Bug#1003040: ITP: asdf-astropy -- ASDF serialization support for astropy

[Ole Streicher]

Package: wnpp
Severity: wishlist
Owner: Ole Streicher 
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-python@lists.debian.org, 
debian-as...@lists.debian.org

* Package name: asdf-astropy
  Version : 0.1.2
  Upstream Author : The ASDF Developers
* URL : https://github.com/astropy/asdf-astropy
* License : BSD-3-Clause
  Programming Lang: Python
  Description : ASDF serialization support for astropy

This package includes plugins that provide ASDF serialization support
for astropy objects. The plugins are automatically enabled when the
package is installed. ASDF (Advanced Scientific Data Format) is a
proposed next generation interchange format for scientific data,
mainly used by the Space Telescope Science Institude (STScI).

It is a new build dependency of the gwcs package. I will
maintain it within the Debian Astro team in Salsa:

https://salsa.debian.org/debian-astro-team/asdf-astropy

Best regards

Ole

Re: DPT repositories checks/"violations" report

[Scott Kitterman]

On Sunday, January 2, 2022 7:50:02 PM EST Louis-Philippe Véronneau wrote:
> On 2021-12-12 01 h 23, Sandro Tosi wrote:
> 
> >> I think there's still one point we need to figure out: how to make
> >> these remarks known to the packages maintainers, instead of all of
> >> them just being in a text file.
> > 
> > 
> > This is still an open point, and i welcome ideas
> 
> 
> Is there a reason why we shouldn't just file bugs in the BTS? I get it's
> not the perfect tool for that, but it would certainly help reach the
> maintainers.
> 
> Using a common usertag would also make it easier to find and fix these
> issues en masse ;)

Since this is all about team Git repositories, someone should just fix them 
(modulo the one about using pypi, which I think we mostly agree isn't 
something someone unfamiliar with the package can 'fix').

Scott K

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Re: sphinxext-opengraph new upstream version and tests

[Chiara Marmo]

Thanks Jeroen for your comments and clarifications.

Using @builddeps@ may seem attractive at first, but is best reserved
> for autopkgtests that actually do a full build. In most other cases
> redundant extra stuff gets installed that's only needed at build
> time, such as dh-python and setuptools in this case.
>

I believe I have reduced the dependencies to the ones needed for the tests.

The debhelper compat level could do with a bump to the current
> version. Other than that, things look fine.
>

Version bumped.

Ready for upload?
Thanks!
Best,

Chiara

Re: DPT repositories checks/"violations" report

[Louis-Philippe Véronneau]

On 2021-12-12 01 h 23, Sandro Tosi wrote:
>> I think there's still one point we need to figure out: how to make
>> these remarks known to the packages maintainers, instead of all of
>> them just being in a text file.
> 
> This is still an open point, and i welcome ideas

Is there a reason why we shouldn't just file bugs in the BTS? I get it's
not the perfect tool for that, but it would certainly help reach the
maintainers.

Using a common usertag would also make it easier to find and fix these
issues en masse ;)

-- 
  ⢀⣴⠾⠻⢶⣦⠀
  ⣾⠁⢠⠒⠀⣿⡁  Louis-Philippe Véronneau
  ⢿⡄⠘⠷⠚⠋   po...@debian.org / veronneau.org
  ⠈⠳⣄


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Re: Transfering packages from Debian Med to DPT (Was: Please enable me transfering python-bioblend to Debian Med team)

[Andreas Tille]

Am Sun, Jan 02, 2022 at 11:25:40AM +0100 schrieb Andreas Tille:
> Am Sun, Jan 02, 2022 at 10:00:09AM +0100 schrieb Andreas Tille:
> > ...
> Continuing with moving packages from Debian Med to Debian Python Team
 
> python-duckpy 3.2.0-2
> python3-duckpy : simple Python library for searching on DuckDuckGo

Moved to Debian Python Team

> python-easydev 0.12.0+dfsg-1
> python3-easydev : common utilities to ease the development of
> Python packages (Python 3)

Moved to Debian Python Team

> python-etelemetry 0.2.0-4
> python3-etelemetry : lightweight Python3 client to communicate
> with the etelemetry server

That's pretty clearly a Debian Med topic

> python-hdmedians 0.14.2-3
> python3-hdmedians : high-dimensional medians in Python3

Moved to Debian Python Team

> python-leidenalg 0.8.8-1
> python3-leidenalg : Python3 implementation of the Leiden algorithm in C++

Seems pretty related to Debian Med topic even if not that obvious.

> python-lzstring 1.0.4-1.1
> python3-lzstring : LZ-based compression algorithm for Python
> (Python 3 version)

Moved to Debian Python Team

> python-matplotlib-venn 0.11.6-2
> python3-matplotlib-venn : Python 3 plotting area-proportional two-
> and three-way Venn diagrams

Moved to Debian Python Team

> python-multipletau 0.3.3+ds-3
> python-multipletau-doc : documentation for multipletau Python module
> python3-multipletau : multiple-tau algorithm for Python3/NumPy

Moved to Debian Python Team

> python-multisplitby 0.0.1-4
> python3-multisplitby : Python3 module to create iterables split on
> arbitrary separators

Moved to Debian Python Team

> python-ncls 0.0.63+ds-1
> python3-ncls : datastructure for interval overlap queries

Moved to Debian Python Team

> python-pipdeptree 2.2.0-2
> python3-pipdeptree : display dependency tree of the installed
> Python 3 packages

Moved to Debian Python Team

> python-pyflow 1.1.20-3
> python3-pyflow : lightweight parallel task engine for Python

Workflows are a very hot topic in Debian Med team.  If there is no strong
reason to move this package to Debian Python team I'd prefer to leave it
where it is.

> python-pynndescent 0.5.2+dfsg-1
> python3-pynndescent : nearest neighbor descent for approximate
> nearest neighbors

Moved to Debian Python Team Git but source does not build - most
possibly due problems with Python3.10 and numba.  The latest upstream
version fails as well (with even more errors).  I'd be happy if someone
from Debian Python Team could serve as Uploader and care for this.

> python-pypubsub 4.0.3-5
> python3-pubsub : Python 3 publish-subcribe library

Moved to Debian Python Team

I'll continue with the next batch soon.

Kind regards

  Andreas.

> python-sinfo 0.3.1-2
> python3-sinfo : print different version information for loaded modules
> python-spectra 0.0.11-3
> python3-spectra : Easy color scales and color conversion for
> Python (Python 3 version)
> python-stdlib-list 0.8.0-4
> python3-stdlib-list : List of Python Standard Libraries (2.6-7, 3.2-9)
> python-streamz 0.6.3-1
> python3-streamz : build pipelines to manage continuous streams of data
> python-stubserver 1.1-2
> python3-stubserver : mock tester of external web dependencies for Python
> python-tinyalign 0.2-5
> python3-tinyalign : numerical representation of differences between 
> strings
> python-typechecks 0.1.0+ds-2
> python3-typechecks : express constraints on types
> python-upsetplot 0.6.0-2
> python3-upsetplot : Draw Lex et al.'s UpSet plots with Pandas and 
> Matplotlib
> python-wdlparse 0.1.0-2
> python3-wdlparse : Workflow Description Language (WDL) parser for Python
> python-wordcloud 1.8.1+dfsg-2
> python3-wordcloud : little word cloud generator in Python
> python-xopen 1.2.1-3
> python3-xopen : Python3 module to open compressed files transparently
> smart-open 5.2.1-3
> python3-smart-open : utils for streaming large files
> sorted-nearest 0.0.31+dfsg-1
> python3-sorted-nearest : Cython helper library for pyranges
> sphinxcontrib-autoprogram 0.1.7-1
> python3-sphinxcontrib.autoprogram : automated documentation of CLI
> programs for Sphinx (Python 3)
> 
> Thanks,
> -- 
> Sandro "morph" Tosi
> My website: http://sandrotosi.me/
> Me at Debian: http://wiki.debian.org/SandroTosi
> Twitter: https://twitter.com/sandrotosi
> 

-- 
http://fam-tille.de

Re: sphinxext-opengraph new upstream version and tests

[Jeroen Ploemen]

On Fri, 31 Dec 2021 17:25:34 -1000
Chiara Marmo  wrote:

> I think the configuration is better now, as the CI passed too.

Using @builddeps@ may seem attractive at first, but is best reserved
for autopkgtests that actually do a full build. In most other cases
redundant extra stuff gets installed that's only needed at build
time, such as dh-python and setuptools in this case.

In addition, python packages that run tests at build time typically
have the full set of module dependencies as build-deps that one also
expects to find as deps on the (main) binary pkg. For such packages,
using @builddeps@ causes dependencies of the package being tested to
get duplicated as test deps, meaning any missing ones - for example
resulting from a packaging or helper application bug - could easily
be overlooked. After all, the autopkgtest would pass even for a
severely broken binary package with all python deps missing.

> Please let me know if the package is ready for the upload.

The debhelper compat level could do with a bump to the current
version. Other than that, things look fine.

> Also, happy new year 2022 to all the people on the list!

Indeed!


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Re: Transfering packages from Debian Med to DPT (Was: Please enable me transfering python-bioblend to Debian Med team)

[Andreas Tille]

Am Sun, Jan 02, 2022 at 10:00:09AM +0100 schrieb Andreas Tille:
> ...
Continuing with moving packages from Debian Med to Debian Python Team

> > python-ciso8601 2.2.0-1
> > python3-ciso8601 : fast ISO8601 date time parser for Python written in C

Moved to Debian Python Team

> > python-colormap 1.0.4-2
> > python3-colormap : ease manipulation of matplotlib colormaps and
> > color codecs (Python 3)

Moved to Debian Python Team

> > python-colormath 3.0.0-1.1
> > python3-colormath : Abstracts common color math operations (Python
> > 3 version)

Moved to Debian Python Team 

> > python-cooler 0.8.11-1
> > python3-cooler : library for a sparse, compressed, binary persistent 
> > storage
> > python3-cooler-examples : library for a sparse, compressed, binary
> > persistent storage (examples)

Should remain in Debian Med team (see
   https://lists.debian.org/debian-python/2022/01/msg2.html )

> > python-depinfo 1.7.0-1
> > python3-depinfo : retrieve and print Python 3 package dependencies

Moved to Debian Python Team 

> > python-fitbit 0.3.1-2
> > python-fitbit-doc : FitBit REST API Client Implementation - 
> > Documentation
> > python3-fitbit : FitBit REST API Client Implementation - Python 3

Should remain in Debian Med team (see   


https://lists.debian.org/debian-python/2022/01/msg2.html )  

  

Will be continued later.

Kind regards

Andreas.

> > python-duckpy 3.2.0-2
> > python3-duckpy : simple Python library for searching on DuckDuckGo
> > python-easydev 0.12.0+dfsg-1
> > python3-easydev : common utilities to ease the development of
> > Python packages (Python 3)
> > python-etelemetry 0.2.0-4
> > python3-etelemetry : lightweight Python3 client to communicate
> > with the etelemetry server
> > python-hdmedians 0.14.2-3
> > python3-hdmedians : high-dimensional medians in Python3
> > python-leidenalg 0.8.8-1
> > python3-leidenalg : Python3 implementation of the Leiden algorithm in 
> > C++
> > python-lzstring 1.0.4-1.1
> > python3-lzstring : LZ-based compression algorithm for Python
> > (Python 3 version)
> > python-matplotlib-venn 0.11.6-2
> > python3-matplotlib-venn : Python 3 plotting area-proportional two-
> > and three-way Venn diagrams
> > python-multipletau 0.3.3+ds-3
> > python-multipletau-doc : documentation for multipletau Python module
> > python3-multipletau : multiple-tau algorithm for Python3/NumPy
> > python-multisplitby 0.0.1-4
> > python3-multisplitby : Python3 module to create iterables split on
> > arbitrary separators
> > python-ncls 0.0.63+ds-1
> > python3-ncls : datastructure for interval overlap queries
> > python-pipdeptree 2.2.0-2
> > python3-pipdeptree : display dependency tree of the installed
> > Python 3 packages
> > python-pyflow 1.1.20-3
> > python3-pyflow : lightweight parallel task engine for Python
> > python-pynndescent 0.5.2+dfsg-1
> > python3-pynndescent : nearest neighbor descent for approximate
> > nearest neighbors
> > python-pypubsub 4.0.3-5
> > python3-pubsub : Python 3 publish-subcribe library
> > python-sinfo 0.3.1-2
> > python3-sinfo : print different version information for loaded modules
> > python-spectra 0.0.11-3
> > python3-spectra : Easy color scales and color conversion for
> > Python (Python 3 version)
> > python-stdlib-list 0.8.0-4
> > python3-stdlib-list : List of Python Standard Libraries (2.6-7, 3.2-9)
> > python-streamz 0.6.3-1
> > python3-streamz : build pipelines to manage continuous streams of data
> > python-stubserver 1.1-2
> > python3-stubserver : mock tester of external web dependencies for Python
> > python-tinyalign 0.2-5
> > python3-tinyalign : numerical representation of differences between 
> > strings
> > python-typechecks 0.1.0+ds-2
> > python3-typechecks : express constraints on types
> > python-upsetplot 0.6.0-2
> > python3-upsetplot : Draw Lex et al.'s UpSet plots with Pandas and 
> > Matplotlib
> > python-wdlparse 0.1.0-2
> > python3-wdlparse : Workflow Description Language (WDL) parser for Python
> > python-wordcloud 1.8.1+dfsg-2
> > python3-wordcloud : little word cloud generator in Python
> > python-xopen 1.2.1-3
> > python3-xopen : Python3 module to open compressed files transparently
> > smart-open 5.2.1-3
> > python3-smart-open : utils for streaming large files
> > sorted-nearest 0.0.31+dfsg-1
> > python3-sorted-nearest : Cython helper library for pyranges
> > sphinxcontrib-autoprogram 0.1.7-1
> > python3-sphinxcontrib.autoprogram : automated documentation of CLI
> > programs for Sphinx (Python 3)
> > 
> > Thanks,
> > -- 
> > Sandro "morph" Tosi
> > My website: http://sandrotosi.me/
> > Me at 

Re: Transfering packages from Debian Med to DPT (Was: Please enable me transfering python-bioblend to Debian Med team)

[Andreas Tille]

Am Sun, Jan 02, 2022 at 01:04:46PM +0530 schrieb Nilesh Patra:
> Before you/someone else makes a move, some of these packages are 
> bioinformatics
> and are better suited for med team:
> 
> * indexed-gzip - This one is mainly for NIFTI image files

I fully agree here but I'd be happy to habd this over (and just did so)
since I feel the competence for NIFTI quite sparsely settled in our team
and thus I consider it well hosted in Debian Python Team.

> * python-anndata - For gene annotation

ACK (and wrote this also in my mail.

> * python-fitbit - For FITBIT API (more in med domain)
> * python-cooler - For genomic interaction data
> 
> There are probably more, but please do not move these ^^
 
I will not move these.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: Transfering packages from Debian Med to DPT (Was: Please enable me transfering python-bioblend to Debian Med team)

[Andreas Tille]

Am Sat, Jan 01, 2022 at 09:28:10PM -0500 schrieb Sandro Tosi:
> > In general we are open to hand over general packages that are not
> > directly touching the medical / biological field to competent hands.  So
> > just ping me and I'll try to respond as quick as possible.
> 
> with UDD-mirror U now, i was able to generate the below list. This
> is in no way a request to move them, just a potential source of data
> for your consideration
> 
> arcp 0.2.1-3
> python3-arcp : (Archive and Package) URI parser and generator

Moved to Debian Python Team

> enlighten 1.7.2-1
> python3-enlighten : console progress bar module for Python3
> python3-enlighten-doc : console progress bar module for Python3
> (documentation)
> python3-enlighten-examples : console progress bar module for
> Python3 (examples)

Moved to Debian Python Team - I packaged version 1.8.0 which is the
last one that does not need the module prefixed (which is a new
dependency since version 1.9.0).  Unfortunately the build time test
fails with:

...
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ProxyError('Cannot connect to 
proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection 
refused'))': /simple/blessed/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ProxyError('Cannot connect to 
proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection 
refused'))': /simple/blessed/
ERROR: Could not find a version that satisfies the requirement 
backports.functools-lru-cache>=1.2.1 (from blessed)
ERROR: No matching distribution found for backports.functools-lru-cache>=1.2.1

=== log end 
ERROR: could not install deps [blessed]; v = 
InvocationError('/build/enlighten-1.8.0/.tox/py310/bin/python -m pip install 
blessed', 1)
___ summary 
ERROR:   py310: could not install deps [blessed]; v = 
InvocationError('/build/enlighten-1.8.0/.tox/py310/bin/python -m pip install 
blessed', 1)
E: pybuild pybuild:367: test: plugin distutils failed with: exit code=1: cd 
/build/enlighten-1.8.0/.pybuild/cpython3_3.10/build; tox -c 
/build/enlighten-1.8.0/tox.ini --sitepackages -e py310
I: pybuild base:237: cd /build/enlighten-1.8.0/.pybuild/cpython3_3.9/build; tox 
-c /build/enlighten-1.8.0/tox.ini --sitepackages -e py39


May be you want to have a look to finalise the move to Debian Python Tem.

> h5sparse 0.1.0-4
> python3-h5sparse : Scipy sparse matrix in HDF5

Moved to Debian Python Team

> indexed-gzip 1.6.4-1
> python3-indexed-gzip : fast random access of gzip files in Python

Moved to Debian Python Team

> pyrle 0.0.33-2
> python3-pyrle : run length arithmetic in Python

Moved to Debian Python Team

> python-anndata 0.7.8-2
> python3-anndata : annotated gene by sample numpy matrix
^^
I think this package is nicely maintained by Debian Med team since it is
in the field of bioinformatics.

> python-avro 1.10.2+dfsg-1
> python3-avro : Apache Avro serialization system (Python 3 library)

Moved to Debian Python Team.  After upgrading to latest upstream version
the build ends with

...
==
ERROR: test_server_with_path (avro.test.test_ipc.TestIPC)
--
Traceback (most recent call last):
  File 
"/build/python-avro-1.11.0+dfsg/.pybuild/cpython3_3.9_avro/build/avro/test/test_ipc.py",
 line 35, in test_server_with_path
client_with_custom_path = avro.ipc.HTTPTransceiver("apache.org", 80, 
"/service/article")
  File 
"/build/python-avro-1.11.0+dfsg/.pybuild/cpython3_3.9_avro/build/avro/ipc.py", 
line 442, in __init__
self.conn.connect()
  File "/usr/lib/python3.9/http/client.py", line 946, in connect
self.sock = self._create_connection(
  File "/usr/lib/python3.9/socket.py", line 823, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/lib/python3.9/socket.py", line 954, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -3] Temporary failure in name resolution

--
Ran 396 tests in 10.738s

FAILED (errors=1, skipped=2)

Unfortunately my time to investigate into this ends now.



I will continue with your list ... and wished moves in the other
direction could be as simple and unbureaucratic as it can be.

Kind regards

   Andreas.


> python-ciso8601 2.2.0-1
> python3-ciso8601 : fast ISO8601 date time parser for Python written in C
> python-colormap 1.0.4-2
> python3-colormap : ease manipulation of matplotlib colormaps and
> color codecs (Python 3)
>