merge dev/emc into ocean stochastic branch

.codecov.yml

@@ -3,6 +3,11 @@ coverage:
         project:
             default:
                 threshold: 100%
+                base: parent
         patch:
             default:
                 threshold: 100%
+                base: parent
+comment:
+    # This must be set to the number of test cases (TCs)
+    after_n_builds: 8

.gitignore

@@ -2,7 +2,19 @@
 *.swp
 *~
 html
-*.log
+
+
+# Build output
+*.o
+*.mod
 MOM6
-build/
-deps/
+
+
+# Autoconf
+aclocal.m4
+autom4te.cache/
+config.log
+config.status
+configure
+/Makefile
+Makefile.mkmf

.gitlab-ci.yml

@@ -32,13 +32,11 @@ setup:
     - git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && cd tests
     # Install / update testing scripts
     - git clone https://github.com/adcroft/MRS.git MRS
-    - (cd MRS ; git checkout xanadu-fms)
     # Update MOM6-examples and submodules
     - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
     - (cd MOM6-examples/src/MOM6 && git submodule update)
     - test -d MOM6-examples/src/LM3 || make -f MRS/Makefile.clone clone_gfdl -s
     - make -f MRS/Makefile.clone MOM6-examples/.datasets -s
-    #- (cd MOM6-examples/src/mkmf && git pull https://github.com/adcroft/mkmf.git add_coverage_mode)
     - env > gitlab_session.log
     # Cache everything under tests to unpack for each subsequent stage
     - cd ../ ; time tar zcf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz tests
@@ -62,7 +60,7 @@ gnu:ocean-only-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{solo_driver,dynamic_symmetric} ../../../src ../../MOM6-examples/src/FMS
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{solo_driver,dynamic_symmetric,ext*} ../../../src ../../MOM6-examples/src/FMS
     - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
@@ -75,7 +73,7 @@ gnu:ice-ocean-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic,ext*} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
     - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
@@ -118,7 +116,7 @@ run:
     - time tar zxf $CACHE_DIR/build-intel-repro-$CI_PIPELINE_ID.tgz
     - time tar zxf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz
     # time tar zxf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz
-    - (echo '#!/bin/tcsh';echo 'make -f MRS/Makefile.tests all -B') > job.sh
+    - (echo '#!/bin/tcsh';echo 'make -f MRS/Makefile.tests all') > job.sh
     - sbatch --clusters=c3,c4 --nodes=29 --time=0:34:00 --account=gfdl_o --qos=debug --job-name=mom6_regressions --output=log.$CI_PIPELINE_ID --wait job.sh
     - cat log.$CI_PIPELINE_ID
     - test -f restart_results_gnu.tar.gz

.gitmodules

@@ -4,9 +4,3 @@
 [submodule "pkg/GSW-Fortran"]
 	path = pkg/GSW-Fortran
 	url = https://github.com/TEOS-10/GSW-Fortran.git
-[submodule "pkg/MOM6_DA_hooks"]
-	path = pkg/MOM6_DA_hooks
-	url = https://github.com/MJHarrison-GFDL/MOM6_DA_hooks.git
-[submodule "pkg/geoKdTree"]
-	path = pkg/geoKdTree
-	url = https://github.com/travissluka/geoKdTree.git

.testing/.gitignore

@@ -1,3 +1,6 @@
-config.mk
-work/
-results/
+# Test output
+/config.mk
+/build/
+/work/
+/results/
+/deps/