Merge develop into main for v1.14.0 release

.github/dependabot.yml

@@ -8,8 +8,7 @@ updates:
       interval: "weekly"
     assignees:
       - "xylar"
-      - "altheaden"
     reviewers:
       - "xylar"
-      - "altheaden"
+      - "andrewdnolan"
 

.github/workflows/build_workflow.yml

@@ -27,7 +27,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     steps:
       - id: skip_check
@@ -37,7 +37,7 @@ jobs:
           paths_ignore: ${{ env.PATHS_IGNORE }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Cache Conda
@@ -53,21 +53,22 @@ jobs:
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v2
         with:
-          activate-environment: "mpas_analysis_ci"
-          miniforge-version: latest
-          channels: conda-forge
-          channel-priority: strict
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
+          environment-name: mpas_analysis_dev
+          init-shell: bash
+          condarc: |
+            channel_priority: strict
+            channels:
+                - conda-forge
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install mpas_analysis
         run: |
-          conda create -n mpas_analysis_dev --file dev-spec.txt \
-              python=${{ matrix.python-version }}
-          conda activate mpas_analysis_dev
+          conda install -y --file dev-spec.txt \
+            python=${{ matrix.python-version }}
           python -m pip install --no-deps --no-build-isolation -vv -e .
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
@@ -76,7 +77,6 @@ jobs:
            CHECK_IMAGES: False
         run: |
           set -e
-          conda activate mpas_analysis_dev
           pip check
           pytest --pyargs mpas_analysis
           mpas_analysis --help
@@ -85,9 +85,5 @@ jobs:
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Build Sphinx Docs
         run: |
-          conda activate mpas_analysis_dev
-          # sphinx-multiversion expects at least a "main" branch
-          git branch main || echo "branch main already exists."
           cd docs
-          sphinx-multiversion . _build/html
-
+          DOCS_VERSION=test make versioned-html

.github/workflows/docs_workflow.yml

@@ -20,7 +20,7 @@ jobs:
         shell: bash -l {0}
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -37,52 +37,60 @@ jobs:
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v2
         with:
-          activate-environment: "mpas_analysis_ci"
-          miniforge-version: latest
-          channels: conda-forge
-          channel-priority: strict
-          auto-update-conda: false
-          python-version: ${{ env.PYTHON_VERSION }}
+          environment-name: mpas_analysis_dev
+          init-shell: bash
+          condarc: |
+            channel_priority: strict
+            channels: 
+                - conda-forge
+          create-args: >-
+            python=${{ env.PYTHON_VERSION }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install mpas_analysis
         run: |
           git config --global url."https://github.com/".insteadOf "[email protected]:"
-          conda create -n mpas_analysis_dev --file dev-spec.txt \
+          conda install -y --file dev-spec.txt \
             python=${{ env.PYTHON_VERSION }}
-          conda activate mpas_analysis_dev
           python -m pip install -vv --no-deps --no-build-isolation -e .
 
       - name: Build Sphinx Docs
         run: |
           set -e
-          conda activate mpas_analysis_dev
           pip check
           mpas_analysis sync diags --help
           cd docs
-          sphinx-multiversion . _build/html
+          DOCS_VERSION=${{ github.ref_name }} make versioned-html
       - name: Copy Docs and Commit
         run: |
           set -e
-          conda activate mpas_analysis_dev
           pip check
           mpas_analysis sync diags --help
           cd docs
           # gh-pages branch must already exist
           git clone https://github.com/MPAS-Dev/MPAS-Analysis.git --branch gh-pages --single-branch gh-pages
+
+          # Only replace docs in a directory with the destination branch name with latest changes. Docs for
+          # releases should be untouched.
+          rm -rf gh-pages/${{ github.ref_name }}
+
+          # don't clobber existing release versions (in case we retroactively fixed them)
+          cp -r _build/html/${{ github.ref_name }} gh-pages/
+
+          mkdir -p gh-pages/shared
+          cp shared/version-switcher.js gh-pages/shared/version-switcher.js
+
+          # Update the list of versions with all versions in the gh-pages directory.
+          python generate_versions_json.py
+
           # Make sure we're in the gh-pages directory.
           cd gh-pages
           # Create `.nojekyll` (if it doesn't already exist) for proper GH Pages configuration.
           touch .nojekyll
           # Add `index.html` to point to the `develop` branch automatically.
           printf '<meta http-equiv="refresh" content="0; url=./develop/index.html" />' > index.html
-          # Only replace docs in a directory with the destination branch name with latest changes. Docs for
-          # releases should be untouched.
-          rm -rf ${{ github.head_ref || github.ref_name }}
-          # don't clobber existing release versions (in case we retroactively fixed them)
-          cp -r -n ../_build/html/* .
           # Configure git using GitHub Actions credentials.
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"

.gitignore

@@ -99,3 +99,6 @@ ENV/
 /chrysalis_test_suite/
 /cori_test_suite/
 /compy_test_suite/
+
+# vscode settings
+.vscode/

README.md

@@ -54,8 +54,8 @@ environment):
 ``` bash
 conda config --add channels conda-forge
 conda config --set channel_priority strict
-conda create -y -n mpas_dev --file dev-spec.txt
-conda activate mpas_dev
+conda create -y -n mpas_analysis_dev --file dev-spec.txt
+conda activate mpas_analysis_dev
 python -m pip install --no-deps --no-build-isolation -e .
 ```
 
@@ -64,16 +64,16 @@ for MPAS-Tools or geometric\_features), you should first comment out the other
 package in `dev-spec.txt`.  Then, you can install both packages in the same
 development environment, e.g.:
 ``` bash
-conda create -y -n mpas_dev --file tools/MPAS-Tools/conda_package/dev-spec.txt \
+conda create -y -n mpas_analysis_dev --file tools/MPAS-Tools/conda_package/dev-spec.txt \
     --file analysis/MPAS-Analysis/dev-spec.txt
-conda activate mpas_dev
+conda activate mpas_analysis_dev
 cd tools/MPAS-Tools/conda_package
 python -m pip install --no-deps --no-build-isolation -e .
 cd ../../../analysis/MPAS-Analysis
 python -m pip install --no-deps --no-build-isolation -e .
 ```
 Obviously, the paths to the repos may be different in your local clones.  With
-the `mpas_dev` environment as defined above, you can make changes to both
+the `mpas_analysis_dev` environment as defined above, you can make changes to both
 `mpas_tools` and `mpas-analysis` packages in their respective branches, and
 these changes will be reflected when refer to the packages or call their
 respective entry points (command-line tools).
@@ -294,8 +294,7 @@ developers".  Then run:
 To generate the `sphinx` documentation, run:
 ```
 cd docs
-make clean
-make html
+DOCS_VERSION=test make clean versioned-html
 ```
 The results can be viewed in your web browser by opening:
 ```

ci/recipe/meta.yaml

@@ -1,5 +1,6 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.13.0" %}
+{% set version = "1.14.0" %}
+{% set python_min = "3.10" %}
 
 package:
   name: {{ name|lower }}
@@ -9,49 +10,52 @@ source:
   path: ../..
 
 build:
-    number: 0
-    script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vv .
-    noarch: python
+  number: 0
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vv
+  noarch: python
+  entry_points:
+    - mpas_analysis = mpas_analysis.__main__:main
+    - download_analysis_data = mpas_analysis.download_data:download_analysis_data
 
 requirements:
   host:
-    - python >=3.9
+    - python {{ python_min }}
     - pip
-    - setuptools
+    - setuptools >=60
   run:
-    - python >=3.9
+    - python >={{ python_min }},<3.13
     - cartopy >=0.18.0
     - cartopy_offlinedata
     - cmocean
     - dask
     - esmf >=8.4.2,<9.0.0
-    - esmf=*=mpi_mpich_*
     - f90nml
     - geometric_features >=1.6.1
     - gsw
     - lxml
     - mache >=1.11.0
     - matplotlib-base >=3.9.0
-    - mpas_tools >=0.34.1,<1.0.0
+    - mpas_tools >=1.3.0,<2.0.0
     - nco >=4.8.1,!=5.2.6
     - netcdf4
     - numpy >=2.0,<3.0
     - pandas
     - pillow >=10.0.0,<11.0.0
     - progressbar2
     - pyproj
-    - pyremap >=1.2.0,<2.0.0
+    - pyremap >=2.0.0,<3.0.0
     - python-dateutil
     - requests
     - scipy >=1.7.0
-    - setuptools
     - shapely >=2.0,<3.0
+    - tranche >=0.2.3
     - xarray >=0.14.1
 
 test:
   requires:
     - pytest
     - pip
+    - python {{ python_min }}
   imports:
     - mpas_analysis
     - pytest
@@ -78,5 +82,6 @@ about:
 
 extra:
   recipe-maintainers:
+    - andrewdnolan
     - xylar
     - jhkennedy

configs/alcf/job_script.cooley.bash

@@ -6,7 +6,7 @@
 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 ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=cooley
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/compy/job_script.compy.bash

@@ -11,7 +11,7 @@ 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 ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=compy
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/job_script.default.bash

@@ -8,7 +8,7 @@
 export OMP_NUM_THREADS=1
 
 source ~/mambaforge/etc/profile.d/conda.sh
-conda activate mpas_dev
+conda activate mpas_analysis_dev
 # if you are on an E3SM supported machine, you can specify it:
 # export E3SMU_MACHINE=chrysalis
 

configs/lanl/job_script.lanl.bash

@@ -8,7 +8,7 @@
 
 source /users/xylar/climate/mambaforge/etc/profile.d/conda.sh
 source /users/xylar/climate/mambaforge/etc/profile.d/mamba.sh
-mamba activate mpas_dev
+mamba activate mpas_analysis_dev
 
 export HDF5_USE_FILE_LOCKING=FALSE
 

configs/lcrc/job_script.anvil.bash

@@ -12,7 +12,7 @@ export OMP_NUM_THREADS=1
 source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_anvil.sh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=anvil
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/lcrc/job_script.chrysalis.bash

@@ -10,7 +10,7 @@ export OMP_NUM_THREADS=1
 source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=chrysalis
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/nersc/job_script.cori-haswell.bash

@@ -20,7 +20,7 @@ export OMP_NUM_THREADS=1
 source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_cori-haswell.sh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=cori-haswell
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/nersc/job_script.cori-knl.bash

@@ -20,7 +20,7 @@ export OMP_NUM_THREADS=1
 source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_cori-knl.sh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=cori-knl
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/nersc/job_script.pm-cpu.bash

@@ -14,7 +14,7 @@ export OMP_NUM_THREADS=1
 source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_pm-cpu.sh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=pm-cpu
 
 export HDF5_USE_FILE_LOCKING=FALSE

configs/olcf/job_script.olcf.bash

@@ -10,7 +10,7 @@
 source /gpfs/alpine/proj-shared/cli115/e3sm-unified/load_latest_e3sm_unified_andes.csh
 # alternatively, you can load your own development environment
 # source ~/mambaforge/etc/profile.d/conda.sh
-# conda activate mpas_dev
+# conda activate mpas_analysis_dev
 # export E3SMU_MACHINE=anvil
 
 export HDF5_USE_FILE_LOCKING=FALSE