Merge pull request #995 from MPAS-Dev/develop

Merge develop into main for v1.10.0 release

Author: xylar

azure-pipelines.yml

@@ -21,12 +21,12 @@ jobs:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
-      Python39:
-        python.version: '3.9'
       Python310:
         python.version: '3.10'
       Python311:
         python.version: '3.11'
+      Python312:
+        python.version: '3.12'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -37,27 +37,22 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda update --yes --all
-      conda install --yes mamba
-      # workaround based on recent failures
-      rm /usr/share/miniconda/pkgs/cache/*.json
-      mamba install --yes conda-build boa
-    displayName: Update conda base environment
+      conda create --yes --name build_env conda-build
+    displayName: Create build environment
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
-      conda activate
-      # workaround based on recent failures
-      rm /usr/share/miniconda/pkgs/cache/*.json
-      conda mambabuild -m "ci/python${PYTHON_VERSION}.yaml" "ci/recipe"
+      conda activate build_env
+      conda build -m "ci/python${PYTHON_VERSION}.yaml" "ci/recipe"
     displayName: Build MPAS-Analysis
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
       conda activate
-      mamba create --yes --quiet --name mpas -c ${CONDA_PREFIX}/conda-bld/ \
+      conda create --yes --quiet --name mpas \
+          -c ${CONDA_PREFIX}/envs/build_env/conda-bld/ \
           python=$PYTHON_VERSION mpas-analysis pytest
     displayName: Create Anaconda mpas environment
 
@@ -72,7 +67,8 @@ jobs:
       set -e
       eval "$(conda shell.bash hook)"
       conda activate
-      mamba create --yes --quiet --name docs -c ${CONDA_PREFIX}/conda-bld/ \
+      conda create --yes --quiet --name docs \
+          -c ${CONDA_PREFIX}/envs/build_env/conda-bld/ \
           python=$PYTHON_VERSION mpas-analysis sphinx mock sphinx_rtd_theme \
           tabulate "m2r2>=0.3.3" "mistune<2"
     condition: eq(variables['python.version'], '3.10')
@@ -151,7 +147,7 @@ jobs:
   strategy:
     matrix:
       Python310:
-        python.version: '3.10'
+        python.version: '3.11'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -162,28 +158,25 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda update --yes --all
-      conda install --yes mamba
-      # workaround based on recent failures
-      rm /usr/share/miniconda/pkgs/cache/*.json
-      mamba install --yes conda-build boa
-    displayName: Update conda base environment
+      conda create --yes --name build_env conda-build
+    displayName: Create build environment
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
-      conda activate
+      conda activate build_env
       # workaround based on recent failures
       rm /usr/share/miniconda/pkgs/cache/*.json
-      conda mambabuild -m "ci/python${PYTHON_VERSION}.yaml" "ci/recipe"
+      conda build -m "ci/python${PYTHON_VERSION}.yaml" "ci/recipe"
     displayName: Build MPAS-Analysis
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
       conda activate
-      mamba create --yes --quiet --name mpas -c ${CONDA_PREFIX}/conda-bld/ \
-           python=$PYTHON_VERSION mpas-analysis pytest
+      conda create --yes --quiet --name mpas \
+          -c ${CONDA_PREFIX}/envs/build_env/conda-bld/ \
+          python=$PYTHON_VERSION mpas-analysis pytest
       conda activate mpas
       pip install git+https://github.com/pydata/xarray.git
 

ci/python3.9.yaml renamed to ci/python3.12.yaml

@@ -5,4 +5,4 @@ pin_run_as_build:
     min_pin: x.x
     max_pin: x.x
 python:
-- 3.9.* *_cpython
+- 3.12.* *_cpython

ci/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.9.1" %}
+{% set version = "1.10.0" %}
 
 package:
   name: {{ name|lower }}
@@ -43,7 +43,7 @@ requirements:
     - pillow >=10.0.0,<11.0.0
     - progressbar2
     - pyproj
-    - pyremap >=0.0.14,<0.1.0
+    - pyremap >=1.2.0,<2.0.0
     - python-dateutil
     - requests
     - scipy

dev-spec.txt

@@ -26,7 +26,7 @@ pandas
 pillow >=10.0.0,<11.0.0
 progressbar2
 pyproj
-pyremap>=0.0.14,<0.1.0
+pyremap>=1.2.0,<2.0.0
 python-dateutil
 requests
 scipy

docs/developers_guide/api.rst

@@ -61,6 +61,7 @@ Ocean tasks
 .. autosummary::
    :toctree: generated/
 
+   ConservationTask
    ClimatologyMapSST
    ClimatologyMapSSS
    ClimatologyMapMLD
@@ -75,6 +76,7 @@ Ocean tasks
    ClimatologyMapWaves
    IndexNino34
    MeridionalHeatTransport
+   OceanHistogram
    StreamfunctionMOC
    TimeSeriesOHCAnomaly
    TimeSeriesTemperatureAnomaly

docs/tutorials/dev_getting_started.rst

@@ -642,24 +642,16 @@ climate index.
     ## options related to producing time series plots, often to compare against
     ## observations and previous runs
 
-    # start and end years for timeseries analysis. Use endYear = end to indicate
-    # that the full range of the data should be used.  If errorOnMissing = False,
-    # the start and end year will be clipped to the valid range.  Otherwise, out
-    # of bounds values will lead to an error.  In a "control" config file used in
-    # a "main vs. control" analysis run, the range of years must be valid and
-    # cannot include "end" because the original data may not be available.
+    # start and end years for timeseries analysis.  Out-of-bounds values will lead
+    # to an error.
     startYear = 1
     endYear = 5
 
     [index]
     ## options related to producing nino index.
 
-    # start and end years for El Nino 3.4 analysis. Use endYear = end to indicate
-    # that the full range of the data should be used.  If errorOnMissing = False,
-    # the start and end year will be clipped to the valid range.  Otherwise, out
-    # of bounds values will lead to an error.  In a "control" config file used in
-    # a "main vs. control" analysis run, the range of years must be valid and
-    # cannot include "end" because the original data may not be available.
+    # start and end years for El Nino 3.4 analysis.  Out-of-bounds values will lead
+    # to an error.
     startYear = 1
     endYear = 5
 

docs/tutorials/getting_started.rst

@@ -443,24 +443,16 @@ climate index.
     ## options related to producing time series plots, often to compare against
     ## observations and previous runs
 
-    # start and end years for timeseries analysis. Use endYear = end to indicate
-    # that the full range of the data should be used.  If errorOnMissing = False,
-    # the start and end year will be clipped to the valid range.  Otherwise, out
-    # of bounds values will lead to an error.  In a "control" config file used in
-    # a "main vs. control" analysis run, the range of years must be valid and
-    # cannot include "end" because the original data may not be available.
+    # start and end years for timeseries analysis.  Out-of-bounds values will lead
+    # to an error.
     startYear = 1
     endYear = 5
 
     [index]
     ## options related to producing nino index.
 
-    # start and end years for El Nino 3.4 analysis. Use endYear = end to indicate
-    # that the full range of the data should be used.  If errorOnMissing = False,
-    # the start and end year will be clipped to the valid range.  Otherwise, out
-    # of bounds values will lead to an error.  In a "control" config file used in
-    # a "main vs. control" analysis run, the range of years must be valid and
-    # cannot include "end" because the original data may not be available.
+    # start and end years for timeseries analysis.  Out-of-bounds values will lead
+    # to an error.
     startYear = 1
     endYear = 5
 

docs/users_guide/analysis_tasks.rst

@@ -37,6 +37,7 @@ Analysis Tasks
    tasks/oceanRegionalProfiles
    tasks/regionalTSDiagrams
    tasks/oceanHistogram
+   tasks/conservation
 
    tasks/climatologyMapSeaIceConcNH
    tasks/climatologyMapSeaIceThickNH

docs/users_guide/config/index.rst

@@ -13,22 +13,15 @@ determine the start and end years of climate indices (such as El Ni |n~| o
   [index]
   ## options related to producing nino index.
 
-  # start and end years for El Nino 3.4 analysis. Use endYear = end to indicate
-  # that the full range of the data should be used.  If errorOnMissing = False,
-  # the start and end year will be clipped to the valid range.  Otherwise, out
-  # of bounds values will lead to an error.  In a "control" config file used in
-  # a "main vs. control" analysis run, the range of years must be valid and
-  # cannot include "end" because the original data may not be available.
+  # start and end years for El Nino 3.4 analysis.  Out-of-bounds values will lead
+  # to an error.
   startYear = 1
-  endYear = end
+  endYear = 20
 
 Start and End Year
 ------------------
 
 A custom config file should specify a start and end year for time axis.
-If ``errorOnMissing = False`` in the ``input`` section and the start or end
-year is beyond the range of the simulation, the range will be reduced to those
-dates with available data and a warning message will be displayed.  If
-``errorOnMissing = True``, out of range year will produce an error.
+Out of range year will produce an error.
 
 

docs/users_guide/config/timeSeries.rst

@@ -16,23 +16,16 @@ for anomalies::
   # only the anomaly over a later span of years is of interest.
   # anomalyRefYear = 249
 
-  # start and end years for timeseries analysis. Use endYear = end to indicate
-  # that the full range of the data should be used.  If errorOnMissing = False,
-  # the start and end year will be clipped to the valid range.  Otherwise, out
-  # of bounds values will lead to an error.  In a "control" config file used in
-  # a "main vs. control" analysis run, the range of years must be valid and
-  # cannot include "end" because the original data may not be available.
+  # start and end years for timeseries analysis.  Out-of-bounds values will lead
+  # to an error.
   startYear = 1
-  endYear = end
+  endYear = 20
 
 Start and End Year
 ------------------
 
 A custom config file should specify a start and end year for time series.
-If ``errorOnMissing = False`` in the ``input`` section and the start or end
-year is beyond the range of the simulation, the range will be reduced to those
-dates with available data and a warning message will be displayed.  If
-``errorOnMissing = True``, out of range year will produce an error.
+Out of range year will produce an error.
 
 
 Anomaly Reference Year