Your message dated Fri, 10 Jan 2025 16:01:40 +0000
with message-id <[email protected]>
and subject line Bug#1092352: fixed in spectral-cube 0.6.5-7
has caused the Debian Bug report #1092352,
regarding FTBFS: test_oned_collapse_beams[True] fails
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1092352: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1092352
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: spectral-cube
Version: 0.6.5-6
Severity: serious
Tags: patch
Justification: ftbfs
Forwarded: https://github.com/radio-astro-tools/spectral-cube/issues/935
spectral-cube FTBFS in unstable due to a change somewhere between
python3-dask 2024.5.2+dfsg-1 and 2024.12.1+dfsg-1. (This dask upload
and the associated dask.distributed upload fix four other RC bugs
between them, so I'm keen to get them into testing.) Here's the test
log:
I: pybuild base:311: cd
/build/reproducible-path/spectral-cube-0.6.5/.pybuild/cpython3_3.13_spectral-cube/build;
python3.13 -m pytest
============================= test session starts
==============================
platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
rootdir: /build/reproducible-path/spectral-cube-0.6.5
configfile: setup.cfg
plugins: doctestplus-1.3.0, astropy-header-0.2.2, arraydiff-0.6.1,
astropy-0.11.0, remotedata-0.4.1, mock-3.14.0, filter-subpackage-0.2.0,
typeguard-4.4.1, hypothesis-6.122.1, cov-5.0.0
collected 1719 items
spectral_cube/spectral_axis.py . [
0%]
spectral_cube/tests/test_analysis_functions.py ................... [
1%]
spectral_cube/tests/test_casafuncs.py ......sssssssssssssss [
2%]
spectral_cube/tests/test_cube_utils.py ....... [
2%]
spectral_cube/tests/test_dask.py .s..s.......s [
3%]
spectral_cube/tests/test_io.py ....................... [
4%]
spectral_cube/tests/test_masks.py ...................................... [
7%]
...............................................XX.... [
10%]
spectral_cube/tests/test_moments.py .................................... [
12%]
........................................................................ [
16%]
........................................................................ [
20%]
........ [
21%]
spectral_cube/tests/test_performance.py ...s.. [
21%]
spectral_cube/tests/test_projection.py .......................x......... [
23%]
.....xxx.......x........................................................ [
27%]
.................. [
28%]
spectral_cube/tests/test_regrid.py ..........ssss....s.................s [
30%]
ss....sssssssssssss [
31%]
spectral_cube/tests/test_spectral_axis.py .............................. [
33%]
...................... [
34%]
spectral_cube/tests/test_spectral_cube.py .............................. [
36%]
........................................................................ [
40%]
........................................................................ [
45%]
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49%]
..............................s.....s...........sssss................... [
53%]
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57%]
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61%]
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65%]
ssssssss......ssssssssssss......ssssssssssss......ssssss................ [
70%]
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74%]
..ssssss......ssssssssssss......ssssssssssss......ssssssssssss......ssss [
78%]
ssssssss......ssssss.................................s.s.F............xx [
82%]
xx....................................................................ss [
86%]
ss............................xxxxxxxx..............sss................. [
91%]
....... [
91%]
spectral_cube/tests/test_stokes_spectral_cube.py ....................... [
92%]
........................................................................ [
97%]
..... [
97%]
spectral_cube/tests/test_subcubes.py ..ssssssssssssssssssss [
98%]
spectral_cube/tests/test_visualization.py ....ssssssss [
99%]
spectral_cube/tests/test_wcs_utils.py ............
[100%]
=================================== FAILURES
===================================
________________________ test_oned_collapse_beams[True]
________________________
data_sdav_beams =
PosixPath('/tmp/pytest-of-cjwatson/pytest-0/test_oned_collapse_beams_True_0/sdav_beams.fits')
use_dask = True
def test_oned_collapse_beams(data_sdav_beams, use_dask):
# Check that an operation along the spatial dims returns an
appropriate
# spectrum
cube, data = cube_and_raw(data_sdav_beams, use_dask=use_dask)
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = cube.mean(axis=(1,2))
assert isinstance(spec, VaryingResolutionOneDSpectrum)
# data has a redundant 1st axis
> np.testing.assert_equal(spec.value, data.mean(axis=(1,2,3)))
spectral_cube/tests/test_spectral_cube.py:1531:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_
args = (<built-in function eq>, array([0.49465334, 0.53732362, 0.37316832,
0.35550457]), array([0.49465334, 0.53732362, 0.37316832, 0.35550457]))
kwds = {'err_msg': '', 'header': 'Arrays are not equal', 'strict': False,
'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not equal
E
E Mismatched elements: 1 / 4 (25%)
E Max absolute difference: 1.11022302e-16
E Max relative difference: 2.06620925e-16
E x: array([0.494653, 0.537324, 0.373168, 0.355505])
E y: array([0.494653, 0.537324, 0.373168, 0.355505])
/usr/lib/python3.13/contextlib.py:85: AssertionError
----------------------------- Captured stderr call
-----------------------------
WARNING: StokesWarning: Cube is a Stokes cube, returning spectral cube for I
component [spectral_cube.io.core]
------------------------------ Captured log call
-------------------------------
WARNING astropy:logger.py:244 StokesWarning: Cube is a Stokes cube,
returning spectral cube for I component
=========================== short test summary info
============================
FAILED
spectral_cube/tests/test_spectral_cube.py::test_oned_collapse_beams[True]
= 1 failed, 1487 passed, 212 skipped, 17 xfailed, 2 xpassed in 257.65s
(0:04:17) =
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/build/reproducible-path/spectral-cube-0.6.5/.pybuild/cpython3_3.13_spectral-cube/build;
python3.13 -m pytest
(3.12 behaves the same way; I've omitted it for brevity.)
This looks like the first issue in
https://github.com/radio-astro-tools/spectral-cube/issues/935. I tried
cherry-picking a couple of patches from there, and that fixed it. Would
you consider doing the same in unstable? I've attached a possible
debdiff.
Thanks,
--
Colin Watson (he/him) [[email protected]]
diff -Nru spectral-cube-0.6.5/debian/changelog
spectral-cube-0.6.5/debian/changelog
--- spectral-cube-0.6.5/debian/changelog 2024-12-17 07:12:11.000000000
+0000
+++ spectral-cube-0.6.5/debian/changelog 2025-01-07 14:19:23.000000000
+0000
@@ -1,3 +1,10 @@
+spectral-cube (0.6.5-6.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * mean -> nanmean in failing test (closes: #-1).
+
+ -- Colin Watson <[email protected]> Tue, 07 Jan 2025 14:19:23 +0000
+
spectral-cube (0.6.5-6) unstable; urgency=medium
* Remove six dependency (Closes: #1090171)
diff -Nru spectral-cube-0.6.5/debian/patches/series
spectral-cube-0.6.5/debian/patches/series
--- spectral-cube-0.6.5/debian/patches/series 2024-12-17 07:11:57.000000000
+0000
+++ spectral-cube-0.6.5/debian/patches/series 2025-01-07 14:19:23.000000000
+0000
@@ -6,3 +6,4 @@
Don-t-run-LMV-test-on-big-endian-archs.patch
Fix-test-for-Astropy-7.patch
Remove-six-dependency.patch
+test-nanmean.patch
diff -Nru spectral-cube-0.6.5/debian/patches/test-nanmean.patch
spectral-cube-0.6.5/debian/patches/test-nanmean.patch
--- spectral-cube-0.6.5/debian/patches/test-nanmean.patch 1970-01-01
01:00:00.000000000 +0100
+++ spectral-cube-0.6.5/debian/patches/test-nanmean.patch 2025-01-07
14:19:23.000000000 +0000
@@ -0,0 +1,25 @@
+From: "Adam Ginsburg (keflavich)" <[email protected]>
+Date: Mon, 6 Jan 2025 11:13:06 -0500
+Subject: mean -> nanmean in failing test
+
+Origin: other,
https://github.com/radio-astro-tools/spectral-cube/pull/929/commits/63d92273e7f423afd1f9080db93a95300a9a5064
+Origin: other,
https://github.com/radio-astro-tools/spectral-cube/pull/929/commits/beb1233fb51cbbf8c3199a72512a37971f25b1d2
+Last-Update: 2025-01-07
+---
+ spectral_cube/tests/test_spectral_cube.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/spectral_cube/tests/test_spectral_cube.py
b/spectral_cube/tests/test_spectral_cube.py
+index bbc1aaa..4ccd135 100644
+--- a/spectral_cube/tests/test_spectral_cube.py
++++ b/spectral_cube/tests/test_spectral_cube.py
+@@ -1528,7 +1528,8 @@ def test_oned_collapse_beams(data_sdav_beams, use_dask):
+ spec = cube.mean(axis=(1,2))
+ assert isinstance(spec, VaryingResolutionOneDSpectrum)
+ # data has a redundant 1st axis
+- np.testing.assert_equal(spec.value, data.mean(axis=(1,2,3)))
++ # we changed to assert_almost_equal in 2025 because, for no known reason,
epsilon-level differences crept in
++ np.testing.assert_almost_equal(spec.value, np.nanmean(data, axis=(1,2,3)))
+ assert cube.unit == spec.unit
+ assert spec.header['BUNIT'] == cube.header['BUNIT']
+
--- End Message ---
--- Begin Message ---
Source: spectral-cube
Source-Version: 0.6.5-7
Done: Ole Streicher <[email protected]>
We believe that the bug you reported is fixed in the latest version of
spectral-cube, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Ole Streicher <[email protected]> (supplier of updated spectral-cube package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 10 Jan 2025 14:12:25 +0100
Source: spectral-cube
Architecture: source
Version: 0.6.5-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Astronomy Team
<[email protected]>
Changed-By: Ole Streicher <[email protected]>
Closes: 1092352
Changes:
spectral-cube (0.6.5-7) unstable; urgency=medium
.
[ Colin Watson ]
* mean -> nanmean in failing test (Closes: #1092352)
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