Debian Bug report logs - #994617
h5py: please be more forgiving about mismatching HDF5 versions

Toggle useless messages

Message #3 received at submit@bugs.debian.org (full text, mbox, reply):

From: Mattia Rizzolo <mattia@debian.org>

To: submit@bugs.debian.org

Subject: h5py: please be more forgiving about mismatching HDF5 versions

Date: Sat, 18 Sep 2021 18:13:54 +0200

[Message part 1 (text/plain, inline)]

Package: python3-h5py
Version: 3.3.0-2
Severity: minor

Dear maintainer,

I'm currently seeting this while running a python's package testsuite:

=============================== warnings summary ===============================
../../../../../usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py:36

  /usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py:36: UserWarning: h5py is running against HDF5 1.10.7 when it was built against 1.10.6, this may cause problems
    _warn(("h5py is running against HDF5 {0} when it was built against {1}, "


-- Docs: https://docs.pytest.org/en/stable/warnings.html


Now, whilst I appreciate that might be true for really different
versions, the concept of ABI is there for a reason, and I trust the
Debian's package version restrictions to prevent me from installing a
combination of hdf5 and h5py that is incompatible.

As such, I'd ask if you could either disable that warning, or at least
make it emit is only when there is a really different version that could
indeed cause problem.

Thank you.

-- 
regards,
                        Mattia Rizzolo

GPG Key: 66AE 2B4A FCCF 3F52 DA18  4D18 4B04 3FCD B944 4540      .''`.
More about me:  https://mapreri.org                             : :'  :
Launchpad user: https://launchpad.net/~mapreri                  `. `'`
Debian QA page: https://qa.debian.org/developer.php?login=mattia  `-

[signature.asc (application/pgp-signature, inline)]

Message #8 received at 994617@bugs.debian.org (full text, mbox, reply):

From: Drew Parsons <dparsons@debian.org>

To: Debian Bug Tracking System <994617@bugs.debian.org>

Subject: Re: h5py: please be more forgiving about mismatching HDF5 versions

Date: Thu, 04 Nov 2021 01:48:34 +0100

Source: h5py
Followup-For: Bug #994617

Hi Mattia, historically hdf5 has not been entirely ABI-stable, see 
https://forum.hdfgroup.org/t/c-c-abi-stability-and-binary-compatibility-between-patch-versions/5312
https://forum.hdfgroup.org/t/another-abi-breakage/5503

The test was added in https://github.com/h5py/h5py/pull/867
Not entirely clear what the context of the test is (the upstream
issues references in the PR seem to discuss being unable to read the
libhdf5 version on Windows).

But the h5py test was added in 2017, while HDF5 was still discussion
ABI [in]stability in 2019. But 1.10.2 and 1.10.3 were released in
2018, after which HDF5 seems to be identifying ABI correctly.

They include binary compatibility reports in their Release Notes
e.g.
https://portal.hdfgroup.org/display/support/HDF5%201.10.8#compatibility1108

https://portal.hdfgroup.org/display/support/HDF5%201.10.3#compatibility
identifies an incompatibility between 1.10.2 and 1.10.3
HDF5 1.10.3 introduced ABI 103

But their binary incompatibilities seem to be correctly reflected in
ABI sonames.  The discussion in 2019 addressed 1.10.1 and 1.10.2. They
considered 1.10.2 the proper stable release (in 2018), and updated the ABI for
1.10.3 as needed (also in 2018).

python3-h5py-serial and python3-h5py-mpi declare their dependency on
the appropriate ABI-versioned libhdf5 so you're right, that should
capture compatibility satisfactorily.


So should be safe to relax the runtime version test.
I'll keep the spirit of it by reducing it to a minor version
comparison.

Drew

Message #13 received at 994617-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 994617-close@bugs.debian.org

Subject: Bug#994617: fixed in h5py 3.3.0-4

Date: Thu, 04 Nov 2021 01:50:27 +0000

Source: h5py
Source-Version: 3.3.0-4
Done: Drew Parsons <dparsons@debian.org>

We believe that the bug you reported is fixed in the latest version of
h5py, 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 994617@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Drew Parsons <dparsons@debian.org> (supplier of updated h5py 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Thu, 04 Nov 2021 02:27:38 +0100
Source: h5py
Architecture: source
Version: 3.3.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Closes: 994617 998215
Changes:
 h5py (3.3.0-4) unstable; urgency=medium
 .
   * Team upload.
   * add debian patches
     - skip_ros_test_no_net.patch skips test_ros3 (catches OSError) if
       network is not available. Needed since libhdf5 is now built with
       ROS (S3) support, but network access is not available on buildd
       servers. Closes: #998215.
     - relax_hdf5_version_test.patch relaxes HDF5 version test to only
       compare major.minor version.  Patches can be assumed to be
       compatibility (will depend on libhdf5 ABI-versioned library
       packages in any case). Closes: #994617.
   * remove deprecated windows/stdint.h from debian/copyright
   * suppress pytest-xvfb with -p no:xvfb not --no-xvfb
Checksums-Sha1:
 d8b4f40c8b3beefac6c98b108281c1cc4fe0d74a 2729 h5py_3.3.0-4.dsc
 4f8798ea0ca10387e74b2d118aa96b831933001f 18388 h5py_3.3.0-4.debian.tar.xz
Checksums-Sha256:
 9af672406d2d9663e3fea2723d4b337e99692309b86b692d979526eb0c74ef3e 2729 h5py_3.3.0-4.dsc
 cff913c029c6e9c4283826d8090f78b9e57bbe9b5392aecd772a7dadc88c2687 18388 h5py_3.3.0-4.debian.tar.xz
Files:
 23265784baf80589e938efd28b6a31ec 2729 python optional h5py_3.3.0-4.dsc
 ed9a7443ff70e78465e352db2a5078a7 18388 python optional h5py_3.3.0-4.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=F7sj
-----END PGP SIGNATURE-----

Send a report that this bug log contains spam.