Merge branch develop into master

ci/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "MPAS-Analysis" %}
-{% set version = "1.7.1" %}
+{% set version = "1.7.2" %}
 
 package:
   name: {{ name|lower }}
@@ -27,6 +27,7 @@ requirements:
     - cartopy_offlinedata
     - cmocean
     - dask
+    - esmf=*=nompi_*
     - f90nml
     - geometric_features >=0.5.0
     - gsw

dev-spec.txt

@@ -8,6 +8,7 @@ cartopy >=0.18.0
 cartopy_offlinedata
 cmocean
 dask
+esmf=*=nompi_*
 f90nml
 geometric_features>=0.5.0
 gsw

docs/Makefile

@@ -13,7 +13,7 @@ help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 clean:
-	rm -rf *obs_table.rst generated obs
+	rm -rf users_guide/*obs_table.rst developers_guide/generated users_guide/obs
 	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile

docs/conf.py

@@ -92,13 +92,13 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
-                    'design_docs/template.md']
+                    'design_docs/template.md', 'design_docs/template.rst']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -131,7 +131,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 
 # -- Options for HTMLHelp output ------------------------------------------
@@ -201,19 +201,27 @@
         ('http://mpas-dev.github.io/MPAS-Tools/stable/', None)}
 
 
+cwd = os.getcwd()
+os.chdir('users_guide')
+
 # Build some custom rst files
-xmlFileName = '../mpas_analysis/obs/observational_datasets.xml'
+xmlFileName = '../../mpas_analysis/obs/observational_datasets.xml'
 for component in ['ocean', 'seaice']:
-    build_rst_table_from_xml(xmlFileName, '{}_obs_table.rst'.format(component),
+    build_rst_table_from_xml(xmlFileName,
+                             f'{component}_obs_table.rst',
                              component)
 
 build_obs_pages_from_xml(xmlFileName)
 build_quick_start()
 
+os.chdir(cwd)
+
 for mdFileName in glob('design_docs/*.md'):
+    if os.path.basename(mdFileName) == 'template.md':
+        continue
     output = m2r2.parse_from_file(mdFileName)
     rstFileName = os.path.splitext(mdFileName)[0]+'.rst'
-    outFile = open(rstFileName, 'w')
-    outFile.write(output)
+    with open(rstFileName, 'w') as outFile:
+        outFile.write(output)
 
 github_doc_root = 'https://github.com/rtfd/recommonmark/tree/master/doc/'

docs/design_docs/index.rst

@@ -0,0 +1,16 @@
+Design Documents
+================
+
+.. toctree::
+   :titlesonly:
+
+   generalized_horizontal_interpolation
+   config_file_reorganization
+   timekeeping_reorg
+   generalize_calendar
+   variable_mapping_reorg
+   parallel_tasks
+   remapper
+   analysis_task_template
+   prerequisite_tasks
+   eddykineticenergy

docs/api.rst → docs/developers_guide/api.rst

@@ -38,7 +38,7 @@ Analysis tasks
 Base Class
 ----------
 
-.. currentmodule:: mpas_analysis.shared.analysis_task
+.. currentmodule:: mpas_analysis.shared
 
 .. autosummary::
    :toctree: generated/
@@ -187,8 +187,13 @@ Climatology
    MpasClimatologyTask.get_file_name
 
    RemapMpasClimatologySubtask
+   RemapMpasClimatologySubtask.setup_and_check
+   RemapMpasClimatologySubtask.run_task
+   RemapMpasClimatologySubtask.add_comparison_grid_descriptor
    RemapMpasClimatologySubtask.get_masked_file_name
    RemapMpasClimatologySubtask.get_remapped_file_name
+   RemapMpasClimatologySubtask.customize_masked_climatology
+   RemapMpasClimatologySubtask.customize_remapped_climatology
 
    RemapObservedClimatologySubtask
    RemapObservedClimatologySubtask.get_observation_descriptor

docs/index.rst

@@ -6,50 +6,49 @@
 MPAS-Analysis
 =============
 
-.. image:: _static/sst_example.png
+.. image:: users_guide/_static/sst_example.png
    :width: 300 px
    :align: center
 
 Analysis for simulations produced with Model for Prediction Across Scales
 (MPAS) components and the Energy Exascale Earth System Model (E3SM), which
 used those components.
 
-User's Guide
-============
 .. toctree::
+   :caption: User's guide
    :maxdepth: 2
 
-   quick_start
-   tutorials
-   configuration
-   analysis_tasks
-   components
-   observations
+   users_guide/quick_start
+   users_guide/configuration
+   users_guide/analysis_tasks
+   users_guide/components
+   users_guide/observations
 
-Developer's Guide
-=================
 .. toctree::
+   :caption: Developer's guide
    :maxdepth: 2
 
-   api
-   design_docs
+   developers_guide/api
 
-Indices and tables
-==================
+   design_docs/index
 
-* :ref:`genindex`
+.. toctree::
+   :caption: Tutorials
+   :maxdepth: 1
+
+   tutorials/getting_started
+   tutorials/dev_getting_started
+   tutorials/dev_understand_a_task
+   tutorials/dev_add_task
 
-Authors
-=======
 .. toctree::
+   :caption: Authors
    :maxdepth: 1
 
    authors
 
-Versions
-========
 .. toctree::
+   :caption: Versions
    :maxdepth: 1
 
    versions
-