Merge pull request #1077 from MPAS-Dev/develop

Merge develop into main for v1.13.0 release

Author: xylar

.github/pull_request_template.md

@@ -4,15 +4,15 @@ Please add a description of what is accomplished in the PR here at the top:
 -->
 
 <!--
-Below are a few things we ask you or your reviewers to kindly check. 
+Below are a few things we ask you or your reviewers to kindly check.
 ***Remove checks that are not relevant by deleting the line(s) below.***
 -->
 Checklist
 * [ ] User's Guide has been updated
 * [ ] If this PR adds a new analysis task, it has also been added to the user's guide
 * [ ] Developer's Guide has been updated
 * [ ] API documentation in the Developer's Guide (`api.rst`) has any new or modified class, method and/or functions listed
-* [ ] Documentation has been [built locally](https://mpas-dev.github.io/MPAS-Analysis/latest/users_guide/quick_start.html#generating-documentation) and changes look as expected
+* [ ] Documentation has been [built locally](https://mpas-dev.github.io/MPAS-Analysis/develop/users_guide/quick_start.html#generating-documentation) and changes look as expected
 * [ ] `Testing` comment in the PR documents testing used to verify the changes
 
 <!--

.github/workflows/build_workflow.yml

@@ -27,7 +27,8 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
     steps:
       - id: skip_check
         uses: fkirc/skip-duplicate-actions@master
@@ -45,10 +46,10 @@ jobs:
           # Increase this value to reset cache if conda-dev-spec.template has not changed in the workflow
           CACHE_NUMBER: 0
         with:
-          path: ~/conda_pkgs_dir
+          path: ~/conda_pkgs_dir_py${{ matrix.python-version }}
           key:
             ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('dev-spec.txt,setup.py') }}
+            hashFiles('dev-spec.txt,pyproject.toml') }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
@@ -58,7 +59,7 @@ jobs:
           miniforge-version: latest
           channels: conda-forge
           channel-priority: strict
-          auto-update-conda: true
+          auto-update-conda: false
           python-version: ${{ matrix.python-version }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}

.github/workflows/docs_workflow.yml

@@ -9,6 +9,9 @@ on:
   release:
     types: [published]
 
+env:
+  PYTHON_VERSION: "3.13"
+
 jobs:
   publish-docs:
     runs-on: ubuntu-latest
@@ -40,15 +43,15 @@ jobs:
           miniforge-version: latest
           channels: conda-forge
           channel-priority: strict
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+          auto-update-conda: false
+          python-version: ${{ env.PYTHON_VERSION }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install mpas_analysis
         run: |
           git config --global url."https://github.com/".insteadOf "[email protected]:"
           conda create -n mpas_analysis_dev --file dev-spec.txt \
-            python=${{ matrix.python-version }}
+            python=${{ env.PYTHON_VERSION }}
           conda activate mpas_analysis_dev
           python -m pip install -vv --no-deps --no-build-isolation -e .
 

MANIFEST.in

@@ -0,0 +1,12 @@
+include mpas_analysis/*.cfg
+include mpas_analysis/obs/analysis_input_files
+include mpas_analysis/obs/sose_10000km_input_files
+include mpas_analysis/obs/observational_datasets.xml
+
+include mpas_analysis/configuration/*.cfg
+include mpas_analysis/shared/html/templates/*
+include mpas_analysis/shared/plot/ScientificColourMaps7/*/*.xml
+include mpas_analysis/shared/plot/SciVisColorColormaps/*.xml
+include mpas_analysis/shared/plot/SciVisColorCustom/*.xml
+include mpas_analysis/test/test*/*
+include mpas_analysis/test/test*/*/*

ci/python3.13.yaml

@@ -0,0 +1,8 @@
+channel_sources:
+- conda-forge,defaults
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.13.* *_cp313

ci/python3.9.yaml

@@ -0,0 +1,8 @@
+channel_sources:
+- conda-forge,defaults
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython

ci/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.12.0" %}
+{% set version = "1.13.0" %}
 
 package:
   name: {{ name|lower }}
@@ -12,29 +12,27 @@ build:
     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
     - pip
+    - setuptools
   run:
     - python >=3.9
     - cartopy >=0.18.0
     - cartopy_offlinedata
     - cmocean
     - dask
-    - esmf >=8.4.2,<8.7.0
+    - esmf >=8.4.2,<9.0.0
     - esmf=*=mpi_mpich_*
     - f90nml
-    - geometric_features >=1.4.0
+    - geometric_features >=1.6.1
     - gsw
     - lxml
     - mache >=1.11.0
     - matplotlib-base >=3.9.0
-    - mpas_tools >=0.34.0
+    - mpas_tools >=0.34.1,<1.0.0
     - nco >=4.8.1,!=5.2.6
     - netcdf4
     - numpy >=2.0,<3.0
@@ -61,6 +59,8 @@ test:
     - pip check
     - pytest --pyargs mpas_analysis
     - mpas_analysis --help
+    - mpas_analysis --list
+    - mpas_analysis --plot_colormaps
     - download_analysis_data --help
 
 about:

dev-spec.txt

@@ -7,15 +7,15 @@ cartopy >=0.18.0
 cartopy_offlinedata
 cmocean
 dask
-esmf >=8.4.2,<8.7.0
+esmf >=8.4.2,<9.0.0
 esmf=*=mpi_mpich_*
 f90nml
-geometric_features>=1.4.0
+geometric_features>=1.6.1
 gsw
 lxml
 mache >=1.11.0
 matplotlib-base>=3.9.0
-mpas_tools>=0.34.1
+mpas_tools>=0.34.1,<1.0.0
 nco>=4.8.1,!=5.2.6
 netcdf4
 numpy>=2.0,<3.0

docs/authors.rst

@@ -19,6 +19,7 @@ Contributors
 * Greg Streletz
 * Adrian Turner
 * Luke Van Roekel
+* Elizabeth Hunke
 
 For a list of all the contributions:
 https://github.com/MPAS-Dev/MPAS-Analysis/graphs/contributors

docs/conf.py

@@ -15,7 +15,7 @@
 import os
 import m2r2
 from glob import glob
-import mpas_analysis
+import mpas_analysis.version
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 if on_rtd:
     os.environ['PROJ_LIB'] = '{}/{}/share/proj'.format(
@@ -87,9 +87,9 @@
     release = version
 else:
     # The short X.Y.Z version.
-    version = mpas_analysis.__version__
+    version = mpas_analysis.version.__version__
     # The full version, including alpha/beta/rc tags.
-    release = mpas_analysis.__version__
+    release = mpas_analysis.version.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -187,9 +187,9 @@
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
     'xarray': ('http://xarray.pydata.org/en/stable/', None),
     'geometric_features':
-        ('http://mpas-dev.github.io/geometric_features/stable/', None),
+        ('http://mpas-dev.github.io/geometric_features/main/', None),
     'mpas_tools':
-        ('http://mpas-dev.github.io/MPAS-Tools/stable/', None)}
+        ('http://mpas-dev.github.io/MPAS-Tools/master/', None)}
 
 
 cwd = os.getcwd()