Merge pull request #640 from JCSDA-internal/release/mpas-1.0

Release/mpas 1.0

.gitattributes

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+*.nc filter=lfs diff=lfs merge=lfs -text
+*.graph.info* filter=lfs diff=lfs merge=lfs -text

.github/pull_request_template.md

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+Use this template to give a detailed message describing the change you want to make to the code.
+If you are unclear on what should be written here, see  https://github.com/wrf-model/WRF/wiki/Making-a-good-pull-request-message for more guidance
+
+The title of this pull request should be a brief "purpose" for this change.
+
+--- Delete this line and those above before hitting "Create pull request" ---
+
+TYPE: choose one of [bug fix, maintenance, enhancement, new feature, feature removed, no impact, text only]
+
+DESCRIPTION OF CHANGES: One or more paragraphs describing problem, solution, and required changes.
+
+ISSUE: For use when this PR closes a Zenhub issue. E.g., for issue number 123,
+
+Fixes #123
+
+
+LIST OF MODIFIED FILES: list of changed files (use `git diff --name-status develop` to get formatted list)
+
+TESTS CONDUCTED: Explicitly state what testing was performed.

.gitignore

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+# Ignore these files anywhere in the tree
+*.pyc

CI/CMakeLists.txt

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+# (C) Copyright 2017-2020 UCAR
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+#
+# MPAS/JEDI bundle
+#
+
+cmake_minimum_required( VERSION 3.12 )
+project( mpas-bundle VERSION 1.0.0 LANGUAGES C CXX Fortran )
+
+## ECBuild integration
+include(GNUInstallDirs)
+set( INSTALL_LIB_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING "Library installation directory" FORCE ) #Force ecbuild to use the default platform lib install location
+set( ECBUILD_DEFAULT_BUILD_TYPE Release CACHE STRING "ECBuild default build type" FORCE)
+set( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
+set( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib )
+set( CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib )
+find_package(ecbuild)
+include( ecbuild_bundle )
+ecbuild_bundle_initialize()
+
+ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda-internal/jedi-cmake.git" )
+
+# ecmwf repos are already available in CI containers. Disabled here
+#option(BUNDLE_SKIP_ECKIT "Don't build eckit" "OFF" ) # Build eckit unless user passes -DBUNDLE_SKIP_ECKIT=ON
+#ecbuild_bundle( PROJECT eckit     GIT "https://github.com/ecmwf/eckit.git" )
+#ecbuild_bundle( PROJECT fckit     GIT "https://github.com/ecmwf/fckit.git" )
+#ecbuild_bundle( PROJECT atlas     GIT "https://github.com/ecmwf/atlas.git" )
+
+#TODO: When mpas-bundle becomes a public repo, consider changing the default value of BUNDLE_SKIP_ROPP-UFO to "ON"
+
+option(BUNDLE_SKIP_ROPP-UFO "Don't build ROPP-UFO"  "OFF") # Skip ropp-ufo build unless user passes -DBUNDLE_SKIP_ROPP-UFO=ON
+ecbuild_bundle( PROJECT ropp-ufo  GIT "https://github.com/jcsda-internal/ropp-test.git" )
+option(BUNDLE_SKIP_GSW "Don't build GSW"       "ON") # Skip gsw build unless user passes -DBUNDLE_SKIP_GSW=OFF
+ecbuild_bundle( PROJECT gsw       GIT "https://github.com/jcsda-internal/GSW-Fortran.git" )
+ecbuild_bundle( PROJECT crtm      GIT "https://github.com/jcsda-internal/crtm.git" )
+ecbuild_bundle( PROJECT rttov     GIT "https://github.com/jcsda-internal/rttov.git" )
+ecbuild_bundle( PROJECT oops      GIT "https://github.com/jcsda-internal/oops.git" )
+ecbuild_bundle( PROJECT saber     GIT "https://github.com/jcsda-internal/saber.git" )
+ecbuild_bundle( PROJECT ioda      GIT "https://github.com/jcsda-internal/ioda.git" )
+ecbuild_bundle( PROJECT ufo       GIT "https://github.com/jcsda-internal/ufo.git" )
+
+# ioda and ufo test data
+#---------------------------------
+
+# If IODA branch is being built set GIT_BRANCH_FUNC to IODA's current branch.
+# If a tagged version of IODA is being built set GIT_TAG_FUNC to ioda's current tag. In this case,
+# IODA test files will be download from UCAR DASH and ioda-data repo will not be cloned.
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+
+#find_branch_name(REPO_DIR_NAME ioda)
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+#if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+#  ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
+#endif()
+
+# same procedure for ufo-data
+find_branch_name(REPO_DIR_NAME ufo)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
+endif()
+
+# same procedure for mpas-jedi-data
+find_branch_name(REPO_DIR_NAME mpas-jedi)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT mpas-jedi-data GIT "https://github.com/JCSDA-internal/mpas-jedi-data.git" )
+endif()
+
+
+set(MPAS_CORES atmosphere init_atmosphere CACHE STRING "MPAS-Model: cores to build.")
+set(MPAS_DOUBLE_PRECISION "ON" CACHE STRING "MPAS-Model: Use double precision 64-bit Floating point.")
+
+ecbuild_bundle( PROJECT MPAS     GIT "https://github.com/jcsda-internal/MPAS-Model.git" )
+ecbuild_bundle( PROJECT mpas-jedi GIT "https://github.com/jcsda-internal/mpas-jedi")
+
+ecbuild_bundle_finalize()
+
+include(cmake/cdash-integration.cmake)
+include(CTest)

CI/buildspec_clang.yml

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+version: 0.2
+
+env:
+  parameter-store:
+    GIT_USER: "/CodeBuild/Git_USER"
+    GIT_PASS: "/CodeBuild/Git_PASS"
+
+phases:
+  install:
+    commands:
+      - echo Executing install phase
+      - echo $CODEBUILD_RESOLVED_SOURCE_VERSION
+      - echo $CODEBUILD_SOURCE_REPO_URL
+      - echo $CODEBUILD_SOURCE_VERSION
+
+      - echo $CODEBUILD_WEBHOOK_MERGE_COMMIT
+      - echo $CODEBUILD_WEBHOOK_PREV_COMMIT
+      - echo $CODEBUILD_WEBHOOK_HEAD_REF
+      - echo $CODEBUILD_WEBHOOK_ACTOR_ACCOUNT_ID
+      - echo $CODEBUILD_WEBHOOK_EVENT
+      - echo $CODEBUILD_WEBHOOK_TRIGGER
+      - echo $CODEBUILD_WEBHOOK_BASE_REF
+
+      # Codebuild only runs on PUSH events if HEAD_REF
+      # is refs/heads/develop (merge to develop). In this
+      # case CODEBUILD_GIT_BRANCH="develop"
+
+      - if [ "$CODEBUILD_WEBHOOK_EVENT" = "PUSH" ];
+        then export CODEBUILD_GIT_BRANCH="develop";
+        echo "Merging to develop";
+        else export CODEBUILD_GIT_BRANCH=${CODEBUILD_WEBHOOK_HEAD_REF#refs/heads/};
+        fi
+
+      - echo "CODEBUILD_GIT_BRANCH=${CODEBUILD_GIT_BRANCH}"
+      - echo "CODEBUILD_SOURCE_VERSION=${CODEBUILD_SOURCE_VERSION}"
+
+  pre_build:
+    commands:
+      - echo Executing pre_build phase
+      - mkdir /build_container
+      - mkdir /jcsda
+      - git lfs install # creates .gitconfig
+
+      #  Set crtm branch name
+      - export CRTM_JEDI_BRANCH="release/crtm_jedi"
+
+      - if [ "$CODEBUILD_GIT_BRANCH" = "develop" ];
+        then export CODEBUILD_GIT_BRANCH_FORK="release-stable";
+        export CODEBUILD_GIT_BRANCH_CRTM=${CRTM_JEDI_BRANCH};
+        else export CODEBUILD_GIT_BRANCH_FORK=${CODEBUILD_GIT_BRANCH};
+        export CODEBUILD_GIT_BRANCH_CRTM=${CODEBUILD_GIT_BRANCH};
+        echo "CODEBUILD_GIT_BRANCH_FORK=${CODEBUILD_GIT_BRANCH_FORK}";
+        fi
+
+      # Upload branch name and commit sha as CodeBuild artifact to S3
+      - mkdir -p /jcsda/artifacts
+      - echo ${CODEBUILD_GIT_BRANCH} > /jcsda/artifacts/branch_name.txt
+      - echo ${CODEBUILD_RESOLVED_SOURCE_VERSION} > /jcsda/artifacts/commit_sha.txt
+
+      - cd CI
+
+      ##  jedi core repos
+      # oops
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/oops $CODEBUILD_GIT_BRANCH oops /jcsda/mpas-bundle develop
+
+      # saber
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/saber $CODEBUILD_GIT_BRANCH saber /jcsda/mpas-bundle develop
+
+      # ioda
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ioda $CODEBUILD_GIT_BRANCH ioda /jcsda/mpas-bundle develop
+
+      # ufo
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ufo $CODEBUILD_GIT_BRANCH ufo /jcsda/mpas-bundle develop
+
+      # crtm
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/crtm $CODEBUILD_GIT_BRANCH_CRTM crtm /jcsda/mpas-bundle $CRTM_JEDI_BRANCH
+
+      ##  internal repos
+      #  mpas-model
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/MPAS-Model $CODEBUILD_GIT_BRANCH_FORK MPAS /jcsda/mpas-bundle release-stable
+
+      #  mpas-jedi
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/mpas-jedi $CODEBUILD_GIT_BRANCH mpas-jedi /jcsda/mpas-bundle develop
+
+      # mpas-jedi-data
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/mpas-jedi-data $CODEBUILD_GIT_BRANCH mpas-jedi-data /jcsda/mpas-bundle develop
+
+      # jedi-cmake
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/jedi-cmake $CODEBUILD_GIT_BRANCH jedicmake /jcsda/mpas-bundle develop
+
+      # ropp
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ropp-test $CODEBUILD_GIT_BRANCH ropp-ufo /jcsda/mpas-bundle develop
+
+      # rttov
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/rttov $CODEBUILD_GIT_BRANCH rttov /jcsda/mpas-bundle develop
+
+      # ufo-test
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ufo-data $CODEBUILD_GIT_BRANCH ufo-data /jcsda/mpas-bundle develop
+
+      # move CMakeLists.txt
+      - cp CMakeLists.txt /jcsda/mpas-bundle
+      - cp -r cmake /jcsda/mpas-bundle/
+      # cdash upload setup
+      - cp /jcsda/mpas-bundle/cmake/CTestConfig.cmake /jcsda/mpas-bundle
+
+  build:
+    on-failure: CONTINUE
+    commands:
+      - echo Executing build phase
+      - echo $CODEBUILD_BUILD_SUCCEEDING
+      - export BUILD_STATUS="0"
+      - echo $BUILD_STATUS
+
+      # configure and build
+      - cd /build_container
+
+      - ecbuild -Wno-dev -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCDASH_OVERRIDE_GIT_BRANCH=$CODEBUILD_GIT_BRANCH -DCTEST_UPDATE_VERSION_ONLY=FALSE /jcsda/mpas-bundle/
+      - ls /build_container
+      - cd /build_container/mpas-jedi
+      - cp ../DartConfiguration.tcl .
+      - sed -i 's/mpas-bundle/mpas-bundle\/mpas-jedi/' DartConfiguration.tcl
+      - sed -i 's/build_container/build_container\/mpas-jedi/' DartConfiguration.tcl
+      - cat DartConfiguration.tcl
+
+      - make -j4
+
+      - if [ "$CODEBUILD_BUILD_SUCCEEDING" = "1" ];
+        then export BUILD_STATUS="1";
+        echo "Build passed";
+        fi
+      - echo $BUILD_STATUS
+
+      - cd /build_container/mpas-jedi
+      - ctest -C RelWithDebInfo -D ExperimentalTest -E compare_mpasjedi_hofx
+
+    finally:
+      - cd /build_container/mpas-jedi
+      - ctest -C RelWithDebInfo -D ExperimentalSubmit -M Continuous -- --track Continuous --group Continuous
+
+  post_build:
+    commands:
+      - echo Executing post_build phase
+      - echo $CODEBUILD_BUILD_SUCCEEDING
+      - echo $BUILD_STATUS
+
+      # upload find cdash url and upload it as CodeBuild artifact to S3
+      - if [ "$BUILD_STATUS" = "1" ];
+        then echo "Build & tests passed, find cdash url";
+        bash /jcsda/mpas-bundle/mpas-jedi/CI/cdash-url.sh /build_container/mpas-jedi/Testing;
+        url=$(bash /jcsda/mpas-bundle/mpas-jedi/CI/cdash-url.sh /build_container/mpas-jedi/Testing);
+        echo $url;
+        echo ${url} > /jcsda/artifacts/cdash-url.txt;
+        cat /jcsda/artifacts/cdash-url.txt;
+        else echo "Build failed";
+        fi
+
+artifacts:
+  files:
+    - '/jcsda/artifacts/*'
+  name: mpas-clang-url