Merge branch 'develop' into feature/scatwind_single_solution

MetOffice · Oct 31, 2023 · 5ec69f4 · 5ec69f4
2 parents 712afa9 + 9451099
commit 5ec69f4
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Showing 3 changed files with 47 additions and 33 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,6 +7,10 @@ on:
   pull_request:
     branches: [develop]
 
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/develop' }}
+
 env:
   REPO: ${{ github.event.repository.name }}
   BUNDLE: pr-${{ github.event.number }}
@@ -16,116 +20,118 @@ jobs:
     name: gnu 11.3.1 (UKMO)
     if: github.repository_owner == 'MetOffice'
     runs-on: jedi-self-hosted-rg
-    
+
     steps:
-      - name: pre-submit cleanup
+      - name: Pre-submit cleanup
         run: |
-          ls -la ./
           rm -fr ./${{ env.BUNDLE }} || true
-          ls -la ./
-      - name: checkout current
+          ls -lgo ./
+      - name: Checkout current
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/${{ env.REPO }}
-      - name: initiate bundle
+      - name: Initiate bundle
         run: cp ./${{ env.BUNDLE }}/${{ env.REPO }}/ci/* ./${{ env.BUNDLE }}/
 
-      - name: checkout jedicmake
+      - name: Checkout jedicmake
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/jedicmake
           repository: JCSDA-internal/jedi-cmake
           submodules: true
           token: ${{ secrets.GH_PAT }}
 
-      - name: checkout oops
+      - name: Checkout oops
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/oops
           repository: JCSDA-internal/oops
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt oops ${{ github.head_ref }}
+      - name: Checkout attempt for oops@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/oops
 
-      - name: checkout ioda
+      - name: Checkout ioda
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ioda
           repository: JCSDA-internal/ioda
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ioda ${{ github.head_ref }}
+      - name: Checkout attempt for ioda@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ioda
 
-      - name: checkout ufo
+      - name: Checkout ufo
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ufo
           repository: JCSDA-internal/ufo
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ufo ${{ github.head_ref }}
+      - name: Checkout attempt for ufo@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ufo
 
-      - name: build and test
+      - name: Build and Test
         run: |
           az acr login --name ngmssboxjediacr
           docker run --rm \
             --entrypoint=/usr/local/src/${REPO}/${BUNDLE}/build-and-test \
             --workdir=/usr/local/src/${REPO}/${BUNDLE} \
             --volume ${PWD}/${BUNDLE}:/usr/local/src/${REPO}/${BUNDLE} \
-            'ngmssboxjediacr.azurecr.io/jedibase:alma9' \
-          && rm -fr ${{github.workspace}}/${{env.BUNDLE}}
+            'ngmssboxjediacr.azurecr.io/jedibase:alma9'
+
+      - name: Cleanup workspace
+        working-directory: ${{github.workspace}}
+        run: rm -fr ${{ env.BUNDLE }} || true
 
   build2:
     name: gnu 9.4.0 (JCSDA)
     if: github.repository_owner == 'MetOffice'
     runs-on: ubuntu-latest
 
     steps:
-      - name: checkout current
+      - name: Checkout current
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/${{ env.REPO }}
       - name: initiate bundle
         run: cp ./${{ env.BUNDLE }}/${{ env.REPO }}/ci/* ./${{ env.BUNDLE }}/
 
-      - name: checkout jedicmake
+      - name: Checkout jedicmake
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/jedicmake
           repository: JCSDA-internal/jedi-cmake
           submodules: true
           token: ${{ secrets.GH_PAT }}
 
-      - name: checkout oops
+      - name: Checkout oops
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/oops
           repository: JCSDA-internal/oops
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt oops ${{ github.head_ref }}
+      - name: Checkout attempt for oops@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/oops
 
-      - name: checkout ioda
+      - name: Checkout ioda
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ioda
           repository: JCSDA-internal/ioda
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ioda ${{ github.head_ref }}
+      - name: Checkout attempt for ioda@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ioda
 
-      - name: checkout ufo
+      - name: Checkout ufo
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ufo
           repository: JCSDA-internal/ufo
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ufo ${{ github.head_ref }}
+      - name: Checkout attempt for ufo@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ufo
 
@@ -143,52 +149,52 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: checkout current
+      - name: Checkout current
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/${{ env.REPO }}
       - name: initiate bundle
         run: cp ./${{ env.BUNDLE }}/${{ env.REPO }}/ci/* ./${{ env.BUNDLE }}/
 
-      - name: checkout jedicmake
+      - name: Checkout jedicmake
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/jedicmake
           repository: JCSDA-internal/jedi-cmake
           submodules: true
           token: ${{ secrets.GH_PAT }}
 
-      - name: checkout oops
+      - name: Checkout oops
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/oops
           repository: JCSDA-internal/oops
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt oops ${{ github.head_ref }}
+      - name: Checkout attempt for oops@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/oops
 
-      - name: checkout ioda
+      - name: Checkout ioda
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ioda
           repository: JCSDA-internal/ioda
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ioda ${{ github.head_ref }}
+      - name: Checkout attempt for ioda@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ioda
 
-      - name: checkout ufo
+      - name: Checkout ufo
         uses: actions/checkout@v4
         with:
           path: ./${{ env.BUNDLE }}/ufo
           repository: JCSDA-internal/ufo
           token: ${{ secrets.GH_PAT }}
-      - name: matching branch checkout attempt ufo ${{ github.head_ref }}
+      - name: Checkout attempt for ufo@${{ github.head_ref }}
         if: github.event_name == 'pull_request'
         run: ./${{ env.BUNDLE }}/get-ref-branch ./${{ env.BUNDLE }}/ufo
 
-      - name: build and test
+      - name: Build and Test
         run: |
           docker run --rm \
             --entrypoint=/usr/local/src/${REPO}/${BUNDLE}/build-and-test \

diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
@@ -7,6 +7,8 @@ project( opsinputs-ci VERSION 0.1 LANGUAGES C CXX Fortran )
 
 set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
 set( ENABLE_OMP ON CACHE BOOL "Compile with OpenMP" )
+option(ENABLE_IODA_DATA "Obtain ioda test data from ioda-data repository (vs tarball)" ON)
+option(ENABLE_UFO_DATA "Obtain ufo test data from ufo-data repository (vs tarball)" ON)
 
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/jedicmake")
 if(NOT DEFINED jedicmake_DIR)

diff --git a/ci/build-and-test b/ci/build-and-test
@@ -2,6 +2,8 @@
 #
 # (C) Crown Copyright 2023, the Met Office. All rights reserved.
 #
+# shellcheck disable=SC2317
+# shellcheck source=/dev/null
 set -euo pipefail
 
 finally() {
@@ -11,6 +13,10 @@ finally() {
         cd /
         rm -fr "${WORKD}"
     fi
+    if [[ -d ${BASE:-} ]]; then
+        cd /
+        rm -fr "$BASE" 2>/dev/null || true
+    fi
 }
 
 # -- HERE is /usr/local/src/<REPONAME>/pr-<#> (cf ../.github/workflow/ci.yml)