Merge pull request #1241 from JCSDA-internal/release/1.1.0

Release/1.1.0

Author: Mark Miesch

.codecov.yml

@@ -6,6 +6,13 @@ coverage:
   precision: 2
   round: down
   range: "70...100"
+  status:
+    project:
+      default:
+        threshold: 0.05%
+    patch:
+      default:
+        threshold: 2%
 
 ignore:
   - "src/test"

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Use this template to report bugs
+title: "[Bug]"
+labels: 'bug'
+assignees: ''
+
+---
+
+## Current behavior (describe the bug)
+>[Be sure to add a Pipeline, Label, Estimate, Assignees, and Epic](https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/inside/practices/issues.html)
+
+## To Reproduce
+
+> What computer are you running on?
+
+> What compilers/modules are you using?
+
+> Steps to reproduce the behavior
+
+1.
+2.
+3.
+...
+
+## Expected behavior
+
+## Additional information (optional)

.github/ISSUE_TEMPLATE/config.yaml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: JCSDA
+    url: https://jcsda.org/
+    about: JCSDA web site
+  - name: Forums
+    url: https://forums.jcsda.org/
+    about: JCSDA user/developer forums

.github/ISSUE_TEMPLATE/general-issue.md

@@ -0,0 +1,26 @@
+---
+name: General issue template
+about: Use this template for general issues
+title: "[New issue]"
+labels: ''
+assignees: ''
+
+---
+
+## Description
+>Provide a detailed description of this issue.
+>What problem needs to be fixed? What new capability needs to be added?
+>If this is a bug, describe the current behavior (or use the bug template).
+>[Be sure to add a Pipeline, Label, Estimate, Assignees, and Epic](https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/inside/practices/issues.html)
+
+## Requirements
+
+>If this is a new feature: What does the new code need to accomplish? Does it require new software dependencies (e.g. new jedi-stack components or new python modules?)
+>If this is a bugfix: What is the expected behavior?
+
+## Acceptance Criteria (Definition of Done)
+>What does it mean for this to be finished?
+
+## Dependencies
+>What must be done before this can be done? Add issue dependencies in ZenHub as appropriate
+>Does this block progress on other issues? Add this issue as a dependency to other ZenHub issues as appropriate

CI/CMakeLists.txt

@@ -1,4 +1,4 @@
-  
+
 # (C) Copyright 2017 UCAR
 #
 # This software is licensed under the terms of the Apache Licence Version 2.0
@@ -8,25 +8,21 @@
 # OOPS bundle
 #
 
-project( oops-bundle C CXX Fortran )
+cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
 
-cmake_minimum_required( VERSION 3.3.2 FATAL_ERROR )
+project( oops-bundle VERSION 1.0.0 LANGUAGES C CXX Fortran )
 
-set( CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_CURRENT_SOURCE_DIR}/ecbuild/cmake;${CMAKE_MODULE_PATH}")
+find_package(ecbuild REQUIRED)
+list( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 include( ecbuild_bundle )
 
 set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
 
 ecbuild_bundle_initialize()
 
-ecbuild_requires_macro_version( 2.7 )
-
-ecbuild_add_option( FEATURE OMP
-                    DEFAULT ON
-                    DESCRIPTION "Use OpenMP" )
-
-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 oops  GIT "https://github.com/jcsda-internal/oops.git" )
 
 ecbuild_bundle_finalize()
+
+include(cmake/cdash-integration.cmake)
+include(CTest)

CI/buildspec_clang.yml

@@ -1,6 +1,7 @@
 version: 0.2
 
 env:
+  shell: bash
   parameter-store:
     GIT_USER: "/CodeBuild/Git_USER"
     GIT_PASS: "/CodeBuild/Git_PASS"
@@ -21,7 +22,15 @@ phases:
       - echo $CODEBUILD_WEBHOOK_TRIGGER
       - echo $CODEBUILD_WEBHOOK_BASE_REF
 
-      - if [ "$CODEBUILD_WEBHOOK_EVENT" = "PULL_REQUEST_MERGED" ];
+      - gh_source=$(pwd)
+      - echo ${gh_source}
+      - echo $CODEBUILD_SRC_DIR
+
+      # Codebuild only runs on PUSH events if HEAD_REF
+      # is refs/heads/develop (merge to develop). In this
+      # case CODEBUILD_GIT_BRANCH="develop"
+
+      - if [ "$CODEBUILD_WEBHOOK_EVENT" = "PUSH" ];
         then export CODEBUILD_GIT_BRANCH="develop";
         echo "Merging to develop";
         else export CODEBUILD_GIT_BRANCH=${CODEBUILD_WEBHOOK_HEAD_REF#refs/heads/};
@@ -31,9 +40,9 @@ phases:
       - echo "CODEBUILD_SOURCE_VERSION=${CODEBUILD_SOURCE_VERSION}"
 
       - echo "check for same branch names, except for develop"
-      - if ! [ "$CODEBUILD_GIT_BRANCH" = "develop" ]; then 
+      - if ! [ "$CODEBUILD_GIT_BRANCH" = "develop" ]; then
         pip install boto3;
-        pip install pygithub; 
+        pip install pygithub;
         python CI/update_webhook_branchname.py $CODEBUILD_GIT_BRANCH $CODEBUILD_RESOLVED_SOURCE_VERSION;
         fi
 
@@ -45,15 +54,34 @@ phases:
       - echo ${CODEBUILD_RESOLVED_SOURCE_VERSION} > artifacts/commit_sha.txt
 
       # get jedi-build-package
-      - git clone https://$GIT_USER:[email protected]/jcsda-internal/jedi-build-package
+      - git clone -b feature/ecbuild35 https://$GIT_USER:[email protected]/jcsda-internal/jedi-build-package
 
       - cd jedi-build-package
       - pip install --user -e .
 
-      - ~/.local/bin/jedi-build --gh-token=$GIT_PASS -j 4 --env-id=docker-clang --branch-map atlas:release-stable fckit:release-stable -br ${CODEBUILD_GIT_BRANCH} -p oops -vvv -3 -u --submit-dashboard --site CodeBuild --abort-on-build-errors --abort-on-test-errors
+      - ~/.local/bin/jedi-build --gh-token=$GIT_PASS -j 4 --env-id=docker-clang --branch-map atlas:release-stable fckit:release-stable -br ${CODEBUILD_GIT_BRANCH} -p oops -vvv -3 -u --submit-dashboard --site CodeBuild --abort-on-build-errors --abort-on-test-errors --cleanup=False 2>&1 | tee jedi_build_output.txt ; test ${PIPESTATUS[0]} -eq 0
+
+      #find CDASH URL
+      - Done_path_line=$(grep 'Done.xml' jedi_build_output.txt | tail -1)
+      - echo $Done_path_line
+      - Done_path=$(echo ${Done_path_line} | sed 's/Uploaded://')
+      - echo $Done_path
+      - cat $Done_path
+      # retrieve buildID from Done.xml
+      - buildID=$(cat $Done_path | grep -o -P '(?<=buildId>).*(?=</build)')
+      - echo ${buildID}
+      - url=https://cdash.jcsda.org/buildSummary.php?buildid=${buildID}
+      - echo ${url}
+
+      #create artifacts
+      - mkdir -p /jcsda/artifacts/
+      - echo ${url} > /jcsda/artifacts/cdash-url.txt
+      - cat /jcsda/artifacts/cdash-url.txt
+      - echo ${CODEBUILD_GIT_BRANCH} > /jcsda/artifacts/branch_name.txt
+      - echo ${CODEBUILD_RESOLVED_SOURCE_VERSION} > /jcsda/artifacts/commit_sha.txt
+      - ls  /jcsda/artifacts/
 
-      
 artifacts:
   files:
-    - 'artifacts/*'
-  name: artifact-oops-clang
+    - '/jcsda/artifacts/*'
+  name: oops-clang-url

CI/buildspec_gnu.yml

@@ -12,6 +12,8 @@ phases:
 
       - echo $CODEBUILD_RESOLVED_SOURCE_VERSION
       - echo $CODEBUILD_SOURCE_REPO_URL
+      - org_name=$(echo $CODEBUILD_SOURCE_REPO_URL | awk '{split($0,org,"/"); print org[4]}')
+      - echo $org_name
       - echo $CODEBUILD_SOURCE_VERSION
 
       - echo $CODEBUILD_WEBHOOK_MERGE_COMMIT
@@ -22,7 +24,11 @@ phases:
       - echo $CODEBUILD_WEBHOOK_TRIGGER
       - echo $CODEBUILD_WEBHOOK_BASE_REF
 
-      - if [ "$CODEBUILD_WEBHOOK_EVENT" = "PULL_REQUEST_MERGED" ];
+      # Codebuild only runs on PUSH events if HEAD_REF
+      # is refs/heads/develop (merge to develop). In this
+      # case CODEBUILD_GIT_BRANCH="develop"
+
+      - if [ "$CODEBUILD_WEBHOOK_EVENT" = "PUSH" ];
         then export CODEBUILD_GIT_BRANCH="develop";
         echo "Merging to develop";
         else export CODEBUILD_GIT_BRANCH=${CODEBUILD_WEBHOOK_HEAD_REF#refs/heads/};
@@ -31,102 +37,108 @@ phases:
       - echo "CODEBUILD_GIT_BRANCH=${CODEBUILD_GIT_BRANCH}"
       - echo "CODEBUILD_SOURCE_VERSION=${CODEBUILD_SOURCE_VERSION}"
 
-      - echo MPI setup for Docker
-      - mkdir -p /var/run/sshd
-      - ssh-keygen -A 
-      - sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config
-      - sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config
-      - sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
-
-      - groupadd jcsda -g 9999
-      - useradd jcsdauser
-      - mkdir -p /jcsda /build_container
-      - chown -R jcsdauser:jcsda /build_container  /usr/local
-      - chmod 6755 /jcsda /build_container /usr/local
-
-      - mkdir /jcsda/.ssh ; echo "StrictHostKeyChecking no" > /jcsda/.ssh/config
-      - mkdir -p /jcsda/.openmpi
-      - mkdir -p /jcsda/oops-bundle
-      - mkdir -p /home/jcsdauser/.openmpi
-        
-      - cp CI/default-mca-params.conf /home/jcsdauser/.openmpi/mca-params.conf
-      - cat /home/jcsdauser/.openmpi/mca-params.conf
-      - chown -R jcsdauser:jcsda /jcsda/
-
-      - su - jcsdauser -c "ssh-keygen -f /jcsda/.ssh/id_rsa -t rsa -N ''
-        && chmod 600 /jcsda/.ssh/config
-        && chmod 700 /jcsda/.ssh
-        && cp /jcsda/.ssh/id_rsa.pub /jcsda/.ssh/authorized_keys
-        && echo MPI setup for Docker done"
-
   pre_build:
     commands:
       - echo Executing pre_build phase
+      - mkdir -p /jcsda/oops-bundle
 
       - git lfs install
-      - cp ~/.gitconfig /home/jcsdauser/
-      - cp CI/CMakeLists.txt /jcsda/oops-bundle
-
+      - cp ~/.gitconfig /home/jedi/
       - cd CI
-        
+
       - if [ "$CODEBUILD_GIT_BRANCH" = "develop" ];
         then export CODEBUILD_GIT_BRANCH_FORK="release-stable";
         else export CODEBUILD_GIT_BRANCH_FORK=${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 /jcsda/artifacts
+      - echo ${CODEBUILD_GIT_BRANCH} > /jcsda/artifacts/branch_name.txt
+      - echo ${CODEBUILD_RESOLVED_SOURCE_VERSION} > /jcsda/artifacts/commit_sha.txt
+
       # oops
-      - ./clone.sh $GIT_USER $GIT_PASS jcsda/oops $CODEBUILD_GIT_BRANCH oops /jcsda/oops-bundle develop
-      # fckit
-      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/fckit $CODEBUILD_GIT_BRANCH_FORK fckit /jcsda/oops-bundle release-stable
-      # atlas
-      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/atlas $CODEBUILD_GIT_BRANCH_FORK atlas /jcsda/oops-bundle release-stable
+      - ./clone.sh $GIT_USER $GIT_PASS jcsda-internal/oops $CODEBUILD_GIT_BRANCH oops /jcsda/oops-bundle develop
+
+      # move CMakeLists.txt from oops/CI to bundle directory
+      - cp CMakeLists.txt /jcsda/oops-bundle/CMakeLists.txt
+
+      # cdash upload setup
+      - mkdir /jcsda/oops-bundle/cmake
+      - cp cmake/CTestCustom.ctest.in /jcsda/oops-bundle/cmake/
+      - cp cmake/cdash-integration.cmake /jcsda/oops-bundle/cmake/
+      - cp cmake/CTestConfig.cmake /jcsda/oops-bundle/
 
-      - cd /jcsda/oops-bundle
-      - ls
- 
   build:
+    on-failure: CONTINUE
     commands:
       - echo Executing build phase
-      - su - jcsdauser -c "cd /build_container 
+      - export BUILD_STATUS="0"
+      - echo $BUILD_STATUS
+      - echo $CODEBUILD_BUILD_SUCCEEDING
+
+      # configure and build
+      - su - jedi -c "cd /home/jedi
         && ls
         && export FC=mpifort
         && export CC=mpicc
         && export CXX=mpicxx
-        &&  cmake -DCMAKE_MODULE_PATH=/usr/local/share/ecbuild/cmake/ -DCMAKE_BUILD_TYPE=Debug -DENABLE_GPROF=ON -DCMAKE_CXX_COMPILER=$(which g++) -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_Fortran_COMPILER=$(which gfortran) /jcsda/oops-bundle/
-        && cd oops
-        && make -j4"
+        && ecbuild -Wno-dev -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCDASH_OVERRIDE_GIT_BRANCH=$CODEBUILD_GIT_BRANCH -DCTEST_UPDATE_VERSION_ONLY=FALSE -DENABLE_GPROF=ON /jcsda/oops-bundle/"
 
-      - export BUILD_STATUS="0"
-      - echo $BUILD_STATUS
-      - echo $CODEBUILD_BUILD_SUCCEEDING
+      - su - jedi -c "cd /home/jedi/oops
+        && export FC=mpifort
+        && export CC=mpicc
+        && export CXX=mpicxx
+        && cp ../DartConfiguration.tcl .
+        && sed -i 's/oops-bundle/oops-bundle\/oops/' DartConfiguration.tcl
+        && sed -i 's/jedi/jedi\/oops/' DartConfiguration.tcl
+        && cat DartConfiguration.tcl
+        && make -j4"
 
       - if [ "$CODEBUILD_BUILD_SUCCEEDING" = "1" ];
         then export BUILD_STATUS="1";
         echo "Build passed";
         fi
       - echo $BUILD_STATUS
 
-      - su - jcsdauser -c "cd /build_container 
-        && ls
+      # run ctest and upload to cdash
+      - su - jedi -c "cd /home/jedi/oops
+        && export FC=mpifort
+        && export CC=mpicc
+        && export CXX=mpicxx
+        && ctest -C RelWithDebInfo -D ExperimentalTest -E test_qg_4dvar_saddlepoint"
+
+    finally:
+       - su - jedi -c "cd /home/jedi/oops
         && export FC=mpifort
         && export CC=mpicc
         && export CXX=mpicxx
-        && cd oops
-        && ctest"
- 
+        && ctest -C RelWithDebInfo -D ExperimentalSubmit -M Continuous -- --track Continuous --group Continuous"
+
   post_build:
     commands:
       - echo Executing post_build phase
       - echo $CODEBUILD_BUILD_SUCCEEDING
-      - if [ "$BUILD_STATUS" = "1" ] && [ "$CODEBUILD_BUILD_SUCCEEDING" = "0" ];
-        then echo "Build passed, rerun failed tests";
-        su - jcsdauser -c "cd /build_container/oops
-        && ctest -VV --rerun-failed";
+      - 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/oops-bundle/oops/CI/cdash-url.sh /home/jedi/oops/Testing;
+        url=$(bash /jcsda/oops-bundle/oops/CI/cdash-url.sh /home/jedi/oops/Testing);
+        echo $url;
+        echo ${url} > /jcsda/artifacts/cdash-url.txt;
+        cat /jcsda/artifacts/cdash-url.txt;
         else echo "Build failed";
         fi
+
       - echo 'Connect to CodeCov'
-      - cd /build_container/oops
+      - cd /home/jedi/oops
       - pwd
       - ls
-      - bash /jcsda/oops-bundle/oops/CI/codecov_script.sh
+      - bash /jcsda/oops-bundle/oops/CI/codecov_script_$org_name.sh
+
+artifacts:
+  files:
+    - '/jcsda/artifacts/*'
+  name: oops-gnu-url