Merge pull request #995 from MPAS-Dev/develop

Merge develop into main for v1.10.0 release
MPAS-Dev · Mar 22, 2024 · 79bc218 · 79bc218
2 parents 83c4054 + f24f15c
commit 79bc218
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diff --git a/azure-pipelines.yml b/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
 

diff --git a/ci/python3.9.yaml → ci/python3.12.yaml b/ci/python3.9.yaml → 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
diff --git a/ci/recipe/meta.yaml b/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

diff --git a/dev-spec.txt b/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

diff --git a/docs/developers_guide/api.rst b/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

diff --git a/docs/tutorials/dev_getting_started.rst b/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
 

diff --git a/docs/tutorials/getting_started.rst b/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
 

diff --git a/docs/users_guide/analysis_tasks.rst b/docs/users_guide/analysis_tasks.rst
@@ -37,6 +37,7 @@ Analysis Tasks
    tasks/oceanRegionalProfiles
    tasks/regionalTSDiagrams
    tasks/oceanHistogram
+   tasks/conservation
 
    tasks/climatologyMapSeaIceConcNH
    tasks/climatologyMapSeaIceThickNH

diff --git a/docs/users_guide/config/index.rst b/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.
 
 
diff --git a/docs/users_guide/config/timeSeries.rst b/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

diff --git a/docs/users_guide/tasks/climatologyMapAntarcticMelt.rst b/docs/users_guide/tasks/climatologyMapAntarcticMelt.rst
@@ -4,7 +4,7 @@ climatologyMapAntarcticMelt
 ===========================
 
 An analysis task for comparison of Antarctic maps of melt rates against
-observations from `Adusumilli et al. (2020) <https://doi.org/10.1038/s41561-020-0616-z>`_.
+observations from `Paolo et al. (2023) <https://doi.org/10.5194/tc-17-3409-2023>`_.
 
 Component and Tags::
 
@@ -76,7 +76,7 @@ For more details, see:
 Observations
 ------------
 
-:ref:`adusumilli_melt`
+:ref:`paolo_melt`
 
 Example Result
 --------------

diff --git a/docs/users_guide/tasks/conservation.rst b/docs/users_guide/tasks/conservation.rst
@@ -0,0 +1,63 @@
+.. _task_conservation:
+
+conservation
+============
+
+An analysis task for plotting histograms of 2-d variables of climatologies
+in ocean regions.
+
+Component and Tags::
+
+  component: ocean
+  tags: timeseries, conservation
+
+Configuration Options
+---------------------
+
+The following configuration options are available for this task:
+
+.. code-block:: cfg
+
+    [conservation]
+    ## options related to producing time series plots, often to compare against
+    ## observations and previous runs
+    
+    # the year from which to compute anomalies if not the start year of the
+    # simulation.  This might be useful if a long spin-up cycle is performed and
+    # 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.
+    startYear = 1
+    endYear = end
+    
+    # Plot types to generate. The following plotTypes are supported:
+    #    total_energy_flux : Total energy flux
+    #    absolute_energy_error : Energy error
+    #    ice_salt_flux : Salt flux related to land ice and sea ice
+    #    absolute_salt_error : Salt conservation error
+    #    total_mass_flux : Total mass flux
+    #    total_mass_change : Total mass anomaly
+    #    land_ice_mass_change : Mass anomaly due to land ice fluxes
+    #    land_ice_ssh_change : SSH anomaly due to land ice fluxes
+    #    land_ice_mass_flux_components : Mass fluxes from land ice
+    plotTypes = 'land_ice_mass_flux_components'
+    
+    # line colors for the main, control and obs curves
+    # see https://matplotlib.org/stable/gallery/color/named_colors.html
+    # and https://matplotlib.org/stable/tutorials/colors/colors.html
+    mainColor = black
+    controlColor = tab:red
+
+
+Example Result
+--------------
+
+.. image:: examples/total_mass_flux.png
+   :width: 500 px
+   :align: center
diff --git a/docs/users_guide/tasks/examples/total_mass_flux.png b/docs/users_guide/tasks/examples/total_mass_flux.png
diff --git a/docs/users_guide/tasks/timeSeriesAntarcticMelt.rst b/docs/users_guide/tasks/timeSeriesAntarcticMelt.rst
@@ -4,8 +4,9 @@ timeSeriesAntarcticMelt
 =======================
 
 An analysis task for plotting time series of mean melt rates per ice shelf or
-Antarctic region along with observations from `Rignot et al. (2013)`_
-and `Adusumilli et al. (2020) <https://doi.org/10.1038/s41561-020-0616-z>`_.
+Antarctic region along with observations from `Rignot et al. (2013)`_,
+`Adusumilli et al. (2020) <https://doi.org/10.1038/s41561-020-0616-z>`_,
+and `Paolo et al. (2023) <https://doi.org/10.5194/tc-17-3409-2023>`_.
 
 Component and Tags::
 

diff --git a/docs/versions.rst b/docs/versions.rst
@@ -20,6 +20,7 @@ Documentation    On GitHub
 `v1.7.2`_        `1.7.2`_
 `v1.8.0`_        `1.8.0`_
 `v1.9.0`_        `1.9.0`_
+`v1.10.0`_       `1.10.0`_
 ================ ===============
 
 .. _`stable`: ../stable/index.html
@@ -38,6 +39,7 @@ Documentation    On GitHub
 .. _`v1.7.2`: ../1.7.2/index.html
 .. _`v1.8.0`: ../1.8.0/index.html
 .. _`v1.9.0`: ../1.9.0/index.html
+.. _`v1.10.0`: ../1.10.0/index.html
 .. _`main`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/main
 .. _`develop`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/develop
 .. _`1.2.6`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.2.6
@@ -54,3 +56,4 @@ Documentation    On GitHub
 .. _`1.7.2`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.7.2
 .. _`1.8.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.8.0
 .. _`1.9.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.9.0
+.. _`1.10.0`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/1.10.0
diff --git a/mpas_analysis/__init__.py b/mpas_analysis/__init__.py
@@ -3,5 +3,5 @@
 import matplotlib as mpl
 mpl.use('Agg')
 
-__version_info__ = (1, 9, 1)
+__version_info__ = (1, 10, 0)
 __version__ = '.'.join(str(vi) for vi in __version_info__)