Package: src:mdanse Version: 2.0.1-2 User: [email protected] Usertags: python3.15 Tags: patch, ftbfs, forky, sid Severity: important
Hi! While rebuilding the python related packages against the Python 3.15rc2 version we found that mdanse fails to build from source [1]. The error is: E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/usr/lib/python3/dist-packages/rdkit/__init__.py This happened because rdkit is only building against the default Python version (3.14 in this case), while mdanse is trying to build against all versions. However, while looking into this I realized that there's no reason this package should be arch:any, it should be arch:all instead. Switching to arch:all and dropping the unused related dependencies makes the package build successfully. In the process of looking into this issue, I also ran into a test error tolerance problem when building in arm64. By moving to arch:all that issue will likely not be visible, but it's still good to make it possible to build mdanse on arm64. I've applied these fixes in the sandbox [2] to verify that it builds successfully, please consider applying the patch to support the upcoming 3.15 version. Setting the severity to important for now. Once Python 3.15 is released, it will be added to python3-defaults and this bug will become release critical. Happy hacking, [1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4749251/ [2]: https://debusine.debian.net/debian/r-python-python3.15/ -- "Can you imagine what I would do if I could do all I can?" -- Sun Tzu Saludos /\/\ /\ >< `/
diff --git a/debian/changelog b/debian/changelog index 8ba5fe50..9eb0010c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,11 @@ +mdanse (2.0.1-3) UNRELEASED; urgency=medium + + * Team upload. + * Build python3-mdanse as arch:all + * Add patch to relax the test tolerance + + -- Maximiliano Curia <[email protected]> Fri, 18 Sep 2026 11:46:02 +0200 + mdanse (2.0.1-2) unstable; urgency=medium * Fix d/copyright syntax. diff --git a/debian/control b/debian/control index 534e72f7..9b5208e9 100644 --- a/debian/control +++ b/debian/control @@ -7,11 +7,9 @@ Section: science Build-Depends: debhelper-compat (= 13), dh-sequence-python3, - cython3, dbus-daemon <!nocheck>, pybuild-plugin-pyproject, python3-all, - python3-all-dev, python3-ase <!nocheck>, python3-h5py <!nocheck>, python3-mdanalysis, @@ -33,12 +31,11 @@ Vcs-Git: https://salsa.debian.org/science-team/mdanse.git Package: python3-mdanse Section: python -Architecture: any +Architecture: all Depends: python3-rdkit (>= 202503.1-5~), ${misc:Depends}, ${python3:Depends}, - ${shlibs:Depends}, python3-vtk9, Description: Molecular Dynamics Analysis for Neutron Scattering Experiments This is the module containing the command-line utilities and diff --git a/debian/patches/relax-test-tolerance.patch b/debian/patches/relax-test-tolerance.patch new file mode 100644 index 00000000..4624547f --- /dev/null +++ b/debian/patches/relax-test-tolerance.patch @@ -0,0 +1,19 @@ +Description: Relax tolerance for DynamicCoherentStructureFactor test + On architectures such as arm64, floating point differences cause a maximum + absolute difference of ~1.1e-5 in the ideal DCSF dataset, which slightly + exceeds the atol=1e-5 tolerance. Relax atol to 2e-5. +Author: Maximiliano Curia <[email protected]> +Forwarded: no +Last-Update: 2026-09-18 + +--- a/MDANSE/Tests/UnitTests/Analysis/test_grouping.py ++++ b/MDANSE/Tests/UnitTests/Analysis/test_grouping.py +@@ -113,7 +113,7 @@ + ("PairDistributionFunction", ["pdf", "rdf", "tcf"], "equal", 1e-10, 1e-7), + ("StaticStructureFactor", ["ssf"], "equal", 1e-10, 1e-7), + ("XRayStaticStructureFactor", ["xssf"], "equal", 1e-10, 1e-7), +- ("DynamicCoherentStructureFactor", ["dcsf"], "b_coherent", 1e-5, 1e-4), ++ ("DynamicCoherentStructureFactor", ["dcsf"], "b_coherent", 2e-5, 1e-4), + ("CurrentCorrelationFunction", ["ccf"], "b_coherent", 1e-6, 1e-7), + ("DynamicIncoherentStructureFactor", ["disf"], "b_incoherent", 1e-10, 1e-7), + ("ElasticIncoherentStructureFactor", ["eisf"], "b_incoherent", 1e-10, 1e-7), diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 00000000..cab0e035 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +relax-test-tolerance.patch
-- debian-science-maintainers mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
