Add user documentation

.gitignore

@@ -18,6 +18,7 @@ coverage.xml
 .tox
 
 docs/_build
+docs/generated
 
 # ide
 .idea

CHANGELOG.md

@@ -6,6 +6,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## Unreleased
 
+Added:
+ - Documentation for the package, including readthedocs integration ([#40](https://github.com/EXCITED-CO2/xarray-regrid/pull/40)).
 
 ## v0.2.3 (2024-02-29)
 

docs/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = xarray-regrid
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/changelog_link.rst

@@ -0,0 +1,2 @@
+.. include:: ../CHANGELOG.md
+   :parser: myst_parser.sphinx_

docs/conf.py

@@ -0,0 +1,115 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+#
+
+import datetime
+from importlib.metadata import version as get_version
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# General information about the project.
+project = "xarray-regrid"
+current_year = datetime.datetime.now().year
+copyright = f"2023-{current_year}, Bart Schilperoort"
+author = "Bart Schilperoort"
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+# The short X.Y version.
+version = get_version("xarray_regrid").split("+")[0]
+# The full version, including alpha/beta/rc tags.
+release = get_version("xarray_regrid")
+
+# -- General configuration ------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "autoapi.extension",
+    #"myst_parser",
+    "myst_nb",
+]
+
+extlinks = {
+    "issue": ("https://github.com/excited-CO2/xarray-regrid/issues/%s", "GH#%s"),
+    "pr": ("https://github.com/excited-CO2/xarray-regrid/pull/%s", "PR#%s"),
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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", "data"]
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+# Myst_nb options
+nb_execution_mode = "off"
+
+# -- Use autoapi.extension to run sphinx-apidoc -------
+
+autoapi_dirs = ["../src"]
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    "**": [
+        "globaltoc.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
+
+html_logo = "./assets/logo.png"
+
+# -- Options for Intersphinx
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+}

docs/getting_started.rst

@@ -0,0 +1,38 @@
+Quickstart
+==========
+
+``xarray-regrid`` allows you to regrid xarray Datasets or DataArrays to a new resolution.
+You can install xarray-regrid with pip:
+
+.. code:: shell
+
+   pip install xarray-regrid
+
+
+To use the package, import ``xarray_regrid``. This will register the ``.regrid`` 'accessor' so it can be used.
+Next load in the data you want to regrid, and the data with a grid you want to regrid to:
+
+.. code:: python
+
+    import xarray_regrid
+    import xarray
+
+    ds = xr.open_dataset("input_data.nc")
+    ds_grid = xr.open_dataset("target_grid.nc")
+
+    ds = ds.regrid.linear(ds_grid)
+
+    # or, for example:
+    ds = ds.regrid.conservative(ds_grid, latitude_coord="lat")
+
+
+Multiple regridding methods are available:
+
+* `linear interpolation <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.linear>`_ (``.regrid.linear``)
+* `nearest-neighbor <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.conservative>`_ (``.regrid.nearest``)
+* `cubic interpolation  <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.cubic>`_ (``.regrid.cubic``)
+* `conservative regridding <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.conservative>`_ (``.regrid.conservative``)
+
+Additionally, a zonal statistics `method to compute the most common value <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.most_common>`_
+is available (``.regrid.most_common``).
+This can be used to upscale very fine categorical data to a more course resolution.

docs/index.rst

@@ -0,0 +1,65 @@
+.. toctree::
+  :maxdepth: 3
+  :hidden:
+
+  self
+
+
+.. toctree::
+  :maxdepth: 3
+  :caption: User Guide
+  :hidden:
+
+  Quickstart <getting_started>
+  Example Notebooks <notebooks/index>
+
+
+.. toctree::
+  :maxdepth: 3
+  :caption: Technical information
+  :hidden:
+
+  Changelog <changelog_link>
+
+xarray-regrid: Regridding utilities for xarray
+**********************************************
+
+|PyPI| |DOI|
+
+Overview
+========
+
+``xarray-regrid`` extends xarray with regridding methods, making it possibly to easily and effiently regrid between two rectilinear grids. 
+
+The following methods are supported:
+
+* `Linear <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.linear>`_
+* `Nearest-neighbor <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.nearest>`_
+* `Conservative <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.conservative>`_
+* `Cubic <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.cubic>`_
+* `"Most common value" (zonal statistics) <autoapi/xarray_regrid/regrid/index.html#xarray_regrid.regrid.Regridder.most_common>`_
+
+Note that "Most common value" is designed to regrid categorical data to a coarse resolution. For regridding categorical data to a finer resolution, please use "nearest-neighbor" regridder.
+
+For usage examples, please refer to the `quickstart guide <getting_started>`_ and the `example notebooks <notebooks/index>`_.
+
+Installing
+==========
+
+.. code:: shell
+
+   pip install xarray-regrid
+
+
+Acknowledgements
+================
+
+This package was developed under Netherlands eScience Center grant `NLESC.OEC.2022.017 <https://research-software-directory.org/projects/excited>`_.
+
+Some methods were inspired by discussions in the `Pangeo <https://pangeo.io>`_ community.
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/xarray-regrid.svg?style=flat
+   :target: https://pypi.python.org/pypi/xarray-regrid/
+
+.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10203304.svg
+   :target: https://doi.org/10.5281/zenodo.10203304

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=xarray-regrid
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/notebooks/index.rst

@@ -0,0 +1,21 @@
+
+Example Notebooks
+~~~~~~~~~~~~~~~~~
+
+To benchmark the library against some more standard tools, we have created some notebooks.
+
+Most notebooks compare the methods implemented in xarray-regrid against more standard tools (CDO, ESMF).
+
+.. toctree::
+  :maxdepth: 1
+  :caption: Benchmarks
+
+  benchmarks/benchmarking_bilinear.ipynb
+  benchmarks/benchmarking_conservative.ipynb
+  benchmarks/benchmarking_nearest.ipynb
+
+.. toctree::
+  :maxdepth: 1
+  :caption: Demos
+
+  demos/demo_most_common.ipynb

pyproject.toml

@@ -49,11 +49,20 @@ dev = [
   "mypy",
   "pytest",
   "pytest-cov",
+  "cftime",  # required for decode time of test netCDF files
   "pandas-stubs", # Adds typing for pandas.
 ]
+docs = [  # Required for ReadTheDocs
+  "myst_parser",
+  "sphinx",
+  "myst-nb",
+  "sphinx_rtd_theme",
+  "sphinx-autoapi",
+  "coverage[toml]",
+]
 
 [tool.hatch.version]
-path = "src/xarray_regrid/__about__.py"
+path = "src/xarray_regrid/__init__.py"
 
 [tool.hatch.envs.default]
 features = ["dev", "benchmarking"]
@@ -70,9 +79,18 @@ coverage = [
   "pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/",
 ]
 
+[tool.hatch.envs.docs]
+features = ["docs"]
+
+[tool.hatch.envs.docs.scripts]
+build = ["(cd docs && make html)"]
+
 [tool.ruff]
 target-version = "py310"
 line-length = 88
+exclude = [
+  "docs",
+]
 
 [tool.ruff.lint]
 select = [
@@ -158,3 +176,4 @@ check_untyped_defs = true
 warn_return_any = true
 warn_unused_ignores = true
 show_error_codes = true
+exclude = ["tests/*", "docs"]

src/xarray_regrid/__init__.py

@@ -8,3 +8,5 @@
     "create_regridding_dataset",
     "methods",
 ]
+
+__version__ = "0.2.3"

src/xarray_regrid/methods/__init__.py

@@ -0,0 +1,3 @@
+"""Implementation of the regridding methods."""
+# Note: this file is only required due to sphinx autoapi
+#  https://github.com/readthedocs/sphinx-autoapi/issues/298