pyuvdata 2.4.3__tar.gz → 2.4.4__tar.gz

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/.github/workflows/publish-to-test-pypi.yaml

@@ -19,8 +19,8 @@ jobs:
       matrix:
         buildplat:
           - [ubuntu-20.04, manylinux, x86_64]
-          - [macos-12, macosx, x86_64]
-          - [macos-12, macosx, arm64]
+          - [macos-13, macosx, x86_64]
+          - [macos-14, macosx, arm64]
           - [windows-2019, win, AMD64]
         python: ["cp310", "cp311", "cp312"]
     steps:
@@ -29,17 +29,16 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.18.1
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
           CIBW_TEST_REQUIRES: "-r ci/test_requirements.txt"
-          CIBW_TEST_COMMAND: "python -m pytest --pyargs pyuvdata"
-          CIBW_TEST_SKIP: "*-macosx_arm64"
+          CIBW_TEST_COMMAND: "python -m pytest --pyargs pyuvdata -n auto"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: ${{ matrix.python }}-${{ startsWith(matrix.buildplat[1], 'macosx') && 'macosx' || matrix.buildplat[1] }}
+          name: cibw-wheels-${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
           path: ./wheelhouse/*.whl
 
   make_sdist:
@@ -53,36 +52,31 @@ jobs:
       - name: Build SDist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: sdist
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   upload_all:
     needs: [build_wheels, make_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
           path: dist
-      - name: Move folders around
-        working-directory: dist
-        run: |
-          for dir in `ls .`; do
-            cd $dir
-            mv * ..
-            cd ..
-            rmdir $dir
-          done
+          merge-multiple: true
+
       - name: Upload to test PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.5.0
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.test_pypi_password }}
           repository_url: https://test.pypi.org/legacy/
 
       - name: Upload to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.5.0
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.pypi_password }}

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/.github/workflows/warning_test.yaml

@@ -24,7 +24,7 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON }}
 

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '(^docs/conf.py|^docs/references/|^pyuvdata/data/|^pyuvdata/uvdata/src/
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
         - id: trailing-whitespace
         - id: check-added-large-files
@@ -30,7 +30,7 @@ repos:
           - pep8-naming>=0.13.3
 
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.4.2
     hooks:
       - id: black
 

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/CHANGELOG.md

@@ -3,6 +3,20 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [2.4.4] - 2024-6-7
+
+### Changed
+- updated minimum cython dependency to 3.0.
+- Updated minimum optional dependency versions: astropy-healpix>=1.0.2
+
+### Fixed
+- Fixed a bug writing UVData objects to UVFITS formats with extra phase center catalog
+entries resulted in an error on read.
+- Fixed a bug where calling `UVData._set_app_coords_helper` with extra phase center
+catalog entries resulted in an error.
+- Bug in which `correct_cable_len` defaulted to `None` instead of `True`
+for `read_mwa_corr_fits`.
+
 ## [2.4.3] - 2024-3-25
 
 ### Added

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyuvdata
-Version: 2.4.3
+Version: 2.4.4
 Summary: an interface for astronomical interferometeric datasets in python
 Home-page: https://github.com/RadioAstronomySoftwareGroup/pyuvdata
 Author: Radio Astronomy Software Group
@@ -13,6 +13,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: astropy>=6.0
@@ -20,6 +21,7 @@ Requires-Dist: docstring-parser>=0.15
 Requires-Dist: h5py>=3.4
 Requires-Dist: numpy>=1.23
 Requires-Dist: pyerfa>=2.0.1.1
+Requires-Dist: pyyaml>=5.4.1
 Requires-Dist: scipy>=1.7.3
 Requires-Dist: setuptools>=61
 Requires-Dist: setuptools_scm!=7.0.0,!=7.0.1,!=7.0.2
@@ -27,12 +29,10 @@ Provides-Extra: astroquery
 Requires-Dist: astroquery>=0.4.4; extra == "astroquery"
 Provides-Extra: casa
 Requires-Dist: python-casacore>=3.5.2; extra == "casa"
-Provides-Extra: cst
-Requires-Dist: pyyaml>=5.4.1; extra == "cst"
 Provides-Extra: hdf5-compression
 Requires-Dist: hdf5plugin>=3.2.0; extra == "hdf5-compression"
 Provides-Extra: healpix
-Requires-Dist: astropy_healpix>=0.6; extra == "healpix"
+Requires-Dist: astropy_healpix>=1.0.2; extra == "healpix"
 Provides-Extra: lunar
 Requires-Dist: lunarsky>=0.2.2; extra == "lunar"
 Provides-Extra: novas
@@ -41,18 +41,16 @@ Requires-Dist: novas_de405; extra == "novas"
 Provides-Extra: all
 Requires-Dist: astroquery>=0.4.4; extra == "all"
 Requires-Dist: python-casacore>=3.5.2; extra == "all"
-Requires-Dist: pyyaml>=5.4.1; extra == "all"
 Requires-Dist: hdf5plugin>=3.2.0; extra == "all"
-Requires-Dist: astropy_healpix>=0.6; extra == "all"
+Requires-Dist: astropy_healpix>=1.0.2; extra == "all"
 Requires-Dist: lunarsky>=0.2.2; extra == "all"
 Requires-Dist: novas; extra == "all"
 Requires-Dist: novas_de405; extra == "all"
 Provides-Extra: test
 Requires-Dist: astroquery>=0.4.4; extra == "test"
 Requires-Dist: python-casacore>=3.5.2; extra == "test"
-Requires-Dist: pyyaml>=5.4.1; extra == "test"
 Requires-Dist: hdf5plugin>=3.2.0; extra == "test"
-Requires-Dist: astropy_healpix>=0.6; extra == "test"
+Requires-Dist: astropy_healpix>=1.0.2; extra == "test"
 Requires-Dist: lunarsky>=0.2.2; extra == "test"
 Requires-Dist: novas; extra == "test"
 Requires-Dist: novas_de405; extra == "test"
@@ -60,7 +58,7 @@ Requires-Dist: pytest>=6.2.5; extra == "test"
 Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: pytest-cases>=3.8.3; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: cython; extra == "test"
+Requires-Dist: cython>=3.0; extra == "test"
 Requires-Dist: coverage; extra == "test"
 Requires-Dist: pre-commit; extra == "test"
 Provides-Extra: doc
@@ -70,9 +68,8 @@ Requires-Dist: pypandoc; extra == "doc"
 Provides-Extra: dev
 Requires-Dist: astroquery>=0.4.4; extra == "dev"
 Requires-Dist: python-casacore>=3.5.2; extra == "dev"
-Requires-Dist: pyyaml>=5.4.1; extra == "dev"
 Requires-Dist: hdf5plugin>=3.2.0; extra == "dev"
-Requires-Dist: astropy_healpix>=0.6; extra == "dev"
+Requires-Dist: astropy_healpix>=1.0.2; extra == "dev"
 Requires-Dist: lunarsky>=0.2.2; extra == "dev"
 Requires-Dist: novas; extra == "dev"
 Requires-Dist: novas_de405; extra == "dev"
@@ -80,7 +77,7 @@ Requires-Dist: pytest>=6.2.5; extra == "dev"
 Requires-Dist: pytest-xdist; extra == "dev"
 Requires-Dist: pytest-cases>=3.8.3; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
-Requires-Dist: cython; extra == "dev"
+Requires-Dist: cython>=3.0; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: matplotlib; extra == "dev"
@@ -234,19 +231,18 @@ Required:
 * numpy >= 1.23
 * pyerfa >= 2.0.1.1
 * python >= 3.10
+* pyyaml >= 5.4.1
 * scipy >= 1.7.3
 * setuptools_scm <7.0|>=7.0.3
 
 Optional:
 
-* astropy-healpix >= 0.6 (for working with beams in HEALPix formats)
+* astropy-healpix >= 1.0.2 (for working with beams in HEALPix formats)
 * astroquery >= 0.4.4 (for enabling phasing to ephemeris objects using JPL-Horizons)
 * hdf5plugin >= 3.2.0 (for enabling bitshuffle and other hdf5 compression filters in uvh5 files)
 * lunarsky >=0.2.2 (for working with simulated datasets for lunar telescopes)
 * novas and novas_de405 (for using the NOVAS library for astrometry)
 * python-casacore >= 3.5.2 (for working with CASA measurement sets)
-* pyyaml >= 5.4.1 (for working with settings files for CST beam files)
-
 
 The numpy and astropy versions are important, so make sure these are up to date.
 
@@ -298,7 +294,7 @@ you will need the following packages:
 * pytest >= 6.2
 * pytest-cases >= 3.8.3
 * pytest-cov
-* cython >=0.23
+* cython >=3.0
 * coverage
 * pre-commit
 * matplotlib

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/README.md

@@ -145,19 +145,18 @@ Required:
 * numpy >= 1.23
 * pyerfa >= 2.0.1.1
 * python >= 3.10
+* pyyaml >= 5.4.1
 * scipy >= 1.7.3
 * setuptools_scm <7.0|>=7.0.3
 
 Optional:
 
-* astropy-healpix >= 0.6 (for working with beams in HEALPix formats)
+* astropy-healpix >= 1.0.2 (for working with beams in HEALPix formats)
 * astroquery >= 0.4.4 (for enabling phasing to ephemeris objects using JPL-Horizons)
 * hdf5plugin >= 3.2.0 (for enabling bitshuffle and other hdf5 compression filters in uvh5 files)
 * lunarsky >=0.2.2 (for working with simulated datasets for lunar telescopes)
 * novas and novas_de405 (for using the NOVAS library for astrometry)
 * python-casacore >= 3.5.2 (for working with CASA measurement sets)
-* pyyaml >= 5.4.1 (for working with settings files for CST beam files)
-
 
 The numpy and astropy versions are important, so make sure these are up to date.
 
@@ -209,7 +208,7 @@ you will need the following packages:
 * pytest >= 6.2
 * pytest-cases >= 3.8.3
 * pytest-cov
-* cython >=0.23
+* cython >=3.0
 * coverage
 * pre-commit
 * matplotlib

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/azure-piplines.yml

@@ -164,7 +164,7 @@ jobs:
       cd ../pyuvsim
       pip install --no-deps .
       mkdir test-reports
-      python -m pytest pyuvsim --junitxml=test-reports/xunit.xml
+      python -m pytest --junitxml=test-reports/xunit.xml
     displayName: run pyuvsim tests
 
 - job: SSINS

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/pyuvdata_min_deps_tests.yml

@@ -8,11 +8,12 @@ dependencies:
   - scipy>=1.5
   - numpy>=1.23
   - pyerfa>=2.0
+  - pyyaml>=5.4.1
   - coverage
   - pytest>=6.2.0
   - pytest-cases>=3.8.3
   - pytest-cov
   - pytest-xdist
-  - cython
+  - cython>=3.0
   - setuptools_scm<7.0|>=7.0.3
   - pip

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/pyuvdata_min_versions_tests.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - astropy==6.0.0
-  - astropy-healpix==0.6
+  - astropy-healpix==1.0.2
   - astroquery==0.4.4
   - docstring_parser==0.15
   - h5py==3.4.0
@@ -18,7 +18,7 @@ dependencies:
   - pytest-cases==3.8.3
   - pytest-cov
   - pytest-xdist
-  - cython
+  - cython==3.0.0
   - setuptools==61
   - setuptools_scm==7.0.3
   - pip

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/pyuvdata_tests.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - astropy>=6.0
-  - astropy-healpix>=0.6
+  - astropy-healpix>=1.0.2
   - astroquery>=0.4.4
   - docstring_parser>=0.15
   - h5py>=3.4
@@ -19,7 +19,7 @@ dependencies:
   - pytest-cases>=3.8.3
   - pytest-cov
   - pytest-xdist
-  - cython
+  - cython>=3.0
   - setuptools_scm<7.0|>=7.0.3
   - pip
   - pip:

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/pyuvdata_tests_windows.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - astropy>=6.0
-  - astropy-healpix>=0.6
+  - astropy-healpix>=1.0.2
   - astroquery>=0.4.4
   - docstring_parser>=0.15
   - h5py>=3.4
@@ -18,7 +18,7 @@ dependencies:
   - pytest-cases>=3.8.3
   - pytest-cov
   - pytest-xdist
-  - cython
+  - cython>=3.0
   - setuptools_scm<7.0|>=7.0.3
   - pip
   - pip:

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/ci/test_requirements.txt

@@ -3,3 +3,4 @@ packaging
 pytest>=6.2.5
 pytest-cov
 pytest-cases>=3.8.3
+pytest-xdist

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/docs/references/uvh5_memo.tex

@@ -28,7 +28,8 @@
 \author{Paul La Plante, and the pyuvdata team}
 \date{November 28, 2018\\
 Revised April 2, 2021\\
-Revised July 14, 2022
+Revised July 14, 2022\\
+Revised April 17, 2024
 }
 
 \begin{document}
@@ -165,8 +166,10 @@ interoperability between different HDF5 implementations.
 \item \textbf{Ntimes}: \textit{int} The number of time samples present in the
   data. (\textit{Ntimes})
 \item \textbf{uvw\_array}: \textit{float} An array of the uvw-coordinates
-  corresponding to each observation in the data. This is a two-dimensional array of
-  size (Nblts, 3). Units are in meters. (\textit{uvw\_array})
+  corresponding to each observation in the data. Baselines are specified as from
+  \verb+ant_1_array+ to \verb+ant_2_array+, implying the position of antenna 2
+  minus the position of antenna 1. This is a two-dimensional array of size
+  (Nblts, 3). Units are in meters. (\textit{uvw\_array})
 \item \textbf{time\_array}: \textit{float} An array of the Julian Date
   corresponding to the temporal midpoint of the corresponding baseline's
   integration. This is a one-dimensional array of size
@@ -274,7 +277,7 @@ And may include:
 	\end{itemize} (\textit{phase\_center\_catalog})
 \item \textbf{phase\_center\_id\_array}: \textit{int}
 A one dimensional array of length Nblts containing the cat\_id from the phase\_center\_catalog
-that each baseline-time is phased to. (\textit{phase\_center\_id\_array})
+that each baseline-time is phased to. \\(\textit{phase\_center\_id\_array})
 \item \textbf{phase\_center\_app\_ra}: \textit{float}
 Apparent right ascension of the phase center in the topocentric frame of the observatory, in radians.
 This is a one-dimensional array of size Nblts. In the event that there are multiple phase centers,
@@ -296,8 +299,8 @@ baseline-time in this calculation. This is set to zero for unprojected phase typ
 (\textit{phase\_center\_frame\_pa})
 
 \item \textbf{version}: \textit{string} The version of the HDF5 file. The latest
-  version (and the one described in this memo) is Version 1.0. Note it should be
-  a string, such as \verb+`1.0'+. See Sec.~\ref{sec:version_history} for the
+  version (and the one described in this memo) is Version 1.1. Note it should be
+  a string, such as \verb+"1.1"+. See Sec.~\ref{sec:version_history} for the
   version history of the HDF5 specification. (No corresponding UVData attribute)
 \end{itemize}
 
@@ -418,10 +421,12 @@ $j$ is as follows \cite{tms}:
 That is, the baseline vector defined by the $uvw$ coordinates is directed from
 antenna $i$ to antenna $j$ (so the baseline vector can be computed as
 $\vb{r_j} - \vb{r_i}$, where $\vb{r}$ is the position vector of a given
-antennas), and the data corresponding to antenna $j$ is conjugated. Note that if
-a file is generated with the opposite convention, it is usually sufficient to
-multiply $uvw$ coordinates by $-1$ to generate a self-consistent dataset, as
-well as conjugating the data in the \verb+data_array+.
+antennas), and the data corresponding to antenna $j$ is conjugated. Following
+the specification of the baselines, antenna $i$ is given by \verb+ant_1_array+
+and $j$ by \verb+ant_2_array+. Note that if a file is generated with the opposite
+convention, it is usually sufficient to multiply $uvw$ coordinates by $-1$ to
+generate a self-consistent dataset, as well as conjugate the data in the
+\verb+data_array+.
 
 \subsection{Flags Dataset}
 \label{sec:flags}

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/environment.yaml

@@ -3,10 +3,10 @@ channels:
   - conda-forge
 dependencies:
   - astropy>=6.0
-  - astropy-healpix>=0.6
+  - astropy-healpix>=1.0.2
   - astroquery>=0.4.4
   - coverage
-  - cython>=0.23
+  - cython>=3.0
   - docstring_parser>=0.15
   - h5py>=3.4
   - hdf5plugin>=3.2.0

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61",
             "wheel",
             "setuptools_scm!=7.0.0,!=7.0.1,!=7.0.2",
             "oldest-supported-numpy",
-            "cython>=0.23"]
+            "cython>=3.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.isort]

{pyuvdata-2.4.3 → pyuvdata-2.4.4}/pyuvdata/tests/test_utils.py

@@ -4382,9 +4382,10 @@ def test_determine_blt_order_size_1():
 
 
 def test_antnums_to_baseline_miriad_convention():
-    ant1 = np.array([0, 1, 2, 3, 0, 0]) + 1  # Ant1 array should be 1-based
-    ant2 = np.array([0, 1, 2, 3, 255, 256]) + 1  # Ant2 array should be 1-based
-    bl_gold = np.array([257, 514, 771, 1028, 67840, 67841], dtype="uint64")
+    ant1 = np.array([1, 2, 3, 1, 1, 1, 255, 256])  # Ant1 array should be 1-based
+    ant2 = np.array([1, 2, 3, 254, 255, 256, 1, 2])  # Ant2 array should be 1-based
+    bl_gold = np.array([257, 514, 771, 510, 511, 67840, 65281, 65538], dtype="uint64")
+
     n_ant = 256
     bl = uvutils.antnums_to_baseline(ant1, ant2, n_ant, use_miriad_convention=True)
     assert np.allclose(bl, bl_gold)