Merge branch 'main' into rajeeja/zonal-mean-analytic-band

Author: rajeeja

.gitignore

@@ -141,6 +141,7 @@ test/dask-worker-space/
 /dask-worker-space/
 .vscode/
 generated/
+.ipynb_checkpoints/
 
 # Test grid files.
 test/meshfiles/*.g
@@ -150,9 +151,13 @@ test/write_*
 
 # Autogenerated docs
 docs/user_api/_autosummary/
-
 docs/notebook-examples.txt
-
+docs/*-examples-gallery.txt
+docs/user-guide/oQU120.data.nc
+docs/user-guide/oQU120.grid.nc
+docs/user-guide/oQU480.data.nc
+docs/user-guide/oQU480.grid.nc
+docs/user-guide/psi_healpix.nc
 
 # benchmarking
 benchmarks/env

docs/api.rst

@@ -176,8 +176,16 @@ Constructors
    UxDataArray.from_xarray
    UxDataArray.from_healpix
 
+Selection & Indexing
+~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: generated/
+
+   UxDataArray.isel
+
 Grid Accessor
-~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: generated/
@@ -200,13 +208,21 @@ Constructors
    UxDataset.from_healpix
 
 Grid Accessor
-~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: generated/
 
    UxDataset.uxgrid
 
+Selection & Indexing
+~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: generated/
+
+   UxDataset.isel
+
 
 Conversion Methods
 ------------------

docs/conf.py

@@ -61,6 +61,11 @@ def __getattr__(cls, name):
     "sphinx_copybutton",
 ]
 
+suppress_warnings = [
+    # mystnb doesn't recognize MIME type 'application/vnd.holoviews_load.v0+json'
+    # from the holoviews plots and otherwise spams the build with warnings
+    "mystnb.unknown_mime_type",
+]
 
 # nbsphinx_execute = "never"
 # jupyter_execute_notebooks = "off"
@@ -74,17 +79,18 @@ def __getattr__(cls, name):
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
-    "iris": ("https://scitools-iris.readthedocs.io/en/latest", None),
-    "numpy": ("https://numpy.org/doc/stable", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy", None),
-    "numba": ("https://numba.pydata.org/numba-doc/latest", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "iris": ("https://scitools-iris.readthedocs.io/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "numba": ("https://numba.readthedocs.io/en/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
-    "dask": ("https://docs.dask.org/en/latest", None),
-    "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),
+    "dask": ("https://docs.dask.org/en/stable/", None),
+    "cftime": ("https://unidata.github.io/cftime/", None),
+    "rasterio": ("https://rasterio.readthedocs.io/en/stable/", None),
+    "sparse": ("https://sparse.pydata.org/en/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    "cartopy": ("https://cartopy.readthedocs.io/stable/", None),
 }
 
 
@@ -136,7 +142,15 @@ def __getattr__(cls, name):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = [
+    "_build",
+    "**.ipynb_checkpoints",
+    # Not included (yet)
+    "examples/template.ipynb",
+    "user-guide/custom-grid.ipynb",
+    "user-guide/spatial-hashing.ipynb",
+    "user-guide/template.ipynb",
+]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
@@ -172,7 +186,7 @@ def __getattr__(cls, name):
     "use_repository_button": True,
     "use_issues_button": True,
     "home_page_in_toc": False,
-    "navbar_footer_text": "",
+    # "navbar_footer_text": "",
     # "extra_footer": "<p></p>",
     "logo": {
         "image_light": "_static/images/logos/uxarray_logo_h_dark.svg",

docs/contributing.rst

@@ -69,8 +69,9 @@ Some important UXarray resources are as follows:
 
 * `UXarray documentation <https://uxarray.readthedocs.io/>`_
   houses significant documentation such as :ref:`quickstart`, :ref:`installation`,
-  :ref:`contributing` (i.e. this document), :ref:`examples`, :ref:`tutorials`,
-  and :ref:`api`.
+  :ref:`contributing` (i.e. this document),
+  examples (:ref:`gallery` or :ref:`userguide`),
+  :ref:`tutorials`, and :ref:`api`.
 
 * `UXarray Milestones <https://github.com/UXARRAY/uxarray/milestones>`_ and
   `UXarray Roadmap <https://github.com/orgs/UXARRAY/projects/2/views/17>`_ shows
@@ -515,24 +516,24 @@ as follows:
   into your Conda environment for UXarray development).
 
 * Test scripts themselves are not intended to use ``pytest`` through implementation.
-Instead, ``pytest`` should be used only for running test scripts as follows::
+  Instead, ``pytest`` should be used only for running test scripts as follows::
 
     $ pytest test/<test_script_name>.py
 
-, or::
+  , or::
 
     $ python -m pytest test/<test_script_name>.py
 
-, the latter of which will also add the current directory to ``sys.path``.
+  , the latter of which will also add the current directory to ``sys.path``.
 
-Not using ``pytest`` for implementation allows the unit tests to be also run
-by using (a number of benefits/conveniences coming from using ``pytest`` can be
-seen `here <https://docs.pytest.org/en/7.1.x/how-to/unittest.html#how-to-use-unittest-based-tests-with-pytest>`_
-though)::
+  Not using ``pytest`` for implementation allows the unit tests to be also run
+  by using (a number of benefits/conveniences coming from using ``pytest`` can be
+  seen `here <https://docs.pytest.org/en/7.1.x/how-to/unittest.html#how-to-use-unittest-based-tests-with-pytest>`_
+  though)::
 
     $ python -m unittest test/<test_script_name>.py
 
-Also, all of the test scripts can be run at once with the following command::
+  Also, all of the test scripts can be run at once with the following command::
 
     $ pytest test
 
@@ -541,7 +542,7 @@ Also, all of the test scripts can be run at once with the following command::
   the test scripts.
 
 * Reference results (i.e. expected output or ground truth for not all but the most cases)
-should not be magic values (i.e. they need to be justified and/or documented).
+  should not be magic values (i.e. they need to be justified and/or documented).
 
 * Recommended, but not mandatory, implementation approach is as follows:
 
@@ -602,7 +603,7 @@ The docstrings must contain:
 ~~~~~~~~~~~~~~~~~~~~~~
 
 As we mentioned a few times throughout this guide, UXarray has a static `documentation
-<https://uxarray.readthedocs.io/>`_ :ref:`index` page that is being generated automatically from the
+<https://uxarray.readthedocs.io/>`_ page that is being generated automatically from the
 repository's code structure. However, there needs to be some manual additions to the
 proper documentation index file(s) for the automation to work.
 

docs/gallery.rst

@@ -1,8 +1,6 @@
 .. currentmodule:: uxarray
 
-.. _examples:
-
-.. math::
+.. _gallery:
 
 Gallery
 =======

docs/getting-started/quick-overview.ipynb

@@ -52,7 +52,7 @@
     "collapsed": false
    },
    "source": [
-    "## Opening a Dataset|"
+    "## Opening a Dataset"
    ]
   },
   {
@@ -322,7 +322,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
+   "pygments_lexer": "ipython3",
    "version": "2.7.6"
   }
  },

docs/index.rst

@@ -112,6 +112,7 @@ around the `UGRID <http://ugrid-conventions.github.io/ugrid-conventions/>`_ conv
     GitHub Discussions <https://github.com/UXARRAY/uxarray/discussions>
     GitHub Issues <https://github.com/UXARRAY/uxarray/issues>
     UGRID Conventions <https://ugrid-conventions.github.io/ugrid-conventions/>
+    contributing
 
 .. raw:: html
 

docs/user-guide/advanced-plotting.ipynb

@@ -48,7 +48,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
+   "pygments_lexer": "ipython3",
    "version": "2.7.6"
   }
  },

docs/user-guide/area_calc.ipynb

@@ -1843,7 +1843,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 7. Demonstrate the Need for Area Correction During Zonal Averaging Calculations Etc.\n",
+    "## 7. Demonstrate the Need for Area Correction During Zonal Averaging Calculations Etc.\n",
     "\n",
     "When performing zonal averaging, it is common practice to calculate the intersection of faces with lines of constant latitude and longitude. \n",
     "\n",

docs/user-guide/data-structures.ipynb

@@ -410,7 +410,7 @@
     "\n",
     "The `UxDataset` class is used for pairing one or more data variables with an unstructured grid. It operates similarly to a `xarrary.Dataset`, with the addition of unstructured-grid specific functionality and is linked to an instance of a `Grid`.\n",
     "\n",
-    "```{info}\n",
+    "```{tip}\n",
     "More information about `xarray.Dataset` can be found [here](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html).\n",
     "```\n"
    ]
@@ -544,7 +544,7 @@
     "\n",
     "While a `UxDataset` represents one or more data variables linked to some unstructured grid, a `UxDataArray` represent a single data variable. Alternatively, one can think of a `UxDataset` as a collection of one or more `UxDataArray` instances.\n",
     "\n",
-    "```{info}\n",
+    "```{tip}\n",
     "More information about `xarray.DataArray` can be found [here](https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html).\n",
     "```\n",
     "\n",