Merge pull request #972 from MPAS-Dev/develop

Merge develop to main for 1.9.0 release

Author: xylar

.travis.yml

@@ -18,9 +18,9 @@ matrix:
     - name: "python-3.8"
       python: 3.8
       env: CONDA_ENV=py38
-    - name: "python-3.7-xarray-master"
+    - name: "python-3.7-xarray-main"
       python: 3.7
-      env: CONDA_ENV=py37-xarray-master
+      env: CONDA_ENV=py37-xarray-main
 
 env:
   global:

README.md

@@ -5,16 +5,16 @@ Analysis for simulations produced with Model for Prediction Across Scales
 (MPAS) components and the Energy Exascale Earth System Model (E3SM), which
 used those components.
 
-![sea surface temperature](docs/_static/sst_example.png)
+![sea surface temperature](docs/users_guide/_static/sst_example.png)
 
 ## conda-forge
 
 ### Current build status
 
 <table><tr><td>All platforms:</td>
     <td>
-      <a href="https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=6243&branchName=master">
-        <img src="https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/mpas-analysis-feedstock?branchName=master">
+      <a href="https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=6243&branchName=main">
+        <img src="https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/mpas-analysis-feedstock?branchName=main">
       </a>
     </td>
   </tr>
@@ -127,7 +127,7 @@ for more details.
   3. If you installed the `mpas-analysis` package, run:
      `mpas_analysis myrun.cfg`.  This will read the configuration
      first from `mpas_analysis/default.cfg` and then replace that
-     configuraiton with any changes from from `myrun.cfg`
+     configuration with any changes from from `myrun.cfg`
   4. If you want to run a subset of the analysis, you can either set the
      `generate` option under `[output]` in your config file or use the
      `--generate` flag on the command line.  See the comments in
@@ -178,7 +178,7 @@ Note: for older runs, mpas-seaice files will be named:
   * `mpascice.rst.0002-01-01_00000.nc`
   * `streams.cice`
   * `mpas-cice_in`
-  Also, for older runs mpaso-in will be named:
+  Also, for older runs `mpaso_in` will be named:
   * `mpas-o_in`
 
 
@@ -221,13 +221,13 @@ If you are running from a git repo:
   2. If using the `mpas-analysis` conda package, download the job script and/or
      sample config file from the
      [example configs directory](https://github.com/MPAS-Dev/MPAS-Analysis/tree/develop/configs).
-  2. Modify the number of parallel tasks, the run name, the output directory
+  3. Modify the number of parallel tasks, the run name, the output directory
      and the path to the config file for the run.
-  3. Note: the number of parallel tasks can be anything between 1 and the
+  4. Note: the number of parallel tasks can be anything between 1 and the
      number of analysis tasks to be performed.  If there are more tasks than
      parallel tasks, later tasks will simply wait until earlier tasks have
      finished.
-  4. Submit the job using the modified job script
+  5. Submit the job using the modified job script
 
 
 

azure-pipelines.yml

@@ -2,7 +2,7 @@
 trigger:
   branches:
     include:
-    - master
+    - main
     - develop
   tags:
     include:
@@ -11,7 +11,7 @@ trigger:
 pr:
   branches:
     include:
-    - master
+    - main
     - develop
 
 jobs:
@@ -37,7 +37,11 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda install --yes "conda<22.11.0" conda-build mamba boa
+      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
 
   - bash: |
@@ -70,7 +74,7 @@ jobs:
       conda activate
       mamba create --yes --quiet --name docs -c ${CONDA_PREFIX}/conda-bld/ \
           python=$PYTHON_VERSION mpas-analysis sphinx mock sphinx_rtd_theme \
-          tabulate m2r2 "mistune<2"
+          tabulate "m2r2>=0.3.3" "mistune<2"
     condition: eq(variables['python.version'], '3.10')
     displayName: Create Anaconda docs environment
 
@@ -93,7 +97,7 @@ jobs:
       if [[ "$(Build.SourceBranch)" == "refs/heads/develop" ]]; then
         export DOCS_VERSION="latest"
         deploy=True
-      elif [[ "$(Build.SourceBranch)" == "refs/heads/master" ]]; then
+      elif [[ "$(Build.SourceBranch)" == "refs/heads/main" ]]; then
         export DOCS_VERSION="stable"
         deploy=True
       elif [[ "$(Build.SourceBranch)" == refs/tags/* ]]; then
@@ -141,7 +145,7 @@ jobs:
     displayName: build and deploy docs
 
 - job:
-  displayName: xarray-master
+  displayName: xarray-main
   pool:
     vmImage: 'ubuntu-latest'
   strategy:
@@ -158,7 +162,11 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda install --yes python=$PYTHON_VERSION "conda<22.11.0" conda-build mamba boa
+      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
 
   - bash: |
@@ -187,53 +195,3 @@ jobs:
       conda activate mpas
       pytest --pyargs mpas_analysis
     displayName: pytest
-
-- job:
-  displayName: osx
-  pool:
-    vmImage: 'macOS-latest'
-  strategy:
-    matrix:
-      Python39:
-        python.version: '3.9'
-      Python310:
-        python.version: '3.10'
-      Python311:
-        python.version: '3.11'
-
-  steps:
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-
-  - bash: sudo chown -R 501:20 /usr/local/miniconda/pkgs
-    displayName: Fix permissions
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda config --add channels conda-forge
-      conda config --set channel_priority strict
-      conda install --yes "conda<22.11.0" conda-build mamba boa
-    displayName: Update conda base environment
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda activate
-      conda mambabuild -m "ci/python${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
-    displayName: Create Anaconda mpas environment
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda activate mpas
-      pytest --pyargs mpas_analysis
-    displayName: pytest

ci/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.8.0" %}
+{% set version = "1.9.0" %}
 
 package:
   name: {{ name|lower }}
@@ -18,37 +18,37 @@ build:
 
 requirements:
   host:
-    - python >=3.7
+    - python >=3.8
     - pip
   run:
-    - python >=3.7
+    - python >=3.8
     - bottleneck
     - cartopy >=0.18.0
     - cartopy_offlinedata
     - cmocean
     - dask
-    - esmf >=8.0.0,<8.3.0
-    - esmf=*=nompi_*
+    - esmf >=8.4.2,<8.5.0
+    - esmf=*=mpi_mpich_*
     - f90nml
-    - geometric_features >=0.5.0
+    - geometric_features >=1.2.0
     - gsw
     - lxml
-    - mache >=1.1.2
-    - matplotlib-base >=3.0.2
-    - mpas_tools >=0.14.0
+    - mache >=1.11.0
+    - matplotlib-base >=3.6.0,!=3.7.2
+    - mpas_tools >=0.16.0
     - nco >=4.8.1
     - netcdf4
     - numpy
     - pandas
-    - pillow
+    - pillow >=10.0.0,<11.0.0
     - progressbar2
     - pyproj
     - pyremap >=0.0.14,<0.1.0
     - python-dateutil
     - requests
     - scipy
     - setuptools
-    - shapely
+    - shapely >=2.0,<3.0
     - xarray >=0.14.1
 
 test:

configs/alcf/job_script.cooley.bash

@@ -5,7 +5,7 @@
 
 source /lus/theta-fs0/projects/ccsm/acme/tools/e3sm-unified/load_latest_e3sm_unified_cooley.sh
 # alternatively, you can load your own development environment
-# source ~/miniconda3/etc/profile.d/conda.sh
+# source ~/mambaforge/etc/profile.d/conda.sh
 # conda activate mpas_dev
 # export E3SMU_MACHINE=cooley
 

configs/compy/job_script.compy.bash

@@ -10,7 +10,7 @@ export OMP_NUM_THREADS=1
 
 source /share/apps/E3SM/conda_envs/load_latest_e3sm_unified_compy.sh
 # alternatively, you can load your own development environment
-# source ~/miniconda3/etc/profile.d/conda.sh
+# source ~/mambaforge/etc/profile.d/conda.sh
 # conda activate mpas_dev
 # export E3SMU_MACHINE=compy
 

configs/job_script.default.bash

@@ -7,7 +7,7 @@
 
 export OMP_NUM_THREADS=1
 
-source ~/miniconda3/etc/profile.d/conda.sh
+source ~/mambaforge/etc/profile.d/conda.sh
 conda activate mpas_dev
 # if you are on an E3SM supported machine, you can specify it:
 # export E3SMU_MACHINE=chrysalis