Initial CI implementation (#55)

Add CI using JCSDA docker image.
--------

Co-authored-by: Yaswant Pradhan <[email protected]>

.github/workflows/ci.yml

@@ -0,0 +1,67 @@
+name: CI
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout current repo
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: checkout jedicmake
+        uses: actions/checkout@v3
+        with:
+          path: ci/jedicmake
+          repository: JCSDA-internal/jedi-cmake
+          submodules: true
+          token: ${{ secrets.GH_PAT }}
+
+      - name: checkout oops
+        uses: actions/checkout@v3
+        with:
+          path: ci/oops
+          repository: JCSDA-internal/oops
+          token: ${{ secrets.GH_PAT }}
+
+      - name: checkout ioda
+        uses: actions/checkout@v3
+        with:
+          path: ci/ioda
+          repository: JCSDA-internal/ioda
+          token: ${{ secrets.GH_PAT }}
+
+      - name: checkout ufo
+        uses: actions/checkout@v3
+        with:
+          path: ci/ufo
+          repository: JCSDA-internal/ufo
+          token: ${{ secrets.GH_PAT }}
+
+      - name: checkout atlas-orca
+        uses: actions/checkout@v3
+        with:
+          path: ci/atlas-orca
+          repository: ECMWF/atlas-orca
+
+      - name: checkout atlas-data
+        uses: actions/checkout@v3
+        with:
+          path: ci/atlas-data
+          repository: MetOffice/atlas-data
+          lfs: true
+          token: ${{ secrets.GH_PAT }}
+
+      - name: build and test
+        run: |
+          docker run --rm \
+            --entrypoint=/usr/local/src/orca-jedi/ci/build-and-test.sh \
+            --workdir=/usr/local/src/orca-jedi/ci \
+            --volume $PWD:/usr/local/src/orca-jedi \
+            'jcsda/docker-gnu-openmpi-dev:latest'

README.rst

@@ -1,3 +1,5 @@
+.. image:: https://github.com/MetOffice/orca-jedi/actions/workflows/ci.yml/badge.svg
+
 orca-jedi
 =========
 

ci/CMakeLists.txt

@@ -0,0 +1,23 @@
+# (C) Copyright 2022 Met Office
+#
+# 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.
+
+cmake_minimum_required( VERSION 3.18 FATAL_ERROR )
+
+project( orca-jedi-ci VERSION 1.0 LANGUAGES C CXX Fortran )
+
+set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
+set( ENABLE_OMP ON CACHE BOOL "Compile with OpenMP" )
+
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/jedicmake" EXCLUDE_FROM_ALL)
+if(NOT DEFINED jedicmake_DIR)
+  set(jedicmake_DIR "${CMAKE_BINARY_DIR}/jedicmake")
+endif()
+
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/atlas-orca" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/oops" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ioda" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ufo" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/orca-jedi")
+enable_testing()

ci/build-and-test.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+set -euo pipefail
+
+finally() {
+    trap '' ERR
+    trap '' EXIT
+    if [[ -d "${WORKD:-}" ]]; then
+        cd /
+        rm -fr "${WORKD}"
+    fi
+}
+
+HERE="$(cd "$(dirname "$0")" && pwd)"
+THIS="$(basename "$0")"
+NPROC=${NPROC:-2}
+WORKD="$(mktemp -d "${THIS}-XXXXXX" -t)"
+
+trap finally ERR
+trap finally EXIT
+
+cd "${WORKD}"
+
+source /opt/spack-environment/activate.sh
+
+echo "
+-------------------------------
+gcc version $(gcc -dumpversion ||:)
+$(ecbuild --version ||:)
+atlas version $(atlas --version ||:)
+eckit version $(eckit-version ||:)
+ectrans version $(ectrans --version ||:)
+fckit version $(fckit --version ||:)
+fiat version $(fiat --version ||:)
+lz4 version $(lz4 --version ||:)
+odc version $(odc --version ||:)
+-------------------------------
+"
+
+rm -f "${HERE}/orca-jedi"
+ln -s '..' "${HERE}/orca-jedi"
+ecbuild -S "${HERE}"
+make -j "${NPROC}"
+
+if [[ ! -f share/plugins/atlas-orca.yml ]]; then
+ echo "ERROR atlas-orca.yml not found!" | tee >(cat >&2)
+ exit 1
+fi
+
+env OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
+    ATLAS_TRACE=1 ATLAS_DEBUG=1 \
+    LD_LIBRARY_PATH="${HERE}/lib:${LD_LIBRARY_PATH}" \
+    ATLAS_DATA_PATH="${HERE}/atlas-data" \
+    ctest -j "${NPROC}" -V --output-on-failure --test-dir "./orca-jedi"
+
+exit

src/tests/orca-jedi/CMakeLists.txt

@@ -9,7 +9,7 @@ ecbuild_add_test( TARGET  test_orcajedi_nemo_io_field_reader.x
 LIST( APPEND ATLAS_TEST_ENVIRONMENT
     ATLAS_ORCA_CACHING=1
     ATLAS_CACHE_PATH=${CMAKE_BINARY_DIR}/share
-    PLUGINS_MANIFEST_PATH=${CMAKE_BINARY_DIR}/atlas-orca/share/plugins )
+    PLUGINS_MANIFEST_PATH=${CMAKE_BINARY_DIR}/share/plugins )
 
 ecbuild_add_test( TARGET  test_orcajedi_nemo_io_field_writer.x
                   SOURCES test_nemo_io_field_writer.cc