Merge remote-tracking branch 'origin/main' into 355-zarr-python-v3-and-zarr-v3

Author: FedeMPouzols

.github/workflows/python-testing-basic-schema-install.yml

@@ -0,0 +1,31 @@
+name: "Tests schemas are importable on a basic xradio install"
+
+on:
+  push:
+    paths-ignore:
+      - '**.md'
+      - '**.rst'
+  pull_request:
+    paths-ignore:
+      - '**.md'
+      - '**.rst'
+
+jobs:
+  test_schema:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.13
+
+    - name: Install base xradio
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Test that schemas are importable
+      run: python -c "import xradio.measurement_set; import xradio.schema.check"

.github/workflows/python-testing-linux.yml

@@ -17,4 +17,5 @@ jobs:
     with:
       cov_project: "xradio"
       test-path: "tests/"
-    secrets: inherit
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -16,7 +16,7 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - python-casacore
+        - casacore
 
 # Configuration for Sphinx documentation
 sphinx:

README.md

@@ -8,6 +8,7 @@ Xarray Radio Astronomy Data IO is still in development.
 [![Coverage](https://codecov.io/gh/casangi/xradio/branch/main/graph/badge.svg)](https://codecov.io/gh/casangi/xradio/branch/main/xradio)
 [![Documentation Status](https://readthedocs.org/projects/xradio/badge/?version=latest)](https://xradio.readthedocs.io)
 [![Version Status](https://img.shields.io/pypi/v/xradio.svg)](https://pypi.python.org/pypi/xradio/)
+[![Benchmarks](https://img.shields.io/badge/Benchmarks-Tests-orange)](https://casangi.github.io/benchviper/xradio)
 
 # Installing
 XRADIO can be installed in virtual environments via pip. It is recommended to use the conda environment manager from [miniforge](https://github.com/conda-forge/miniforge) to create a clean, self-contained runtime where XRADIO and all its dependencies can be installed, for example:

docs/source/conf.py

@@ -91,6 +91,11 @@
 
 nitpicky = True
 
+# Ignore nitpicky warnings related to Python built-ins and the like
+# (https://stackoverflow.com/questions/11417221/sphinx-autodoc-gives-warning-pyclass-reference-target-not-found-type-warning)
+# (https://bugs.python.org/issue11975)
+nitpick_ignore = [("py:class", "optional")]
+
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "astropy": ("https://docs.astropy.org/en/stable", None),

docs/source/image_data/tutorials/image_schema_proposal.ipynb

@@ -33,23 +33,28 @@
     "    - Add types to all data variables and dataset.\n",
     "\n",
     "## Image Types\n",
-    "    sky\n",
-    "    flag\n",
-    "    point_spread_function\n",
-    "    primary_beam\n",
-    "    mask\n",
-    "    beam_fit_params_sky\n",
-    "    beam_fit_params_point_spread_function\n",
-    "    visibility_normalization\n",
-    "    description:\n",
-    "    date:\n",
+    "    sky: Image of the sky.\n",
+    "    flag: A boolean image defining any invalid pixels.\n",
+    "    point_spread_function: The instrumental response or \"dirty beam.\" Represents how a point source would appear given the uv-coverage and weighting scheme. Used by deconvolution algorithms to model and remove sidelobe artifacts. Determines the resolution of the image. Should be unity at the peak.\n",
+    "    primary_beam : The effective antenna power pattern projected onto the sky, describing how sensitivity falls off from the pointing center. Values range from 1.0 at center to ~0 at the edges. \n",
+    "    mask : A boolean image defining the region(s) where the deconvolution algorithm is allowed to place clean components. \n",
+    "    beam_fit_params_sky: The Gaussian fit of the resolution element. Note that this would be the same as the beam_fit_params_point_spread_function except when the sky image is convolved to a common beam.\n",
+    "    beam_fit_params_point_spread_function: The Gaussian fit to the peak of the point_spread_function.\n",
+    "    visibility_normalization: The aggregate of the image weights and used to normalize the gridded visibilities.\n",
+    "    description: String description.\n",
+    "    date: Date created.\n",
     "\n",
-    "    visibility*\n",
-    "    visibility_normalization*\n",
-    "    uv_sampling*\n",
-    "    uv_sampling_normalization*\n",
-    "    aperture*\n",
-    "    aperture_normalization*\n",
+    "    visibility* : Gridded Visibilities\n",
+    "    uv_sampling* : Gridded Weights\n",
+    "    uv_sampling_normalization* : Normalization used by uv_sampling.\n",
+    "    aperture* : Gridded weighted apertures. Used to calculate the primary_beam.\n",
+    "    aperture_normalization* : Normalization used by aperture.\n",
+    "\n",
+    "\n",
+    "Examples of sky (each would be its own data group):\n",
+    "SKY_DECONVOLVED\n",
+    "SKY_MODEL\n",
+    "SKY_RESIDUAL\n",
     "\n",
     "* UV plain. Only used internally and for debugging.\n",
     "    "

docs/source/measurement_set/schema.rst

@@ -264,10 +264,13 @@ Value Keys
 Scan Intents
 ~~~~~~~~~~~~
 
-Scan intents to be used with :py:class:`~xradio.measurement_set.schema.VisibilityXds` and
-:py:class:`~xradio.measurement_set.schema.SpectrumXds`,
-in the ``intents`` field of the
-:py:class:`~xradio.measurement_set.schema.ObservationInfoDict`:
+Scan intents to be used with
+:py:class:`~xradio.measurement_set.schema.VisibilityXds` and
+:py:class:`~xradio.measurement_set.schema.SpectrumXds`, in the
+``scan_intents`` field of the
+:py:class:`~xradio.measurement_set.schema.ScanArray`.  The format to
+be used is ``[intent]#[subintent]``, where the possible values for
+``[intent]`` are:
 
 * ``CALIBRATE AMPLI`` : Amplitude calibration scan
 * ``CALIBRATE ANTENNA PHASE`` : Requested by EVLA.
@@ -300,10 +303,7 @@ in the ``intents`` field of the
 * ``TEST`` : used for development.
 * ``UNSPECIFIED`` : Unspecified scan intent
 
-Sub-scan intents to be used with :py:class:`~xradio.measurement_set.schema.VisibilityXds` and
-:py:class:`~xradio.measurement_set.schema.SpectrumXds`,
-in the ``intents`` field of the
-:py:class:`~xradio.measurement_set.schema.ObservationInfoDict`:
+Possible values for ``[subintent]``:
 
 * ``ON SOURCE`` : on-source measurement
 * ``OFF SOURCE`` : off-source measurement

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xradio"
-version = "v1.1.1"
+version = "v1.1.3"
 description = " Xarray Radio Astronomy Data IO"
 authors = [
     {name = "Jan-Willem Steeb", email="jsteeb@nrao.edu"},

src/xradio/__init__.py

@@ -1,14 +0,0 @@
-# import os
-# from toolviper.utils.logger import setup_logger
-
-
-# _logger_name = "xradio"
-# if os.getenv("VIPER_LOGGER_NAME") != _logger_name:
-#     os.environ["VIPER_LOGGER_NAME"] = _logger_name
-#     setup_logger(
-#         logger_name="xradio",
-#         log_to_term=True,
-#         log_to_file=False,  # True
-#         log_file="xradio-logfile",
-#         log_level="DEBUG",
-#     )

src/xradio/_utils/_casacore/casacore_from_casatools.py

@@ -48,7 +48,7 @@
 )
 
 import numpy as np
-import toolviper.utils.logger as logger
+from xradio._utils.logging import xradio_logger
 
 casaconfig.config.data_auto_update = False
 casaconfig.config.measures_auto_update = False
@@ -335,13 +335,13 @@ def taql(self, taqlcommand="TaQL expression"):
         tb_query = taqlcommand.replace("$mtable", tablename).replace(
             "$gtable", tablename
         )
-        logger.debug(f"tb_query_from: {tb_query_from.name()}")
-        logger.debug(f"tb_query_cmd:  {tb_query}")
+        xradio_logger().debug(f"tb_query_from: {tb_query_from.name()}")
+        xradio_logger().debug(f"tb_query_cmd:  {tb_query}")
         tb_query_to = _wrap_table(swig_object=tb_query_from._swigobj.taql(tb_query))
         if not is_open:
             tb_query_from.close()
             shutil.rmtree(tablename)
-        logger.debug(f"tb_query_to: {tb_query_to.name()}")
+        xradio_logger().debug(f"tb_query_to: {tb_query_to.name()}")
         return tb_query_to
 
     def getcolshapestring(self, *args, **kwargs):