Bringing master up to date

.gitignore

@@ -2,3 +2,4 @@
 build
 _static
 _templates
+*.swp

.travis.yml

@@ -0,0 +1,38 @@
+env:
+  global:
+  - secure: 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
+  - secure: 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
+  - secure: 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
+branches:
+  only:
+  - develop
+language: cpp
+services:
+  - docker
+before_install:
+  - echo $TRAVIS_PULL_REQUEST
+  - echo $TRAVIS_PULL_REQUEST_BRANCH
+  - echo $TRAVIS_BRANCH
+  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
+  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
+  - pwd
+  - ls 
+  - cd CI
+  - REPO_SOURCE_DIR=${TRAVIS_BUILD_DIR}/jcsda/src_repo
+  # should use develop after issue with parallel ufo testing is solved
+  - git clone https://${GH_TOKEN}@github.com/jcsda-internal/jedi-build-package.git ${REPO_SOURCE_DIR}/jedi_build_package
+
+  - docker pull jcsda/docker-clang-mpich-dev
+  - docker images
+
+script:
+  - docker run -d -t --env GH_TOKEN=$GH_TOKEN --env AWS_ACCESS_KEY_ID=$aws_access_key_id --env GH_BRANCH=$BRANCH --env AWS_SECRET_ACCESS_KEY=$aws_secret_access_key --name clang_container -v ${REPO_SOURCE_DIR}/jedi_build_package:/jcsda/src_repo jcsda/docker-clang-mpich-dev
+
+  - docker exec clang_container bash -c 'mkdir ~/.aws'  
+  - docker exec clang_container bash -c 'echo [default] >> ~/.aws/credentials '  
+  - docker exec clang_container bash -c 'echo aws_access_key_id = $aws_access_key_id >> ~/.aws/credentials'  
+  - docker exec clang_container bash -c 'echo aws_secret_access_key = $aws_secret_access_key >> ~/.aws/credentials'
+  - docker exec clang_container bash -c 'ls /jcsda/src_repo'
+  - docker exec clang_container bash -c 'cd /jcsda/src_repo && pip install --user -e .'
+
+  - docker exec clang_container bash -c 'cd /jcsda/src_repo && ~/.local/bin/jedi-build --gh-token=$GH_TOKEN -j 4 --env-id=travis-clang --branch-map atlas:release-stable fckit:release-stable crtm:release/crtm_jedi -br $GH_BRANCH -p ufo -vvv -3 -u --submit-dashboard --site TravisCI --abort-on-build-errors --abort-on-test-errors'

CI/CMakeLists.txt

@@ -0,0 +1,47 @@
+
+# (C) Copyright 2017 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.
+
+#
+# UFO bundle
+#
+
+cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
+
+project( ufo-bundle LANGUAGES C CXX Fortran )
+
+find_package(ecbuild)
+set( CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_CURRENT_SOURCE_DIR}/ecbuild/cmake;${CMAKE_MODULE_PATH}")
+include( ecbuild_bundle )
+
+set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
+
+ecbuild_bundle_initialize()
+ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/JCSDA/jedi-cmake.git" )
+
+option("BUNDLE_SKIP_ECKIT" "Don't build eckit" "ON") #Skip eckit build unless user passes -DBUNDLE_SKIP_ECKIT=OFF
+ecbuild_bundle( PROJECT eckit GIT "https://github.com/JCSDA/eckit.git" )
+ecbuild_bundle( PROJECT fckit GIT "https://github.com/JCSDA/fckit.git" )
+ecbuild_bundle( PROJECT atlas GIT "https://github.com/JCSDA/atlas.git" )
+
+ecbuild_bundle( PROJECT oops GIT "https://github.com/JCSDA/oops.git" )
+ecbuild_bundle( PROJECT saber GIT "https://github.com/JCSDA/saber.git" )
+#ecbuild_bundle( PROJECT gsw  GIT "https://github.com/JCSDA/GSW-Fortran.git" BRANCH develop  UPDATE )
+ecbuild_bundle( PROJECT crtm GIT "https://github.com/JCSDA/crtm.git" )
+ecbuild_bundle( PROJECT ioda GIT "https://github.com/JCSDA/ioda.git" )
+ecbuild_bundle( PROJECT ufo  GIT "https://github.com/JCSDA/ufo.git" )
+
+
+# Build Doxygen documentation
+option(BUILD_UFO_BUNDLE_DOC "Build documentation" OFF)
+if(BUILD_UFO_BUNDLE_DOC)
+   add_subdirectory( Documentation )
+endif(BUILD_UFO_BUNDLE_DOC)
+
+ecbuild_bundle_finalize()
+
+include(cmake/cdash-integration.cmake)
+include(CTest)
+

CI/buildspec_clang.yml

@@ -0,0 +1,149 @@
+version: 0.2
+
+env:
+  parameter-store:
+    GIT_USER: "/CodeBuild/Git_USER"
+    GIT_PASS: "/CodeBuild/Git_PASS"
+
+phases:
+  install:
+    commands:
+      - echo Executing install phase
+      - 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=${CODEBUILD_SOURCE_VERSION}"
+
+  pre_build:
+    commands:
+      - echo Executing pre_build phase
+      - mkdir /build_container
+      - mkdir /jcsda
+      - cd CI
+
+      - git lfs install # creates .gitconfig
+
+      #  Set crtm branch name
+      - export CRTM_JEDI_BRANCH="v2.3-jedi"
+
+      - if [ "$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
+
+      ##  public repos
+      # ufo
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda/ufo $CODEBUILD_GIT_BRANCH ufo /jcsda/ufo-bundle develop
+
+      # crtm
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda/crtm $CODEBUILD_GIT_BRANCH_CRTM crtm /jcsda/ufo-bundle $CRTM_JEDI_BRANCH
+
+      # ioda
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda/ioda $CODEBUILD_GIT_BRANCH ioda /jcsda/ufo-bundle develop
+
+      # saber
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda/saber $CODEBUILD_GIT_BRANCH saber /jcsda/ufo-bundle develop
+
+      # oops
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda/oops $CODEBUILD_GIT_BRANCH oops /jcsda/ufo-bundle develop
+
+
+      ##  ecmwf repos
+      # atlas
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/atlas $CODEBUILD_GIT_BRANCH_FORK atlas /jcsda/ufo-bundle release-stable
+
+      #fckit
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/fckit $CODEBUILD_GIT_BRANCH_FORK fckit /jcsda/ufo-bundle release-stable
+
+
+      ##  internal repos
+      # jedi-cmake
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/jedi-cmake $CODEBUILD_GIT_BRANCH jedicmake /jcsda/ufo-bundle develop
+
+      # ioda-engines
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ioda-engines $CODEBUILD_GIT_BRANCH ioda_engines /jcsda/ufo-bundle develop
+
+      # rttov
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/rttov $CODEBUILD_GIT_BRANCH rttov /jcsda/ufo-bundle develop
+
+      # ropp
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/ropp-test $CODEBUILD_GIT_BRANCH ropp-ufo /jcsda/ufo-bundle develop
+
+      # geos-aero
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/geos-aero $CODEBUILD_GIT_BRANCH geos-aero /jcsda/ufo-bundle develop
+
+      #gsw
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/GSW-Fortran $CODEBUILD_GIT_BRANCH gsw /jcsda/ufo-bundle develop
+
+      # move CMakeLists.txt
+      - cp CMakeLists.txt /jcsda/ufo-bundle
+      - cp -r cmake /jcsda/ufo-bundle/
+      - cd /jcsda/ufo-bundle
+
+      - ls
+      - cd /jcsda/ufo-bundle
+      - ls
+
+      - sed -i 's/BRANCH develop  UPDATE//' CMakeLists.txt
+      - sed -i 's/BRANCH develop //' CMakeLists.txt
+      - sed -i 's/BRANCH release-stable UPDATE//' CMakeLists.txt
+      - sed -i -e '/ecbuild_bundle( PROJECT ufo/i\
+        ecbuild_bundle( PROJECT ropp-ufo  GIT "https://github.com/JCSDA/ropp-test.git" )' CMakeLists.txt
+      - sed -i -e '/ecbuild_bundle( PROJECT ufo/i\
+        ecbuild_bundle( PROJECT geos-aero  GIT "https://github.com/JCSDA/geos-aero.git" )' CMakeLists.txt
+
+  build:
+    commands:
+      - echo Executing build phase
+      - echo $CODEBUILD_BUILD_SUCCEEDING
+      - export BUILD_STATUS="0"
+      - echo $BUILD_STATUS
+
+      - cd /build_container
+      - ecbuild -DBUILD_RTTOV=1 /jcsda/ufo-bundle/
+      - cd ufo
+      - make -j4
+
+      - if [ "$CODEBUILD_BUILD_SUCCEEDING" = "1" ];
+        then export BUILD_STATUS="1";
+        echo "Build passed";
+        fi
+      - echo $BUILD_STATUS
+
+      - cd /build_container/ufo
+      - ctest
+
+  post_build:
+    commands:
+      - echo Executing post_build phase
+      - echo $CODEBUILD_BUILD_SUCCEEDING
+      - if [ "$BUILD_STATUS" = "1" ] && [ "$CODEBUILD_BUILD_SUCCEEDING" = "0" ];
+        then echo "Build passed, rerunning failed tests";
+        cd /build_container/ufo;
+        ctest -VV --rerun-failed;
+        else echo "Build failed";
+        fi