Re: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl" returned

2022-03-22 Thread Andreas Tille
Hi, Am Wed, Mar 23, 2022 at 12:19:40AM +1100 schrieb Hugh McMaster: > On Mon, 28 Feb 2022 at 16:40, Hugh McMaster wrote: > > > I did some testing and found that pygame 2.1.0 is the first recent > > version not affected by the FreeType test issue. > > > > I'll keep digging, but I'd strongly

Thank you for helpful responses (Re: python-catalogue: AttributeError: type object 'EntryPoint' has no attribute '_from_text')

2022-03-18 Thread Andreas Tille
Hi, I'd like to use the chance to express that I'm really thankful for every helpful response I received here on this list. My work in Debian touches a lot of techniques and I can't gather expertise in every single one. It also happens that web searches I'm doing are not always as successful as

python-catalogue: AttributeError: type object 'EntryPoint' has no attribute '_from_text'

2022-03-17 Thread Andreas Tille
Hi, I intend to package python-catalogue[1] but there is a test suite issue (see salsa-ci for complete log[2]): platform linux -- Python 3.10.3, pytest-6.2.5, py-1.10.0, pluggy-1.0.0 rootdir: /builds/python-team/packages/python-catalogue/debian/output/source_dir collected 8 items

Please care for arm64 autopkgtest of rdflib (Was: Any reason not to upload rdflib 6 to unstable)

2022-02-27 Thread Andreas Tille
Am Thu, Feb 24, 2022 at 09:54:24PM +0100 schrieb Andreas Tille: > Am Thu, Feb 24, 2022 at 01:40:51PM +0100 schrieb Andreas Tille: > > > > On the other hand in the current situation with two open RC bugs all > > other packages are broken anyway and will be removed from testing

Any reason not to upload rdflib 6 to unstable (Was: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13)

2022-02-24 Thread Andreas Tille
Am Thu, Feb 24, 2022 at 01:40:51PM +0100 schrieb Andreas Tille: > > On the other hand in the current situation with two open RC bugs all > other packages are broken anyway and will be removed from testing if > we do not act upon the issue. So may be we should upload to unstable?

Re: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-24 Thread Andreas Tille
Hi Nilesh, Am Thu, Feb 24, 2022 at 06:00:03PM +0530 schrieb Nilesh Patra: > On 2/24/22 3:36 PM, Andreas Tille wrote: > > I tried to follow your suggestion to upgrade rdflib to version 6 in Git. > > Unfortunately I'm stumbling upon a different issue in the new test > > suit

Re: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-24 Thread Andreas Tille
Control: tags -1 confirmed Control: tags -1 help Hi Jonas, > Please consider releasing rdflib v6 which in my brief testing is > compatible with pyparser v3. I tried to follow your suggestion to upgrade rdflib to version 6 in Git. Unfortunately I'm stumbling upon a different issue in the new

Re: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl" returned

2022-02-22 Thread Andreas Tille
Hi Stefano, Am Wed, Feb 23, 2022 at 01:56:11AM + schrieb Stefano Rivera: > Hi Andreas (2022.02.22_07:57:25_+) > > I've put all developers mentioned as Uploader in CC. Given that the > > last non-team upload was two years ago which might have lead to the > > situation that following

Re: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl" returned

2022-02-21 Thread Andreas Tille
Control: tags -1 confirmed Hi, I had a look into this issue since a Debian Med package received a testing removal warning. I can confirm the build fails with Segmentation fault in the build time test suite. I realised that this package is lagging quite a bit behind upstream and my

Re: Should we allow Janitor to commit directly to all DPT packages?

2022-02-19 Thread Andreas Tille
Am Fri, Feb 18, 2022 at 02:31:13AM +0530 schrieb Nilesh Patra: > On 2/18/22 2:23 AM, Sandro Tosi wrote: > > thanks for bringing the perspective of how things are done in the Med > > team, but it feels none of the points you mentioned nor the specific > > Med team workflow apply here, > > I

Re: Should we allow Janitor to commit directly to all DPT packages?

2022-02-17 Thread Andreas Tille
Hi, Am Thu, Feb 17, 2022 at 12:39:54PM -0500 schrieb Sandro Tosi: > I receive notifications for all MRs opened against DPT packages, and > Janitor's are always pretty much ready to merge as is, and so i think > we should let Janitor commit directly to the team packages. I admit I'm hesitating a

Re: New version of mayavi2 fails to build

2022-02-17 Thread Andreas Tille
Hi Scott, Am Thu, Feb 17, 2022 at 11:27:12AM -0500 schrieb Scott Talbert: > Looking at the full log, it appears as if something in the build process is > trying to open an X display and fails. Perhaps try running dh_auto_build > with Xvfb? Yes, thanks for the very helpful hint Andreas.

New version of mayavi2 fails to build

2022-02-17 Thread Andreas Tille
Hi, as you can see in Salsa-CI build log[1] the new version of mayavi2 fails with something like: ... File "/builds/python-team/packages/mayavi2/debian/output/source_dir/mayavi/mlab.py", line 16 in File "", line 228 in _call_with_frames_removed File "", line 850 in exec_module File "",

Re: scikit-learn in unstable FTBFS on arm64, armel, armhf, i386, ppc64el and s390x

2022-02-17 Thread Andreas Tille
Hi, Am Wed, Feb 16, 2022 at 12:09:23PM +0100 schrieb John Paul Adrian Glaubitz: > > So, I have skimmed over the build logs and one of the main issues is the use > of > -march flags to enforce a certain baseline [1]: > > powerpc64le-linux-gnu-gcc: error: unrecognized command-line option >

Re: [Help] Re: python-envisage: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-14 Thread Andreas Tille
Hi Scott, thanks a lot for your hints. Am Sun, Feb 13, 2022 at 10:28:15PM -0500 schrieb Scott Talbert: > I spent some time looking into this. The problem is that upstream includes > binary eggs (which are Python version specific) as part of its test suite. > The problem here is that there are

[Help] Re: python-envisage: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-09 Thread Andreas Tille
Control: tags -1 help Hi, I've updated python-envisage in Salsa[1] to the latest upstream version and bumped its failing predepends to their according latest upstream and fixed all bugs in those. For envisage I'm stumbling upon a Python3.10 related bug I'd like to ask for help: ...

Re: Help for python-subby needed

2022-02-01 Thread Andreas Tille
Am Tue, Feb 01, 2022 at 08:26:54AM -0500 schrieb Scott Kitterman: > > Add build-depends on pybuild-plugin-pyproject. > > Drop build-depends on flit. > > Drop the "export PYBUILD_SYSTEM=flit" line in d/rules. Thanks, this works now. > That should get you close. Yep. Thanks a lot

Re: Help for python-subby needed

2022-02-01 Thread Andreas Tille
Am Sat, Jan 29, 2022 at 01:50:22AM +0500 schrieb Andrey Rahmatullin: > On Fri, Jan 28, 2022 at 09:48:00PM +0100, Andreas Tille wrote: > > Hi, > > > > I need python-subby as a new dependency for some Debian Med package. > > Unfortunately it does not build easily[1]: &

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2022-01-29 Thread Andreas Tille
Hi Louis-Philippe, Am Sat, Jan 29, 2022 at 06:59:48PM -0500 schrieb Louis-Philippe Véronneau: > CleverCSV and ordered-set went through NEW 2 days ago, so I tweaked what > Andreas had done and uploaded the latest upstream version of deepdiff to > unstable. :-) Thanks a lot Andreas. --

Help for python-subby needed

2022-01-28 Thread Andreas Tille
Hi, I need python-subby as a new dependency for some Debian Med package. Unfortunately it does not build easily[1]: dh_auto_build -O--buildsystem=pybuild E: pybuild pybuild:367: build: plugin flit failed with: Neither [project] nor [tool.flit.metadata] found in pyproject.toml E: pybuild

python-schedule should be probably moved to Debian Python Team

2022-01-18 Thread Andreas Tille
Hi, I've just fixed #1002316 by upgrading to latest upstream version. When looking at the package it might make sense to move it to Debian Python team instead of private maintainership. I'd volunteer to move the package over if all involved people agree. Kind regards Andreas. --

Re: Please enable me transfering python-bioblend to Debian Med team

2022-01-15 Thread Andreas Tille
Am Sat, Jan 15, 2022 at 07:23:14PM + schrieb Stefano Rivera: > > Could you process this transfer please? Moving python-bioblend from > > python->med team. > > You have maintainer access in -med and owner in -python, hence please > > consider transferring this. > > Transferred:

Re: Please enable me transfering python-bioblend to Debian Med team

2022-01-11 Thread Andreas Tille
Hi, I think we sorted out that the request to move python-bioblend to Debian Med is valid. I'm CCing Debian Python team maintainers to get this finally done. I'm not sure whether making me the owner of that actual repository is sufficient to enable me transfering the archive. Alternatively I

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

2022-01-03 Thread Andreas Tille
Am Sun, Jan 02, 2022 at 09:00:27PM +0100 schrieb Andreas Tille: ... Continuing with moving packages from Debian Med to Debian Python Team > python-sinfo 0.3.1-2 > python3-sinfo : print different version information for loaded modules Moved to Debian Python Team. > python-spectra

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

2022-01-02 Thread 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 lib

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

2022-01-02 Thread 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 T

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

2022-01-02 Thread 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

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

2022-01-02 Thread 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

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2021-12-27 Thread Andreas Tille
Hi Louis-Philippe, Am Mon, Dec 27, 2021 at 04:35:44PM -0500 schrieb Louis-Philippe Véronneau: > >> https://github.com/rspeer/ordered-set > > I've just uploaded this one to NEW, it's packaged at: > > https://salsa.debian.org/python-team/packages/python-ordered-set Nice. > >>

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2021-12-25 Thread Andreas Tille
Hi Michael, Am Fri, Dec 24, 2021 at 11:49:49PM +0100 schrieb Michael Banck: > AFAICT, the newer deepdiff requires the following unpackaged modules: > > https://github.com/rspeer/ordered-set > https://github.com/alan-turing-institute/CleverCSV Added as "TODO" entry in d/changelog > It

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

2021-12-23 Thread Andreas Tille
Hi Sandro, Am Thu, Dec 23, 2021 at 09:52:49AM -0500 schrieb Sandro Tosi: > > Thus I moved mypy now and moved it to DPT[2]. Feel free to add yourself > > to Uploaders and upload with the new location. > > thanks! You are welcome. > > Sandro, do you have any other packages in mind? > > too

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2021-12-23 Thread Andreas Tille
Hi Michael, Am Thu, Dec 23, 2021 at 12:16:05PM +0100 schrieb Michael Banck: > On Thu, Dec 23, 2021 at 10:57:47AM +0100, Andreas Tille wrote: > > seems I was able to create repositories and simply my script to do so > > starting with an existing local repository failed for reasons I

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

2021-12-23 Thread Andreas Tille
Hi, Am Thu, Dec 23, 2021 at 02:07:45PM +0530 schrieb Nilesh Patra: > On 12/23/21 1:54 PM, Andreas Tille wrote: > > Hi again, > > > > by chance I learned that I do not have permissions to create > > repositories in salsa:python-team/packages thus moving packages

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2021-12-23 Thread Andreas Tille
. E: pybuild pybuild:355: test: plugin custom failed with: exit code=1: python3.10 setup.py test Kind regards Andreas. Am Thu, Dec 23, 2021 at 09:21:55AM +0100 schrieb Andreas Tille: > Hi, > > Am Thu, Dec 23, 2021 at 12:53:36AM -0500 schrieb Louis-Philippe Véronneau: > > One

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

2021-12-23 Thread Andreas Tille
Wed, Dec 22, 2021 at 10:06:10PM +0100 schrieb Andreas Tille: > Hi Sandro, > > Am Wed, Dec 22, 2021 at 03:13:28PM -0500 schrieb Sandro Tosi: > > > Please note: The people involved are the same. We are members of > > > both teams but consider the Debian Med

Re: Moving deepdiff to the Python Team? (and maybe taking over)

2021-12-23 Thread Andreas Tille
Team upload. + * Move package to Debian Python Team + + -- Andreas Tille Thu, 23 Dec 2021 09:07:37 +0100 + deepdiff (3.3.0-2) unstable; urgency=medium * Team upload diff --git a/debian/control b/debian/control index 8cccbb3..48149c9 100644 --- a/debian/control +++ b/debian/control @@ -1,7 +1,8

Re: Please enable me transfering python-bioblend to Debian Med team

2021-12-22 Thread Andreas Tille
Hi Sandro, Am Wed, Dec 22, 2021 at 03:13:28PM -0500 schrieb Sandro Tosi: > > Please note: The people involved are the same. We are members of > > both teams but consider the Debian Med team more appropriate. We > > are simply missing the permissions to do the move properly. > > since you're

Re: Please enable me transfering python-bioblend to Debian Med team

2021-12-22 Thread Andreas Tille
Am Wed, Dec 22, 2021 at 06:13:32PM +0100 schrieb Pierre-Elliott Bécue: > > Andreas Tille wrote on 21/12/2021 at 15:43:11+0100: > > > Ping? Could any admin of Debian Python Team help out? We can simply > > recreate the repository in Debian Med and move on ... but that m

Re: Please enable me transfering python-bioblend to Debian Med team

2021-12-21 Thread Andreas Tille
Ping? Could any admin of Debian Python Team help out? We can simply recreate the repository in Debian Med and move on ... but that might be confusing for users who will find two clones in differen teams. Thank you, Andreas. Am Sun, Dec 19, 2021 at 05:06:43PM +0100 schrieb Andreas Tille: >

Please enable me transfering python-bioblend to Debian Med team

2021-12-19 Thread Andreas Tille
Hi, we want to take over python-bioblend to Debian Med team. Unfortunately the transfer procedure requires owner permissions to remove the package from the old place. Could someone grant Nilesh Patra or me owner permissions on this package? Alternatively I can grant maintainer permissions to

Re: Ball fails its autopkgtest - how to properly deal with sip files?

2021-12-14 Thread Andreas Tille
Control: tags -1 pending I've fixed the dh_installdocs issue in Git[1] but wanted to solve the autopkgtest issue as well. At first I provided the proper module name[2] which brought me back to the old discussion here: Am Thu, Sep 23, 2021 at 11:59:50PM +0200 schrieb Étienne Mollier: > Hi

[help] pymol: Deprecation warning during startup

2021-12-14 Thread Andreas Tille
Hi, I think I've fixed the issue[1] and it works nicely at command line. Unfortunately Salsa-CI[2] shows a new issue AttributeError: module 'importlib' has no attribute 'util' which I do not understand at all since at command line there is the attribute 'util'. Any hint would be welcome

Re: numba: FTBFS with Python 3.10

2021-12-09 Thread Andreas Tille
Hi, I've commited version 0.54.1 to Git since I assume that we have better chances for Python3.10 support in the more recent upstream version. Unfortunately the build stops with dh_auto_clean -O--buildsystem=pybuild I: pybuild base:237: python3.10 setup.py clean ... from distutils import

[Help] diskcache: FTBFS now even earlier due to Python3.10

2021-11-29 Thread Andreas Tille
Control: tags -1 help Hi, currently I'm running into ERROR: py310: could not install deps [django>=2.2.*, pytest, pytest-cov, pytest-django, pytest-xdist]; v = InvocationError("/build/diskcache-5.2.1/.tox/py310/bin/python -m pip install 'django>=2.2.*' pytest pytest-cov pytest-django

[help] New error in test cases of bmtk

2021-11-22 Thread Andreas Tille
Hi, I think I've found a patch[1] to solve the original issue which just seems to be a floating point precision issue. However, meanwhile there is another less simple issue: ERRORS _ ERROR collecting

Re: Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

2021-11-03 Thread Andreas Tille
Control: tags -1 pending Hi Stuart, Am Wed, Nov 03, 2021 at 09:43:40AM +1100 schrieb Stuart Prescott: > > > > Extension error: > > > > You must configure the bibtex_bibfiles setting > > > > make[2]: *** [Makefile:40: html] Error 2 > > this is sphinxcontrib-bibtex saying that you need to add the

Re: Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

2021-11-02 Thread Andreas Tille
Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 https://github.com/cogent3/cogent3/issues/977 Hi, I wonder whether someone on the Python list might come up with some help Am Sun, Oct 24, 2021 at 01:57:39PM +0200 schrieb Lucas Nussbaum: > Source: python-cogent > Version:

Re: Potential issue with numpy

2021-09-29 Thread Andreas Tille
On Wed, Sep 29, 2021 at 11:27:23AM -0400, Sandro Tosi wrote: > Please do report bugs in the BTS when there's a problem with a package #995318 Kind regards Andreas. -- http://fam-tille.de

Potential issue with numpy

2021-09-29 Thread Andreas Tille
Hi, in the issue I filed against nipype I was asked to try to rebuild numpy and see whether this might make a diffence. So I tried dget http://deb.debian.org/debian/pool/main/n/numpy/numpy_1.19.5-1.dsc cd numpy-1.19.5 and have rebuild it in a recent pbuilder environment. This ends up in

Placement of *.so files to be found by Python modules (Was: ont-fast5-api)

2021-05-27 Thread Andreas Tille
Hi, there is a problem with ont-fast5-api[0] On Wed, May 26, 2021 at 03:22:21AM +0530, Nilesh Patra wrote: > However, one problem - I'm being verbose so we are in loop: >

How can I override module name in autopkgtest-pkg-python

2021-03-03 Thread Andreas Tille
Hi, I worked on the package python-cython-blis[1] (there is no specific reason to have it in Debian Science scope - I just found an existing repository there and continued with this). The package works nicely - but the autopkgtest (in Salsa CI[2] does not): autopkgtest [19:46:36]: test

Re: diskcache: ERROR: tox config file (either pyproject.toml, tox.ini, setup.cfg) not found

2021-01-25 Thread Andreas Tille
On Mon, Jan 25, 2021 at 12:45:08PM -0500, Sandro Tosi wrote: > and that's because > https://github.com/grantjenks/python-diskcache/blob/master/tox.ini is > not included in the pypi package (and, independently, the reason i > start packaging tarballs from github, it's just easier than getting >

diskcache: ERROR: tox config file (either pyproject.toml, tox.ini, setup.cfg) not found

2021-01-25 Thread Andreas Tille
Hi, to update python-cobra I need diskcache as new dependency. Yaroslav I assume it is OK if I team-hijacked your ITP. I injected the packaging into the existing but empty repository[1]. Unfortunately I have no idea about tox and thus I need help to solve this: dh_auto_test

macsyfinder: Upstream released Python3 version but "error: 'setuptools' is not supported. Please use 'pip' instead."

2021-01-14 Thread Andreas Tille
Control: tags -1 - upstream Hi, upstream has released a Python3 version of macsyfinder which I pushed to Git[1]. When trying to build I get a strange error: dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root

Re: Bug#980005: lumpy-sv: lumpyexpress fails with no args

2021-01-12 Thread Andreas Tille
Control: tags -1 confirmed Control: tags -1 help Hi, I confirm I can reproduce the issue in a minimal chroot while the lumpyexpress command prints the help screen as expected. This smells like a missing dependency but I do not have any idea which one. It seems there is a similar known issue

Re: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

2020-12-08 Thread Andreas Tille
On Tue, Dec 08, 2020 at 11:11:27PM +0500, Andrey Rahmatullin wrote: > https://github.com/nipy/nipy/issues/461 As far as I can see that's included into 0.4.3~rc1. Yaroslav, would you mind commenting on this? It would be great to have some kind of 0.4.3~rc2 to get nipy fixed. Kind regards

Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

2020-12-08 Thread Andreas Tille
Control: tags -1 pending Control: tags -1 help Hi, I've updated nipy Git[1] to version 0.4.3~rc1 which solves the originally reported issue. However, there are some remaining failures in the build time test: ... == ERROR:

Python3.9 issue: '"yield from" can't be applied to "Condition"' (Was: Bug#976779: mypy FTBFS with only python 3.9)

2020-12-08 Thread Andreas Tille
Control: tags -1 pending Control: tags -1 help On Mon, Dec 07, 2020 at 11:24:34PM +0200, Adrian Bunk wrote: > ... > #set -e; for v in 3.9; do > set -e; for v in 3.8; do \ > PATH=$PATH:/<>/debian/mypy/usr/bin/ python$v -m pytest -n > auto \ > -o testpaths=mypy/test -o

Re: Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)

2020-10-30 Thread Andreas Tille
Control: tags -1 upstream Control: forewarded -1 https://github.com/sanger-pathogens/gubbins/issues/286 On Fri, Oct 30, 2020 at 02:38:03PM +0500, Andrey Rahmatullin wrote: > python/gubbins/common.py::parse_and_run() constructs an absolute path for > the executable and then passes it to

Re: Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)

2020-10-30 Thread Andreas Tille
Control: tags -1 help Control: forwarded -1 Aidan Delaney Hi, I admit I have no idea what might have caused these pkg_resources related errors and how to fix these. Any help would be welcome Andreas. On Sun, Sep 27, 2020 at 08:45:17PM +0200, Lucas Nussbaum wrote: > Source: gubbins >

Re: Issues when reading mailboxes from alioth-lists.debian.net

2020-08-19 Thread Andreas Tille
On Wed, Aug 19, 2020 at 10:31:55PM +0530, Nilesh Patra wrote: > > For me the error goes way for me when I change line 781 in > /usr/lib/python3.8/mailbox.py > to: > > msg.set_from(from_line[5:].decode('utf-8')) > > May be this is a minor feature enhancement since at the moment messages with

Issues when reading mailboxes from alioth-lists.debian.net

2020-08-19 Thread Andreas Tille
Hi, in the teammetrics project I'm trying to parse mailboxes. This worked with Python2 but after porting the code to Python3 I get some encoding troubles. A specific one seem to be an error in the mailbox module. Please run the attached script test_mbox which downloads one of the critical mbox

Help with new sphinx version needed (Was: Bug#966983: Most likely fixed in sphinx (2.4.3-5))

2020-08-11 Thread Andreas Tille
Hi, I need some help with a sphinx error for python-skbio: On Tue, Aug 11, 2020 at 10:26:10AM +0200, Sebastiaan Couwenberg wrote: > On 8/11/20 9:41 AM, Andreas Tille wrote: > > On Tue, Aug 11, 2020 at 07:17:30AM +0200, Sebastiaan Couwenberg wrote: > >> A smiliar issue was rep

Thanks (Was: pyarrow: Could NOT find Python3 (missing: Python3_LIBRARIES Python3_INCLUDE_DIRS))

2020-07-22 Thread Andreas Tille
On Wed, Jul 22, 2020 at 09:43:01AM -0400, Scott Talbert wrote: > > Any idea why these variables are not sensibly set automatically and what > > I can do to provide these? > > Try adding python3-all-dev to Build-Depends. Thanks - that was simple. ;-) Kind regards, Andreas. --

pyarrow: Could NOT find Python3 (missing: Python3_LIBRARIES Python3_INCLUDE_DIRS)

2020-07-22 Thread Andreas Tille
Hi, I intend to package pyarrow[1] as a precondition for some Debian Med package. Unfortunately I get: ... -- Build output directory: /build/python-pyarrow-0.17.1/build/temp.linux-x86_64-3.8/release CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146

Help needed to run tests in biocore-ntnu-ncls

2020-06-13 Thread Andreas Tille
Hi DPMT, Steffen Möller has prepared biocore-ntnu-ncls[1] in the Debian Med COVID-19 effort. I did a review and realised that the build time test does not work: ... ERRORS _ ERROR collecting

Please transfer package presto from DPMT to med-team

2020-05-29 Thread Andreas Tille
Hi, as you can read here https://lists.debian.org/debian-med/2020/05/msg00249.html we would like to maintain presto in Debian Med. Unfortunately I do not have permissions to transfer the repository. Please either give me permissions or some kind soul could do the transfer to move the

Re: Bug#953970: Taking over DPMT (Was: python-boto: autopkgtest failure with Python 3.8 as default)

2020-05-16 Thread Andreas Tille
On Mon, May 11, 2020 at 10:20:24PM -0400, Noah Meyerhans wrote: > Control: tags -1 + patch > > > I'll move this package to a cloud-team repository and prepare an upload > > to unstable on Monday if nobody beats me to it. > > https://salsa.debian.org/cloud-team/python-boto/-/merge_requests/1

Re: Taking over DPMT (Was: python-boto: autopkgtest failure with Python 3.8 as default)

2020-05-10 Thread Andreas Tille
Hi, this bug stays a source of autoremoval warnings noise. I wonder if someone might take action on this to move the package to team maintenance. Eric suggested the cloud team which is perfectly fine for me - but can this please made happen. It should not be that hard once the repository is

Source only upload of validators

2020-04-28 Thread Andreas Tille
Hi Harley, thanks for packaging validators as streamlit predepencency for our COVID-19 sprint. I've done a source-only upload to enable testing migration of this package. I've done some automatic updates using routine-update. Thanks again Andreas. -- http://fam-tille.de

pauvre is missing sklearn despite the package is installed

2020-04-27 Thread Andreas Tille
Hi, the Debian Med team is busy to package python-pauvre[1] which is part of our COVID-19 sprint. I think Etienne Mollier and I have put the packaging in quite some shape in Git[1]. However, when I try to test the included CLI interface I get: $ pauvre -h Traceback (most recent call last):

Re: Please move logbook to Debian Python Modules team (Was: src:logbook: Requires a package outside of Main)

2020-04-15 Thread Andreas Tille
ular automatic packaging enhancements done which finally lead to a better quality. Kind regards Andreas. > On Wed, Apr 15, 2020 at 9:01 AM Andreas Tille wrote: > > > > Hi Salsa admins, > > > > please be so kind to transfer > > > > https:

Re: Please move logbook to Debian Python Modules team (Was: src:logbook: Requires a package outside of Main)

2020-04-15 Thread Andreas Tille
you :). > > Cheers, > > On 4/14/20 11:16 AM, Inaki Malerba wrote: > > El 14/4/20 a las 10:43, Andreas Tille escribió: > >> Hi Agustin and Iñaki, > >> > >> I wonder whether you would like to maintain the logbook package in > >> Debian Pytho

Please move logbook to Debian Python Modules team (Was: src:logbook: Requires a package outside of Main)

2020-04-14 Thread Andreas Tille
Hi Agustin and Iñaki, I wonder whether you would like to maintain the logbook package in Debian Python Modules team (by setting the mailing list as Maintainer and you two serve as Uploaders.) This would possibly enhance the number of people who are watching this package and would simplify doing

Thanks to Olek and Scott and for sure all other contributors (Was: Fwd: [covid] New Contributor for biohackathon)

2020-04-09 Thread Andreas Tille
Hi, currently I'm experiencing a situation which I described in several of my talks[1]: For me a team means: Waking up in the morning and realising that somebody else has solved your problem from yesterday. Thanks a lot to all who contributed and let me enjoy my sleep at night

[Help] Re: Bug#953052: psychopy: python2 dependencies

2020-04-08 Thread Andreas Tille
Control: tags -1 help Hi DPMT, I need to admit I'm currentl overwhelmed with COVID-19 hackathon. A quick view does not really show any suspicious things to me. Any help (including team upload / NMU) would be appreciated. Kind regards Andreas. On Tue, Mar 03, 2020 at 09:34:24PM +0100,

Re: [RFC] python-cobra, python3-sbml5

2020-04-05 Thread Andreas Tille
On Sun, Apr 05, 2020 at 03:40:56PM +0530, Nilesh Patra wrote: > > > '_libsbml' file which corresponds to libsbml (with python3-sbml5 as a > > > provide) package. When I dug into looking at libsbml, I noticed that the > > > relevant file (libsbml.py) which throws error > > > is generated with

Re: [RFC] python-cobra, python3-sbml5

2020-04-05 Thread Andreas Tille
Hi Nilesh, On Sat, Apr 04, 2020 at 06:53:55PM +0530, Nilesh Patra wrote: > > >From the logs, in the last message[2] it looks like an import-error for > '_libsbml' file which corresponds to libsbml (with python3-sbml5 as a > provide) package. When I dug into looking at libsbml, I noticed that the

Taking over DPMT (Was: python-boto: autopkgtest failure with Python 3.8 as default)

2020-03-30 Thread Andreas Tille
Hi Emmanuel, thanks a lot for your patch. Please note that you crafted it against GIt which is lagging behind the latest NMU. I intended to apply it anyway - but it does not solve == ERROR: test_constructor

Re: Python help needed for test suite in multiqc

2020-03-26 Thread Andreas Tille
Hi Andrey, On Thu, Mar 26, 2020 at 12:34:11AM +0500, Andrey Rahmatullin wrote: > http://bugs.debian.org/954640 Thanks a lot. Multiqc builds with humanfriendly from Git. Kind regards Andreas. -- http://fam-tille.de

Python help needed for test suite in multiqc

2020-03-25 Thread Andreas Tille
Hi Python folks, the Debian Med team intends to package multiqc[1]. When running the build time tests I get: ... debian/rules override_dh_auto_test make[1]: Verzeichnis „/build/multiqc-1.8+dfsg“ wird betreten cp -a multiqc*.egg-info

Re: cannot allocate memory in static TLS block

2020-03-17 Thread Andreas Tille
Hi Faidon, On Tue, Mar 17, 2020 at 01:29:59PM +0200, Faidon Liambotis wrote: > Hi Andreas, > > Thanks for reaching out. It sounds like this is already reported as > #951704 (Cc'ed now). OK. > I'll need to give this a closer look, but I hope I > can have an update within the next couple of

Re: cannot allocate memory in static TLS block

2020-03-15 Thread Andreas Tille
Hi Faidon, could you imagine to build jemalloc with --disable-initial-exec-tls as Sergio suggests below to fix the issue in drmaa (and possibly other packages)? Should I open a separate bug report against jemalloc to request this? Kind regards Andreas. On Sat, Mar 14, 2020 at 05:18:49PM

cannot allocate memory in static TLS block (Was: Bug#953832: drmaa: autopkgtest failure: RuntimeError: Could not find drmaa library)

2020-03-14 Thread Andreas Tille
Control: tags -1 help Control: retitle -1 cannot allocate memory in static TLS block Hi Paul, On Fri, Mar 13, 2020 at 11:09:31PM +0100, Paul Gevers wrote: > > raise RuntimeError(('Could not find drmaa library. Please specify > its ' + > RuntimeError: Could not find drmaa library. Please

Re: Help for issues with lazyarray needed

2020-03-05 Thread Andreas Tille
On Thu, Mar 05, 2020 at 02:27:13PM +0530, Nilesh Patra wrote: > > I had tried this, > I think Passing [:-1] in the mask2 initialisation would fix this. We also > need to cast this into a numpy array. > ... > > I'll try this by midnight today. If I can, I'll try a fix for this, and > make a MR,

Help for issues with lazyarray needed

2020-03-05 Thread Andreas Tille
Control: tags -1 pending Hi, I have updated lazyarray in Git[1] (by moving it to Debian Science team). The old package was lagging way behind upstream and a Python3 port is available by upstream so I just create the python3-lazyarray package fixing the open bugs. Unfortunately there is an open

Help needed to make pkgconfig finding just built lib

2020-02-27 Thread Andreas Tille
Control: tags -1 help Hi, I'm trying to drop biosig4c++ with Python3 only in Git[1]. Unfortunately I get: make[3]: Entering directory '/build/biosig4c++-1.9.5/python' python3 setup.py build Traceback (most recent call last): File "setup.py", line 11, in PKG=pkgconfig.parse('libbiosig')

Re: Bug#950063: influxdb-python FTBFS with pandas 0.25.3

2020-02-20 Thread Andreas Tille
On Thu, Feb 20, 2020 at 10:31:41AM -0500, Alexandre Viau wrote: > On Thu, Feb 20, 2020 at 4:15 AM Andreas Tille wrote: > > Regarding your wish to remove you from Maintainers: I did not intend to > > take over the package from you personally. I rather wanted to do >

Re: influxdb-python FTBFS with pandas 0.25.3

2020-02-20 Thread Andreas Tille
Hi Alexandre, On Wed, Feb 19, 2020 at 09:51:43AM -0500, Alexandre Viau wrote: > Feel free to move influxdb-python to DPMT. Thanks. > However, if you do, please remove me from the maintainers and > delete/move the existing salsa project. For sure I can transfer the project on Salsa. Regarding

Re: influxdb-python FTBFS with pandas 0.25.3

2020-02-05 Thread Andreas Tille
Hi Alexandre, since a Debian Med package is affected as reverse-depends of influxdb-python I had a look. Unfortunately this Python package is not maintained by the Python modules team. I would consider it a good idea to move this package into team maintenance. I'd volunteer to do that move but

Re: Bug#937177: obitools: Python2 removal in sid/bullseye

2020-01-12 Thread Andreas Tille
Control: tags -1 help Hi Scott, On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote: > On Fri, 30 Aug 2019 07:28:59 + Matthias Klose wrote: > ... > > I don't see any evidence of upstream progress on converting to python3. This seems to be correct. > This > package is

Re: python-datrie: FTBFS with recent hypothesis version

2020-01-09 Thread Andreas Tille
On Thu, Jan 09, 2020 at 07:45:09PM +0100, Michael Crusoe wrote: > https://patches.ubuntu.com/p/python-datrie/python-datrie_0.7.1-3ubuntu1.patch > > I can confirm that this patch fixes the build and I've opened a merge > request at >

Re: Removing python-xmlbuilder from Debian

2019-12-25 Thread Andreas Tille
On Wed, Dec 25, 2019 at 12:26:59PM +0100, Thomas Goirand wrote: > Currently, the only reverse dependency of this package is > python-pbcommand. Not in unstable. > So we have 2 choices: > > 1/ Fix python-xmlbuilder > 2/ Get python-xmlbuilder and python-pbcommand removed from Debian. > > Your

Re: kmer: Python2 removal in sid/bullseye

2019-12-19 Thread Andreas Tille
Hi Scott, thanks a lot for your hint. On Thu, Dec 19, 2019 at 01:34:08PM -0500, Scott Talbert wrote: > > The 'file' class doesn't exist anymore in Python 3. You'll have to rewrite > myfile to not use it. OK, I simply went with ... @@ -608,6 +608,11 @@ Last-Update: Thu, 19 Dec 2019 10:43:09

Re: kmer: Python2 removal in sid/bullseye

2019-12-19 Thread Andreas Tille
Control: tags -1 help Hi, I tried to convert kmer to Python3 in Git[1]. Unfortunately I'm stumbling upon an issue in the test suite: ... python3 /usr/bin/../lib/atac/bin/AtacDriver.py /tmp/atac-test.doxZJ4/results/work/LeprvsTuber.matches.extended Traceback (most recent call last): File

Re: Help needed (Was: Bug#943083: libncl: Python2 removal in sid/bullseye)

2019-12-16 Thread Andreas Tille
On Mon, Dec 16, 2019 at 01:31:02PM +0500, Andrey Rahmatullin wrote: > On Mon, Dec 16, 2019 at 09:17:50AM +0100, Andreas Tille wrote: > > inputParentPath = lineIter.next().strip() > > AttributeError: '_io.StringIO' object has no attribute 'next' > This should be changed to ne

Help needed (Was: Bug#943083: libncl: Python2 removal in sid/bullseye)

2019-12-16 Thread Andreas Tille
Control: tags -1 help Hi, I tried 2to3 on the Python files belonging to libncl test suite. Upstream is using a somehow complex method to read config files. Before trying a complete rewrite I wonder whether someone might be able to make some sense out of: ... make check-local make[4]: Entering

Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 10:49:45PM +0500, Andrey Rahmatullin wrote: > > I think at least this is solved now: > > > > > > https://salsa.debian.org/med-team/pdb2pqr/commit/1f4ee901456641140ef18ca8e91e4701e1175410 > > Nice catch, "env.Append(LIBS=[python_lib])" where "python_lib = 'python' + >

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 03:16:32PM +0100, Andreas Tille wrote: > > ... > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib > -lpython3.7m -lpython3.7 > /usr/bin/ld: cannot find -lpy

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 05:46:42PM +0500, Andrey Rahmatullin wrote: > > > > Thanks for that additional hint. I can confirm that I checked whether > > pkgconfig can be used before I was asking here. But we seem to agree > > that this is not the case. I admit I have no real clue how to convince

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