Add initial documentation

.github/workflows/readthedocs.yml

@@ -0,0 +1,22 @@
+# .github/workflows/documentation-links.yml
+
+name: readthedocs/actions
+on:
+  pull_request_target:
+    types:
+      - opened
+    # Execute this action only on PRs that touch
+    # documentation files.
+    # paths:
+    #   - "doc/**"
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "xarray-ms"

.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_install:
+      - pip install poetry==1.8.3
+      - poetry config virtualenvs.create false
+      - poetry install --with docs
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py

README.rst

@@ -0,0 +1,116 @@
+xarray-ms
+=========
+
+xarray-ms presents a Measurement Set v4 view (MSv4) over
+`CASA Measurement Sets <https://casa.nrao.edu/Memos/229.html>`_ (MSv2).
+It provides access to MSv2 data via the xarray API, allowing MSv4 compliant applications
+to be developed on well-understood MSv2 data.
+
+.. code-block:: python
+
+  >>> import xarray_ms
+  >>> import xarray
+  >>> ds = xarray.open_dataset("/data/L795830_SB001_uv.MS/",
+                               chunks={"time": 2000, "baseline": 1000})
+  >>> ds
+    <xarray.Dataset> Size: 70GB
+    Dimensions:                     (time: 28760, baseline: 2775, frequency: 16,
+                                    polarization: 4, uvw_label: 3)
+    Coordinates:
+        antenna1_name               (baseline) object 22kB dask.array<chunksize=(1000,), meta=np.ndarray>
+        antenna2_name               (baseline) object 22kB dask.array<chunksize=(1000,), meta=np.ndarray>
+        baseline_id                 (baseline) int64 22kB dask.array<chunksize=(1000,), meta=np.ndarray>
+      * frequency                   (frequency) float64 128B 1.202e+08 ... 1.204e+08
+      * polarization                (polarization) <U2 32B 'XX' 'XY' 'YX' 'YY'
+      * time                        (time) float64 230kB 1.601e+09 ... 1.601e+09
+    Dimensions without coordinates: baseline, uvw_label
+    Data variables:
+        EFFECTIVE_INTEGRATION_TIME  (time, baseline) float64 638MB dask.array<chunksize=(2000, 1000), meta=np.ndarray>
+        FLAG                        (time, baseline, frequency, polarization) uint8 5GB dask.array<chunksize=(2000, 1000, 16, 4), meta=np.ndarray>
+        TIME_CENTROID               (time, baseline) float64 638MB dask.array<chunksize=(2000, 1000), meta=np.ndarray>
+        UVW                         (time, baseline, uvw_label) float64 2GB dask.array<chunksize=(2000, 1000, 3), meta=np.ndarray>
+        VISIBILITY                  (time, baseline, frequency, polarization) complex64 41GB dask.array<chunksize=(2000, 1000, 16, 4), meta=np.ndarray>
+        WEIGHT                      (time, baseline, frequency, polarization) float32 20GB dask.array<chunksize=(2000, 1000, 16, 4), meta=np.ndarray>
+    Attributes:
+        antenna_xds:          <xarray.Dataset> Size: 4kB\nDimensions:           (...
+        version:              0.0.1
+        creation_date:        2024-09-10T14:29:22.587984+00:00
+        data_description_id:  0
+
+Measurement Set v4
+------------------
+
+NRAO_/SKAO_ are developing a new xarray-based `Measurement Set v4 specification <msv4-spec_>`_.
+While there are many changes some of the major highlights are:
+
+* xarray_ is used to define the specification.
+* MSv4 data consists of Datasets of ndarrays on a regular time-channel grid.
+  MSv2 data is tabular and, while in many instances the time-channel grid is regular,
+  this was not guaranteed, especially after MSv2 datasets had been transformed by various tasks.
+
+
+xarray_ Datasets are self-describing and they are therefore easier to reason about and work with.
+Additionally, the regularity of data will make writing MSv4-based software less complex.
+
+xradio
+------
+
+`casangi/xradio <xradio_>`_ provides a reference implementation that converts
+CASA v2 Measurement Sets to Zarr v4 Measurement Sets using the python-casacore_
+package.
+
+Why xarray-ms?
+--------------
+
+* By developing against an MSv4 xarray view over MSv2 data,
+  developers can develop applications on well-understood data,
+  and then seamlessly transition to newer formats.
+  Data can also be exported to newer formats (principally zarr_) via xarray's
+  native I/O routines.
+  However, the xarray view of either format looks the same to the software developer.
+
+* xarray-ms builds on xarray's
+  `backend API <https://docs.xarray.dev/en/stable/internals/how-to-add-new-backend.html>`_:
+  Implementing a formal CASA MSv2 backend has a number of automatically benefits:
+
+  * Use of xarray's internal I/O routines such as ``open_dataset`` or ``to_zarr``.
+  * Use of xarray's `lazy loading mechanism <xarray_lazy_>`_.
+  * Automatic access to any `chunked array types <xarray_chunked_arrays_>`_
+    supported by xarray including, but not limited to dask_.
+  * Arbitrary chunking along any xarray dimension.
+
+* xarray-ms uses arcae_, a high-performance backend to CASA Tables implementing
+  a subset of python-casacore_'s interface.
+* Some limited support for irregular MSv2 data via padding.
+
+Work in Progress
+----------------
+
+.. warning::
+
+  xarray-ms is currently under active development and does not yet
+  have feature parity with xradio_.
+
+.. warning::
+
+  The Measurement Set v4 specification is currently under active development.
+
+Most measures information and many secondary sub-tables are currently missing.
+However, the most important parts of the ``MAIN`` tables,
+as well as the ``ANTENNA``, ``POLARIZATON`` and ``SPECTRAL_WINDOW``
+sub-tables are implemented and should be sufficient to start
+developing software that uses xarray-ms.
+
+.. _SKAO: https://www.skao.int/
+.. _NRAO: https://public.nrao.edu/
+.. _msv4-spec: https://docs.google.com/spreadsheets/d/14a6qMap9M5r_vjpLnaBKxsR9TF4azN5LVdOxLacOX-s/
+.. _xradio: https://github.com/casangi/xradio
+.. _dask-ms: https://github.com/ratt-ru/dask-ms
+.. _arcae: https://github.com/ratt-ru/arcae
+.. _dask: https://www.dask.org/
+.. _python-casacore: https://github.com/casacore/python-casacore/
+.. _xarray: https://github.com/pydata/xarray
+.. _xarray_backend: https://docs.xarray.dev/en/stable/internals/how-to-add-new-backend.html
+.. _xarray_lazy: https://docs.xarray.dev/en/latest/internals/internal-design.html#lazy-indexing-classes
+.. _xarray_chunked_arrays: https://docs.xarray.dev/en/latest/internals/chunked-arrays.html
+.. _zarr: https://zarr.dev/

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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)

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/source/api.rst

@@ -0,0 +1,8 @@
+API
+===
+
+Opening Measurement Sets
+------------------------
+
+.. autoclass:: xarray_ms.backend.msv2.entrypoint.MSv2PartitionEntryPoint
+    :members: open_dataset, open_datatree

doc/source/conf.py

@@ -0,0 +1,65 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+# type: ignore
+
+project = "xarray-ms"
+copyright = "2024, Simon Perkins"
+author = "Simon Perkins"
+release = "0.2.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+  "sphinx.ext.autodoc",
+  "sphinx.ext.autosummary",
+  "sphinx.ext.extlinks",
+  "sphinx_copybutton",
+  "sphinx.ext.doctest",
+  "sphinx.ext.napoleon",
+  "sphinx.ext.intersphinx",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_preprocess_types = False
+napoleon_type_aliases = None
+napoleon_attr_annotations = True
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+
+extlinks = {
+  "issue": ("https://github.com/ratt-ru/xarray-ms/issues/%s", "GH#"),
+  "pr": ("https://github.com/ratt-ru/xarray-ms/pull/%s", "GH#"),
+}
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+  "dask": ("https://dask.pydata.org/en/stable", None),
+  "numpy": ("https://numpy.org/doc/stable/", None),
+  "python": ("https://docs.python.org/3/", None),
+  "xarray": ("https://docs.xarray.dev/en/stable", None),
+}

doc/source/index.rst

@@ -0,0 +1,20 @@
+.. xarray-ms documentation master file, created by
+   sphinx-quickstart on Tue Sep 10 10:36:27 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+xarray-ms documentation
+=======================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   install
+   api

doc/source/install.rst

@@ -0,0 +1,59 @@
+Installation
+============
+
+.. code-block:: bash
+
+    $ pip install xarray-ms
+
+Development
+===========
+
+Firstly, install Python `Poetry <poetry_>`_.
+
+.. _poetry: https://python-poetry.org/
+
+Then, the following commands will install the required dependencies,
+optional testing dependencies, documentation and development dependencies
+in a suitable virtual environment:
+
+.. code-block:: bash
+
+  $ cd /code/arcae
+  $ poetry env use 3.11
+  $ poetry install -E testing --with doc --with dev
+  $ poetry run pre-commit install
+  $ poetry shell
+
+The pre-commit hooks can be manually executed as follows:
+
+.. code-block:: bash
+
+  $ poetry run pre-commit run -a
+
+
+Test Suite
+----------
+
+Run the following command within the arcae source code directory to
+execute the test suite
+
+.. code-block:: bash
+
+  $ cd /code/arcae
+  $ poetry install -E testing --with dev
+  $ poetry run py.test -s -vvv tests/
+
+
+Documentation
+-------------
+
+Run the following command within the doc sub-directory to
+build the Sphinx documentation
+
+.. code-block:: bash
+
+  $ cd /code/arcae
+  $ poetry install --with doc
+  $ poetry shell
+  $ cd doc
+  $ make html

doc/source/readme.rst

@@ -0,0 +1 @@
+.. include:: ../../README.rst

pyproject.toml

@@ -21,6 +21,21 @@ testing = ["dask", "distributed", "pytest"]
 [tool.poetry.plugins."xarray.backends"]
 "xarray-ms:msv2" = "xarray_ms.backend.msv2.entrypoint:MSv2PartitionEntryPoint"
 
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pre-commit = "^3.8.0"
+
+[tool.poetry.group.doc]
+optional = true
+
+[tool.poetry.group.doc.dependencies]
+sphinx = "^8.0.2"
+pygments = "^2.18.0"
+sphinx-copybutton = "^0.5.2"
+pydata-sphinx-theme = "^0.15.4"
+
 [tool.ruff]
 line-length = 88
 indent-width = 2