Merge pull request #1526 from JCSDA-internal/release/mpas-1.0

Release/mpas 1.0
JCSDA · Sep 21, 2021 · 69a6475 · 69a6475
2 parents 2af9b91 + 2b7c010
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -9,7 +9,7 @@
 
 cmake_minimum_required( VERSION 3.12 )
 
-project( ufo VERSION 1.1.0 LANGUAGES C CXX Fortran )
+project( ufo VERSION 1.2.0 LANGUAGES C CXX Fortran )
 
 ## Ecbuild integration
 find_package( ecbuild 3.3.2 REQUIRED )

diff --git a/LICENSE → LICENSE.md b/LICENSE → LICENSE.md
@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright 2017-2021 UCAR
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

diff --git a/README.md b/README.md
@@ -1,14 +1,15 @@
-GNU:[![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVjRjeGRXc2EyQit2Z3J4YXNWYjl3dGpWaFMyc0V4UkxGR25PS29VSXN1Z3ExbjJwNHBjRVZCUUptV243dlNWUFFtSmdxS1k5VHBwK25HeHdNbXJmTlFRPSIsIml2UGFyYW1ldGVyU3BlYyI6InM4dW1jYjE1enUxU216Y3UiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-ufo-gnu/history?region=us-east-1)
+### Continuous integration:
+| Platform      |  JCSDA-internal       | JCSDA      |
+| ------------- | ------------- |------------- |
+| GNU           | [![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVngyM2gvQ3d4dzRMb1c0ZmJKa2xnWmtTTHFhVEFoWFZNTHFBNWZTQ3ZrUlhVeldqNHFRQlVxbHJrRUs5MDlPRkhvZkt6K1kyaUs1UkJzaEpSSkZaRllNPSIsIml2UGFyYW1ldGVyU3BlYyI6IjJtd3F5dlk0WDhuUGRrWGkiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/ufo-internal-gnu/history) | [![AWS-gnu](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVjRjeGRXc2EyQit2Z3J4YXNWYjl3dGpWaFMyc0V4UkxGR25PS29VSXN1Z3ExbjJwNHBjRVZCUUptV243dlNWUFFtSmdxS1k5VHBwK25HeHdNbXJmTlFRPSIsIml2UGFyYW1ldGVyU3BlYyI6InM4dW1jYjE1enUxU216Y3UiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/automated-testing-ufo-gnu/history)
+| Intel         | [![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiSnVxeG5qNndXd3JyZk1MaHJKODRCVlJXRTNnV2NnSGNzUGMxcFNaY3NnK3oyS0hHaklCdG8vK0VDeFZlSVFRLzhDZVBOMExPM29ncVQ2Z255KzVXWmg4PSIsIml2UGFyYW1ldGVyU3BlYyI6ImRtQ09kb0RjVG5ObWI2Vm8iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/ufo-internal-intel/history) | [![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVjRjeGRXc2EyQit2Z3J4YXNWYjl3dGpWaFMyc0V4UkxGR25PS29VSXN1Z3ExbjJwNHBjRVZCUUptV243dlNWUFFtSmdxS1k5VHBwK25HeHdNbXJmTlFRPSIsIml2UGFyYW1ldGVyU3BlYyI6InM4dW1jYjE1enUxU216Y3UiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/automated-testing-ufo-gnu/history)
+| CLANG         | [![AWS-clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiWEI0Z2xCa0NpdlpNVTdLNEJGRWR5aEJ5NkpKdjNTT2ZQMURJWG5GNFZQUjV4Mkc4R1I2M3NGbEtUYzM2MCthdzZDeDVjS0NVSjB1R3h1TUFCYkdNb0RrPSIsIml2UGFyYW1ldGVyU3BlYyI6ImdrWGZnaXhzSG9pcDBMa0IiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/ufo-internal-clang/history) | [![AWS-clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVU1vbVR2Y0twa3NpWHRoMUhraGlreU9Da2t5RVpZQk9kV3NrL2hTc0szdXRlaCszVzhHRndrd0VqcnpSb2lyL2VCRXNtK1Y4WG5LRHVxbldteFArU2IwPSIsIml2UGFyYW1ldGVyU3BlYyI6IkpQUTRlaThyRWVkWEJjNEwiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/469205354006/projects/automated-testing-ufo-clang/history)  
+| Code Coverage | [![codecov](https://codecov.io/gh/JCSDA/ufo/branch/develop/graph/badge.svg?token=nxhUKP82Pd)](https://codecov.io/gh/JCSDA-internal/ufo) |
 
-INTEL:[![AWS-intel](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiUGxUMXUrdkNTVURCcjlwaTFlVlZ5eklHWGNodVdlWko2M0phM0lTRVIrWS9OcWQraWpwN3FvL240N2FDZWdEZGF3dU9vSHZHS1lFbEVJd2M5M1NWWHUwPSIsIml2UGFyYW1ldGVyU3BlYyI6Ii8xWTZDL0VxV1hNSE1LVHMiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-ufo-intel/history?region=us-east-1)
-
-CLANG: [![AWS_clang](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiVU1vbVR2Y0twa3NpWHRoMUhraGlreU9Da2t5RVpZQk9kV3NrL2hTc0szdXRlaCszVzhHRndrd0VqcnpSb2lyL2VCRXNtK1Y4WG5LRHVxbldteFArU2IwPSIsIml2UGFyYW1ldGVyU3BlYyI6IkpQUTRlaThyRWVkWEJjNEwiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=develop)](https://us-east-1.console.aws.amazon.com/codesuite/codebuild/projects/automated-testing-ufo-clang/history?region=us-east-1)
-
-[![codecov](https://codecov.io/gh/JCSDA/ufo/branch/develop/graph/badge.svg?token=nxhUKP82Pd)](https://codecov.io/gh/JCSDA/ufo)
 
 Unified Forward Operators for Joint Effort for Data assimilation Integration (JEDI) project.
 
-(C) Copyright 2017-2019 UCAR.
+(C) Copyright 2017-2021 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.

diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -909,7 +909,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-#EXCLUDE                =  @CMAKE_CURRENT_SOURCE_DIR@/../src/util
+EXCLUDE                =  @CMAKE_CURRENT_SOURCE_DIR@/../test/testinput/reference/README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1126,13 +1126,6 @@ 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

diff --git a/docs/mainpage.h b/docs/mainpage.h
@@ -0,0 +1,12 @@
+#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 Unified Forward Operator (UFO)
+ *
+ * UFO provides the observational operators needed to compute departures and innovations. In other words, it enables the comparison between model forecasts and observations that lies at the heart of the data assimilation process. UFO also provides related functionality related to observations such as quality control (QC) filters and variational bias correction.
+ *
+  */
diff --git a/ewok/aircraft.yaml b/ewok/aircraft.yaml
diff --git a/ewok/jedi-gdas/airs_aqua.yaml b/ewok/jedi-gdas/airs_aqua.yaml
@@ -40,22 +40,17 @@ obs bias:
     predictors:
     - name: constant
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &airs_aqua_tlapse $(experiment_dir)/{{current_cycle}}/airs_aqua.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &airs_aqua_tlapse $(experiment_dir)/{{current_cycle}}/airs_aqua.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *airs_aqua_tlapse
+      tlapse: *airs_aqua_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 #  Wavenumber Check

diff --git a/ewok/jedi-gdas/amsua_aqua.yaml b/ewok/jedi-gdas/amsua_aqua.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_aqua_tlapse $(experiment_dir)/{{current_cycle}}/amsua_aqua.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_aqua_tlapse $(experiment_dir)/{{current_cycle}}/amsua_aqua.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_aqua_tlapse
+      tlapse: *amsua_aqua_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_metop-a.yaml b/ewok/jedi-gdas/amsua_metop-a.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_metop-a_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-a.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_metop-a_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-a.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_metop-a_tlapse
+      tlapse: *amsua_metop-a_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_metop-b.yaml b/ewok/jedi-gdas/amsua_metop-b.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_metop-b_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-b.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_metop-b_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-b.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_metop-b_tlapse
+      tlapse: *amsua_metop-b_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_metop-c.yaml b/ewok/jedi-gdas/amsua_metop-c.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_metop-c_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-c.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_metop-c_tlapse $(experiment_dir)/{{current_cycle}}/amsua_metop-c.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_metop-c_tlapse
+      tlapse: *amsua_metop-c_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_n15.yaml b/ewok/jedi-gdas/amsua_n15.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_n15_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n15.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_n15_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n15.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_n15_tlapse
+      tlapse: *amsua_n15_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_n18.yaml b/ewok/jedi-gdas/amsua_n18.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_n18_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n18.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_n18_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n18.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_n18_tlapse
+      tlapse: *amsua_n18_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/amsua_n19.yaml b/ewok/jedi-gdas/amsua_n19.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &amsua_n19_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n19.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &amsua_n19_tlapse $(experiment_dir)/{{current_cycle}}/amsua_n19.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *amsua_n19_tlapse
+      tlapse: *amsua_n19_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList

diff --git a/ewok/jedi-gdas/atms_n20.yaml b/ewok/jedi-gdas/atms_n20.yaml
@@ -20,27 +20,18 @@ obs bias:
   variational bc:
     predictors:
     - name: constant
-    - name: cosine_of_latitude_times_orbit_node
-      options:
-        preconditioner: 0.01
-    - name: sine_of_latitude
     - name: lapse_rate
-      options:
-        order: 2
-        tlapse: &atms_n20_tlapse $(experiment_dir)/{{current_cycle}}/atms_n20.{{background_time}}.tlapse.txt
+      order: 2
+      tlapse: &atms_n20_tlapse $(experiment_dir)/{{current_cycle}}/atms_n20.{{background_time}}.tlapse.txt
     - name: lapse_rate
-      options:
-        tlapse: *atms_n20_tlapse
+      tlapse: *atms_n20_tlapse
     - name: emissivity
     - name: scan_angle
-      options:
-        order: 4
+      order: 4
     - name: scan_angle
-      options:
-        order: 3
+      order: 3
     - name: scan_angle
-      options:
-        order: 2
+      order: 2
     - name: scan_angle
 obs filters:
 - filter: BlackList