[Debian-pan-maintainers] Bug#1114723: tomwer: FTBFS with NumPy 2.3
roehling at debian.org
roehling at debian.org
Mon Sep 8 20:44:43 BST 2025
Source: tomwer
Version: 1.4.8-1
Severity: important
User: debian-python at lists.debian.org
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, tomwer failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
h5py/_debian_h5py_serial/h5f.pyx:122: FileNotFoundError
------------------------------ Captured log call -------------------------------
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/scores/params.py", line 173, in load_from_dict
self.score_method = ScoreMethod.from_value(dict_["score_method"])
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/scores/params.py", line 105, in score_method
self._score_method = ScoreMethod.from_value(method)
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/saaxis/params.py", line 94, in load_from_dict
self.mode = ReconstructionMode.from_value(dict_["mode"])
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/saaxis/params.py", line 59, in mode
mode = ReconstructionMode.from_value(mode)
WARNING nxtomo.paths.nxtomo:nxtomo.py:447 version of the NXtomo not found. Will take the latest one (1.4)
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/saaxis/saaxis.py", line 433, in run
mode = ReconstructionMode.from_value(params.mode)
WARNING silx.DEPRECATION:deprecation.py:136 Function from_value is deprecated since silx version 2.1.1. Use 'Enum(value)' instead.
File "/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/reconstruction/nabu/nabucommon.py", line 208, in __init__
self._target = Target.from_value(target)
PROCESS_SUCCEED tomwer.core.process.reconstruction.saaxis.saaxis:processlog.py:60 cor scores of slice {'slice': 4} for scan NXtomo scan(master_file: tmp/tmpg5h_t7yy/tmpg5h_t7yy.h5, entry: entry) computed.
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/tomoscan/framereducer/framereducerbase.py:4
/usr/lib/python3/dist-packages/tomoscan/framereducer/framereducerbase.py:4: DeprecationWarning: numpy.core.numerictypes is deprecated and has been renamed to numpy._core.numerictypes. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.numerictypes.generic.
from numpy.core.numerictypes import generic as numy_generic
../../../../../../usr/lib/python3/dist-packages/pytools/persistent_dict.py:52
/usr/lib/python3/dist-packages/pytools/persistent_dict.py:52: RecommendedHashNotFoundWarning: Unable to import recommended hash 'siphash24.siphash13', falling back to 'hashlib.sha256'. Run 'python3 -m pip install siphash24' to install the recommended hash.
warn("Unable to import recommended hash 'siphash24.siphash13', "
../../../../../../usr/lib/python3/dist-packages/orangecanvas/utils/localization/__init__.py:5
/usr/lib/python3/dist-packages/orangecanvas/utils/localization/__init__.py:5: DeprecationWarning: import 'orangecanvas.localization', not 'orangecanvas.utils.localization'
warnings.warn(
../../../../../../usr/lib/python3/dist-packages/orangecanvas/utils/localization/si.py:5
/usr/lib/python3/dist-packages/orangecanvas/utils/localization/si.py:5: DeprecationWarning: import 'orangecanvas.localization.si', not 'orangecanvas.utils.localization.si'
warnings.warn(
tomwer/core/tests/test_utils.py::test_flat_field_normalization
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/utils/normalization.py:54: RuntimeWarning: divide by zero encountered in divide
corrrectedImage = (imgData - dark) / (flat - dark)
tomwer/core/process/tests/test_data_watcher.py: 24 warnings
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/control/datawatcher/datawatcherobserver.py:533: DeprecationWarning: isSet() is deprecated, use is_set() instead
if self.observations.scanReadyEvent.isSet():
tomwer/core/process/tests/test_data_watcher.py: 20 warnings
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/control/datawatcher/datawatcher.py:292: DeprecationWarning: isSet() is deprecated, use is_set() instead
if self.observationThread.scanReadyEvent.isSet():
tomwer/core/scan/tests/test_future_scan.py::test_simple_future_tomo_obj
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/scan/tests/test_future_scan.py:23: DeprecationWarning: There is no current event loop
future = asyncio.Future()
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
/usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
return matrix(data, dtype=dtype, copy=False)
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
tomwer/core/utils/tests/test_image.py::test_scale_img2_to_img1
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/utils/image.py:125: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
float(vec1[0]) * (img_2 * img_2) + float(vec1[1]) * img_2 + float(vec1[2])
tomwer/core/process/control/tests/test_email.py::test_format_email_info
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/control/emailnotifier.py:119: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).
"timestamp": datetime.utcnow().isoformat(timespec="seconds"),
tomwer/core/process/drac/tests/test_icat_processed_dataset.py: 54 warnings
tomwer/core/process/drac/tests/test_icat_raw_dataset.py: 16 warnings
/build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build/tomwer/core/process/drac/dracbase.py:165: DeprecationWarning: 'mode' parameter is deprecated and will be removed in Pillow 13 (2026-10-15)
img = Image.fromarray(image.astype(numpy.uint8), mode="L")
tomwer/core/process/reconstruction/tests/test_saaxis.py: 20 warnings
/usr/lib/python3.13/multiprocessing/popen_fork.py:67: DeprecationWarning: This process (pid=91) is multi-threaded, use of fork() may lead to deadlocks in the child.
self.pid = os.fork()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tomwer/core/process/reconstruction/tests/test_saaxis.py::TestSAAxisProcess::test
=========== 1 failed, 122 passed, 23 skipped, 147 warnings in 11.32s ===========
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/tomwer-1.4.8/.pybuild/cpython3_3.13_tomwer/build; python3.13 -m pytest -v tomwer/core/*/test_* tomwer/core/*/*/test_* tomwer/core/*/*/*/test_* tomwer/core/*/*/*/*/test_*
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T12:32:11Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2457366/
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/164170/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Cheers
Timo
More information about the Debian-pan-maintainers
mailing list