uvcombine 1.0.0__tar.gz

uvcombine-1.0.0/.github/workflows/main.yml

@@ -0,0 +1,36 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+    - main
+    tags:
+    - '*'
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  tests:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v3
+    with:
+      display: true
+      libraries: |
+        apt:
+          - '^libxcb.*-dev'
+          - libxkbcommon-x11-dev
+          - libegl1
+      envs: |
+        - linux: build_docs
+        - linux: py310-test
+        - linux: py310-test-casa
+        - linux: py312-test-dev
+        - linux: py313-test-all
+        - macos: py310-test-all
+        - macos: py311-test-all
+        - macos: py312-test-all
+        - macos: py313-test-dev
+        - windows: py310-test-all
+        - windows: py311-test-all
+        - windows: py312-test-all
+        - windows: py313-test-dev
+

uvcombine-1.0.0/.github/workflows/pre-commit.yml

@@ -0,0 +1,17 @@
+name: pre-commit
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - uses: pre-commit/action@v3.0.1

uvcombine-1.0.0/.github/workflows/publish.yml

@@ -0,0 +1,49 @@
+name: Build and upload to PyPI
+
+on:
+  push:
+    branches:
+    - main
+    tags:
+    - '*'
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build_sdist_and_wheel:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.12'
+      - name: Install build
+        run: python -m pip install build
+      - name: Build sdist and wheel
+        run: python -m build --sdist --wheel --outdir dist/ .
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [build_sdist_and_wheel]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/uvcombine
+    permissions:
+      id-token: write  # required for PyPI trusted publishing (OIDC)
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

uvcombine-1.0.0/.gitignore

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+# Compiled files
+*.py[cod]
+*.a
+*.o
+*.so
+__pycache__
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/version.py
+*/cython_version.py
+htmlcov
+.coverage
+MANIFEST
+
+# Sphinx
+docs/api
+docs/_build
+
+# Eclipse editor project files
+.project
+.pydevproject
+.settings
+
+# Pycharm editor project files
+.idea
+
+# Packages/installer info
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.cache
+.tox
+.*.sw[op]
+*~
+
+# Mac OSX
+.DS_Store
+
+*.ipynb_checkpoints
+examples/*.png
+*.png
+
+# Backup files left behind by editors/CASA sessions
+*.pybck
+*.ipynbbck
+*.orig
+casapy-*.log
+casa-*.log
+ipython-*.log
+ipython_log_*.py
+*.last

uvcombine-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.9.1
+    hooks:
+      - id: nbstripout

uvcombine-1.0.0/.readthedocs.yml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+
+# Install regular dependencies.
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: docs/conf.py
+  builder: html
+  fail_on_warning: true

uvcombine-1.0.0/CHANGES.rst

@@ -0,0 +1,28 @@
+1.0.0 (2026-09-10)
+------------------
+First release on PyPI. Requires Python 3.10+ and astropy 6.1+.
+
+Highlights:
+
+- Feathering of high-resolution (interferometric) and low-resolution
+  (single-dish) images with ``feather_simple``, and of spectral cubes with
+  ``feather_simple_cube``, including dask-backed, memory-limited processing of
+  large cubes (#25, #34)
+- uv-overlap consistency checks and single-dish flux scale factors with
+  ``feather_compare``, ``feather_plot`` and ``uvcombine.scale_factor`` (#16)
+- Tests comparing ``feather_simple`` with CASA's ``feather`` task (#23)
+
+Changes leading up to 1.0.0:
+
+- Remove the remaining ``turbustat`` imports and make ``statsmodels`` an
+  optional dependency, installed with ``pip install "uvcombine[stats]"`` (#58)
+- Fix ``find_scale_factor(method='distrib')`` returning exp(scale factor)
+  when the likelihood fit is not used, including when statsmodels is not
+  installed (#58)
+- Vendor TurbuStat's ``pspec`` to drop the runtime ``turbustat`` dependency (#57)
+- Handle unitless axes in ``feather_plot`` (#54)
+- Remove old deprecated code (#48)
+- Replace astropy's defunct ``ProgressBar`` with ``tqdm`` (#44)
+- Switch PyPI publishing to trusted publishing (OIDC) and add the missing
+  ``LICENSE.rst`` (#52)
+- Docs, CI and packaging maintenance (#29, #30, #38, #47, #51, #53, #55, #56)

uvcombine-1.0.0/LICENSE.rst

@@ -0,0 +1,34 @@
+Copyright (c) 2015-2026, uvcombine developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Licenses of bundled code
+=========================
+
+``uvcombine/pspec.py`` is adapted from TurbuStat
+(https://github.com/Astroua/TurbuStat), which is distributed under the
+MIT license reproduced at the top of that file.

uvcombine-1.0.0/MANIFEST.in

@@ -0,0 +1,16 @@
+include README.md
+include CHANGES.rst
+include LICENSE.rst
+include pyproject.toml
+
+recursive-include *.pyx *.c *.pxd
+recursive-include docs *
+recursive-include licenses *
+recursive-include cextern *
+recursive-include scripts *
+
+prune build
+prune docs/_build
+prune docs/api
+
+global-exclude *.pyc *.o

uvcombine-1.0.0/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: uvcombine
+Version: 1.0.0
+Summary: Combination of high- and low-resolution radio astronomical data.
+Author: Adam Ginsburg
+Author-email: Eric Koch <koch.eric.w@gmail.com>
+License-Expression: BSD-3-Clause
+Project-URL: homepage, https://uvcombine.readthedocs.org
+Project-URL: documentation, https://uvcombine.readthedocs.org
+Project-URL: repository, https://github.com/radio-astro-tools/uvcombine
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+Requires-Dist: astropy>=6.1
+Requires-Dist: numpy>=1.8
+Requires-Dist: scipy
+Requires-Dist: packaging>=19
+Requires-Dist: setuptools>=62.3.3
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: reproject>=0.13
+Requires-Dist: spectral-cube>=0.4.0
+Requires-Dist: radio-beam>=0.3.5
+Requires-Dist: tqdm
+Provides-Extra: docs
+Requires-Dist: sphinx-astropy; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=5; extra == "test"
+Requires-Dist: pytest-astropy>=0.10; extra == "test"
+Requires-Dist: pytest-cov>=3; extra == "test"
+Requires-Dist: scikit-image>=0.24; extra == "test"
+Provides-Extra: dev
+Requires-Dist: numpy>=0.0.dev0; extra == "dev"
+Requires-Dist: astropy>=0.0.dev0; extra == "dev"
+Requires-Dist: spectral-cube>=0.0.dev0; extra == "dev"
+Requires-Dist: radio-beam>=0.0.dev0; extra == "dev"
+Provides-Extra: notebooks
+Requires-Dist: pre-commit; extra == "notebooks"
+Requires-Dist: nbstripout; extra == "notebooks"
+Provides-Extra: stats
+Requires-Dist: statsmodels; extra == "stats"
+Provides-Extra: all
+Requires-Dist: uvcombine[docs,stats,test]; extra == "all"
+Dynamic: license-file
+
+uvcombine
+=========
+
+uvcombine provides tools for combining high-resolution images with missing large angular scales (Fourier-domain short-spacings)
+with low-resolution images containing the short/zero spacing, including:
+
+* Feathering two images
+* Feathering two cubes (including for large cubes using spectral-cube's dask implementation)
+* uv-overlap consistency tests and measuring the single dish flux scaling factor.
+
+See the `documentation <https://uvcombine.readthedocs.io/en/latest/>`_ for more information.
+Worked notebook examples of the uvcombine functionality can be found in the `examples <https://github.com/radio-astro-tools/uvcombine/tree/main/examples>`_ directory.
+
+Install the latest release from PyPI with::
+
+    pip install uvcombine
+
+Development
+^^^^^^^^^^^
+
+Example notebooks under ``examples/`` are kept free of cell outputs on ``main`` so
+diffs stay reviewable. This is enforced by a ``pre-commit`` hook (`nbstripout
+<https://github.com/kynan/nbstripout>`_) plus a CI check that fails if a notebook
+with outputs is pushed. To set up the hook locally::
+
+    pip install -e ".[notebooks]"
+    pre-commit install
+
+Notebooks with their outputs executed are kept on the ``with-output`` branch
+instead; it is refreshed manually (not by CI) whenever an example notebook changes.
+
+radio-astro-tools
+^^^^^^^^^^^^^^^^^
+
+This package is part of the radio-astro-tools project. See
+`radio-astro-tools <https://radio-astro-tools.github.io/>`_ for more information.
+

uvcombine-1.0.0/README.rst

@@ -0,0 +1,37 @@
+uvcombine
+=========
+
+uvcombine provides tools for combining high-resolution images with missing large angular scales (Fourier-domain short-spacings)
+with low-resolution images containing the short/zero spacing, including:
+
+* Feathering two images
+* Feathering two cubes (including for large cubes using spectral-cube's dask implementation)
+* uv-overlap consistency tests and measuring the single dish flux scaling factor.
+
+See the `documentation <https://uvcombine.readthedocs.io/en/latest/>`_ for more information.
+Worked notebook examples of the uvcombine functionality can be found in the `examples <https://github.com/radio-astro-tools/uvcombine/tree/main/examples>`_ directory.
+
+Install the latest release from PyPI with::
+
+    pip install uvcombine
+
+Development
+^^^^^^^^^^^
+
+Example notebooks under ``examples/`` are kept free of cell outputs on ``main`` so
+diffs stay reviewable. This is enforced by a ``pre-commit`` hook (`nbstripout
+<https://github.com/kynan/nbstripout>`_) plus a CI check that fails if a notebook
+with outputs is pushed. To set up the hook locally::
+
+    pip install -e ".[notebooks]"
+    pre-commit install
+
+Notebooks with their outputs executed are kept on the ``with-output`` branch
+instead; it is refreshed manually (not by CI) whenever an example notebook changes.
+
+radio-astro-tools
+^^^^^^^^^^^^^^^^^
+
+This package is part of the radio-astro-tools project. See
+`radio-astro-tools <https://radio-astro-tools.github.io/>`_ for more information.
+

uvcombine-1.0.0/config_template.py

@@ -0,0 +1,6 @@
+import os
+here = os.path.dirname(os.path.abspath('.'))
+datapath=[os.path.join(here, '.casa', 'data')]
+measurespath=datapath[0]
+measures_auto_update=True
+data_auto_update=True

uvcombine-1.0.0/docs/Makefile

@@ -0,0 +1,134 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+#This is needed with git because git doesn't create a dir if it's empty
+$(shell [ -d "_static" ] || mkdir -p _static)
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)
+	-rm -rf api
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Astropy.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Astropy.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Astropy"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Astropy"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."