Hello,
I am the maintainer of silx
I have this problem with the gui application
$ silx view
Traceback (most recent call last):
File "/usr/bin/silx", line 33, in <module>
sys.exit(load_entry_point('silx==1.1.2', 'console_scripts', 'silx')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/silx/__main__.py", line 67, in main
status = launcher.execute(sys.argv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/silx/utils/launcher.py", line 294, in
execute
return command.execute(command_argv)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/silx/utils/launcher.py", line 128, in
execute
status = func(argv)
^^^^^^^^^^
File "/usr/lib/python3/dist-packages/silx/app/view/main.py", line 214, in main
mainQt(options)
File "/usr/lib/python3/dist-packages/silx/app/view/main.py", line 156, in
mainQt
import silx.gui.utils.matplotlib # noqa
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/silx/gui/utils/matplotlib.py", line 39,
in <module>
from pkg_resources import parse_version
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3328,
in <module>
@_call_aside
^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3303,
in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3341,
in _initialize_master_working_set
working_set = WorkingSet._build_master()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 631, in
_build_master
ws.require(__requires__)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 969, in
require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 829, in
resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 871, in
_resolve_dist
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'h5py' distribution was not found and
is required by 'hdf5plugin silx'
So the entry point do not find the h5py package even if python3-h5py is
installed via python3-h5py-serial
I reported the issue to the h5py maintainer via this bug report.
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1051781
This package is a bit special since it provide a serial implementation
python3-h5py-serial and an MPI one via the
python3-h5py-mpi. both packages are co-installable.
In each of these packages there is an
/usr/lib/python3/dist-packages/h5py._debian_h5py_serial-3.7.0.dist-info/METADATA
/usr/lib/python3/dist-packages/h5py._debian_h5py_serial-3.7.0.dist-info/RECORD
/usr/lib/python3/dist-packages/h5py._debian_h5py_serial-3.7.0.dist-info/WHEEL
/usr/lib/python3/dist-packages/h5py._debian_h5py_serial-3.7.0.dist-info/top_level.txt
and
/usr/lib/python3/dist-packages/h5py._debian_h5py_mpi-3.7.0.dist-info/METADATA
/usr/lib/python3/dist-packages/h5py._debian_h5py_mpi-3.7.0.dist-info/RECORD
/usr/lib/python3/dist-packages/h5py._debian_h5py_mpi-3.7.0.dist-info/WHEEL
/usr/lib/python3/dist-packages/h5py._debian_h5py_mpi-3.7.0.dist-info/top_level.txt
On Debian the two versions are named h5py._debian_h5py_serial and
h5py._debian_h5py_mpi
This organisation is specific to Debian since upstream provide only one version
of the h5py package.
On Debian we are able to co-install and MPI and a serial version of this
library linked
to the serial or mpi version of the hdf5 library.
the differences are
$ diff
/usr/lib/python3/dist-packages/h5py._debian_h5py_serial-3.7.0.dist-info/METADATA
/usr/lib/python3/dist-packages/h5py._debian_h5py_mpi-3.7.0.dist-info/METADATA
2c2
< Name: h5py.-debian-h5py-serial
---
> Name: h5py.-debian-h5py-mpi
30a31
> Requires-Dist: mpi4py (>=3.0.2)
so the name and a dependecy to the mpi4py package.
for the RECORD part the installed files are located in two different
directory, so they are totally different.
top_level.txt WHEEL are identical
There is a generic python3-h5py which is used in the B-D of packages depending
on h5py.
It is almost empty but depends on one of the two implementations.
$ dpkg -L python3-h5py
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/python3-h5py
/usr/share/doc/python3-h5py/README.Debian
/usr/share/doc/python3-h5py/README.rst
/usr/share/doc/python3-h5py/changelog.Debian.gz
/usr/share/doc/python3-h5py/copyright
$ apt show python3-h5py
Package: python3-h5py
Version: 3.7.0-8
Priority: optional
Section: python
Source: h5py
Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Installed-Size: 22,5 kB
Depends: python3-h5py-serial | python3-h5py-mpi
This package does not provide a dist-info named h5py. So all entry points which
depends on h5py will failed (like silx)
bookworm is affected by this issue. Nevertheless I do not know how many
packages have this issue, the rdepends on python3-h5py is like this
Dépend: dioptas
Dépend: invesalius
Dépend: mcaller
Dépend: ont-fast5-api
Dépend: pbhoney
Dépend: poretools
Dépend: pycoqc
Dépend: pyfr
Dépend: python3-anndata (>= 3)
Dépend: python3-astrodendro (>= 0.2.0)
Dépend: python3-bayespy
Dépend: python3-binoculars
Dépend: python3-biom-format
Dépend: python3-bioxtasraw
Dépend: python3-bmtk
Dépend: python3-cooler (>= 2.5)
Dépend: python3-dipy
Dépend: python3-fabio
Dépend: python3-genx
Dépend: python3-glue (>= 2.10)
Dépend: python3-guidata (>= 3.0)
Dépend: python3-h5netcdf
Dépend: python3-hdf5plugin
Dépend: python3-hdf5storage
Dépend: python3-hdf-compass
Dépend: python3-hdmf (>= 2.10)
Dépend: python3-hdmf (<< 4)
Dépend: python3-hickle (>= 2.10.0)
Dépend: python3-hydroffice.bag
Dépend: python3-hyperspy (>= 2.3)
Dépend: python3-keras
Dépend: python3-keras-applications
Dépend: python3-loompy
Dépend: python3-mintpy
Dépend: python3-mofapy
Dépend: python3-nabu (>= 3.0)
Dépend: python3-openems
Dépend: python3-pyfai
Dépend: python3-pygac
Dépend: python3-pyhst2-cuda
Dépend: python3-pymca5
Dépend: python3-pynwb (>= 2.9~)
Dépend: python3-pyspectral
Dépend: python3-sardana
Dépend: python3-sasdata
Dépend: python3-sasview
Dépend: python3-silx
Dépend: python3-skbio (>= 3.6.0)
Dépend: python3-taurus
Dépend: python3-tomoscan (>= 3.0)
Dépend: python3-unifrac (>= 3.3.0)
Dépend: python3-xraylarch (>= 3.2)
Dépend: python3-xrayutilities
Dépend: python3-yt
Dépend: q2-feature-table
Dépend: q2-quality-control
Dépend: q2-types
Dépend: siconos-mechanics-tools (>= 2.8.0-1)
Dépend: tombo
Est en conflit avec: python3-h5py-serial (<< 2.10.0-3~)
python3-h5py
Recommande: pan-data-reduction-frameworks
Recommande: pizzly
Recommande: pysph-viewer
Recommande: python3-bcbio
Recommande: python3-geotiepoints
Recommande: python3-meshio
Recommande: python3-pbcore
Recommande: python3-satpy
Reverse Depends:
Suggère: python3-astropy
Suggère: python3-dask
Suggère: python3-h5py-mpi
Suggère: python3-h5py-serial
Suggère: python3-klepto
Suggère: python3-veusz
Suggère: python3-vigra
Suggère: python3-zarr
Suggère: science-nanoscale-physics-dev
- The dependencies are expected to be h5py in all upstream projects. So my
question is how do we provide this egg info , should we use alternative in
order to create the dist-info depending on the packages installed. Is
alternative the right tool for this use case ?
- Is it possible or a desirable expectation from dh_python to failed if there
is entry point expecting no available dist of egg info ? This way we will not
provide non working packages.
- or a lintian check would be more appropriate for this purpose ?
- how do we fix bookworm ?
thanks for your time
Frederic
