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30ee724
enhance the cube header determinator by checking the spectral dimension
keflavich Mar 9, 2023
8695938
add option to specify header
keflavich Mar 13, 2023
6ff0b1a
try to make convolution possible _and_ use memmap'd output
keflavich Mar 13, 2023
3ce0a5a
need non-array truthiness
keflavich Mar 13, 2023
4e54a9c
just raise the exception as is, don't wrap it
keflavich Mar 13, 2023
c8042c2
refactor cube mosaicing to use reproject.coadd
keflavich Mar 13, 2023
96223c4
refactor to allow for direct FITS output
keflavich Mar 13, 2023
3d17483
bitpix dtype
keflavich Mar 13, 2023
c22cb5f
getdata doesn't support mode
keflavich Mar 13, 2023
18d2759
force overwrite
keflavich Mar 13, 2023
54b597e
force overwrite
keflavich Mar 13, 2023
5b3e587
mode for fits
keflavich Mar 13, 2023
0d9c834
hdu0
keflavich Mar 13, 2023
93a5bbe
refactor to use output_array
keflavich Mar 13, 2023
ef924be
allow setting no spectral block size
keflavich Mar 13, 2023
82f9705
add flush
keflavich Mar 13, 2023
97d9b35
need to flush occasionally
keflavich Mar 13, 2023
9091462
allow channel-by-channel mosaicing instead of cube-by-cube
keflavich Mar 14, 2023
bc5a0f2
add progressbar & frequent flush callback
keflavich Mar 14, 2023
f607179
fix some critical typos and enable resuming from partly-written file …
keflavich Mar 14, 2023
1d93c74
restructure a bunch of things that are being done too expensively and…
keflavich Mar 14, 2023
f0503bf
more verbosity & parallelism
keflavich Mar 14, 2023
f9156da
this is very verbose now, but still trying to make verbosity flexible
keflavich Mar 15, 2023
b038a68
allow weights to be included
keflavich Mar 15, 2023
24ef114
add explanations of some choices
keflavich Mar 20, 2023
100a503
when operating on lists of cubes, some may be out of range, and they …
keflavich Sep 4, 2023
cb4a588
need more checks for cubes to be in range
keflavich Sep 5, 2023
1960971
have to account for more corner cases for missing data
keflavich Sep 5, 2023
3115f64
fix more bugs with keep
keflavich Sep 6, 2023
173dff0
refactor neighboring channel chooser
keflavich Sep 8, 2023
9c6ad11
WIP: try making dask do reprojection
keflavich Oct 5, 2022
149fa37
move reproject to top-level dask class
keflavich Sep 9, 2023
8c93603
pass kwargs
keflavich Sep 10, 2023
431b794
comment out the wrapper
keflavich Sep 12, 2023
f1855ba
add some debug things
keflavich Nov 10, 2023
c994147
allow a threshold to be specified for spectral agreement in cube
keflavich Dec 2, 2023
0e28c28
logical bugfix
keflavich Dec 2, 2023
97792e3
update use of reproject kwargs
keflavich Dec 3, 2023
0b8a453
fix typo in header creation
keflavich Dec 3, 2023
cb9f3f9
fix logical error: if the spectral axis is reversed, keeping CRPIX an…
keflavich Dec 3, 2023
6e9fa8a
force dtype in memory-based merge
keflavich Dec 8, 2023
d4ab934
sanity checks, dtype forcing
keflavich Dec 9, 2023
aef2531
add some more checks that the output file is float
keflavich Dec 9, 2023
d9efe55
add an explicit warning
keflavich Dec 9, 2023
a0815d9
dtypes are a pain
keflavich Dec 9, 2023
e59cf0e
Add handling for VRSC -> SC with common beam; optional return footprint
e-koch Dec 29, 2023
4fe9592
Expand test_mosaic_cubes
e-koch Dec 29, 2023
735d9fe
Keep the original projection when combining headers
e-koch Dec 29, 2023
b7a912b
Ensure combined header updates units appropriately
e-koch Dec 29, 2023
af7c9b9
The -1 for the combined spectral axis is returning the wrong shape. L…
e-koch Dec 29, 2023
b836769
Add test for mosaicking in spectral dimension
e-koch Dec 29, 2023
28187a4
Remove CASABM after convolving to a common beam
e-koch Dec 29, 2023
aa393e1
Drop the units check when one cube is dimensionless
e-koch Dec 29, 2023
77fd858
add common beam hack
keflavich Dec 20, 2023
a82f435
remove typo
keflavich Dec 20, 2023
43c021c
Add dask[distributed] to required packages
e-koch Dec 29, 2023
eac9d91
some robustness against beams, better error messaging
keflavich Dec 29, 2023
7e69a40
Allow passing specific dask distributed clients as a kwarg
e-koch Jan 5, 2024
bd0278d
Don't start a dask client as a kwarg
e-koch Jan 5, 2024
6367e31
Remove unused taper kwarg
e-koch Jan 6, 2024
d2d22f7
make progressbar a little more sensible and add debugging things around
keflavich Feb 12, 2024
2cc682c
add failure_returns_pointlike for beam deconvolution
keflavich Jun 15, 2024
2f90596
pass intermediate_memmap to reproject_and_coadd
keflavich Jun 15, 2024
6f8e315
add descs
keflavich Jun 16, 2024
83949f6
reproject_and_coadd does not accept progressbar any more
keflavich Jul 15, 2024
1802dd4
argmax/argmin need to return ints [some test code was removed]
keflavich Oct 18, 2024
4ad60ff
workaround missing mask problem
keflavich Jan 22, 2025
74824e7
need to modify list inplace
keflavich Jan 22, 2025
8654457
workaround didn't work
keflavich Jan 22, 2025
bc67a8f
was supposed to return slices
keflavich Jan 22, 2025
d5523be
add some cube mosaicing tests. they fail. disaster.
keflavich Jan 24, 2025
7f0f2d4
tests caught a few bugs
keflavich Jan 24, 2025
76343fc
testing work
keflavich Jan 24, 2025
1b6df89
add weighted test
keflavich Jan 24, 2025
8c1df2e
handle weight cube slicing - before, we were loading whole weight cub…
keflavich Jan 25, 2025
131b9af
lots of debug statements and fixes. Somehow, every single case is a …
keflavich Jan 25, 2025
5dcc0b1
fix weightcube cut handling
keflavich Jan 26, 2025
13f8ff7
comment out debugs
keflavich Jan 26, 2025
5b8778e
debug statements semi-restored, and catch the case where scubes are d…
keflavich Jan 26, 2025
16eeb72
add extrapolation tolerance parameter & some debug statements to remo…
keflavich Jan 26, 2025
ab1c147
tests pass if we don't try to gather data
keflavich Jan 26, 2025
2320392
fix a dask test error (shouldn't run with dask) and turn off loud debug
keflavich Jan 26, 2025
77feff3
remove a debug statement that CI didn't like
keflavich Jan 26, 2025
de631aa
add missing fixture
keflavich Jan 26, 2025
a97c26d
sometimes warnings are turned off - force them on
keflavich Jan 26, 2025
20cba44
more verbose message when failing because cubes unmatched
keflavich Jan 28, 2025
bcffa26
pass on reproject kwargs & fix logical error: sign(0)=0
keflavich Jan 28, 2025
55ed7ee
Merge remote-tracking branch 'upstream/main' into cubewcs_mosaic_and_…
keflavich Jul 25, 2025
18cdeec
Merge remote-tracking branch 'upstream/main' into cubewcs_mosaic_and_…
keflavich Aug 28, 2025
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116 changes: 116 additions & 0 deletions setup.cfg
Original file line number Diff line number Diff line change
@@ -0,0 +1,116 @@
[metadata]
name = spectral-cube
description = A package for interaction with spectral cubes
long_description = file: README.rst
author = Adam Ginsburg, Tom Robitaille, Chris Beaumont, Adam Leroy, Erik Rosolowsky, and Eric Koch
author_email = [email protected]
license = BSD
url = http://spectral-cube.readthedocs.org
edit_on_github = False
github_project = radio-astro-tools/spectral-cube
version = 0.6.3

[options]
zip_safe = False
packages = find:
install_requires =
astropy
numpy>=1.8.0
radio_beam>=0.3.3
dask[array]
dask[distributed]
joblib
casa-formats-io
packaging
tqdm

[options.extras_require]
test =
pytest-astropy
pytest-cov
regions>=0.7
numpy>=1.24.0
astropy>=5.2.1
zarr<3.0.0 # Unpin if updated. See issue #936
docs =
sphinx-astropy
matplotlib
noviz =
zarr<3.0.0 # Unpin if updated. See issue #936
fsspec
distributed
pvextractor
reproject>=0.9.1
scipy
viz =
aplpy
matplotlib
reproject
pvextractor
viz_extra =
glue-core[qt]
yt ; python_version<'3.8'
dev =
pvextractor
radio-beam
reproject
regions

[options.package_data]
spectral_cube.tests =
data/*
data/*/*

spectral_cube.io.tests = data/*/*

[upload_docs]
upload-dir = docs/_build/html
show-response = 1

[tool:pytest]
minversion = 3.0
norecursedirs = build docs/_build
doctest_plus = enabled
addopts = -p no:warnings
doctest_subpackage_requires =
spectral_cube/vis*.py = aplpy


[coverage:run]
omit =
spectral-cube/__init__*
spectral-cube/conftest.py
spectral-cube/*setup*
spectral-cube/*/tests/*
spectral-cube/tests/test_*
spectral-cube/extern/*
spectral-cube/utils/compat/*
spectral-cube/version*
spectral-cube/wcs/docstrings*
spectral-cube/_erfa/*
*/spectral-cube/__init__*
*/spectral-cube/conftest.py
*/spectral-cube/*setup*
*/spectral-cube/*/tests/*
*/spectral-cube/tests/test_*
*/spectral-cube/extern/*
*/spectral-cube/utils/compat/*
*/spectral-cube/version*
*/spectral-cube/wcs/docstrings*
*/spectral-cube/_erfa/*

[coverage:report]
exclude_lines =
# Have to re-enable the standard pragma
pragma: no cover
# Don't complain about packages we have installed
except ImportError
# Don't complain if tests don't hit assertions
raise AssertionError
raise NotImplementedError
# Don't complain about script hooks
def main\(.*\):
# Ignore branches that don't pertain to this version of Python
pragma: py{ignore_python_version}
# Don't complain about IPython completion helper
def _ipython_key_completions_
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