Merge pull request #1387 from JCSDA-internal/release/mpas-1.0

Release/mpas 1.0

.gitignore

@@ -19,6 +19,7 @@ exp.summary.txt
 CMakeLists.txt.user
 dependencies.mk
 loadmap
+git-hammer-config.json
 
 #Ignore the contents of these directories
 #(html and latex directories are generated by doxygen)

CMakeLists.txt

@@ -11,7 +11,7 @@
 ################################################################################
 
 cmake_minimum_required( VERSION 3.12 )
-project( oops VERSION 1.1.0 LANGUAGES CXX Fortran )
+project( oops VERSION 1.2.0 LANGUAGES CXX Fortran )
 
 ## Ecbuild integration
 find_package( ecbuild 3.3.2 REQUIRED )

LICENSE → LICENSE.md

@@ -188,7 +188,7 @@
       identification within third-party archives.
 
    Copyright 2009-2016 European Centre for Medium-Range Weather Forecasts (ECMWF)
-   Copyright 2017-2020 University Corporation for Atmospheric Research (UCAR)
+   Copyright 2017-2021 University Corporation for Atmospheric Research (UCAR)
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -1,6 +1,9 @@
 Object Oriented Prediction System (OOPS)
 
-GNU: [![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiN2RzbkhSR3o4dm9HN29wRW5laDRMdGlSdGFrNUswWE9pMVJHbmwrQ0EvYWZkNnRjMTFzZWFQL3dUdUpLbmUxNlJXYlFsYmRoaDR5K1NUdCtWNmNvTHFBPSIsIml2UGFyYW1ldGVyU3BlYyI6ImV5OWJFdFRWNWVnMVpwcHEiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-gnu/history?region=us-east-1)
-INTEL: [![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiWG5KM0dQR3VBNWdVVUdJeURwUjhoOXNWYlBYdnpGR2prLzQ4RXk2ZlkrN2llZ2M4S05MeXdWcERMVFZ2RGIxbTRXZFMvTFM5cTRoamFzV3hYanlZVEVNPSIsIml2UGFyYW1ldGVyU3BlYyI6IjZJVnJYL1Z5VktTQWZzZUkiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-intel)
-CLANG: [![AWS-clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiNHdvREpKTnVOT2pneEx6cHpaMjlma3RsUmlLZFQrMmpDR0tNODBrMzA0Z0pFazFKMFloQVc0Q0xkeGRZbW9WSDJ4c2FWSFg0SkZWb1VXVmVQRk5rSTFJPSIsIml2UGFyYW1ldGVyU3BlYyI6InRQckQrWDdaY0l2RkZoWmUiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-clang/history?region=us-east-1)
-[![codecov](https://codecov.io/gh/JCSDA/oops/branch/develop/graph/badge.svg?token=GdDzbEQedm)](https://codecov.io/gh/JCSDA/oops)
+### Continuous integration:
+| Platform      |  JCSDA-internal       | JCSDA      |
+| ------------- | ------------- |------------- |
+| GNU           | [![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiNjVsdE5keGM1Tk5yV3FEd2tiaU5YRFVLWEVUTitBdCs5dm9nc29LNjh0T1plank1bzB2TTB2ZkptT2lUSFNWMklmWWdkNW5IbFR1VXZ1NE12M0JiR3BrPSIsIml2UGFyYW1ldGVyU3BlYyI6IkthTWxpTkZaY21CUklINnciLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/oops-internal-gnu/history) | [![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiN2RzbkhSR3o4dm9HN29wRW5laDRMdGlSdGFrNUswWE9pMVJHbmwrQ0EvYWZkNnRjMTFzZWFQL3dUdUpLbmUxNlJXYlFsYmRoaDR5K1NUdCtWNmNvTHFBPSIsIml2UGFyYW1ldGVyU3BlYyI6ImV5OWJFdFRWNWVnMVpwcHEiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://us-east-1.console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-gnu/history)
+| Intel         | [![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiUkd1YnZqN2RLWWhaOFE5MkdmbGZ5K1I0amlGU3l4Z3h5Ymw2KzR1Z3lhMXNFSEpkK2M2QTlIZk9mdVQ0ZEx5UFMvRDBZa2tUbVd6TkU1QmZPRWEycmNRPSIsIml2UGFyYW1ldGVyU3BlYyI6IjhmY2tER1c5SDVYekJZRS8iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/oops-internal-intel/history) | [![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiWG5KM0dQR3VBNWdVVUdJeURwUjhoOXNWYlBYdnpGR2prLzQ4RXk2ZlkrN2llZ2M4S05MeXdWcERMVFZ2RGIxbTRXZFMvTFM5cTRoamFzV3hYanlZVEVNPSIsIml2UGFyYW1ldGVyU3BlYyI6IjZJVnJYL1Z5VktTQWZzZUkiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://us-east-1.console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-intel/history)
+| CLANG         | [![AWS-clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiL3F2OHVEcmc0WitOTlY3Vm9LV0J3NHREZ0RicUZ6RDFXcFNlODhrRHN6a0RjNlF2TDI0VzM2S0VBKzMxR1BIREdYNmZrRWRUcm9xd0h2ZnhYNzVNc3NJPSIsIml2UGFyYW1ldGVyU3BlYyI6Iit1Y01tZSt4b1VtbGxKeDQiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/oops-internal-clang/history) | [![AWS-clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiNHdvREpKTnVOT2pneEx6cHpaMjlma3RsUmlLZFQrMmpDR0tNODBrMzA0Z0pFazFKMFloQVc0Q0xkeGRZbW9WSDJ4c2FWSFg0SkZWb1VXVmVQRk5rSTFJPSIsIml2UGFyYW1ldGVyU3BlYyI6InRQckQrWDdaY0l2RkZoWmUiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://us-east-1.console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-oops-clang/history)  
+| Code Coverage | [![codecov](https://codecov.io/gh/JCSDA/oops/branch/develop/graph/badge.svg?token=GdDzbEQedm)](https://codecov.io/gh/JCSDA/oops) |

cmake/backtrace_deps.cmake

@@ -0,0 +1,64 @@
+# (C) Copyright 2021 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.
+
+# This CMake file tests which stack trace provider libraries are available on
+# a particular system. This is needed to set appropriate flags for
+# boost stacktrace (used in src/oops/util/signal_trap.cc).
+
+include(CheckCXXSourceCompiles)
+
+# check_cxx_source_compiles uses global flags, unfortunately, so we need to
+# save a bit of state to run the tests.
+
+set(saved_libraries ${CMAKE_REQUIRED_LIBRARIES})
+set(saved_defs ${CMAKE_REQUIRED_DEFINITIONS})
+
+string(CONFIGURE [[
+    #include <iostream>
+    #include <boost/stacktrace.hpp>
+
+    int main() {
+        std::cout << boost::stacktrace::stacktrace() << std::endl;
+        return 0;
+    }
+]] stacktracecode @ONLY)
+
+
+# Different configs
+
+list( APPEND OOPS_STACKTRACE_none_LIBS "")
+set(  OOPS_STACKTRACE_none_DEFS -DBOOST_STACKTRACE_USE_NOOP)
+
+list( APPEND OOPS_STACKTRACE_default_LIBS -ldl)
+set(  OOPS_STACKTRACE_default_DEFS "")
+
+list( APPEND OOPS_STACKTRACE_libbacktrace_LIBS -ldl -lbacktrace)
+list( APPEND OOPS_STACKTRACE_libbacktrace_DEFS -DBOOST_STACKTRACE_USE_BACKTRACE)
+
+list( APPEND OOPS_STACKTRACE_addr2line_LIBS -ldl -lbacktrace)
+list( APPEND OOPS_STACKTRACE_addr2line_DEFS -DBOOST_STACKTRACE_USE_ADDR2LINE)
+find_program(addr2line_PATH addr2line)
+if(addr2line_PATH)
+	message( STATUS "Found addr2line at ${addr2line_PATH}." )
+	list(APPEND OOPS_STACKTRACE_addr2line_DEFS -DBOOST_STACKTRACE_ADDR2LINE_LOCATION=${addr2line_PATH})
+endif()
+
+
+# Test each configuration here.
+foreach ( provider IN ITEMS libbacktrace addr2line default none )
+	list(APPEND CMAKE_REQUIRED_LIBRARIES ${OOPS_STACKTRACE_${provider}_LIBS})
+	list(APPEND CMAKE_REQUIRED_DEFINITIONS ${OOPS_STACKTRACE_${provider}_DEFS})
+	check_cxx_source_compiles("${stacktracecode}" OOPS_STACKTRACE_${provider}_AVAILABLE)
+	set(CMAKE_REQUIRED_LIBRARIES ${saved_libraries})
+	set(CMAKE_REQUIRED_DEFINITIONS ${saved_defs})
+	if ( OOPS_STACKTRACE_${provider}_AVAILABLE )
+		list( APPEND OOPS_STACKTRACE_AVAILABLE_PROVIDERS ${provider} )
+	endif()
+endforeach()
+
+message( STATUS "Boost stacktrace supports these providers: ${OOPS_STACKTRACE_AVAILABLE_PROVIDERS}.")
+list(GET OOPS_STACKTRACE_AVAILABLE_PROVIDERS 0 OOPS_STACKTRACE_PROVIDER)
+message( STATUS "Using this provider for stacktraces: ${OOPS_STACKTRACE_PROVIDER}.")
+

cmake/oops_compiler_flags.cmake

@@ -49,3 +49,5 @@ elseif( CMAKE_CXX_COMPILER_ID MATCHES "Clang" )
 else()
   message( STATUS "C++ compiler with ID ${CMAKE_CXX_COMPILER_ID} will be used with CMake default options")
 endif()
+
+

docs/Doxyfile.in

@@ -1127,13 +1127,6 @@ VERBATIM_HEADERS       = YES
 
 ALPHABETICAL_INDEX     = YES
 
-# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
-# which the alphabetical index list will be split.
-# Minimum value: 1, maximum value: 20, default value: 5.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-COLS_IN_ALPHA_INDEX    = 5
-
 # In case all classes in a project start with a common prefix, all classes will
 # be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
 # can be used to specify a prefix (or a list of prefixes) that should be ignored

docs/mainpage.h

@@ -0,0 +1,11 @@
+#pragma once
+
+// This file defines what appears on the Main Page of the documentation
+// generated by doxygen. The file contains no code, and does not appear
+// in any cpp include statement.
+//
+/*!
+ * \mainpage Object Oriented Prediction System (OOPS)
+ *
+ * OOPS is the top level of JEDI that orchestrates the configuration and execution of applications. This is where DA applications are implemented. OOPS also includes the Lorenz 95 and Quasi-geostrophic toy models that can used to run many of the DA applications.
+ */

ewok/4dvar.yaml

@@ -1,36 +1,36 @@
 cost function:
-  cost type: $(cost_function)
+  cost type: ${cost_function}
   window begin: '{{window_begin}}'
-  window length: $(window_length)
+  window length: ${window_length}
   geometry:
-    $(GEOMETRY)
+    ${GEOMETRY}
   model:
-    $(MODEL)
-  analysis variables: $(an_variables)
+    ${MODEL}
+  analysis variables: ${an_variables}
   background:
-    $(BACKGROUND)
+    ${BACKGROUND}
   background error:
-    $(BACKGROUND_ERROR)
+    ${BACKGROUND_ERROR}
   observations:
-    $(OBSERVATIONS)
+    ${OBSERVATIONS}
   constraints:
-  - $(JC)
+  - ${JC}
 variational:
   minimizer:
-    $(MINIMIZER)
+    ${MINIMIZER}
   iterations:
-  - ninner: $(ninner)
-    gradient norm reduction: $(reduc)
+  - ninner: ${ninner}
+    gradient norm reduction: ${reduc}
     geometry:
-      $(GEOMETRY)
+      ${GEOMETRY}
     linear model:
-      $(LINEAR_MODEL)
+      ${LINEAR_MODEL}
     diagnostics:
-      departures: $(diag)
+      departures: ${diag}
 final:
   diagnostics:
     departures: oman
   prints:
     frequency: PT3H
 output:
-  $(AN_OUTPUT)
+  ${AN_OUTPUT}

ewok/forecast.yaml

@@ -1,9 +1,9 @@
-forecast length: $(forecast_length)
+forecast length: ${forecast_length}
 initial condition:
-  $(FC_INPUT)
+  ${FC_INPUT}
 geometry:
-  $(GEOMETRY)
+  ${GEOMETRY}
 model:
-  $(MODEL)
+  ${MODEL}
 output:
-  $(FC_OUTPUT)
+  ${FC_OUTPUT}

ewok/hofx3d.yaml

@@ -1,9 +1,9 @@
 geometry:
-  $(GEOMETRY)
+  ${GEOMETRY}
 state:
   '{{BACKGROUND}}'
 observations:
-  $(OBSERVATIONS)
+  ${OBSERVATIONS}
 window begin: '{{window_begin}}'
-window length: $(window_length)
+window length: ${window_length}
 

ewok/hofx4d.yaml

@@ -1,9 +1,9 @@
 geometry:
-  $(GEOMETRY)
+  ${GEOMETRY}
 states:
   '{{BACKGROUND}}'
 observations:
-  $(OBSERVATIONS)
+  ${OBSERVATIONS}
 window begin: '{{window_begin}}'
-window length: $(window_length)
+window length: ${window_length}
 

l95/ewok/defaults/an.yaml

@@ -1,2 +1,2 @@
 date: '{{current_cycle}}'
-filename: '$(current_dir)/$(experiment).an.{{current_cycle}}'
+filename: '$(run_dir)/$(experiment).an.{{current_cycle}}'

l95/ewok/defaults/an_output.yaml

@@ -1,5 +1,5 @@
-datadir: '$(current_dir)'
-filename: '$(current_dir)/$(experiment).an.{{current_cycle}}'
+datadir: $(run_dir)
+filename: '$(run_dir)/$(experiment).an.{{current_cycle}}'
 exp: $(experiment)
 ##first: '{% $(window_length) - $(window_offset) %}'
 first: PT3H

l95/ewok/defaults/bg.yaml

@@ -1,2 +1,2 @@
 date: '{{window_begin}}'
-filename: '$(current_dir)/$(experiment).bg.{{current_cycle}}.l95'
+filename: '$(run_dir)/$(experiment).bg.{{current_cycle}}.l95'

l95/ewok/defaults/fc.yaml

@@ -1,2 +1,2 @@
 date: '{{current_cycle}}'
-filename: $(current_dir)/$(experiment).fc.{{current_cycle}}.$(step)
+filename: $(run_dir)/$(experiment).fc.{{current_cycle}}.$(step)

l95/ewok/defaults/fc_output.yaml

@@ -1,4 +1,4 @@
-datadir: $(current_dir)
+datadir: $(run_dir)
 date: '{{current_cycle}}'
 exp: $(experiment)
 frequency: PT3H

l95/ewok/defaults/obs.yaml

@@ -3,8 +3,8 @@ obs operator:
 obs space:
   source: truth
   filetype: obt
-  obsdatain:  '$(current_dir)/input.obs.{{window_begin}}.obt'
-  obsdataout: '$(current_dir)/$(experiment).obs.{{window_begin}}.obt'
+  obsdatain:  '$(run_dir)/input.obs.{{window_begin}}.obt'
+  obsdataout: '$(run_dir)/$(experiment).obs.{{window_begin}}.obt'
 obs error:
   covariance model: diagonal
 r2d2_type: l95_obs

l95/src/executables/EDA.cc

@@ -5,6 +5,7 @@
  * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
  */
 
+#include "lorenz95/instantiateL95ChangeVarFactory.h"
 #include "lorenz95/instantiateLocalizationFactory.h"
 #include "lorenz95/L95Traits.h"
 #include "oops/runs/EnsembleApplication.h"
@@ -13,6 +14,7 @@
 
 int main(int argc,  char ** argv) {
   oops::Run run(argc, argv);
+  lorenz95::instantiateL95ChangeVarFactory();
   lorenz95::instantiateLocalizationFactory();
   oops::EnsembleApplication<oops::Variational <lorenz95::L95Traits, lorenz95::L95ObsTraits> >eda;
   return run.execute(eda);

l95/src/executables/EnsHofX.cc

@@ -8,13 +8,15 @@
  * does it submit to any jurisdiction.
  */
 
+#include "lorenz95/instantiateL95ChangeVarFactory.h"
 #include "lorenz95/L95Traits.h"
 #include "oops/runs/EnsembleApplication.h"
 #include "oops/runs/HofX4D.h"
 #include "oops/runs/Run.h"
 
 int main(int argc,  char ** argv) {
   oops::Run run(argc, argv);
+  lorenz95::instantiateL95ChangeVarFactory();
   oops::EnsembleApplication<oops::HofX4D <lorenz95::L95Traits, lorenz95::L95ObsTraits> > enshofx;
   return run.execute(enshofx);
 }

l95/src/executables/HofX.cc

@@ -8,12 +8,14 @@
  * does it submit to any jurisdiction.
  */
 
+#include "lorenz95/instantiateL95ChangeVarFactory.h"
 #include "lorenz95/L95Traits.h"
 #include "oops/runs/HofX4D.h"
 #include "oops/runs/Run.h"
 
 int main(int argc,  char ** argv) {
   oops::Run run(argc, argv);
+  lorenz95::instantiateL95ChangeVarFactory();
   oops::HofX4D<lorenz95::L95Traits, lorenz95::L95ObsTraits> hofx;
   return run.execute(hofx);
 }

l95/src/executables/LETKF.cc

@@ -5,12 +5,14 @@
  * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
  */
 
+#include "lorenz95/instantiateL95ChangeVarFactory.h"
 #include "lorenz95/L95Traits.h"
 #include "oops/runs/LocalEnsembleDA.h"
 #include "oops/runs/Run.h"
 
 int main(int argc,  char ** argv) {
   oops::Run run(argc, argv);
+  lorenz95::instantiateL95ChangeVarFactory();
   oops::LocalEnsembleDA<lorenz95::L95Traits, lorenz95::L95ObsTraits> letkf;
   return run.execute(letkf);
 }

l95/src/executables/Main4dvar.cc

@@ -8,13 +8,15 @@
  * does it submit to any jurisdiction.
  */
 
+#include "lorenz95/instantiateL95ChangeVarFactory.h"
 #include "lorenz95/instantiateLocalizationFactory.h"
 #include "lorenz95/L95Traits.h"
 #include "oops/runs/Run.h"
 #include "oops/runs/Variational.h"
 
 int main(int argc,  char ** argv) {
   oops::Run run(argc, argv);
+  lorenz95::instantiateL95ChangeVarFactory();
   lorenz95::instantiateLocalizationFactory();
   oops::Variational<lorenz95::L95Traits, lorenz95::L95ObsTraits> var;
   return run.execute(var);

l95/src/lorenz95/BackgroundCheck.cc

@@ -10,13 +10,12 @@
 #include <vector>
 
 #include "lorenz95/L95Traits.h"
-#include "oops/interface/ObsFilter.h"
 
 // -----------------------------------------------------------------------------
 namespace lorenz95 {
 // -----------------------------------------------------------------------------
-static oops::FilterMaker<L95ObsTraits,
-       oops::ObsFilter<L95ObsTraits, BackgroundCheck> > makerBackgroundCheck_("Background Check");
+static oops::interface::FilterMaker<L95ObsTraits, BackgroundCheck> makerBackgroundCheck_(
+    "Background Check");
 
 // -----------------------------------------------------------------------------
 BackgroundCheck::BackgroundCheck(const ObsTable & obsdb, const Parameters_ & parameters,
@@ -26,7 +25,7 @@ BackgroundCheck::BackgroundCheck(const ObsTable & obsdb, const Parameters_ & par
 }
 
 // -----------------------------------------------------------------------------
-void BackgroundCheck::postFilter(const ObsVec1D & hofx, const ObsDiags1D &) const {
+void BackgroundCheck::postFilter(const ObsVec1D & hofx, const ObsVec1D &, const ObsDiags1D &) {
   std::vector<float> yobs;
   obsdb_.getdb("ObsValue", yobs);
   size_t inflate = 0;