Re: ncl has not set science-team as maintainer

2024-04-19 Thread Andreas Tille
astair > > On 19/04/2024 09:43, Andreas Tille wrote: > > Hi Alastair, > > > > I've found ncl in the list of packages with t64 transition issues. > > Since I know its a Debian Science package I had a look and realised > > that this package has not set > >

Does anybody intent to adopt openmx -- nano-scale material simulations

2024-04-19 Thread Andreas Tille
Hi, since openmx is listed on the list of blockers for t64 transition and long time orphaned I wonder whether it is better to remove the package from Debian. According popcon its usage has basically zero votes[2] (which might be caused by the fact that it was not included into the last two

ncl has not set science-team as maintainer

2024-04-19 Thread Andreas Tille
Hi Alastair, I've found ncl in the list of packages with t64 transition issues. Since I know its a Debian Science package I had a look and realised that this package has not set Maintainer: Debian Science Maintainers as per team policy (and you as well as possibly others as Uploaders). Do

Re: Action needed for R-pkg Uploaders

2024-03-18 Thread Andreas Tille
ot;Any team member can and *should* upload team maintained packages no matter who is specified as Uploader." BTW, its perfectly welcome to add additional IDs to Uploaders. > Op Mon, Mar 11, 2024 at 03:47:42PM +0100 schreef Andreas Tille: > > > > > > > Joost van Baa

Re: Bug#1065841: Taking over datalad to either Debian Med or Debian Science team

2024-03-12 Thread Andreas Tille
Hi Yaroslav, Am Tue, Mar 12, 2024 at 03:50:22PM -0400 schrieb Yaroslav Halchenko: > Let's keep DataLad under our (NeuroDebian) umbrella for now, since we > are also upstream there and project is active. We are also > working with Vasyl (CCed) to experiment with some semi-automation for > package

Taking over datalad to either Debian Med or Debian Science team

2024-03-11 Thread Andreas Tille
Hi Yaroslav, once we agreed that we should probably move all Neurodebian packages to Debian Med to make it accessible for a bigger team. I was not really active for some time in this attempt. However, bug #1065841 brought datalad on my screen. I would love to see it maintained on Salsa either

Action needed for R-pkg Uploaders

2024-03-11 Thread Andreas Tille
Hi R-pkg team members, as you might have possibly read I nominated myself for DPL for the next term[1]. I will pronounce in my platform clearly that I will stop my uploading activity to rather concentrate on my DPL tasks. I hope I will be able to really stop myself from uploading in case I

Re: Segyio is lagging behind upstream (Was: segyio ftbfs with Python 3.12)

2024-02-21 Thread Andreas Tille
't import the symbols to the std:: > namespace. In general, the headers Standard C++ imports from Standard C > snips the .h and prefixes c, so stdint.h -> cstdint, stdio.h -> cstdio, etc. > > -- Tino Didriksen > > > On Wed, 21 Feb 2024 at 11:16, Andreas Tille wrote: >

Segyio is lagging behind upstream (Was: segyio ftbfs with Python 3.12)

2024-02-21 Thread Andreas Tille
Hi, I've found in the set of patches for segyio other cherry-picked patches to adapt to certain Python3.x versions[1]. The patch kindly suggested by s3v to fix this bug[2] would simply be another cherry-pick from upstream who has meanwhile released a couple of new versions incorporating all

Re: Team-maintenance of visidata in Debian Science team (Was: visidata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

2024-02-08 Thread Andreas Tille
entinel page right now[1]. > Anja Kind regards Andreas. [1] https://blends.debian.org/science/tasks/datamanagement#visidata > On Thu, 8 Feb 2024 at 04:45, Andreas Tille wrote: > > > Hi Anja, > > > > when analysing Python3.12 bugs like this I stumbled upon visidata.

Team-maintenance of visidata in Debian Science team (Was: visidata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

2024-02-08 Thread Andreas Tille
Hi Anja, when analysing Python3.12 bugs like this I stumbled upon visidata. While I have no idea for a fix my first attempt would be to update to the latest upstream version and see whether the bug might be fixed. I would love to help out (with such an upgrade or sponsoring the package.)

Re: Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes

2024-02-03 Thread Andreas Tille
Hi again, Am Fri, Feb 02, 2024 at 09:56:14PM +0100 schrieb Andreas Tille: > Hi Rebecca, > > Am Tue, Jan 30, 2024 at 08:05:35AM + schrieb Rebecca N. Palmer: > > I intend to upload pandas 2.x to unstable soon. These packages have a patch > > in their bug - please upl

Re: Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes

2024-02-02 Thread Andreas Tille
Hi Rebecca, Am Tue, Jan 30, 2024 at 08:05:35AM + schrieb Rebecca N. Palmer: > I intend to upload pandas 2.x to unstable soon. These packages have a patch > in their bug - please upload them (I'm a DM, I can't do that), or if you > think this patch won't work or isn't a good idea, tell me

Re: Bug#1061828: r-cran-plotly: Can't create any plots

2024-01-31 Thread Andreas Tille
Hi again, Am Tue, Jan 30, 2024 at 08:58:58PM +0100 schrieb Przemysław Kopa: > > $ head -n 6 plotly_cran/lib/plotly-main-2.11.1/plotly-latest.min.js > /** > * plotly.js v2.11.1 > * Copyright 2012-2022, Plotly, Inc. > * All rights reserved. > * Licensed under the MIT license > */ I've updated

Re: Bug#1061828: r-cran-plotly: Can't create any plots

2024-01-30 Thread Andreas Tille
Hi Przemysław, Am Tue, Jan 30, 2024 at 08:58:58PM +0100 schrieb Przemysław Kopa: > I've done some investigation. If you uninstall r-cran-plotly and then > install plotly directly from CRAN (same version), then the plot from the > example renders correctly: Thanks a lot, that's extremely helpful.

Re: Bug#1061828: r-cran-plotly: Can't create any plots

2024-01-30 Thread Andreas Tille
Control: tags -1 help Hi Przemyslaw, thanks a lot for your bug report. Its a schame that you have issues with the packaged version of plotly. Am Mon, Jan 29, 2024 at 09:36:55PM +0100 schrieb Przemyslaw Kopa: >Tried a simple scatterplot example: > >library(plotly) >plot_ly(data =

Re: can I help with pyvista packaging?

2024-01-29 Thread Andreas Tille
n, Jan 29, 2024 at 9:18 AM Andreas Tille wrote: > > Maybe its a good thing to discuss this issue at > > debian-pyt...@lists.debian.org (keeping the actual uploaders Gorden and > > Ximin in CC) to check out the blockers for the migration. Finally we > > need to make sure

Re: can I help with pyvista packaging?

2024-01-29 Thread Andreas Tille
an you please manually add me to each one of those with the > > highest possible gitlab permissions, so that I can tweak salsa CI? > > (I am in the science group and therefore I can access every science > > team repo, but only with the lowest gitlab permissions) > > &

How can we deal with lots of RC bugs as a team (and do we need critterding as one example)

2024-01-23 Thread Andreas Tille
Hi, in the Debian Med team we dedicate the time before Christmas in a so called "Advent bug squashing party" to bug fixing. Every team member simply picks bugs from our list of bugs no matter whether these are "own" packages (in terms of the bug fixer is Uploader) or not. Since I tried to fix

Re: Bug#1043240: transition: pandas 1.5 -> 2.1

2024-01-21 Thread Andreas Tille
Hi Rebecca, Am Sun, Jan 21, 2024 at 03:29:21PM + schrieb Rebecca N. Palmer: > > Hence, doing this transition now would involve breaking some reverse > dependencies with no known fix, but given the number of packages involved, > trying to wait until they're all fixed is rather likely to

Re: python-sparse's autopkg tests fail with Python 3.12

2024-01-13 Thread Andreas Tille
Hi Nilesh, Am Sat, Jan 13, 2024 at 04:15:07PM +0530 schrieb Nilesh Patra: > Fixed in Git, please check. Thanks a lot. I'll wait for debci whether bug #1055847 persists. I wonder whether we could close simply #1058485 since the test is passing with current numba. Kind regards Andreas. --

Re: python-sparse's autopkg tests fail with Python 3.12

2024-01-13 Thread Andreas Tille
Hi, thanks to Rebecca's hint I've updated python-sparse in Git to the latest upstream version. I decided to deactivate all patches. When trying to build I'm running into several errors: ModuleNotFoundError: No module named 'sparse._version' [1] This is surely due to the removal of

Debian Med sprint February 16.-18. 2024 in Berlin (in person meeting)

2024-01-10 Thread Andreas Tille
Hi, the Debian Med team will held its yearly in person meeting from Friday, February 16 (evening) until Sunday, February 18 (evening) in Berlin. For more detailed information please visit the Wiki page[1] and if you like to join our small meeting with bug squashing (may be Python 3.12 bug fixing

Re: build-depends on atlas, which is obsolete and scheduled for removal

2023-11-29 Thread Andreas Tille
Control: tags -1 help [Ritika Ramani in CC to inform that Debian tries to get rid of Atlas which also affects phast. see https://bugs.debian.org/1056681] Hi, I tried to replace clapack by LAPACKE. Unfortunately this is not a drop-in replacement. As you can see in the raw(! normal log is to

Help for emmax needed (Was: Removing ATLAS?)

2023-11-29 Thread Andreas Tille
Control: tags -1 help Hi, Am Fri, Jul 14, 2023 at 01:40:22AM +0200 schrieb Sébastien Villemot: > Le lundi 10 juillet 2023 à 22:01 +0200, Andreas Tille a écrit : > > I've checked my responsibility for the dependencies and stumbled about > > emmax > > > > >

Re: Please push your changes to python-xarray

2023-11-13 Thread Andreas Tille
ndreas. > Alastair McKinstry writes: > > > Hi > > > > Apologies I am swamped on this. Please go ahead and apply. > > > > Thanks > > Alastair > > > > On 13/11/2023 12:51, Andreas Tille wrote: > >> Ping? > >> > >> I'd love

Re: Please push your changes to python-xarray

2023-11-13 Thread Andreas Tille
07, 2023 at 09:26:13AM +0100 schrieb Andreas Tille: > Hi Alastair, > > I realised that the Git repository on salsa[1] is lagging a couple of > uploads behind the package pool. Please be so kind to push your changes > to Salsa. > > Thanks a lot for your work on this package &

Please push your changes to python-xarray

2023-11-07 Thread Andreas Tille
Hi Alastair, I realised that the Git repository on salsa[1] is lagging a couple of uploads behind the package pool. Please be so kind to push your changes to Salsa. Thanks a lot for your work on this package Andreas. [1] https://salsa.debian.org/science-team/python-xarray --

r-cran-stanheaders seems to use old tbb interface instead of onetbb

2023-10-25 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/stan-dev/rstan/issues/1101 Hi, I opened an issue on StanHeaders upstream about an issue with rstan and rstanarm. Any help (patch) to port StanHeaders to the new onetbb interface would be welcome. Kind regards Andreas. --

Re: Removing ATLAS?

2023-07-12 Thread Andreas Tille
Hi Rafael, Am Wed, Jul 12, 2023 at 03:34:09PM +0200 schrieb Rafael Laboissière: > When generating the C++ code, the xmds tool tries to link against > libcblas.so, which, currently, only exists in the libatlas-base-dev package. I admit this is actually the reason why any of the packages I'm

Re: Removing ATLAS?

2023-07-11 Thread Andreas Tille
ou can reach upstream it would be great if you could ping them somehow. Kind regards Andreas. > Best, > Steffen > > > Gesendet: Montag, 10. Juli 2023 um 22:01 Uhr > > Von: "Andreas Tille" > > An: debian-science@lists.debian.org > > Betreff: Re: Removing

Re: Removing ATLAS?

2023-07-10 Thread Andreas Tille
Hi Sébastian, Am Sat, Jul 08, 2023 at 10:01:15AM +0200 schrieb Sébastien Villemot: > > So, given all that, I’m inclined to (try to) remove atlas during the > trixie development cycle. Sounds reasonable. > Any thought on this? I've checked my responsibility for the dependencies and stumbled

Re: Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-10 Thread Andreas Tille
Hi Jochen, Am Fri, Jul 07, 2023 at 12:04:29PM +0200 schrieb Jochen Sprickerhof: > > echo "SALSA_TOKEN=" >> ~/.devscripts > echo 'SALSA_CI_CONFIG_PATH="recipes/debian.yml@salsa-ci-team/pipeline"' >> > ~/.devscripts > sudo apt install devscripts > salsa update_safe --group science-team --all

Re: Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-07 Thread Andreas Tille
Hi Jochen, Am Fri, Jul 07, 2023 at 09:48:45AM +0200 schrieb Jochen Sprickerhof: > > I confirm routine-update is going beyond the recommendation but in those > > teams where I'm working (in CC) we have this de-facto standard to use > > this file. Before I change the behaviour of routine-update I

Re: Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-07 Thread Andreas Tille
Control: severity -1 wishlist Hi Christopher, thanks you for the suggestion to enhance routine-update. Am Thu, Jul 06, 2023 at 09:03:23PM +0100 schrieb Christopher Obbard: > routine-update adds a file under the path "debian/salsa-ci.yml". Yes, this is intended. > According to the

Re: Maintenance of OSPRay and its dependency

2023-07-06 Thread Andreas Tille
Hi François, Am Sat, Jul 01, 2023 at 05:47:48PM +0200 schrieb François Mazen: > I'm working on packaging OSPRay [1], and Steve advised to make it team > maintained by the Debian Science Team. I definitely agree because > OSPRay mainly targets scientific applications like VTK or ParaView. Thanks

Re: numba: autopkgtest regression: segmentation fault on arm64

2023-07-03 Thread Andreas Tille
Hi On Sun, 21 May 2023 11:39:29 -0700 Diane Trout wrote: > Unfortunately it also wants llvmlite 0.40.0. Could you please be more verbose about this "unfortunately"? > It'd probably be easier to get upstream to help with debugging 0.57 I fully agree that we should target at latest upstream

Bug#1036753: unblock: debian-science/1.14.5

2023-05-25 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock X-Debbugs-Cc: debian-scie...@packages.debian.org, debian-science@lists.debian.org Control: affects -1 + src:debian-science Please unblock package debian-science [ Reason ] This is the

Re: HDF5 - how about removing gif2h5 subject to several CVE?

2023-05-24 Thread Andreas Tille
Hi Gilles, since nobody responded to your question (I did not respond as well since none of my packages uses this tool) here some opinion from me: No contradiction means agreement - thus just go for it. Thanks a lot for caring for hdf5 libraries Andreas. Am Sat, Feb 25, 2023 at 10:37:58PM

Numba issues for genx for other architectures than amd64 and ppc64el (Was: genx won't start: TypeError: Pen(): arguments did not match any overloaded call)

2023-04-18 Thread Andreas Tille
Hi, I've found genx in the "Cleaner view"[1] due to missing builds[2]. It turns out that for instance for arm64[3] the build fails with tests/test_numba_equivalency.py Fatal Python error: Segmentation fault For armel[4] (and armhf) we get dh_auto_test -a -O--buildsystem=pybuild I:

Re: Packaging liblsl

2023-03-14 Thread Andreas Tille
Hi Enrico, Am Tue, Mar 14, 2023 at 10:55:50AM +0100 schrieb Enrico Zini: > I've been needing to use liblsl[1] for a personal project, I noticed > that it's easily packaged, and it would be straightforward to upload it > to Debian. > > However, the package seems to have a much vaster reach and

Re: Bug#1027215: Bug#1026539: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-03-02 Thread Andreas Tille
Hi Rebecca, Am Thu, Mar 02, 2023 at 09:00:14PM + schrieb Rebecca N. Palmer: > > 1.1.2 isn't the latest version, just the latest that calls the module theano > rather than aesara. (I chose it to package because I didn't want to fully > break compatibility, then abandoned it because I didn't

Re: Bug#1026539: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-03-02 Thread Andreas Tille
Hi Rebecca, Am Wed, Mar 01, 2023 at 10:41:23PM + schrieb Rebecca N. Palmer: > I agree that switching to Aesara is probably the only reasonable option > other than removal. (I'd given up on trying to fix 1.0, and was intending > to let removal happen.) > > However, it's a much bigger change

Re: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-03-01 Thread Andreas Tille
Control: tags -1 pending Hi, > Andrius Merkys wrote: > That said, it is OK to omit keras in bookworm if need be, but I would > like to see it back for trixie. I've spent some time into theano and it builds and runs its test suite in Salsa CI[1]. Since despite some tests are failing in my

Re: Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))

2023-02-09 Thread Andreas Tille
Hi again, Am Thu, Feb 09, 2023 at 05:52:13PM +0100 schrieb Andreas Tille: > > That said, the np.matrix discrepancy was only just fixed recently, in > > December, by > > https://github.com/lmcinnes/umap/pull/946 I've updated the packaging, added the PR, fixed some test issues

Re: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))

2023-02-09 Thread Andreas Tille
Am Thu, Feb 09, 2023 at 04:57:03PM +0100 schrieb Drew Parsons: > tldr; https://github.com/lmcinnes/umap/pull/946 Thanks for the hint. > There's a couple of strange aspects to this problem. The np.matrix seems to > be generated by scipy.sparse. np.matrix is "not recommended" by numpy, but >

[Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))

2023-02-09 Thread Andreas Tille
Control: tags -1 help Am Thu, Feb 09, 2023 at 12:50:45AM +0100 schrieb Santiago Vila: > Package: src:umap-learn > Version: 0.4.5+dfsg-3 > Severity: serious > Tags: ftbfs > > Dear maintainer: > > During a rebuild of all packages in bookworm, your package failed to build: In Salsa CI you can

Re: scikit-learn Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-02-07 Thread Andreas Tille
Am Tue, Feb 07, 2023 at 09:05:28AM +0100 schrieb Drew Parsons: > On 2023-02-07 08:33, Graham Inggs wrote: > > Hi Drew > > > > I think python3-scipy should declare a Breaks on python3-skbio less > > than the version in unstable (0.5.8-3). > > This should sort out the autopkgtest regressions of

Re: Numba not in testing due to lots of autopkgtest errors - how to proceed

2023-02-07 Thread Andreas Tille
Hi Diane, Am Mon, Feb 06, 2023 at 11:23:47AM -0800 schrieb Diane Trout: > I pushed numba 0.56.4+dfsg-2 to unstable, and it should be vastly > better than -1. I quickly counted there's about 13 test failures for > what functionality we can support, those failing tests are currently > getting

Re: We are right before the freeze now - please update anything to latest version that needs updating

2023-02-03 Thread Andreas Tille
Hi Maarten, Am Fri, Feb 03, 2023 at 10:55:14AM +0100 schrieb Maarten van Gompel: > I'll give it a try today and see how far I can get. Hopefully that's > still in time? There will be ABI changes but at least there are no other > packages in debian that depend on our stack besides our own

Re: Numba not in testing due to lots of autopkgtest errors - how to proceed

2023-02-03 Thread Andreas Tille
Hi Graham, Am Fri, Feb 03, 2023 at 11:36:01AM +0200 schrieb Graham Inggs: > I will hint numba 0.56.4+dfsg-1 to migrate to testing now, despite the > autopkgtest regressions, and file an RC bug so we don't lose track of > this. Please don't upload until this has happened. Thanks a lot for your

Re: Numba not in testing due to lots of autopkgtest errors - how to proceed

2023-02-02 Thread Andreas Tille
Hi Graham, Am Thu, Feb 02, 2023 at 08:40:23PM +0200 schrieb Graham Inggs: > On Thu, 2 Feb 2023 at 17:18, Andreas Tille wrote: > > It seems to me that build time tests are working and the failure is > > just in autopkgtest. I'm drawing this conclusion from your latest > >

Re: Numba not in testing due to lots of autopkgtest errors - how to proceed

2023-02-02 Thread Andreas Tille
Hi Diane, Am Wed, Feb 01, 2023 at 02:21:08PM -0800 schrieb Diane Trout: > > > > could you please give an update about the status of numba?  The > > window > > of opportunity is closing soon.  Please be as verbose as possible > > what > > help you might need. > > > > Ok what I've been doing so

Re: We are right before the freeze now - please update anything to latest version that needs updating

2023-02-02 Thread Andreas Tille
Hi Joost, Am Thu, Feb 02, 2023 at 10:39:17AM +0100 schrieb Joost van Baal-Ilić: > Hi Andreas e.a., > > [I guess the same is true for debian-science, re-using your -med post here.] Re-using is fine. ;-) > On Wed, Feb 01, 2023 at 03:14:30PM +0100, Andreas Tille wrote to debian

Numba not in testing due to lots of autopkgtest errors - how to proceed

2023-02-01 Thread Andreas Tille
Hi Diane, could you please give an update about the status of numba? The window of opportunity is closing soon. Please be as verbose as possible what help you might need. In any case thanks for all your work on this heavy package Andreas. -- http://fam-tille.de

Re: Help needed to finalise the oneTBB migration of flexbar

2023-01-29 Thread Andreas Tille
Am Sat, Jan 28, 2023 at 09:06:43AM +0100 schrieb Andreas Tille: > Am Fri, Jan 27, 2023 at 11:12:10PM +0100 schrieb Étienne Mollier: > > favor of funtion tbb::parallel_pipeline). I'm a bit dry for the > > moment and will have the weekend busy, so if someone wants to > > take o

Re: scikit-learn Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-27 Thread Andreas Tille
Am Thu, Jan 26, 2023 at 07:51:23PM + schrieb Rebecca N. Palmer: > Control: tags 1029701 fixed-upstream > > Full log: > https://ci.debian.net/data/autopkgtest/unstable/amd64/s/scikit-learn/30693526/log.gz > > There appear to be at least 2 separate failures here, both known and > probably

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-26 Thread Andreas Tille
Am Thu, Jan 26, 2023 at 05:45:58PM +0100 schrieb Drew Parsons: > > Any solution for this one? > > Probably just needs updating to the latest release. They fixed some things. Latest release is building in my local git. I'll report about issues if I might meet some. Otherwise I'll also upload

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-26 Thread Andreas Tille
Am Thu, Jan 26, 2023 at 04:51:25PM +0100 schrieb Drew Parsons: > On 2023-01-26 16:46, Andreas Tille wrote: > > I've fixed all those Debian Med related issues in testing where you > > filed > > bug reports for. Seems from my point of view the upload of 1.10 is > > fine.

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-26 Thread Andreas Tille
Am Thu, Jan 26, 2023 at 04:51:25PM +0100 schrieb Drew Parsons: > > Thanks Andrea. armel has revealed which tests it needs skipped, so I'll > push scipy 1.10 to unstable after scipy 1.8.1-22 is done migrating to > testing Thanks a lot for all your work on this Andreas. --

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-26 Thread Andreas Tille
Hi Drew, Am Thu, Jan 26, 2023 at 01:46:18PM +0100 schrieb Drew Parsons: > > for the release architectures with autopkgtests, so expect results for > > more architectures to appear over the next few hours. > > [1] https://qa.debian.org/excuses.php?experimental=1=scipy > > Ok, if you're happy with

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-25 Thread Andreas Tille
Am Wed, Jan 25, 2023 at 04:29:59PM +0100 schrieb Drew Parsons: > heh yeah, I was just replying about that :) So at least I was beating you in writing an e-mail! :-P > Are we confident on bringing scipy 1.10 to the new stable? In any case we should probably follow Graham's advise to let things

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-25 Thread Andreas Tille
Am Wed, Jan 25, 2023 at 04:23:58PM +0100 schrieb Andreas Tille: > I'm just building an according package locally and will hopefully upload > soon. ... but Drew Parsons seems to have beaten me. ;-) Thanks also to Drew Andreas. -- http://fam-tille.de

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-25 Thread Andreas Tille
Hi Graham, Am Wed, Jan 25, 2023 at 03:09:54PM +0200 schrieb Graham Inggs: > Please do fix #1029550 in 1.8.1 in testing before uploading 1.10.0 to > unstable. It is one of the last blockers for NumPy. I'm just building an according package locally and will hopefully upload soon. Thanks a lot

Re: Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-25 Thread Andreas Tille
Hi Graham, Am Wed, Jan 25, 2023 at 02:28:37PM +0200 schrieb Graham Inggs: > On Wed, 25 Jan 2023 at 11:43, Andreas Tille wrote: > > I was motivated for this patch by Diane's statement on the Debian Med > > matrix channel that dask and dask.distributed are interconnected. If >

Re: Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-25 Thread Andreas Tille
Hi Graham Am Tue, Jan 24, 2023 at 12:50:41PM +0200 schrieb Graham Inggs: > > On Tue, 24 Jan 2023 at 00:16, Rebecca N. Palmer > wrote: > > The remaining autopkgtest failures blocking pandas are: > > - dipy/amd64 and snakemake/i386 look like random flakiness: please retry > > them. (I think DMs

Help needed to finalise the oneTBB migration of flexbar

2023-01-24 Thread Andreas Tille
Control: tags -1 help Hi, I made some progress[1] in converting flexbar (which seems to be orphaned upstream[2] so we are on our own with the migration - but the program ist interesting anyway) but finally have hit a blocker which you can see in the build in Salsa CI[3]. It would be great if

Please help to reproduce (Was: shiny-server: server-function don't run)

2023-01-22 Thread Andreas Tille
Hi Sebastian, thanks for your bug report and your attempt to track this down by replacing the sockjs files. Please note that neither Nilesh nor I are shiny-server users. Thus it would help if you could provide a possibly small example that helps us reproducing the problem. Kind regards

Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-19 Thread Andreas Tille
Hi, Am Thu, Jan 19, 2023 at 12:52:13AM +0100 schrieb Drew Parsons: > On 2023-01-18 22:31, Rebecca N. Palmer wrote: > > > > This "broken by numpy 1.24" bug looks to me like 17033, not 17630. > > This has what looks like a trivially-backportable patch, though I > > haven't actually tried that: > >

Re: Helping hands needed to upgrade scipy

2023-01-17 Thread Andreas Tille
Hi Drew, Am Wed, Jan 18, 2023 at 02:45:31AM +0100 schrieb Drew Parsons: > On 2023-01-17 18:12, Andreas Tille wrote: > > Hi, > > > > I upgraded the experimental branch of scipy to contain the submodules > > upstream includes. I'm *not* convinced that we need them all

Re: Do we want to keep up pyfr?

2023-01-17 Thread Andreas Tille
Hi Drew, Am Tue, Jan 17, 2023 at 12:43:56PM +0100 schrieb Drew Parsons: > > [1] https://salsa.debian.org/science-team/pyfr > > [2] https://salsa.debian.org/science-team/pyfr/-/jobs/3809459 > > > From the test log, h5py didn't get installed. > > Looking at debian/tests/control, it only has @

Helping hands needed to upgrade scipy

2023-01-17 Thread Andreas Tille
Hi, I upgraded the experimental branch of scipy to contain the submodules upstream includes. I'm *not* convinced that we need them all - hopefully we can get rid of boost (but upstream has some patches here) and scipy-mathjax. For the moment I've tried to build the experimental branch and ended

Do we want to keep up pyfr?

2023-01-16 Thread Andreas Tille
Hi, I pushed some changes to pyfr git[1] including the latest upstream version. Unfortunately the autopkgtest fails[2] with pkg_resources.DistributionNotFound: The 'h5py>=2.10' distribution was not found and is required by pyfr (which is a bit strange since we have h5py 3.7.0.) If someone

Re: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-01-16 Thread Andreas Tille
Hi Thiago, Am Mon, Jan 16, 2023 at 11:08:35AM -0300 schrieb Thiago Franco Moraes: > Done! I removed both python3-theano and python3-keras. Thanks for the quick response. Autopkgtest currently fails due to Bug #1027851 pytorch FTBFS with Python 3.11 as default version I think, I'll wait a

Re: skimage: two build-time tests are failing in latest upload

2023-01-16 Thread Andreas Tille
Hi Ole, Am Mon, Jan 16, 2023 at 12:09:22PM +0100 schrieb Ole Streicher: > > === short test summary info > > > > FAILED > > skimage/color/tests/test_colorconv.py::test_lab_lch_roundtrip_dtypes[float16] > > FAILED > >

Re: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-01-16 Thread Andreas Tille
Hi Thiago, Am Sat, Jan 14, 2023 at 07:50:27PM -0300 schrieb Thiago Franco Moraes: > Hi Rebecca, > > InVesalius can work without Theano (and Keras). It will use Pytorch. Would you mind updating the packaging without Theano? Currently its in its Build-Depends. Would it be sufficient to drop

skimage: two build-time tests are failing in latest upload

2023-01-16 Thread Andreas Tille
Hi Ole, thanks for caring for skimage. I realised that s390x fails building[1] with: === short test summary info FAILED skimage/color/tests/test_colorconv.py::test_lab_lch_roundtrip_dtypes[float16] FAILED

Re: transition: pandas 1.3 -> 1.5

2023-01-10 Thread Andreas Tille
Am Mon, Jan 09, 2023 at 01:44:40PM +0200 schrieb Graham Inggs: > Hi Rebecca > > On Fri, 6 Jan 2023 at 10:30, Rebecca N. Palmer > wrote: > > Should this go ahead before the freeze? I think yes if the new dask > > works, but am open to disagreement. > > Please go ahead. With numpy 1:1.24.1-2

Re: keras orphaned

2023-01-10 Thread Andreas Tille
Hi Stephen, Am Wed, Jan 04, 2023 at 10:38:44PM +0100 schrieb Stephen Sinclair: > I have unfortunately decided to orphan keras and related packages, as there > are errors with the latest numpy that I cannot resolve, and upstream no > longer maintains this software as an independent package from

Debian Med sprint January 21.+22. 2023 (in person meeting)

2022-12-02 Thread Andreas Tille
to arrive may be at Friday 20.1. noon to meet at some place that needs to be determined and if possible stay until Monday 23.1. to do some after sprint socialising in Berlin. Looking forward to see you all Andreas. Am Thu, Dec 01, 2022 at 08:50:12AM +0100 schrieb Andreas Tille: > Hi fo

Re: MRs on salsa and letting janitor automate things

2022-12-01 Thread Andreas Tille
Hi Jelmer, Am Thu, Dec 01, 2022 at 04:04:13PM + schrieb Jelmer Vernooij: > One of the things you don't get when running these scripts manually rather > than > waiting or the janitor is that it verifies the package still builds, passes > autotests and generates binary diffs before

Re: MRs on salsa and letting janitor automate things

2022-12-01 Thread Andreas Tille
Hi again, Am Thu, Dec 01, 2022 at 01:55:43PM +0100 schrieb PICCA Frederic-Emmanuel: > > As I tried to explain, routine-update does all what Janitor is doing > > (please let me know if not than I'd include the actual Janitor code) > > plus other things Janitor can't do. I'm fine with whatever the

Re: MRs on salsa and letting janitor automate things

2022-12-01 Thread Andreas Tille
Hi Stuart, Am Wed, Nov 30, 2022 at 10:58:06AM +1100 schrieb Stuart Prescott: > > While there is a substantial overlap in the feature sets, one is not a > subset of the other. > > - routine-update does some great things like normalising packaging. That's > something Janitor can't do because

Re: MRs on salsa and letting janitor automate things

2022-12-01 Thread Andreas Tille
Hi Dima, Am Tue, Nov 29, 2022 at 06:56:02PM -0800 schrieb Dima Kogan: > Hi Nilesh and Stuart. That email on debian-devel describes my use case > well. My packages are vanilla-enough that there's little value in doing > anything more than Build-Depends: debhelper (>=11) and sticking "11" in >

Debian Med sprint January 2023 (in person meeting)

2022-11-30 Thread Andreas Tille
Hi folks, thanks to Sascha Steinbiss we can have our next in person meeting where we were in 2020 the last time. His employer is offering rooms outside of their office hours (actually Saturday + Sunday). All details are listed at the sprint wiki page:

Re: MRs on salsa and letting janitor automate things

2022-11-29 Thread Andreas Tille
Moin, Am Tue, Nov 29, 2022 at 06:38:00PM +0100 schrieb Christian T. Steigies: > > I admit I share the old fashioned view and we asket Jelmer to not > > run Janitor on Debian Med and R-pkg-team. The rationale is that > > we are running > > > > routine-update > > This sounds cool, but I have

Re: MRs on salsa and letting janitor automate things

2022-11-29 Thread Andreas Tille
Hi, Am Sun, Nov 27, 2022 at 08:29:58AM -0400 schrieb David Bremner: > > Personally I often find it hard to prioritize understanding the MRs from > the janitor, and I'm not comfortable with having a bot commit to a repo > that I am responsible for. Perhaps I'm just old fashioned. I'm an >

Re: MRs on salsa and letting janitor automate things

2022-11-29 Thread Andreas Tille
Am Mon, Nov 28, 2022 at 09:58:33AM + schrieb Jelmer Vernooij: > debhelper-c that > carries debhelper 13. If you're looking to avoid anything that's not available > in e.g. oldstable or ubuntu lts rather than specifically excluding > "debhelper-compat (= X)", the janitor also has a setting for

Re: OCaml support for mcl (Was: Help with mcl needed: util/rand.h missing)

2022-11-28 Thread Andreas Tille
Hi Nilesh, Am Mon, Nov 28, 2022 at 01:44:16PM +0530 schrieb Nilesh Patra: > > I'm in favour of droping the OCaml patch. > > I guess the Ocaml patch was needed for pplacer. Now pplacer FTBFS due to > removed > ocaml patch/binpkg. See Bug#1024889 Ah, yes, sure, I'm blaming my very bad

Re: OCaml support for mcl (Was: Help with mcl needed: util/rand.h missing)

2022-10-28 Thread Andreas Tille
Hi, Am Sat, Oct 29, 2022 at 01:32:59AM +0530 schrieb Nilesh Patra: > > On Wed, Oct 26, 2022 at 11:17:38AM +0200, Andreas Tille wrote: > > Shayan, do you think you can fix this patch you once obtained from some > > project that seems to have stalled since 9 years?

OCaml support for mcl (Was: Help with mcl needed: util/rand.h missing)

2022-10-26 Thread Andreas Tille
Hi Joost, Am Tue, Oct 25, 2022 at 03:41:57PM +0200 schrieb Joost van Baal-Ilić: > > > Do you have any idea where to obtain util/rand.h? > > > > It came with cimfomfa-18-238/util/rand.h > > > > does current cimfomfa no longer ship it? > > I think you have to patch it: replace > > #include

Re: Can't open perl script "/usr/share/vtk9/doxygen//doc_header2doxygen.pl": No such file or directory

2022-10-25 Thread Andreas Tille
Hi, is there any chance to provide doc_header2doxygen.pl in VTK9 packages? Kind regards Andreas. -- http://fam-tille.de

Help with mcl needed: util/rand.h missing

2022-10-25 Thread Andreas Tille
Hi Joost, cimfomfa was quickly accepted in unstable thanks to ftpmaster. So I wanted to build the latest version of mcl but I stumbled upon caml/caml_mcl.c:2:10: fatal error: util/rand.h: No such file or directory 2 | #include "util/rand.h" | ^ Do you have

Re: Uploading cimfomfa

2022-10-13 Thread Andreas Tille
Am Thu, Oct 13, 2022 at 10:28:21AM +0200 schrieb Joost van Baal-Ilić: > [Cc-ing upstream] > > Excellent, yes please, go ahead! Will do, thanks for the ultrafast reply Andreas. > Bye, Thanks, Joost > > On Thu, Oct 13, 2022 at 09:55:48AM +0200, Andreas Tille w

Uploading cimfomfa

2022-10-13 Thread Andreas Tille
Hi Joost, thanks to your previous work I was able to get cimfomfa easily built and I worked down your list of todo/fixme in d/changelog. So I'm basically ready to upload this package which I would need for the new version of mcl. I hope you don't mind if I do so in a team upload to new. Kind

Re: ITA: glm -- C++ library for OpenGL GLSL type-based mathematics

2022-09-03 Thread Andreas Tille
Am Sat, Sep 03, 2022 at 09:47:27PM +0200 schrieb Anton Gladky: > Hi Andrea, > > thanks for taking care of this package! Really appreciate it. > > Please, follow an advices given by Pierre and we will upload > the package, giving you permissions to upload it in the future. > > It could also be

Reduce severity from serious to important

2022-08-15 Thread Andreas Tille
Control: severity -1 important Hi, as discussed on Debian Science the affected test suite errors are ignored for the moment so the package does not FTBFS any more and thus the bug is not serious any more. Since issues are remaining the bugs are not closed yet. Kind regards Andreas. --

Re: scikit-learn testing migration

2022-08-13 Thread Andreas Tille
Hi Nilesh, Am Sat, Aug 13, 2022 at 02:13:05PM +0530 schrieb Nilesh Patra: > > Considering long term maintainance this does not seem to be nice especially > keeping in mind the fact that sklearn is a key package. For sure it is not nice. > I think it is OK to do it _for the moment_ to allow the

Re: scikit-learn testing migration

2022-08-13 Thread Andreas Tille
Hi again, Am Thu, Aug 04, 2022 at 01:25:42PM +0200 schrieb Andreas Tille: > Am Fri, Jul 29, 2022 at 06:09:26AM +0200 schrieb Andreas Tille: > Before we fall into another "do nothing" period: I will upload > scikit-learn restricted to those architectures only which have

Re: scikit-learn testing migration

2022-08-04 Thread Andreas Tille
Hi again, Am Fri, Jul 29, 2022 at 06:09:26AM +0200 schrieb Andreas Tille: > I just like to repeat my point: If the package is to slow on release > architectures, that we will not manage to fix it, it is in the interest > of our users to not support the problematic architectures

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