pyuvdata 3.2.7__tar.gz → 3.2.8__tar.gz

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.github/workflows/macosx_windows_ci.yaml

@@ -19,6 +19,9 @@ jobs:
     name: Run Tests
     env:
       PYTHON: ${{ matrix.python-version }}
+      # Keep the test data in the workspace rather than the per-OS default cache
+      # location, so it can be cached with a single path on every runner.
+      PYUVDATA_DATA_DIR: ${{ github.workspace }}/pooch_cache
     runs-on: ${{ matrix.os }}
     defaults:
      run:
@@ -59,6 +62,16 @@ jobs:
             exit 1;
           fi
 
+      - name: Restore cached test data
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: pooch_cache
+          key: pooch-${{ runner.os }}-${{ hashFiles('src/pyuvdata/datasets.py') }}
+
+      - name: Download any test data not already cached
+        run: |
+          python ci/prefetch_test_data.py "$PYUVDATA_DATA_DIR"
+
       - name: Install
         run: |
           CFLAGS="-DCYTHON_TRACE=1 -DCYTHON_TRACE_NOGIL=1" pip install .

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.github/workflows/numba_test.yaml

@@ -25,7 +25,7 @@ jobs:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version-file: pyproject.toml
 

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.github/workflows/publish-to-test-pypi.yaml

@@ -16,6 +16,8 @@ jobs:
   build_wheels:
     name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
     runs-on: ${{ matrix.buildplat[0] }}
+    env:
+      PYUVDATA_DATA_DIR: ${{ github.workspace }}/pooch_cache
     strategy:
       fail-fast: false
       matrix:
@@ -35,13 +37,38 @@ jobs:
           fetch-depth: 0
           persist-credentials: false
 
+      # Only for the prefetch step below
+      - name: Setup Python
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version-file: pyproject.toml
+
+      # Suppress the cache-poisoning audit for this step, since the only way to fix it
+      # is to allow for lookup-only , which would stop the cache from being restored.
+      # Known issue: https://github.com/zizmorcore/zizmor/issues/2071 -- the ignore can
+      # get removed once the issue is implemented in zizmor.
+      - name: Restore cached test data
+        if: github.event_name != 'release'
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 # zizmor: ignore[cache-poisoning]
+        with:
+          path: pooch_cache
+          key: pooch-${{ runner.os }}-${{ hashFiles('src/pyuvdata/datasets.py') }}
+
+      - name: Download any test data not already cached
+        shell: bash
+        run: |
+          python -m pip install pooch pyyaml
+          python ci/prefetch_test_data.py "$PYUVDATA_DATA_DIR"
+
       - name: Build wheels
-        uses: pypa/cibuildwheel@294735312765b09d24a2fbec22660ce817587d55 # v4.1.0
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074 # v4.2.0
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
           CIBW_TEST_REQUIRES: "-r ci/test_requirements.txt"
           CIBW_TEST_COMMAND: "pytest {project}/tests -n auto"
+          CIBW_ENVIRONMENT: PYUVDATA_DATA_DIR='${{ env.PYUVDATA_DATA_DIR }}'
+          CIBW_ENVIRONMENT_LINUX: PYUVDATA_DATA_DIR=/project/pooch_cache
 
       - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
@@ -79,12 +106,6 @@ jobs:
           path: dist
           merge-multiple: true
 
-      - name: Upload to test PyPI
-        if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
-        with:
-          repository_url: https://test.pypi.org/legacy/
-
       - name: Upload to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.github/workflows/warning_test.yaml

@@ -39,7 +39,7 @@ jobs:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python-version }}
 

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.gitignore

@@ -84,3 +84,6 @@ src/pyuvdata/uvdata/corr_fits.c
 src/pyuvdata/uvdata/src/miriad_wrap.cpp
 
 .vscode/
+
+# test data cache populated by ci/prefetch_test_data.py
+pooch_cache/

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
           args: ['--fix=no']
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.16.3
+    rev: v0.16.7
     hooks:
       - id: ruff
       - id: ruff-format
@@ -30,6 +30,6 @@ repos:
         additional_dependencies: ["bandit[toml]"]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.29.0
+    rev: v1.30.1
     hooks:
     - id: zizmor

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/CHANGELOG.md

@@ -3,6 +3,34 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [3.2.8] - 2025-09-18
+
+### Fixed
+- A bug in `UVData.read_ms` where visibility units could not be parsed when stored in
+a MeasurementSet as a singleton entry/list.
+- A bug in `UVData.write_ms` which caused `corrected_data` and `model_data` not to be
+reordered in the same way that, e.g., `UVData.data_array` was on write.
+- A bug in `UVData.write_ms` which caused `corrected_data` and `model_data` not to be
+conjugated (and inconsistent with `UVData.data_array`) when a mixture of baseline
+conjugation schemes was present.
+- A bug in `UVData.read_ms_cal` and `UVData.write_ms_cal` where gains tables where not
+being conjugated correctly.
+- A bug where the Jones array stored in calibration tables generated ny `UVCal.write_ms_cal`
+could be incorrectly ordered.
+- A bug where `utils.gain_interpolate.time_interp_cal` was not unwrapping phase gains
+along the time axis correctly (mistakenly was using the Jones axis instead).
+- A bug where calling `UVData.conjugate_bls` was not reordering `nsample_array` and
+`flag_array` cross-polarization entries.
+- A bug in `UVData.phase` where near-field phasing ignored `select_mask` and applied the
+near-field correction to every record, overwriting the w-coordinate and rotating the
+visibilities of records belonging to other phase centers.
+
+### Changed
+- `UVData.read_ms` and `UVData.write_ms` now always flip conjugation scheme on read and
+write for non-pyuvdata generated MeasurementSets (it was previously believed that when
+ant1 > ant2, the conjugation scheme may be flipped, but that was a misreading of CASA's
+codebase).
+
 ## [3.2.7] - 2025-08-20
 
 ### Added

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyuvdata
-Version: 3.2.7
+Version: 3.2.8
 Summary: A pythonic interface for radio astronomy interferometry data
 Author-email: Bryna Hazelton <brynah@phys.washington.edu>, Adam Beardsley <adam.beardsley@winona.edu>, Daniel Jacobs <daniel.c.jacobs@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Nicholas Kern <nkern@mit.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Adam Lanman <alanman@mit.edu>, Paul La Plante <paul.laplante@unlv.edu>, Steven Murray <murray.steveng@gmail.com>, Jonathan Pober <jonathan_pober@brown.edu>, Pyxie Star <pyxiestar@gmail.com>
 Maintainer-email: Bryna Hazelton <brynah@phys.washington.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Steven Murray <murray.steveng@gmail.com>

pyuvdata-3.2.8/ci/prefetch_test_data.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+"""
+Download the pyuvdata test data into a shared pooch cache.
+
+The wheel-building jobs run the test suite once per wheel, in an environment with a
+cold cache, so each one re-downloads the whole test dataset from github. Running this
+once on the runner and pointing the test environments at the result via the
+PYUVDATA_DATA_DIR environment variable turns those N downloads into one.
+
+Usage: python ci/prefetch_test_data.py <cache_dir>
+"""
+
+import importlib.util
+import os
+import sys
+import types
+from pathlib import Path
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+SRC = REPO_ROOT / "src" / "pyuvdata"
+
+
+def load_datasets_module():
+    """
+    Load pyuvdata.datasets without importing pyuvdata itself.
+
+    Importing the real package pulls in the compiled extensions, which have not been
+    built yet when this runs. datasets.py only needs DATA_PATH from the parent, so
+    stub out just enough of the package for it to import.
+    """
+    pkg = types.ModuleType("pyuvdata")
+    pkg.__path__ = [str(SRC)]
+    data_pkg = types.ModuleType("pyuvdata.data")
+    data_pkg.DATA_PATH = str(SRC / "data")
+    sys.modules["pyuvdata"] = pkg
+    sys.modules["pyuvdata.data"] = data_pkg
+
+    spec = importlib.util.spec_from_file_location(
+        "pyuvdata.datasets", SRC / "datasets.py"
+    )
+    module = importlib.util.module_from_spec(spec)
+    sys.modules["pyuvdata.datasets"] = module
+    spec.loader.exec_module(module)
+    return module
+
+
+def main():
+    """Fetch every dataset in the registry into the requested cache directory."""
+    if len(sys.argv) != 2:
+        sys.exit(f"usage: {sys.argv[0]} <cache_dir>")
+
+    # pooch reads this when the Pooch object is created, so it has to be set before
+    # datasets.py is executed.
+    cache_dir = Path(sys.argv[1]).resolve()
+    os.environ["PYUVDATA_DATA_DIR"] = str(cache_dir)
+
+    datasets = load_datasets_module()
+    print(f"Caching {len(datasets.fetch_dict)} datasets into {datasets.pup.abspath}")
+
+    for name in datasets.fetch_dict:
+        datasets.fetch_data(name)
+
+    print(f"Done. Cache is at {datasets.pup.abspath}")
+
+
+if __name__ == "__main__":
+    main()

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/docs/conventions.rst

@@ -23,13 +23,16 @@ the position of the first (after which various rotations are applied). The secon
 *ant1-ant2*, where :math:`\mathcal{V}_{12}=\langle V_{1} V_{2}^{*} \rangle`, and the
 *uvw*-coordinate is calculated by taking the position of the first antenna minus
 the second. The pyuvdata software package uses the *ant2-ant1* convention, as does
-MIRIAD; with UVFITS, FHD, and Mir formats use the opposite convention. MeasurementSet
-format (used within CASA) appears to support both conventions, with the convention
-selected based on the number of the antennas in the pair: when the antenna number of
-*ant1* is greater than that of *ant2*, then the *ant2-ant1* convention is used,
-otherwise the *ant1-ant2* convention is used (e.g., the 3-7 baseline would use the
-*ant1-ant2* convention within CASA, whereas the 7-3 baseline would use the *ant2-ant1*
-convention).
+MIRIAD; with UVFITS, FHD, Mir, and MeasurementSet (used within CASA) formats using the
+opposite convention. Note that this also applies to calibration solutions derived from
+the dataset, with the implication being that gains solved in the *ant2-ant1* convention
+are the complex conjugates of those solved in the *ant1-ant2* convention.
+
+Note that separately from the conjugation convention, some platforms have requirements
+for which antenna is listed first in the baseline (e.g., AIPS needs UVFITS files
+recorded with :math:`\text{ant1}<\text{ant2}`), separate from the conjugation
+convention. pyuvdata is able to support so-called "mixed" conventions in this respect,
+with the antenna ordering convention being independent of the conjugation convention.
 
 Phase Center Types
 ------------------

{pyuvdata-3.2.7 → pyuvdata-3.2.8}/src/pyuvdata/datasets.py

@@ -22,6 +22,8 @@ pup = pooch.create(
     version=data_version,
     # If this is a development version, get the data from the "main" branch
     version_dev="main",
+    env="PYUVDATA_DATA_DIR",
+    retry_if_failed=3,
     registry=None,
 )