc -out ./subkey-328B3A0E-secret.asc -d
-#     gpg --allow-secret-key-import --import ./subkey-328B3A0E-secret.asc && rm subkey-328B3A0E-secret.asc
-#     rm subkey-328B3A0E-secret.* || true
-#     unset encrypted_ef4535c39461_key || true
-#     unset encrypted_ef4535c39461_iv || true
-#     gpg --armor --detach-sign -u 328B3A0E --comment 'Mac users can use GPGTools - https://gpgtools.org' \
-#       --comment "Download Izaak Beekman's GPG public key from your" \
-#       --comment 'trusted key server or from' \
-#       --comment 'https://izaakbeekman.com/izaak.pubkey.txt' \
-#       --comment 'Next add it to your GPG keyring, e.g.,' \
-#       --comment '`curl https://izaakbeekman.com/izaak.pubkey.txt | gpg --import`' \
-#       --comment "Make sure you have verified that the release archive's" \
-#       --comment 'SHA256 checksum matches the provided' \
-#       --comment "opencoarrays-${TRAVIS_TAG}-SHA256.txt and ensure that this file" \
-#       --comment "and it's signature are in the same directory. Then" \
-#       --comment 'verify with:' \
-#       --comment '`gpg --verify opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt.asc`' \
-#       "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
-
-# deploy:
-#   provider: releases
-#   api_key:
-#     secure: 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
-#   file:
-#     - "OpenCoarrays-${TRAVIS_TAG}.tar.gz"
-#     - "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
-#     - "opencoarrays-${TRAVIS_TAG}-SHA256.txt.asc"
-#   skip_cleanup: true
-#   on:
-#     tags: true
-#    repo: sourceryinstitute/opencoarrays
 
 notifications:
   webhooks:

Brewfile

@@ -1,20 +1,19 @@
-# Brewfile to install OpenCoarrays prerequisites with [Homebrew] or [Linuxbrew].
+# Brewfile to install OpenCoarrays prerequisites with [Homebrew].
 #
 # TL;DR: `brew tap homebrew/bundle && brew bundle` to install prerequisites
 #
 # Homebrew for Mac OS X can be installed via:
 # `/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
-# Linux brew (lives in userland, no sudo required) can be installed with:
-# `ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/linuxbrew/go/install)"`
+# Homebrew for Linux (lives in userland, no sudo required) can be installed with:
+# `sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"`
 #
 # Once Homebrew/Linuxbrew is installed, execute the following commands to install the required prerequisites:
 # `brew tap homebrew/bundle && brew bundle`
 #
 
 brew 'cmake'
 brew 'gcc'
-brew 'mpich', args: ['cc=gcc-8', 'build-from-source']
-brew 'opencoarrays', args: ['cc=gcc-8', 'build-from-source']
+brew 'mpich' #, args: ['cc=gcc-9', 'build-from-source', 'verbose']
+# brew 'opencoarrays', args: ['cc=gcc-9', 'build-from-source', 'verbose']
 
 # [Homebrew]: http://brew.sh
-# [Linuxbrew]: http://linuxbrew.sh

CMakeLists.txt

@@ -697,8 +697,9 @@ function(add_caf_test name num_caf_img test_target)
     endif()
   endif()
   if( openmpi)
-    set (test_parameters ${test_parameters} --allow-run-as-root)
-    message( STATUS "Open-MPI back end detected, passing --allow-run-as-root to allow tests to pass when run with sudo or as root." )
+    if(NOT DEFINED ENV{TRAVIS})
+      set (test_parameters ${test_parameters} --allow-run-as-root)
+    endif()
   endif()
   set(test_parameters -np ${num_caf_img} ${test_parameters})
   if(DEFINED ARGN)

INSTALL.md

@@ -75,7 +75,16 @@ and re-running CMake.
 ## End-User Installation ##
 
 Most users will find it easiest and fastest to use package management
-software to install OpenCoarrays.  Package management options for
+software to install OpenCoarrays. Below is the status of OpenCoarrays
+in various package managers. If you do not see your favorite package
+manager listed or it is badly out of date, please reach out and ask
+for it to be included or updated, or contribute it yourself. We are
+happy to work with package managers to resolve issues, and adapt our
+build system to play nicely so they don't have to maintain patches.
+
+[![Packaging status][repology-badge]][OC-on-repology]
+
+Package management options for
 macOS, Windows, and Linux are described first below. Also described
 below are options for installing via the Sourcery Institute virtual
 machine or via the bash scripts included that are in the OpenCoarrays
@@ -423,6 +432,9 @@ file.
 
 [URLs]: #
 
+[OC-on-repology]: https://repology.org/project/opencoarrays/versions
+[repology-badge]: https://repology.org/badge/vertical-allrepos/opencoarrays.svg
+
 [FreeBSD ports/packages installation information]: https://www.freebsd.org/doc/en_US.ISO8859-1/books/handbook/ports.html
 [GH all releases badge]: https://img.shields.io/github/downloads/sourceryinstitute/OpenCoarrays/total.svg?style=flat-square
 [GH release badge]: https://img.shields.io/github/release/sourceryinstitute/OpenCoarrays.svg?style=flat-square

README.md

@@ -87,6 +87,17 @@ The default [index.ipynb] notebook is read only, but you can
 execute it, copy it to make changes, or create an entirely
 new [CAF kernel][notebook kernel] notebook.
 
+Packaged Version
+----------------
+
+If you would like to be able to install OpenCoarrays through your
+favorite package manager, please ask them to add it, or contribute it
+yourself. If you see your favorite package manager has an outdated
+version, please ask them to update it, or contribute an update
+yourself.
+
+[![Packaging status][repology-badge]][OC-on-repology]
+
 Getting Started
 ---------------
 
@@ -189,6 +200,9 @@ to aid in development efforts.
 [Jupyter]: https://jupyter.org
 [index.ipynb]: https://nbviewer.jupyter.org/github/sourceryinstitute/jupyter-CAF-kernel/blob/master/index.ipynb
 
+[OC-on-repology]: https://repology.org/project/opencoarrays/versions
+[repology-badge]: https://repology.org/badge/vertical-allrepos/opencoarrays.svg
+
 [build img]: https://img.shields.io/travis/sourceryinstitute/OpenCoarrays.svg?style=flat-square "Build badge"
 [CI Master Branch]: https://travis-ci.org/sourceryinstitute/OpenCoarrays?branch=master "View Travis-CI builds"
 [download img]: https://img.shields.io/github/downloads/sourceryinstitute/OpenCoarrays/total.svg?style=flat-square "Download count badge"

cmake/InstallFileManifest.cmake

@@ -1,3 +1,4 @@
+
 # This script will create and install an install manifest, including SHA256 hashes of each installed file
 # Variables passed from CMake must be set with `install(CODE "set(...)")`
 
@@ -6,7 +7,7 @@ message(STATUS "Generating SHA256 checksumed receipt for all installed assets")
 # Set receipt install destination
 set(RECEIPT_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DATADIR}/${PROJECT_NAME}")
 
-# Mimic cmake_install.cmake's handlin of components
+# Mimic cmake_install.cmake's handling of components
 if(CMAKE_INSTALL_COMPONENT)
   set(HASHED_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.SHA256.txt")
 else()
@@ -16,10 +17,15 @@ endif()
 # Clean out any old install manifest on re-installation, if it exists
 file(REMOVE "${CMAKE_BINARY_DIR}/${HASHED_INSTALL_MANIFEST}")
 
+if(DEFINED ENV{DESTDIR})
+  get_filename_component(ABS_DESTDIR "$ENV{DESTDIR}" ABSOLUTE)
+else()
+  set(ABS_DESTDIR "")
+endif()
 # Loop over files computing hashes
 foreach(file IN LISTS CMAKE_INSTALL_MANIFEST_FILES)
-  file(SHA256 "${file}" _file_sha256)
-  file(RELATIVE_PATH FILE_REL_PATH "${RECEIPT_INSTALL_DIR}" "${file}")
+  file(SHA256 "$ENV{DESTDIR}${file}" _file_sha256)
+  file(RELATIVE_PATH FILE_REL_PATH "${ABS_DESTDIR}${RECEIPT_INSTALL_DIR}" "${ABS_DESTDIR}${file}")
   file(APPEND "${CMAKE_BINARY_DIR}/${HASHED_INSTALL_MANIFEST}" "${_file_sha256}  ${FILE_REL_PATH}\n")
 endforeach()
 file(APPEND "${CMAKE_BINARY_DIR}/${HASHED_INSTALL_MANIFEST}"

developer-scripts/travis/install.osx.sh

@@ -24,22 +24,7 @@ echo "Performing Travis-CI installation phase on macOS..."
 # Update and install via Homebrew on macOS
 brew update > /dev/null
 
-brew install gcc || true
-brew link --overwrite gcc || true
-
-for pkg in ${OSX_PACKAGES}; do
-    brew ls --versions "${pkg}" >/dev/null || brew install "${pkg}" || brew link --overwrite "${pkg}"
-    brew outdated "${pkg}" || brew upgrade "${pkg}"
-done
-
-# Uninstall mpich and openmpi so that we can install our own version
-#brew uninstall --force --ignore-dependencies openmpi || true
-#brew uninstall --force --ignore-dependencies mpich || true
-
-# Building CMake from source is very slow. We should be using binaries instead
-# if [[ "${BUILD_TYPE:-}" == InstallScript ]]; then # uninstall some stuff if present
-#     brew uninstall --force --ignore-dependencies cmake || true
-# fi
+brew outdated
 
 {
     mpif90 --version && mpif90 -show
@@ -51,4 +36,12 @@ done
 type -a cmake || echo "CMake not installed"
 cmake --version || true
 
+echo "CC: ${CC:-none defined}"
+echo "\$CC --version:"
+${CC:-} --version || true
+
+echo "FC: ${FC:-none-defined}"
+echo "\$FC --version:"
+${FC:-} --version || true
+
 echo "Done."