Merge branch 'UXARRAY:main' into main

hongyuchen1030 · Feb 13, 2024 · e5aab20 · e5aab20
2 parents 7738774 + a756811
commit e5aab20
Show file tree

Hide file tree

Showing 68 changed files with 5,425 additions and 2,516 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -18,25 +18,41 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ "ubuntu-latest", "macos-latest", "windows-latest"]
+        os: [ "ubuntu-latest", "macos-latest", "macos-14", "windows-latest"]
         python-version: [ "3.9", "3.10", "3.11"]
     steps:
       - name: Cancel previous runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
+
       - name: checkout
         uses: actions/checkout@v4
         with:
           token: ${{ github.token }}
-      - name: conda_setup
+
+      - name: conda_setup (x64)
+        uses: conda-incubator/setup-miniconda@v3
+        if: matrix.os != 'macos-14'
+        with:
+          activate-environment: uxarray_build
+          channel-priority: strict
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          environment-file: ci/environment.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+
+      - name: conda_setup (ARM64)
         uses: conda-incubator/setup-miniconda@v3
+        if: matrix.os == 'macos-14'
         with:
           activate-environment: uxarray_build
           channel-priority: strict
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
           environment-file: ci/environment.yml
+          installer-url: https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-MacOSX-arm64.sh
 
       - name: Install uxarray
         run: |
@@ -55,7 +71,7 @@ jobs:
           python -m pytest test -v --cov=./uxarray --cov-report=xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.0.1
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -12,4 +12,4 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: actions/[email protected]
-      - uses: pre-commit/[email protected].0
+      - uses: pre-commit/[email protected].1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,4 @@
 repos:
--   repo: https://github.com/pre-commit/mirrors-yapf    # To format the code to conform YAPF
-    rev: v0.31.0
-    hooks:
-      - id: yapf
-        args: ['--in-place', '--recursive', '--style', 'google']
-
 -   repo: https://github.com/myint/docformatter    # To format the doc strings to conform PEP257
     rev: v1.4
     hooks:
@@ -20,3 +14,16 @@ repos:
     - id: end-of-file-fixer        # Makes sure files end with a newline.
     - id: trailing-whitespace      # Checks for any tabs or spaces after the last non-whitespace character on the line.
     - id: check-docstring-first    # Checks that code comes after the docstrings.
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+      exclude: ".test"
+
+    # Run the formatter.
+    - id: ruff-format
+      exclude: ".test"
diff --git a/README.md b/README.md
@@ -1,9 +1,8 @@
 
 
 
-<img src='https://raw.githubusercontent.com/UXARRAY/uxarray/a2d893cf597dd1a6e775f9dad029c662c64a39c7/docs/_static/images/logos/uxarray_logo_quad_tri.svg' width='400'>
+[comment]: <> (<img src='https://raw.githubusercontent.com/UXARRAY/uxarray/a2d893cf597dd1a6e775f9dad029c662c64a39c7/docs/_static/images/logos/uxarray_logo_quad_tri.svg' width='400'>)
 
----
 
 
 
@@ -20,8 +19,8 @@ UXarray aims to address the geoscience community's need for tools that enable
 standard data analysis techniques to operate directly on unstructured grid
 data. UXarray provides Xarray-styled functionality to better read in and use
 unstructured grid datasets that follow standard conventions, including UGRID,
-MPAS, SCRIP, and Exodus formats. This effort is a result of the
-collaboration between Project Raijin (NCAR and Pennsylvania State University)
+MPAS, SCRIP, ESMF, and Exodus grid formats. This effort is a result of the
+collaboration between Project Raijin (NSF NCAR and Pennsylvania State University)
 and the SEATS Project (Argonne National Laboratory, UC Davis, and Lawrence
 Livermore National Laboratory). The UXarray team welcomes community
 members to become part of this collaboration at any level of contribution.
@@ -51,7 +50,7 @@ is receptive to additional functionality requests.
 
 ## Intended Functionality for Grids
 
-* Support for reading and writing UGRID, SCRIP and Exodus formatted grids.
+* Support for reading and writing UGRID, SCRIP ESMF, and Exodus formatted grids.
 * Support for reading and writing shapefiles.
 * Support for arbitrary structured and unstructured grids on the sphere,
   including latitude-longitude grids, grids with only partial coverage of

diff --git a/ci/docs.yml b/ci/docs.yml
@@ -19,6 +19,7 @@ dependencies:
     - jupyter_client
     - scikit-learn
     - sphinx-book-theme
+    - sphinx-autosummary-accessors
     - myst-nb
     - sphinx-design
     - nbsphinx
@@ -30,7 +31,7 @@ dependencies:
     - cartopy
     - pandas<2.1.0
     - geocat-datafiles
+    - spatialpandas
     - pip:
       - antimeridian
       - pyfma
-      - git+https://github.com/holoviz/spatialpandas.git
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -21,8 +21,8 @@ dependencies:
   - scikit-learn
   - scipy
   - shapely
+  - spatialpandas
   - xarray
   - pip:
     - antimeridian
     - pyfma
-    - git+https://github.com/holoviz/spatialpandas.git
diff --git a/ci/install-upstream.sh b/ci/install-upstream.sh
@@ -16,7 +16,7 @@ conda remove -y --force \
     shapely \
     xarray
 
-python -m pip uninstall \
+pip uninstall -y \
     antimeridian \
     spatialpandas
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -10,13 +10,17 @@
 import pathlib
 import yaml
 from sphinx.application import Sphinx
+import sphinx_autosummary_accessors
 from sphinx.util import logging
 from textwrap import dedent, indent
-
-sys.path.insert(0,
-                os.path.abspath('../'))  # Source code dir relative to this file
+import datetime
 
 import uxarray
+import matplotlib.pyplot
+
+__all__ = (uxarray, matplotlib.pyplot)
+
+sys.path.insert(0, os.path.abspath("../"))  # Source code dir relative to this file
 
 LOGGER = logging.getLogger("conf")
 
@@ -25,11 +29,8 @@
 except ImportError:
     from mock import Mock as MagicMock
 
-import matplotlib.pyplot
-
 
 class Mock(MagicMock):
-
     @classmethod
     def __getattr__(cls, name):
         return MagicMock()
@@ -44,48 +45,34 @@ def __getattr__(cls, name):
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'myst_nb',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx_autosummary_accessors",
+    "myst_nb",
     "sphinx_design",
     "nbsphinx",
 ]
 
 mathjax_config = {
-    'tex2jax': {
-        'inlineMath': [['$', '$'], ['\\(', '\\)']],
-        'displayMath': [['$$', '$$'], ['\\[', '\\]']],
-        'processEscapes': True,
-    },
-    'HTML-CSS': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        },
-        'fonts': {
-            'availableFonts': ['TeX'],
-            'preferredFont': 'TeX',
-            'webFont': 'TeX'
-        }
+    "tex2jax": {
+        "inlineMath": [["$", "$"], ["\\(", "\\)"]],
+        "displayMath": [["$$", "$$"], ["\\[", "\\]"]],
+        "processEscapes": True,
     },
-    'CommonHTML': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        }
+    "HTML-CSS": {
+        "linebreaks": {"automatic": True, "width": "container"},
+        "fonts": {"availableFonts": ["TeX"], "preferredFont": "TeX", "webFont": "TeX"},
     },
-    'SVG': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        }
-    }
+    "CommonHTML": {"linebreaks": {"automatic": True, "width": "container"}},
+    "SVG": {"linebreaks": {"automatic": True, "width": "container"}},
 }
 
-mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+mathjax_path = (
+    "https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+)
 
 extlinks = {
     "issue": ("https://github.com/uxarray/uxarray/issues/%s", "GH"),
@@ -104,7 +91,7 @@ def __getattr__(cls, name):
     "cftime": ("https://unidata.github.io/cftime", None),
     "rasterio": ("https://rasterio.readthedocs.io/en/latest", None),
     "sparse": ("https://sparse.pydata.org/en/latest/", None),
-    'xarray': ('http://xarray.pydata.org/en/stable/', None),
+    "xarray": ("http://xarray.pydata.org/en/stable/", None),
 }
 
 napoleon_use_admonition_for_examples = True
@@ -113,36 +100,34 @@ def __getattr__(cls, name):
 autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates", sphinx_autosummary_accessors.templates_path]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 # source_suffix = ['.rst', '.md']
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.ipynb': 'myst-nb',
-    '.myst': 'myst-nb',
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
 }
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'uxarray'
-
-import datetime
+project = "uxarray"
 
 current_year = datetime.datetime.now().year
-copyright = u'{}, Uxarray'.format(current_year)
-author = u'UXARRAY'
+copyright = "{}, Uxarray".format(current_year)
+author = "UXARRAY"
 
 
 # The version info for the project being documented
 def read_version():
-    for line in open('../meta.yaml').readlines():
-        index = line.find('set version')
+    for line in open("../meta.yaml").readlines():
+        index = line.find("set version")
         if index > -1:
-            return line[index + 15:].replace('\" %}', '').strip()
+            return line[index + 15 :].replace('" %}', "").strip()
 
 
 # The short X.Y version.
@@ -163,7 +148,7 @@ def read_version():
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -199,7 +184,7 @@ def read_version():
     use_issues_button=True,
     home_page_in_toc=False,
     navbar_footer_text="",
-    #extra_footer="""<p></p>""",
+    # extra_footer="""<p></p>""",
 )
 
 # The name for this set of Sphinx documents.
@@ -208,23 +193,23 @@ def read_version():
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '_static/images/logos/uxarray_temp_logo.png'
+html_logo = "_static/images/logos/uxarray_temp_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = '_static/images/logos/uxarray_temp_logo.png'
+html_favicon = "_static/images/logos/uxarray_temp_logo.png"
 
 # 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"]
 html_css_files = ["style.css"]
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'uxarraydoc'
+htmlhelp_basename = "uxarraydoc"
 
-autodoc_typehints = 'none'
+autodoc_typehints = "none"
 
 
 # custom scripts for making a gallery of examples notebooks
@@ -233,8 +218,7 @@ def update_gallery(app: Sphinx):
 
     LOGGER.info("creating gallery...")
 
-    notebooks = yaml.safe_load(
-        pathlib.Path(app.srcdir, "gallery.yml").read_bytes())
+    notebooks = yaml.safe_load(pathlib.Path(app.srcdir, "gallery.yml").read_bytes())
 
     items = [
         f"""
@@ -246,7 +230,8 @@ def update_gallery(app: Sphinx):
                 :alt: {item['title']}
             +++
             {item['title']}
-            """ for item in notebooks
+            """
+        for item in notebooks
     ]
 
     items_md = indent(dedent("\n".join(items)), prefix="    ")
@@ -264,5 +249,5 @@ def update_gallery(app: Sphinx):
 
 # Allow for changes to be made to the css in the theme_overrides file
 def setup(app):
-    app.add_css_file('theme_overrides.css')
+    app.add_css_file("theme_overrides.css")
     app.connect("builder-inited", update_gallery)
diff --git a/docs/index.rst b/docs/index.rst
@@ -9,9 +9,9 @@
    :description: Uxarray Python module
    :keywords: weather research and forecasting,
               model, weather, numerical weather prediction, model,
-              matplotlib, cartopy, ncar, ucar, cisl, UC Davis, SEATs, ugrid,
-              national center for atmospheric research,
-              university corporation for atmospheric research
+              matplotlib, cartopy, nsf ncar, ucar, cisl, UC Davis, SEATS, ugrid,
+              nsf national center for atmospheric research, university
+              corporation for atmospheric research
 
 
 .. .. image:: _static/images/nsf.png