Merge pull request #340 from MPAS-Dev/develop

Merge develop to master
MPAS-Dev · Apr 26, 2018 · f7e1d07 · f7e1d07
2 parents e56da52 + dcc0de6
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diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,39 @@
+Copyright (c) 2013,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
+Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
+
+All rights reserved. 
+
+LANS is the operator of the Los Alamos National Laboratory under Contract No.
+DE-AC52-06NA25396 with the U.S. Department of Energy.  UCAR manages the National
+Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the
+National Science Foundation.  The U.S. Government has rights to use, reproduce,
+and distribute this software.  NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY
+LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE
+OF THIS SOFTWARE.  If software is modified to produce derivative works, such
+modified software should be clearly marked, so as not to confuse it with the
+version available from LANS and UCAR.
+
+Additionally, redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1) Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2) Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+3) None of the names of LANS, UCAR or the names of its contributors, if any, may
+be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -103,12 +103,19 @@ for more details.
       * `mpaso.rst.0002-01-01_00000.nc` (or any other mpas-o restart file)
       * `streams.ocean`
       * `mpas-o_in`
-  * mpas-cice files:
-      * `mpascice.hist.am.timeSeriesStatsMonthly.*.nc`
-      * `mpascice.rst.0002-01-01_00000.nc` (or any other mpas-cice restart
+  * mpas-seaice files:
+      * `mpasseaice.hist.am.timeSeriesStatsMonthly.*.nc`
+      * `mpasseaice.rst.0002-01-01_00000.nc` (or any other mpas-seaice restart
         file)
-      * `streams.cice`
-      * `mpas-cice_in`
+      * `streams.seaice`
+      * `mpas-seaice_in`
+
+Note: for older runs, mpas-seaice files will be named:
+  * `mpascice.hist.am.timeSeriesStatsMonthly.*.nc`
+  * `mpascice.rst.0002-01-01_00000.nc`
+  * `streams.cice`
+  * `mpas-cice_in`
+
 
 ## Purge Old Analysis
 

diff --git a/conda/recipe/build.sh b/conda/recipe/build.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/sh
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
+python setup.py install --single-version-externally-managed --record=record.txt
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
@@ -0,0 +1,47 @@
+{% set version = "0.7.5" %}
+
+package:
+    name: mpas_analysis
+    version: {{ version }}
+
+source:
+    path: ../..
+
+build:
+    number: 0
+
+test:
+    requires:
+        - pytest
+    imports:
+        - mpas_analysis
+        - pytest
+    commands:
+        - pytest --pyargs mpas_analysis
+
+requirements:
+    build:
+        - python
+        - setuptools
+    run:
+        - python
+        - numpy
+        - scipy
+        - matplotlib
+        - netcdf4
+        - xarray >=0.10.0
+        - dask
+        - bottleneck
+        - basemap
+        - lxml
+        - nco >=4.7.0
+        - pillow
+
+about:
+    home:  http://gitub.com/MPAS-Dev/MPAS-Analysis
+
+extra:
+    recipe-maintainers:
+        - doutriaux1
+        - xylar
+
diff --git a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil
@@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3
 # placed in the output mappingSubdirectory
 mappingDirectory = /lcrc/group/acme/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.
@@ -142,4 +149,4 @@ polarPlot = False
 ## options related to ocean regions used in several analysis modules
 
 # Directory for region mask files
-regionMaskDirectory = /global/project/projectdirs/acme/mapping/grids/
+regionMaskDirectory = /lcrc/group/acme/mpas_analysis/region_masks 
diff --git a/configs/anvil/job_script.anvil.bash b/configs/anvil/job_script.anvil.bash
@@ -1,4 +1,11 @@
 #!/bin/bash
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # comment out if using debug queue
 #PBS -q acme

diff --git a/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl b/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl
@@ -43,6 +43,13 @@ mpasMeshName = oRRS30to10v3wLI
 # placed in the output mappingSubdirectory
 mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/cori/job_script.cori-haswell.bash b/configs/cori/job_script.cori-haswell.bash
@@ -1,4 +1,11 @@
 #!/bin/bash -l
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # comment out if using debug queue
 #SBATCH --partition=regular

diff --git a/configs/cori/job_script.cori-knl.bash b/configs/cori/job_script.cori-knl.bash
@@ -1,4 +1,11 @@
 #!/bin/bash -l
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # comment out if using debug queue
 #SBATCH --partition=regular

diff --git a/configs/edison/config.20170807.beta1.G_oQU240.edison b/configs/edison/config.20170807.beta1.G_oQU240.edison
@@ -32,6 +32,13 @@ mpasMeshName = oQU240
 # placed in the output mappingSubdirectory
 # mappingDirectory = /dir/for/mapping/files
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison b/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison
@@ -33,6 +33,13 @@ mpasMeshName = oEC60to30v3
 # placed in the output mappingSubdirectory
 mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison b/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison
@@ -43,6 +43,13 @@ mpasMeshName = oEC60to30v3wLI
 # placed in the output mappingSubdirectory
 mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/edison/job_script.edison.bash b/configs/edison/job_script.edison.bash
@@ -1,4 +1,11 @@
 #!/bin/bash -l
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # comment out if using debug queue
 #SBATCH --partition=regular

diff --git a/configs/job_script.default.bash b/configs/job_script.default.bash
@@ -1,4 +1,11 @@
 #!/bin/bash
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # MPAS/ACME job to be analyzed, including paths to simulation data and
 # observations. Change this name and path as needed

diff --git a/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf b/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf
@@ -32,6 +32,13 @@ mpasMeshName = QU60
 # placed in the output mappingSubdirectory
 # mappingDirectory = /dir/for/mapping/files
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/lanl/config.MatchBoth_orig b/configs/lanl/config.MatchBoth_orig
@@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3
 # placed in the output mappingSubdirectory
 mappingDirectory = /turquoise/usr/projects/climate/SHARED_CLIMATE/mpas_analysis/mapping/
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/lanl/job_script.lanl.bash b/configs/lanl/job_script.lanl.bash
@@ -1,4 +1,11 @@
 #!/bin/bash
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # change number of nodes to change the number of parallel tasks
 # (anything between 1 and the total number of tasks to run)

diff --git a/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison b/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison
@@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3
 # placed in the output mappingSubdirectory
 mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping/
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan b/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan
@@ -32,6 +32,13 @@ mpasMeshName = oRRS18to6v3
 # placed in the output mappingSubdirectory
 mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/olcf/job_script.olcf.bash b/configs/olcf/job_script.olcf.bash
@@ -1,4 +1,11 @@
 #!/bin/bash
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 
 # comment out if using debug queue
 #PBS -q batch

diff --git a/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta b/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta
@@ -45,6 +45,13 @@ mpasMeshName = oEC60to30v3wLI
 # placed in the output mappingSubdirectory
 mappingDirectory = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/mapping
 
+# names of namelist and streams files, either a path relative to baseDirectory
+# or an absolute path.
+oceanNamelistFileName = mpas-o_in
+oceanStreamsFileName = streams.ocean
+seaIceNamelistFileName = mpas-cice_in
+seaIceStreamsFileName = streams.cice
+
 [output]
 ## options related to writing out plots, intermediate cached data sets, logs,
 ## etc.

diff --git a/configs/theta/job_script.theta.bash b/configs/theta/job_script.theta.bash
@@ -1,4 +1,11 @@
 #!/bin/bash
+# Copyright (c) 2017,  Los Alamos National Security, LLC (LANS)
+# and the University Corporation for Atmospheric Research (UCAR).
+#
+# Unless noted otherwise source code is licensed under the BSD license.
+# Additional copyright and license information can be found in the LICENSE file
+# distributed with this code, or at http://mpas-dev.github.com/license.html
+#
 #COBALT -t 1:00:00
 #COBALT -n 1
 #COBALT -A OceanClimate

diff --git a/docs/.gitignore b/docs/.gitignore
@@ -1 +1,2 @@
 generated
+*_obs_table.rst
diff --git a/docs/Makefile b/docs/Makefile
@@ -12,9 +12,13 @@ BUILDDIR      = _build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+clean:
+	rm -rf *observationstable.rst
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/__init__.py b/docs/__init__.py
diff --git a/docs/api.rst b/docs/api.rst
@@ -51,7 +51,12 @@ Ocean tasks
    ClimatologyMapSST
    ClimatologyMapSSS
    ClimatologyMapMLD
+   ClimatologyMapSSH
    ClimatologyMapAntarcticMelt
+   ClimatologyMapSoseTemperature
+   ClimatologyMapSoseSalinity
+   ClimatologyMapArgoTemperature
+   ClimatologyMapArgoSalinity
    IndexNino34
    MeridionalHeatTransport
    StreamfunctionMOC