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

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

2019-12-13 Thread Andreas Tille
Hi Andrey, On Fri, Dec 13, 2019 at 05:18:45PM +0500, Andrey Rahmatullin wrote: > On Fri, Dec 13, 2019 at 09:49:47AM +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/Algorithm

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 03:23:19PM +0500, Andrey Rahmatullin wrote: > On Fri, Dec 13, 2019 at 09:49:47AM +0100, Andreas Tille wrote: > > So how can I enable proper linking to -lpython3.7 which is obviously not > > in the library search path (but package libpython3.7 is definitel

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

2019-12-13 Thread Andreas Tille
Hi Scott, On Thu, Dec 12, 2019 at 04:34:09PM -0500, Scott Talbert wrote: > On Thu, 12 Dec 2019, Andreas Tille wrote: > > mkdir -p /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr > > scons \ > >URL="http://localhost/pdb2pqr/; \ > >PREFIX="

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

2019-12-12 Thread Andreas Tille
On Thu, Dec 12, 2019 at 03:49:13PM -0500, Scott Talbert wrote: > > > > That hint was helpful anyway and I get further now. I think now the > > problem is to convince scons to install in $(CURDIR)/debian/tmp which > > seems to try rather /usr/share/pdb2pqr directly: > > Looks like the

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

2019-12-12 Thread Andreas Tille
Hi Scott, On Thu, Dec 12, 2019 at 11:31:09AM -0500, Scott Talbert wrote: > On Thu, 12 Dec 2019, Andreas Tille wrote: > > I don't see any Python3 changes in that repository. Did you push your > changes? Argh, its pushed now. > Anyway, the problem is likely in CopySubActio

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

2019-12-12 Thread Andreas Tille
Control: tags -1 help Hi, it seems pdb2pqr is orphaned upstream. However, it seems to be worth keeping inside Debian thus I tried my luck to port it to Python3 in Git[1]. Unfortunately the build runs into scons: Building targets ... CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")

Re: python-datrie: FTBFS with recent hypothesis version

2019-12-09 Thread Andreas Tille
Hi, I have upgraded python-datrie in Git[1] to latest upstream version (0.8). It shows the same issue - so I admit I have no better clue than reporting the issue upstream which I'd rather leave to the official Uploader of the package. BTW, we probably should expect build issues with Python

[Help] Please switch to Python 3

2019-12-07 Thread Andreas Tille
Control: tags -1 help Hi, I upgraded python-pbcommand Git[1] to latest upstream commit which is work in progress to Python3. Unfortunately I'm facing some remaining test suite errors: ... [gw3] [ 98%] PASSED tests/test_validators.py::TestValidators::test_validate_report

[Help] consensuscore: Python2 removal in sid/bullseye

2019-12-07 Thread Andreas Tille
Control: tags -1 help Hi, I tried to port consensuscore to Python3 in Git[1]. Unfortunately 2to3 was not completely successfully since I get: dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3.8 setup.py build. WARNING: '' not a valid package name; please use only

pytest help needed

2019-12-04 Thread Andreas Tille
Hi, I try to prepare the latest git commit from upstream of python-pbcore[1]. Unfortunately the build time test fails with: ... dh_auto_test I: pybuild base:217: python3.8 setup.py test running pytest running egg_info writing pbcore.egg-info/PKG-INFO writing dependency_links to

Lintian warning for this issue (Was: autopkgtest-pkg-python fails if package name is python-pyMODULENAME)

2019-12-04 Thread Andreas Tille
On Fri, Nov 29, 2019 at 12:02:44PM +0100, Andreas Tille wrote: > > I've opened > > https://salsa.debian.org/cpython-team/python3-defaults/merge_requests/2 > > to clarify this. Comments welcome, particularly if you don't think my > > proposed change reflects consensus. &g

Any reason why python-scipy version 1.3.1 remains in experimental?

2019-12-01 Thread Andreas Tille
Hi, according to the answer to an issue I opened agains scikit-bio[1] the test suite would work with scipy version 1.3.1. I wonder what might be the reason to stick to version 1.2.2 instaed of upgrading to the version in experimental. In case this situation would not change in the next weeks

Re: autopkgtest-pkg-python fails if package name is python-pyMODULENAME (Was: Bug#945768: python-pypubsub: autopkgtest failure: No module named 'pypubsub')

2019-11-29 Thread Andreas Tille
On Fri, Nov 29, 2019 at 10:42:45AM +, Simon McVittie wrote: > > I've opened > https://salsa.debian.org/cpython-team/python3-defaults/merge_requests/2 > to clarify this. Comments welcome, particularly if you don't think my > proposed change reflects consensus. Thanks. This is more clear. I

Re: autopkgtest-pkg-python fails if package name is python-pyMODULENAME (Was: Bug#945768: python-pypubsub: autopkgtest failure: No module named 'pypubsub')

2019-11-28 Thread Andreas Tille
On Thu, Nov 28, 2019 at 11:15:31AM -0500, Sandro Tosi wrote: > > Hmmm, what are the chances to get this applied? I've added > > > >X-Python-Module-Name: pubsub > > > > in Git - but this will not reall fix the test. The only solution I'd see > > otherwise is to deactivate the test. > > if

Re: autopkgtest-pkg-python fails if package name is python-pyMODULENAME (Was: Bug#945768: python-pypubsub: autopkgtest failure: No module named 'pypubsub')

2019-11-28 Thread Andreas Tille
On Thu, Nov 28, 2019 at 04:18:07PM +0100, Ondrej Novy wrote: > > > Is there any trick to enable autopkgtest-pkg-python detecting the correct > > module name? > > > > no (not yet? See: https://salsa.debian.org/ci-team/autodep8/merge_requests/6 > ) Hmmm, what are the chances to get this applied?

autopkgtest-pkg-python fails if package name is python-pyMODULENAME (Was: Bug#945768: python-pypubsub: autopkgtest failure: No module named 'pypubsub')

2019-11-28 Thread Andreas Tille
On Thu, Nov 28, 2019 at 12:46:34PM +0100, Paul Gevers wrote: > Source: python-pypubsub > Version: 4.0.3-2 > X-Debbugs-CC: debian...@lists.debian.org > User: debian...@lists.debian.org > Usertags: regression > > ... > > [1] https://qa.debian.org/excuses.php?package=python-pypubsub > >

Help with upgrading psychopy needed (Was: Python2 removal in sid/bullseye)

2019-11-20 Thread Andreas Tille
Control: tags -1 help Hi, I've tried to upgraded psychopy[1] to the latest upstream version. Unfortunately I failed to run the test suite successfully: dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /build/psychopy-3.2.4+dfsg/.pybuild/cpython3_3.7/build; python3.7 -m pytest

Re: Bug#937657: Issue with numpy under Python 3.8

2019-11-17 Thread Andreas Tille
Hi Graham, On Sun, Nov 17, 2019 at 02:16:29PM +0200, Graham Inggs wrote: > If you look on the numpy tracker page [1], you'll see there is a note: > > "This package is part of the ongoing testing transition known as > python3.8. Please avoid uploads unrelated to this transition, they > would

Re: Bug#937657: Issue with numpy under Python 3.8

2019-11-16 Thread Andreas Tille
Hi Rebecca, On Sat, Nov 16, 2019 at 09:16:17AM +, Rebecca N. Palmer wrote: > I think that just means "numpy hasn't yet been rebuilt for Python 3.8". (In > Python modules that include a C extension, the .py files are shared but the > C part is compiled separately for each Python version.) > >

Issue with numpy under Python 3.8 (Was: python-colormap: Python2 removal in sid/bullseye)

2019-11-15 Thread Andreas Tille
Control: tags -1 help Hi, I have dropped the Python2 package in Git[1] and tried to build which ended up in: ... I: pybuild base:217: cd /build/python-colormap-1.0.2/.pybuild/cpython3_3.8_colormap/build; python3.8 -m nose -v test nose.config: INFO: Ignoring files matching ['^\\.', '^_',

[Help] graphlan: Python2 removal in sid/bullseye

2019-11-08 Thread Andreas Tille
Hi, I started an attempt to port graphlan to Python3 in Git[1] but its autopkgtest throws errors: Running test script ./IBD_biogeography/run.sh . Traceback (most recent call last): File "/usr/bin/graphlan_annotate", line 26, in from src.graphlan_lib import CircTree as CTree File

Help needed for issue in test suite for Python3 (Was: Bug#937698: python-dendropy: Python2 removal in sid/bullseye)

2019-10-08 Thread Andreas Tille
Control: tags -1 help Hi, I have prepared a fix for this package in Git[1]. Unfortunately I'm stumbling upon a test suite error which was discussed with upstream previously. It happens only for Python3 and was ignored before but this strategy seems to be inappropriate now after droping

Re: [Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-18 Thread Andreas Tille
Hi Michael, On Mon, Sep 16, 2019 at 11:56:48AM +0200, Michael Kesper wrote: > But honestly, it should better be ripped out and use > real encryption. The docstring tells so: > The rotor module has been removed from the Python 2.4 > distribution because > > the rotor module uses an insecure

Reviving maintenance of python-pyface

2019-09-18 Thread Andreas Tille
Hi, pyface was lagging extremely behind upstream. To cope with Qt5 and Python3 migration I simply pushed the latest upstream version to the packaging Git[1] == ERROR: pyface.action.tests.test_action_item

Re: [Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-16 Thread Andreas Tille
Hi Peter, On Sun, Sep 15, 2019 at 02:47:50PM +0100, peter green wrote: > > > tmp = rt.encrypt('Cycle{}'.format(pickle.dumps(objSave))) > > > > Thanks to this hint > This hint was *wrong*, it will introduce garbage into the string and the > "rotor" code is clearly designed to work with byte

Python3 issue with Tkinter (Was: Bug#938447: scoary: Python2 removal in sid/bullseye)

2019-09-13 Thread Andreas Tille
Hi, I think I ported scoary successfully to Python3 in Git[1]. The command line applications seem to work but the GUI is just ending with Need the following installed: Tkinter, tkFileDialog, ttk For the more simple inspection I copy here the beginning which leads to this: import sys, os

Re: [Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-13 Thread Andreas Tille
Hi, On Thu, Sep 12, 2019 at 09:08:04PM +0200, Michael Kesper wrote: > > Since I do not have much experience with hashlib I'd be happy if > > someone might be able to proof-read `def Save_Cycle` in > > save_load.py. > > This does not have anything to do with hashlib per se. > It's just the

Re: [Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-12 Thread Andreas Tille
On Thu, Sep 12, 2019 at 01:57:32PM +0500, Andrey Rahmatullin wrote: > > > There are circular imports in the code so you most likely broke that by > > > reordering imports in various files. > > > > s/you most likely broke/2to3 most likely broke/ > 2to3 doesn't do that. You mentioned autopep8, it

Re: 2to3 adds '.' in front dir of "from dir import ..." statements (Was: [MoM] lefse migration to python 3])

2019-09-12 Thread Andreas Tille
Hi Michael, On Thu, Sep 12, 2019 at 09:22:06AM +0200, Michael Kesper wrote: > On 12.09.19 08:30, Thomas Goirand wrote: > > I wont comment on the relative import ambiguity problem, as Ghislain > > replied correctly. However, I do want to comment on 2to3. > > > > I generally recommend against

Re: [Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-12 Thread Andreas Tille
Hi Andrey, On Wed, Sep 11, 2019 at 07:32:33PM +0500, Andrey Rahmatullin wrote: > > $ cycle > > Traceback (most recent call last): > > File "/usr/bin/cycle", line 12, in > > from dialogs import * > > File "/usr/share/cycle/dialogs.py", line 8, in > > from cal_year import cycle, Val >

[Help] Re: Bug#939181: cycle: Python2 removal in sid/bullseye

2019-09-11 Thread Andreas Tille
Control: tags -1 help On Wed, Sep 11, 2019 at 09:33:54AM -0300, Antonio Terceiro wrote: > E: Sub-process /usr/bin/dpkg returned an error code (1) > ~[100]$ cycle > File "/usr/bin/cycle", line 29 > if lang_find: > ^ > TabError: inconsistent use of tabs and spaces in

2to3 adds '.' in front dir of "from dir import ..." statements (Was: [MoM] lefse migration to python 3])

2019-09-09 Thread Andreas Tille
Hi, in the process of the Python3 migration the package lefse was converted using 2to3. The changes can be found in git[1]. I'm wondering about the following diff created by 2to3: - from lefse import * + from .lefse import * When calling a random binary of the resulting binary package

Re: [Help] Bug#938668: tifffile: Python2 removal in sid/bullseye

2019-09-05 Thread Andreas Tille
Hi Andrey, On Thu, Sep 05, 2019 at 11:06:22PM +0500, Andrey Rahmatullin wrote: > > Depends: python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, python3:any, > > python:any > > > > > > How can I get rid of the python:any dependency? > You ship a Python 2 script, /usr/bin/tifffile. It also

[Help] Bug#938668: tifffile: Python2 removal in sid/bullseye

2019-09-05 Thread Andreas Tille
Control: tags -1 help Hi, for some reason I do not understand are the dependencies of the binary package Depends: python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, python3:any, python:any How can I get rid of the python:any dependency? Kind regards Andreas. --

Re: Test suite errors with Python3 (Was: Why is dh_auto_clean calling python2.7? (Was: Bug#937624: python-burrito: ...))

2019-08-31 Thread Andreas Tille
On Sat, Aug 31, 2019 at 04:47:42PM -0400, Sandro Tosi wrote: > burrito.util.ApplicationError: Could not open "/tmp/fixed.txt" > > is the file there? No, that file does not exist. $ grep -R /tmp/fixed.txt burrito/tests/test_util.py:f = open('/tmp/fixed.txt','w') burrito/tests/test_util.py:

Test suite errors with Python3 (Was: Why is dh_auto_clean calling python2.7? (Was: Bug#937624: python-burrito: ...))

2019-08-31 Thread Andreas Tille
Control: tags -1 help On Sat, Aug 31, 2019 at 11:50:16AM +0200, Ondrej Novy wrote: > > I see that python-all is still present in Build-Depends (line 9). > > yep, that's reason. pybulid detects python{,-all} in B-D and if they are > present, it runs clean for Python 2. Thanks for pointing this

Why is dh_auto_clean calling python2.7? (Was: Bug#937624: python-burrito: Python2 removal in sid/bullseye)

2019-08-31 Thread Andreas Tille
Hi, I have removed the Python2 package from d/control and all python-* Build-Depends in Git[1]. However, the build in a pbuilder chroot fails with: dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean Traceback

python-confluent-kafka Python2 migration and maintenance in Debian Python Modules Team

2019-08-01 Thread Andreas Tille
Hi Christos, when inspecting rdepends of python-avro I stumbled upon your package python-confluent-kafka. I checked whether the Python2 package has any further rdepends which does not seem to be the case. Thus we should probably drop it from Debian. While doing so I upgraded the Git

Re: Use debhelper-compat instead of debian/compat

2019-07-22 Thread Andreas Tille
Hi Ondrej On Thu, Jul 18, 2019 at 04:15:38PM -0300, Ondrej Novy wrote: > according to debhelper man package it's recommended to use debhelper-compat > instead of debian/compat file. > > I would like to mass-commit this change to DPMT/PAPT, example: > >

Re: python-intervaltree in Debian Python team maintenance

2019-07-22 Thread Andreas Tille
Hi Hilko, On Mon, Jul 22, 2019 at 11:54:21AM +0200, Hilko Bengen wrote: > * Andreas Tille: > > > I noticed that python-intervaltree is not maintained in Debian Python > > team. I wonder whether you might want to move this package to the > > team repository and follow

python-intervaltree in Debian Python team maintenance

2019-07-21 Thread Andreas Tille
Hi Hilko, I noticed that python-intervaltree is not maintained in Debian Python team. I wonder whether you might want to move this package to the team repository and follow the Debian Python policy (by putting the list as maintainer and you as Uploader). Kind regards and thanks for maintaining

Please remove repositories for python-pytz and pyomo from Salsa

2019-06-26 Thread Andreas Tille
Hi, I realised that https://salsa.debian.org/python-team/modules/python-pytz is hanging around on Salsa but should not. Pytz os packaged as python-tz (see #836261) so this repository should vanish. I please also remove https://salsa.debian.org/python-team/applications/pyomo Pyomo was

Re: Please enable me pushing to python-team/applications

2019-03-28 Thread Andreas Tille
On Thu, Mar 28, 2019 at 02:50:22PM +0100, Piotr Ożarowski wrote: > I added you to the team Andreas, sorry for the delay. Thanks. No need to sorry - I know you are very busy. ;-) I've pushed the changes I did for the atheist upload. Kind regards, Andreas. -- http://fam-tille.de

Re: Packaging python-xrayutilities

2019-03-21 Thread Andreas Tille
On Thu, Mar 21, 2019 at 03:23:52PM +0500, Andrey Rahmatullin wrote: > On Thu, Mar 21, 2019 at 10:09:22AM +, MARIE Alexandre wrote: > > override_dh_installdocs: > > ln -s /usr/share/javascript/mathjax/MathJax.js > > $(CURDIR)/doc/build/html/_static/MathJax.js > > find

Re: Please enable me pushing to python-team/applications

2019-03-21 Thread Andreas Tille
On Thu, Mar 21, 2019 at 09:22:05AM +0100, W. Martin Borgert wrote: > On 2019-03-21 00:47, Thomas Goirand wrote: > > Can't you guys just simply give write access to Andreas? What's the > > issue? Why is it taking so long? This really give the feeling the "team" > > is still very much dysfunctional,

Re: Please enable me pushing to python-team/applications

2019-03-19 Thread Andreas Tille
On Tue, Mar 19, 2019 at 07:18:43PM +0300, Dmitry Shachnev wrote: > > I hope you will be added to the team, but while you are not, why can’t > you just use merge requests? In principle I could do this. However, I provided patches for some PAPT maintained packages on Alioth easily and I'd love to

Re: Please enable me pushing to python-team/applications

2019-03-19 Thread Andreas Tille
can try to assemble single commits on their own than. Sorry, for beeing a bit harsh, but I'm afraid that things like this are effectively preventing newcomers to this team Andreas. On Fri, Mar 15, 2019 at 04:22:50PM +0100, Andreas Tille wrote: > Hi, > > On Fri, Mar 15, 2019 at 0

Re: Please enable me pushing to python-team/applications

2019-03-15 Thread Andreas Tille
Hi, On Fri, Mar 15, 2019 at 02:12:57PM +0100, Ondrej Novy wrote: > Hi, > > ne 24. 2. 2019 v 20:39 odesílatel Andreas Tille napsal: > > > I just have push permissions for python-team/modules but when I tried > > to push changes to atheist to fix #918827, I ha

Re: Please enable me pushing to python-team/applications

2019-03-06 Thread Andreas Tille
Hi again, On Sun, Feb 24, 2019 at 08:39:03PM +0100, Andreas Tille wrote: > I just have push permissions for python-team/modules but when I tried > to push changes to atheist to fix #918827, I have no commit permissions > to https://salsa.debian.org/python-team/applications/atheist .

Please enable me pushing to python-team/applications

2019-02-24 Thread Andreas Tille
Hi, I just have push permissions for python-team/modules but when I tried to push changes to atheist to fix #918827, I have no commit permissions to https://salsa.debian.org/python-team/applications/atheist . Kind regards Andreas. -- http://fam-tille.de

Re: wheel autopkg tests fail (command1 and command2)

2019-02-07 Thread Andreas Tille
Control: tags -1 help Hi, I admit I have no idea what file "tests is seeked in ERROR: file not found: tests Any idea how to fix this? Kind regards Andreas. -- http://fam-tille.de

Re: Build test failure for python-easydev

2019-01-23 Thread Andreas Tille
On Wed, Jan 23, 2019 at 09:58:45AM +, Nick Morrott wrote: > > Cool. Thanks a lot. Your outright contribution was very helpful and > > really welcome. The only change I made is to revert your commit > > 38022ac5 since there is no point in changing the upstream source that > > way. I agree

Re: Build test failure for python-easydev

2019-01-22 Thread Andreas Tille
Hi Nick, On Tue, Jan 22, 2019 at 11:33:09PM +, Nick Morrott wrote: > > I'm a newcomer to the python team, but I'm looking at this at the > > moment to improve by debugging and python packaging. Cool. Thanks a lot. Your outright contribution was very helpful and really welcome. The only

  1   2   3   4   >