Bug#1068008: newer rust needed
Also I thought to try to build deno https://github.com/denoland/deno.git (ITP - #961337) https://bugs.debian.org/961337 deno but it needs ❯ cat rust-toolchain.toml [toolchain] channel = "1.77.2" components = ["rustfmt", "clippy"] so we are indeed well behind :-/ -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1057126: Bug#1067104: Acknowledgement (server stalls: AH00046: child process 2876749 still did not exit, sending a SIGKILL)
"All ingenious is simple" -- thanks for sharing. I might redo following your example but to check more frequently. On Thu, 21 Mar 2024, Peter Krefting wrote: > My workaround is simpler, I have this line in root's crontab: > 5 * * * * curl --silent --max-time 5 --output /dev/null > http://localhost/trac/ || systemctl restart apache2 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1057126: Bug#1067104: Acknowledgement (server stalls: AH00046: child process 2876749 still did not exit, sending a SIGKILL)
I think "my" https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067104
is a duplicate of this one. I blame mod_wsgi since this I believe
started to happen after I started to use it.
FWIW here is a dirty workaround script I just crafted with chatgpt to
monitor/restart apache2 as soon as it starts happening (doesn't happen upon
every maintenance event for me I believe). Let me know if I should gather any
additional information.
#!/bin/bash
set -eu
# Define the lock file and log directory
lock_file="/var/log/apache-scoreboard-restart/lock.lck"
log_dir="/var/log/apache-scoreboard-restart/"
# Ensure the log directory exists
mkdir -p "$log_dir"
# Attempt to acquire a lock
exec 200>"$lock_file"
if ! flock -n 200 ; then
echo "Another instance is running."
exit 0
fi
# Function to perform actions when the specified log line is found
handle_scoreboard_full() {
local timestamp=$(date --iso-8601=seconds)
local log_file="${log_dir}${timestamp}.log"
echo "Logging system information to $log_file."
{ ps auxw -H; echo "---"; lsof; } > "$log_file"
echo "Reloading Apache." >> "$log_file"
service apache2 reload
echo "Sleeping for a minute." >> "$log_file"
sleep 60
}
# Monitor the Apache error log
while true; do
tail --follow=name /var/log/apache2/error.log | while read line
; do
if echo "$line" | grep -q "AH03490: scoreboard is full,
not at MaxRequestWorkers.Increase ServerLimit." ; then
handle_scoreboard_full
break # so we start with a fresh tail
fi
done
done
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW: http://www.linkedin.com/in/yarik
signature.asc
Description: PGP signature
Bug#1065203: Acknowledgement (regression: TypeError: find_username() missing 1 required positional argument: 'ssh_conf')
I submitted MR with this fix and overall small refactoring of the code there to improve functionality at https://salsa.debian.org/debian/dput-ng/-/merge_requests/34 Please review/merge/release -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1067104: server stalls: AH00046: child process 2876749 still did not exit, sending a SIGKILL
Package: apache2 Version: 2.4.57-2 Severity: important Server was working just fine for years and recently started to stall completely after 3-7 days of functioning normally. error logs get filled up first with AH03490 and then eventually with AH00045 messages: [Sun Mar 17 02:26:01.353381 2024] [mpm_event:error] [pid 2649373:tid 139846579189632] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. ... [Sun Mar 17 22:00:42.201774 2024] [mpm_event:error] [pid 2649373:tid 139846579189632] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Sun Mar 17 22:00:42.995574 2024] [mpm_event:error] [pid 2649373:tid 139846579189632] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Sun Mar 17 22:00:42.998488 2024] [mpm_event:notice] [pid 2649373:tid 139846579189632] AH00492: caught SIGWINCH, shutting down gracefully [Sun Mar 17 22:00:46.358981 2024] [core:warn] [pid 2649373:tid 139846579189632] AH00045: child process 2649375 still did not exit, sending a SIGTERM [Sun Mar 17 22:00:46.359064 2024] [core:warn] [pid 2649373:tid 139846579189632] AH00045: child process 2649376 still did not exit, sending a SIGTERM until I restart the beast. $> grep AH03490 error.log | wc -l 70404 $> grep AH00045 error.log | wc -l 48 Server has a number of virtualserver's configured. Seems has started about a month ago $> for e in error.log*; do zgrep AH03490 $e| head -n 1 ; done [Sun Mar 17 02:26:01.353381 2024] [mpm_event:error] [pid 2649373:tid 139846579189632] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Mon Mar 11 16:47:41.181900 2024] [mpm_event:error] [pid 1172065:tid 140192799893376] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Tue Mar 05 00:00:12.307813 2024] [mpm_event:error] [pid 2686718:tid 139644504094592] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Sun Feb 25 03:23:33.382200 2024] [mpm_event:error] [pid 2686718:tid 139644504094592] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Sat Feb 24 01:02:29.148887 2024] [mpm_event:error] [pid 2686718:tid 139644504094592] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. [Tue Feb 13 14:28:00.653754 2024] [mpm_event:error] [pid 2434335:tid 140300052350848] AH03490: scoreboard is full, not at MaxRequestWorkers.Increase ServerLimit. and likely after I configured some wsgi $> zgrep apache /var/log/dpkg.log.* | grep 2024 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 install libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 status half-installed libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 status unpacked libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 configure libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 status unpacked libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:23 status half-configured libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:34:25 status installed libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:51:18 status installed libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:51:19 remove libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:51:19 status half-configured libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:51:21 status half-installed libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:51:21 status config-files libapache2-mod-python:amd64 3.5.0+git20211031.e6458ec-1+deb12u1 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 install libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 status half-installed libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 status unpacked libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 configure libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 status unpacked libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:11 status half-configured libapache2-mod-wsgi-py3:amd64 4.9.4-1+b2 /var/log/dpkg.log.2.gz:2024-02-02 12:52:14 status installed libapache2-mod-wsgi-py3:amd64
Bug#1066931: Acknowledgement (replace debian/1.39 with 1.39 tag)
moreover that added tag was not even annotated as the release tags: hence ❯ git describe 1.38-11-gb182a2e ❯ git describe --tags debian/1.39-8-gb182a2e -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1066931: replace debian/1.39 with 1.39 tag
Package: python3-dput Version: 1.39 Severity: minor Tags: upstream X-Debbugs-Cc: Andreas Tille Hi Andreas, Thanks for taking care about recent release. But I got confused when I didn't see 1.39 tag, and only later detected that you tagged it as debian/1.39 . Unless there is team decision on changing tagging scheme, should we replace debian/1.39 with a more regular for this repo 1.39 tag? ❯ git tag | grep -e '1\.3' 1.3 1.30 1.31 1.32 1.33 1.34 1.35 1.35+deb12u1 1.36 1.37 1.38 debian/1.39 -- System Information: Debian Release: trixie/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'stable-updates'), (100, 'stable-security'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.6.15-amd64 (SMP w/20 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-dput depends on: ii gnupg 2.2.40-1.1 ii python3 3.11.6-1 ii python3-debian 0.1.49 ii python3-xdg 0.28-2 Versions of packages python3-dput recommends: ii debian-keyring 2023.12.24 ii lintian 2.117.0 ii openssh-client 1:9.6p1-4 ii python3-distro-info 1.7 ii python3-jsonschema 4.10.3-2 ii python3-paramiko 2.12.0-2 python3-dput suggests no packages. -- debconf-show failed
Bug#1065841: Taking over datalad to either Debian Med or Debian Science team
Hi Andreas, 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 updates/backports (for neurodebian) and datalad (and some of its ecosystem) packages are the target. Packaging will be on salsa. We might move them under larger Med or Science teams, but not just yet. Re #1065841 specifically -- while trying to build updated package I experienced some odd side-effect (pip started to try to install tqdm) and didn't see immediate reason.I will see how well it goes on debian infra after source only upload (did now). Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1065841: datalad: Please drop dependencies on python3-distutils
Indeed, I think we did using distutils as of 0.18.0 On March 10, 2024 9:33:12 AM EDT, Graham Inggs wrote: >Source: datalad >Version: 0.19.6-1 >Severity: important >Tags: ftbfs >User: debian-pyt...@lists.debian.org >Usertags: python3.12 > >Hi Maintainer > >This package has dependencies, build-dependencies and/or autopkgtest >dependencies on python3-distutils. The python3-distutils binary >package will soon be dropped from python3-stdlib-extensions. > >In fact, there is no module for Python 3.12 in python3-distutils, so >these dependencies may already be unnecessary. > >Regards >Graham > > -- Sent from a phone which beats iPhone.
Bug#1065203: regression: TypeError: find_username() missing 1 required positional argument: 'ssh_conf'
Package: dput-ng Version: 1.38~bpo12+1 Severity: important Used to work fine, today started to fail: ❯ dput neurosmaug git-annex_10.20240227-1~ndall+1_source.changes Uploading git-annex using scp to neurosmaug (host: neurosmaug; directory: /home/neurodebian/deb/builds/ndbuild) running allowed-distribution: check whether a local profile permits uploads to the target distribution running checksum: verify checksums before uploading running suite-mismatch: check the target distribution for common errors running gpg: check GnuPG signatures before the upload Not checking GPG signature due to allow_unsigned_uploads being set. Traceback (most recent call last): File "/usr/bin/dput", line 129, in upload_package(changes, args) File "/usr/lib/python3/dist-packages/dput/uploader.py", line 323, in invoke_dput with uploader(profile['method'], profile, File "/usr/lib/python3.11/contextlib.py", line 137, in __enter__ return next(self.gen) ^^ File "/usr/lib/python3/dist-packages/dput/uploader.py", line 170, in uploader obj.initialize() File "/usr/lib/python3/dist-packages/dput/uploaders/scp.py", line 56, in initialize login = find_username(self._config) ^^^ TypeError: find_username() missing 1 required positional argument: 'ssh_conf' downgrade to Version: 1.38~bpo12+1 resolved the issue. Trickery might be due to "fqdn = neurosmaug" where "neurosmaug" is defined within ~/.ssh/config like Host neurosmaug User neurodebian ForwardAgent no HostName some.sensored.example.com Port Cheers, -- System Information: Debian Release: trixie/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'stable-updates'), (100, 'stable-security'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.6.15-amd64 (SMP w/20 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages dput-ng depends on: ii python3 3.11.6-1 ii python3-dput 1.38~bpo12+1 dput-ng recommends no packages. Versions of packages dput-ng suggests: pn dput-ng-doc pn python3-twitter ii rsync3.2.7-1+b1 -- debconf-show failed
Bug#1014890: RFP: python3-looseversion -- Version numbering for anarchists and software realists
AFAIK nope -- feel welcome to finish it up and upload. Then you can make it follow the desired naming ;) On Wed, 03 Jan 2024, Mike Gabriel wrote: > Has there been any progress on uploading python3-looseversion to unstable, > recently? (I'd suggest naming the src:pkg python-looseversion, though). > I need the LooseVersion() API for python-x2go and if you have dropped > interest in looseversion (or similar), would you be ok with me doing an > initial upload of python-looseversion? > Greets + Thanks for feedback, > Mike -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1059247: stressant: crashes not finding /usr/share/doc/fio/examples/basic-verify.fio
Package: stressant Version: 0.7.0 Severity: important X-Debbugs-Cc: deb...@onerussian.com Dear Maintainer, Decided to try stressant on a freshly installed debian box. But it crashed with yoh@reproiner:~$ stressant --cpu ... INFO: Disk stress test Traceback (most recent call last): File "/usr/bin/stressant", line 491, in main() File "/usr/bin/stressant", line 479, in main testDrive(**vars(args)) File "/usr/bin/stressant", line 401, in testDrive with open(jobFile, 'rb') as source: ^^^ FileNotFoundError: [Errno 2] No such file or directory: '/usr/share/doc/fio/examples/basic-verify.fio' only with apt-file I saw that there is also fio-examples that is only Suggests-ed by fio on which stressant depends. So it seems that stressant might need to Depend on fio-examples *** Reporter, please consider answering these questions, where appropriate *** * What led up to the situation? * What exactly did you do (or not do) that was effective (or ineffective)? * What was the outcome of this action? * What outcome did you expect instead? *** End of the template - remove these template lines *** -- System Information: Debian Release: 12.4 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 6.1.0-16-amd64 (SMP w/4 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages stressant depends on: ii python3 3.11.2-1+b1 ii python3-colorlog 6.7.0-1 ii python3-humanize 4.4.0-1 Versions of packages stressant recommends: ii fio3.33-3 ii hdparm 9.65+ds-1 ii iperf3 3.12-1+deb12u1 ii lshw 02.19.git.2021.06.19.996aaad9c7-2+b1 ii smartmontools 7.3-1+b1 ii stress-ng 0.15.06-2 stressant suggests no packages. -- no debconf information
Bug#861635: any hope for et to get to debian?
didn't check if PPA upstream promotes a good start Re Jason's > Also why is this changed to RFP? because it had been over a year without package materializing, thus it is more of RFP than ITP. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#946244: pretty please
Current versions is way too old. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1031781: neurodebian-popcon.gpg'
Sorry for the delay. Somehow I even didn't get any message on this bug report being filed ... odd On Mon, 20 Feb 2023, Yaroslav Halchenko wrote: > > How do I get rid of this message? > apt-get install neurodebian-archive-keyring > ? > Let me know how it goes... I will look more in detail later. If still > observe the issue, reportbug neurodebian-archive-keyring to provide > detail and so I don't forget about it I was wrong about what package to implicate here: you reported >neurodebian-popularity-contest deinstall and indeed that /usr/share/popularity-contest/neurodebian-popcon.gpg is from that package. So I guess, you did/tried to dpkg --remove neurodebian-popularity-contest (not --purge) and that left the cron script present but without key shipped in the package. That lead to the error. To resolve it, just dpkg --purge neurodebian-popularity-contest which should also remove /etc/popularity-contest.d/neurodebian.conf and as a result to avoid that cron job script try to get that key and report to our popcon server. I think I have a fix... FTR: here is a Dockerfile with which I have created a "test env" (git)smaug:~exppsy[master]neurodebian-trash/debian-1031781 $> cat Dockerfile FROM debian:buster ENV DEBIAN_FRONTEND=noninteractive RUN apt-get -y update RUN apt-get -y install eatmydata RUN eatmydata apt-get -y install sudo gnupg wget locales RUN wget -O /etc/apt/sources.list.d/neurodebian.sources.list http://neuro.debian.net/lists/buster.us-nh.li bre && \ apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 && \ apt-get update -qqq && \ apt-get install -y svgtune # just to pull in neurodebian-popularity-contest and here is invocation to try a "fixed up" version: docker run -it --rm -v $PWD/popcon/neurodebian.conf:/etc/popularity-contest.d/neurodebian.conf neurodebian-debug:1 bash -c 'set -x; echo PARTICIPATE="yes" >> /etc/popularity-contest.conf; dpkg --remove --force -depends neurodebian-popularity-contest; ls -l /etc/cron.daily/popularity-contest /usr/share/popularity-co ntest/neurodebian-popcon.gpg; ls -l /usr/share/doc/neurodebian-popularity-contest; bash -x /etc/cron.dail y/popularity-contest' -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1050471: ITS: impose+
no objections! On Thu, 24 Aug 2023, Bastian Germann wrote: > Source: impose+ > Severity: important > impose+ does not seem to be maintained anymore. I intend to salvage it with > the plan to orphan it in three weeks. Please notify me if you object. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1028157: cython update
On Fri, 11 Aug 2023, Drew Parsons wrote: > ... > > But in any case PR18242 looks simple enough to backport to scipy 1.10.1 . > Would need to be tested first. Get cython3 into experimental so we can > check. Dear Stefano, would you have time for such an endeavor? would be great and highly appreciated! > > - upstream has (and I don't think ever had) no upper bound > > > grep Cython pyproject.toml > > "Cython>=0.29.18", > ... > > CCing Drew Parsons maintaining scipy -- may be he could recall the need > > for upper bound or just make a verdict to drop that upper bound? > The upper bound for scipy is declared in its pyproject.toml, but you're > right it's not declared so in scipy git. > They often add an upper bound in the release tarballs. I think it's a > mechanism so keep released code more manageable, avoiding unanticipated > problems with future versions. ha -- I was not aware of such an act/approach. Just for completeness of understanding of the release process of scipy -- indeed: ❯ wget --quiet https://files.pythonhosted.org/packages/a6/98/fceb84466a74b8fe74ce2dcc3a0a89cb7b4a689d4775e0fb4c95f335ef6a/scipy-1.11.1.tar.gz ❯ tar -Oxf scipy-1.11.1.tar.gz scipy-1.11.1/pyproject.toml | grep Cython "Cython>=0.29.35,<3.0", # when updating version, also update check in meson.build and they do it as a part of the "release tag/branch" preparation process: ❯ git diff master...v1.11.0 -- pyproject.toml | head -n 20 diff --git a/pyproject.toml b/pyproject.toml index f3951dc82..ccab62aec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,37 +8,164 @@ # "pybind11>=2.4.3,<2.5.0", [build-system] +build-backend = 'mesonpy' requires = [ -"wheel", -"setuptools", -"Cython>=0.29.18", -"pybind11>=2.4.3", -"pythran", +"meson-python>=0.12.1,<0.14.0", # already working with 0.13.x series at branch time +"Cython>=0.29.35,<3.0", # when updating version, also update check in meson.build +"pybind11>=2.10.4,<2.11.0", +"pythran>=0.12.0,<0.14.0", # already working with 0.13.x series at branch time +# `wheel` is needed for non-isolated builds, given that `meson-python` in a release specific commit which looks like "done manually" (although I hope not) http://github.com/scipy/scipy/commit/fa053c5b6419267e52a75f11535608fb67c052db ❯ git show fa053c5b6419267e52a75f11535608fb67c052db pyproject.toml commit fa053c5b6419267e52a75f11535608fb67c052db Author: Tyler Reddy Date: Wed May 31 05:05:45 2023 -0600 MAINT: version bounds for 1.11.0rc1 (#18591) The version bounds are easy to mess up--the reference conversation from the last release is linked below: https://github.com/scipy/scipy/pull/17569 The adjustment of version strings to include i.e., `rc1` is normally left to the `REL` commit proper during the release process [skip ci] diff --git a/pyproject.toml b/pyproject.toml index 940cb5760..ccab62aec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,13 +10,13 @@ [build-system] build-backend = 'mesonpy' requires = [ -"meson-python>=0.12.1", -"Cython>=0.29.35", # when updating version, also update check in meson.build -"pybind11>=2.10.4", -"pythran>=0.12.0", +"meson-python>=0.12.1,<0.14.0", # already working with 0.13.x series at branch time +"Cython>=0.29.35,<3.0", # when updating version, also update check in meson.build +"pybind11>=2.10.4,<2.11.0", +"pythran>=0.12.0,<0.14.0", # already working with 0.13.x series at branch time # `wheel` is needed for non-isolated builds, given that `meson-python` # doesn't list it as a runtime requirement (at least in 0.5.0) -"wheel", +"wheel<0.41.0", # NumPy dependencies - to update these, sync from # https://github.com/scipy/oldest-supported-numpy/, and then @@ -62,11 +62,11 @@ maintainers = [ # Note: Python and NumPy upper version bounds should be set correctly in # release branches, see: # https://scipy.github.io/devdocs/dev/core-dev/index.html#version-ranges-for-numpy-and-other-dependencies -requires-python = ">=3.9" +requires-python = ">=3.9,<3.13" dependencies = [ # TODO: update to "pin-compatible" once possible, see # https://github.com/FFY00/meson-python/issues/29 -"numpy>=1.21.6", +"numpy>=1.21.6,<1.28.0", ] readme = "README.rst"
Bug#1028157: cython update
Hi Nilson sorry -- I was not following cython package recently so all kudos to Stefano and other team members for taking good care of it under team maintainership. I think the best would have been to check existing bug reports and follow up on them, thus to minimize traffic I immediately CCing https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028157 Please follow up here and state your interest to see 3.0.0 in debian. Note https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028157#10 The latest version of scipy, 1.11.1, needs Cython>=0.29.35 but also declares Cython<3.0. So we need first check with scipy on either it is ready for cython 3: - upstream has (and I don't think ever had) no upper bound > grep Cython pyproject.toml "Cython>=0.29.18", in git log for scipy upstream I find last record for cython3 compat from v1.5.0rc1~75 in 2020! So scipy was in sync with cython development - for debian package upper bound was introduced in https://salsa.debian.org/python-team/packages/scipy/-/commit/7a469e2435a01468b769f11c14f7e2a5c318fe4a but no detailed reason provided. so might have been general precaution. CCing Drew Parsons maintaining scipy -- may be he could recall the need for upper bound or just make a verdict to drop that upper bound? -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#1014890: ITP: python3-looseversion -- Version numbering for anarchists and software realists
Thank you Alban, done -- join/finish up https://salsa.debian.org/python-team/packages/python-looseversion please On Mon, 19 Jun 2023, Alban Browaeys wrote: > on January 4th of 2023 you retitled this RFP to ITP. > > ITP: python3-looseversion -- Version numbering for anarchists and > software realists > Do you have an early package code or python3-looseversion to share (on > debian salsa or else)? > I will have to create such a package otherwise as salt 3006 depends > upon python3 looseversion (I am building it based upon the salt 3005 > deb pacakging from > openmediavault > https://github.com/openmediavault/packages/tree/master/pool/main/s/salt > ). > So even if you only did an early frame of it that would avoid duplicate > effort. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#999526: Taking over package into Debian Python Team maintenance and fixing bug (Was: mdp: FTBFS with numpy 1.21 (in experimental): dh_auto_test: error: pybuild --test --test-pytest -i python{versi
Hi Andreas, Thank you very much for offering help. I think Tiziano would not mind, so please feel very welcome to a) for the sake of b) or any other goodness you would like to bring ;) Note though that MDP is pretty much inactive project since a few years back. It seems it is still used by some and somewhat maintained upstream, so might indeed be worthwhile keeping afloat in Debian but I would not cry if it got RMed. After/if packaging moves to a new repo on salsa, we can submit a PR to add an empty out debian/ and add stub debian/README to that upstream repo to signal that packaging moved to salsa. Cheers, On Mon, 17 Apr 2023, Andreas Tille wrote: > Hi Tiziano and Yaroslav, > I'd volunteer to >a) take over package into Debian Python Team (including > using Salsa Git and Maintainer address of DPT) and >b) apply the patch and upload the package > I'm not interested in just doing b) and hope you will find the time to > care for the package if you are not happy with a). Please note that > there was an NMU which is not taken over in your repository at Github. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1031803: in `request': undefined method `escape' for URI:Module (NoMethodError)
Package: ghi Version: 1.2.0-1.1 Severity: normal I just installed it since just now discovered, and at the first invocation got a crash, so not sure how usable it is: ❯ ghi list zsh: correct 'ghi' to 'gih' [nyae]? n # NeurodataWithoutBorders/nwb-schema open issues /usr/lib/ruby/vendor_ruby/ghi/client.rb:100:in `request': undefined method `escape' for URI:Module (NoMethodError) path = URI.escape path ^^^ from /usr/lib/ruby/vendor_ruby/ghi/client.rb:76:in `get' from /usr/lib/ruby/vendor_ruby/ghi/commands/list.rb:148:in `block in execute' from /usr/lib/ruby/vendor_ruby/ghi/formatting.rb:509:in `throb' from /usr/lib/ruby/vendor_ruby/ghi/commands/list.rb:146:in `execute' from /usr/lib/ruby/vendor_ruby/ghi/commands/command.rb:17:in `execute' from /usr/lib/ruby/vendor_ruby/ghi.rb:80:in `execute' from /usr/bin/ghi:4:in `' -- System Information: Debian Release: bookworm/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable-security'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.1.0-3-amd64 (SMP w/12 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages ghi depends on: ii git 1:2.39.1-0.1 ii ruby 1:3.1 ii ruby-pygments.rb 2.3.0+ds-2.2 Versions of packages ghi recommends: ii less 590-1.1 ghi suggests no packages. -- debconf-show failed
Bug#787277: running into the same with bullseye -> bookworm upgrade
Happened to me on a new server I received from a vendor with bullseye preinstalled so I don't know exactly if they didn't mess with password there but very unlikely they did. Upon upgrade to bookworm got those persisting errors root@typhon:~# apt-get -f install Reading package lists... Done Building dependency tree... Done Reading state information... Done 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5 not fully installed or removed. After this operation, 0 B of additional disk space will be used. Setting up ca-certificates-java (20230103) ... org.debian.security.InvalidKeystorePasswordException: Cannot open Java keystore. Is the password correct? at org.debian.security.KeyStoreHandler.load(KeyStoreHandler.java:68) at org.debian.security.KeyStoreHandler.(KeyStoreHandler.java:52) at org.debian.security.UpdateCertificates.(UpdateCertificates.java:65) at org.debian.security.UpdateCertificates.main(UpdateCertificates.java:51) Caused by: java.io.IOException: Keystore was tampered with, or password was incorrect at java.base/sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:795) at java.base/sun.security.util.KeyStoreDelegator.engineLoad(KeyStoreDelegator.java:222) at java.base/java.security.KeyStore.load(KeyStore.java:1479) at org.debian.security.KeyStoreHandler.load(KeyStoreHandler.java:66) ... 3 more Caused by: java.security.UnrecoverableKeyException: Password verification failed at java.base/sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:793) ... 6 more dpkg: error processing package ca-certificates-java (--configure): installed ca-certificates-java package post-installation script subprocess returned error exit status 1 dpkg: dependency problems prevent configuration of openjdk-17-jre-headless:amd64: openjdk-17-jre-headless:amd64 depends on ca-certificates-java (>= 20190405~); however: Package ca-certificates-java is not configured yet. dpkg: error processing package openjdk-17-jre-headless:amd64 (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of default-jre-headless: default-jre-headless depends on openjdk-17-jre-headless; however: Package openjdk-17-jre-headless:amd64 is not configured yet. dpkg: error processing package default-jre-headless (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of openjdk-17-jre:amd64: openjdk-17-jre:amd64 depends on openjdk-17-jre-headless (= 17.0.6+10-1); however: Package openjdk-17-jre-headless:amd64 is not configured yet. dpkg: error processing package openjdk-17-jre:amd64 (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of default-jre: default-jre depends on default-jre-headless (= 2:1.17-74); however: Package default-jre-headless is not configured yet. default-jre depends on openjdk-17-jre; however: Package openjdk-17-jre:amd64 is not configured yet. dpkg: error processing package default-jre (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: ca-certificates-java openjdk-17-jre-headless:amd64 default-jre-headless openjdk-17-jre:amd64 default-jre E: Sub-process /usr/bin/dpkg returned an error code (1) root@typhon:~# cat /etc/default/cacerts # defaults for ca-certificates-java # The password which is used to protect the integrity of the keystore. # storepass must be at least 6 characters long. It must be provided to # all commands that access the keystore contents. # Only change this if adding private certificates. #storepass='' # enable/disable updates of the keystore /etc/ssl/certs/java/cacerts cacerts_updates=yes The history of the package on the box: root@typhon:~# zgrep ca-certifica /var/log/dpkg.log* /var/log/dpkg.log:2023-02-18 19:57:08 upgrade ca-certificates:all 20210119 20211016 /var/log/dpkg.log:2023-02-18 19:57:08 status half-configured ca-certificates:all 20210119 /var/log/dpkg.log:2023-02-18 19:57:08 status unpacked ca-certificates:all 20210119 /var/log/dpkg.log:2023-02-18 19:57:08 status half-installed ca-certificates:all 20210119 /var/log/dpkg.log:2023-02-18 19:57:08 status unpacked ca-certificates:all 20211016 /var/log/dpkg.log:2023-02-18 19:57:47 upgrade ca-certificates-java:all 20190909 20230103 /var/log/dpkg.log:2023-02-18 19:57:47 status half-configured ca-certificates-java:all 20190909 /var/log/dpkg.log:2023-02-18 19:57:47 status unpacked ca-certificates-java:all 20190909 /var/log/dpkg.log:2023-02-18 19:57:47 status half-installed ca-certificates-java:all 20190909 /var/log/dpkg.log:2023-02-18 19:57:47
Bug#1026232: RFP: label-studio -- multi-type data labeling and annotation tool with standardized output format
Package: wnpp Severity: wishlist * Package name: label-studio Version : 1.7.0 Upstream Author : Heartexlabs * URL : https://github.com/heartexlabs/label-studio * License : Apache 2.0 Programming Lang: Python Description : multi-type data labeling and annotation tool with standardized output format Label Studio is an open source data labeling tool. It lets you label data types like audio, text, images, videos, and time series with a simple and straightforward UI and export to various model formats. It can be used to prepare raw data or improve existing training data to get more accurate ML models. In my case I am considering to try it for a project to automate data entry QC (see https://github.com/con/noisseur/issues/1) -- if you know anything like that already, please let me know. Notes: - that git repository is a bit "suboptimal" -- >1GB of .git/objects (likely mistakes made in prior history, checkout tree is only about 200MB with all the docs/ images per each release etc). watchout while cloning, might want a shallow clone
Bug#1021619: RFP: python3-lazy-loader -- load subpackages and functions on demand
Package: wnpp Severity: wishlist X-Debbugs-Cc: debian-pyt...@lists.debian.org * Package name: python3-lazy-loader Version : 0.1 Upstream Author : Jarrod Millman * URL : https://github.com/scientific-python/lazy_loader * License : BSD-3 Programming Lang: Python-3 Description : load subpackages and functions on demand lazy_loader makes it easy to load subpackages and functions on demand. I was told that used in skimage and networkx already. Checked that introduced in networkx networkx-2.7rc1~42 bundled inside the source code. In debian we still have 2.6.3, so with the next update it would get it. lazy-loader is considered for adoption in other projects which would eventually get into Debian as well.
Bug#1015102: heudiconv: FTBFS: FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data-reproin]
oh, sorry about that and thanks for the ping!
I fixed it upstream already (the bug is really in datalad), and will
look to release it asap (i.e. now) and then see if we can update package
(might need to also upload new version of dcmstack first)
On Thu, 29 Sep 2022, Nilesh Patra wrote:
> Hi Yaroslav,
> Since you are the upstream for heudiconv, could you please help fix this?
> On Sat, 16 Jul 2022 15:49:48 +0200 Lucas Nussbaum wrote:
> > Source: heudiconv
> > Version: 0.11.3-1
> > Severity: serious
> > Justification: FTBFS
> > Tags: bookworm sid ftbfs
> > User: lu...@debian.org
> > Usertags: ftbfs-20220716 ftbfs-bookworm
> > Hi,
> > During a rebuild of all packages in sid, your package failed to build
> > on amd64.
> > Relevant part (hopefully):
> >dh_auto_test -O--buildsystem=pybuild
> > pybuild --test --test-pytest -i python{version} -p "3.9 3.10"
> > I: pybuild pybuild:300: cp -a heudiconv/tests
> > /<>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/
> > I: pybuild base:239: cd
> > /<>/.pybuild/cpython3_3.9_heudiconv/build; python3.9 -m pytest
> > = test session starts
> > ==
> > platform linux -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0
> > rootdir: /<>
> > collected 99 items / 1 skipped
> > heudiconv/external/tests/test_dlad.py . [
> > 1%]
> > heudiconv/heuristics/test_reproin.py [
> > 9%]
> > heudiconv/tests/test_bids.py ..s [
> > 44%]
> > heudiconv/tests/test_convert.py .. [
> > 54%]
> > heudiconv/tests/test_dicoms.py ... [
> > 57%]
> > heudiconv/tests/test_heuristics.py .F. [
> > 68%]
> > heudiconv/tests/test_main.py .. [
> > 82%]
> > heudiconv/tests/test_queue.py ...[
> > 85%]
> > heudiconv/tests/test_regression.py sss. [
> > 89%]
> > heudiconv/tests/test_tarballs.py . [
> > 90%]
> > heudiconv/tests/test_utils.py .
> > [100%]
> > === FAILURES
> > ===
> > _ test_reproin_largely_smoke[--files
> > /<>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data-reproin]
> > _
> > tmpdir =
> > local('/tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0')
> > heuristic = 'reproin'
> > invocation = '--files
> > /<>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data'
> > @pytest.mark.parametrize('heuristic', ['reproin', 'convertall'])
> > @pytest.mark.parametrize(
> > 'invocation', [
> > "--files %s" % TESTS_DATA_PATH,# our new way with automated
> > groupping
> > "-d %s/{subject}/* -s 01-fmap_acq-3mm" % TESTS_DATA_PATH #
> > "old" way specifying subject
> > # should produce the same results
> > ])
> > @pytest.mark.skipif(Dataset is None, reason="no datalad")
> > def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
> > is_bids = True if heuristic == 'reproin' else False
> > arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
> > % (heuristic, tmpdir)
> > if is_bids:
> > arg += " -b"
> > arg += " --datalad "
> > args = (
> > arg + invocation
> > ).split(' ')
> > # Test some safeguards
> > if invocation == "--files %s" % TESTS_DATA_PATH:
> > # Multiple subjects must not be specified -- only a single one
> > could
> > # be overridden from the command line
> > with pytest.raises(ValueError):
> > runner(args + ['--subjects', 'sub1', 'sub2'])
> > if heuristic != 'reproin':
> > # if subject is not overridden, raise error
> > with pytest.raises(NotImplementedError):
> > runner(args)
> > return
> > runner(args)
> > ds = Dataset(str(tmpdir))
> > assert ds.is_installed()
> > assert not ds.repo.dirty
> > head = ds.repo.get_hexsha()
> > # and if we rerun -- should fail
> > lgr.info(
> > "RERUNNING, expecting to FAIL since the same everything "
> > "and -c specified so we did conversion already"
> > )
> > with pytest.raises(RuntimeError):
> > runner(args)
> > # but there should be nothing new
> > assert not ds.repo.dirty
> > > assert head == ds.repo.get_hexsha()
> > E AssertionError: assert '2c32d90c7252...452338c3a611a' ==
> > '52121805b02b...b36be77769e34'
> > E - 52121805b02b454149686a4ae12b36be77769e34
> > E + 2c32d90c7252c966ebdba876f6f452338c3a611a
> >
Bug#892664: my use case. Petition to have zst support in dpkg
We build both debian and ubuntu backports for http://neuro.debian.net/ . And then we use https://snapshot.debian.org/ engine to provide snapshots over our archive, which we run in a Debian environment. Unfortunately dpkg-deb used by snapshot pukes on Ubuntu packages due to "unknown compression for member 'control.tar.zst'". I would be eager to see this issue addressed. Pretty please! -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#720723: Please do not compress .vym files
Package: vym Version: 2.6.11-3+b2 Followup-For: Bug #720723 Just ran into this 9 yo issue. Should be easy to fix by excluding .vym from being compressed by dh_compress -- System Information: Debian Release: bookworm/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable-security'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.18.0-4-amd64 (SMP w/12 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages vym depends on: ii libc62.34-4 ii libgcc-s1 [libgcc1] 12.2.0-1 ii libqt5core5a 5.15.4+dfsg-5 ii libqt5dbus5 5.15.4+dfsg-5 ii libqt5gui5 5.15.4+dfsg-5 ii libqt5network5 5.15.4+dfsg-5 ii libqt5printsupport5 5.15.4+dfsg-5 ii libqt5svg5 5.15.4-2 ii libqt5widgets5 5.15.4+dfsg-5 ii libqt5xml5 5.15.4+dfsg-5 ii libstdc++6 12.2.0-1 ii unzip6.0-27 ii xsltproc 1.1.35-1 ii zip 3.0-12 vym recommends no packages. Versions of packages vym suggests: ii ruby 1:3.0+1 -- debconf-show failed
Bug#1018335: datalad-container: build-depends on python3-nose or uses it for autopkgtest
FWIW -- I was wrong (got lost in datalad extensions). -container is not yet migrated to pytest but will be shortly! On Mon, 29 Aug 2022, Yaroslav Halchenko wrote: > Next upload will have it using pytest -- we have migrated to pytest > recently upstream > Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1018335: datalad-container: build-depends on python3-nose or uses it for autopkgtest
Next upload will have it using pytest -- we have migrated to pytest recently upstream Cheers, On Sun, 28 Aug 2022, Dmitry Shachnev wrote: > Source: datalad-container > Version: 1.1.6-0.1 > User: python-modules-t...@lists.alioth.debian.org > Usertags: nose-rm > Dear Maintainer, > Your package still uses nose [1], which is an obsolete testing framework for > Python, dead and unmaintained since 2015 [2][3]. > If you received this bug report, it means that your package either has a > build-dependency on python3-nose or uses that package in debian/tests/control. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1014890: RFP: python3-looseversion -- Version numbering for anarchists and software realists
Package: wnpp Severity: wishlist X-Debbugs-Cc: debian-pyt...@lists.debian.org * Package name: python3-looseversion Version : 1.0.1 Upstream Author : Chris Markiewicz * URL : https://github.com/effigies/looseversion * License : Python Programming Lang: Python Description : Version numbering for anarchists and software realists A backwards/forwards-compatible fork of distutils.version.LooseVersion, for times when PEP-440 isn't what you need. . The goal of this package is to be a drop-in replacement for the original LooseVersion. It implements an identical interface and comparison logic to LooseVersion. The only major change is that a looseversion.LooseVersion is comparable to a distutils.version.LooseVersion, which means tools should not need to worry whether all dependencies that use LooseVersion have migrated. . If you are simply comparing versions of Python packages, consider moving to packaging.version.Version, which follows PEP-440. LooseVersion is better suited to interacting with heterogeneous version schemes that do not follow PEP-440. This package would be useful as we plan for adding support for Python 3.12 which would remove distutils.version.LooseVersion and some packages would need to "adjust" somehow. In our DataLad project we likely would just go the way of using this LooseVersion instead of coming up with some "more proper" solution.
Bug#1009381: datalad-container: diff for NMU version 1.1.6-0.1
THANK YOU Adrian! Apparently I have forgotten to upload updated debian package after all those now automated bugfix releases in datalad-container... I will do that now, and if I fail -- your NMU would proudly solve the issue -- no need to cancel. On Thu, 26 May 2022, Adrian Bunk wrote: > Control: tags 1009381 + patch > Control: tags 1009381 + pending > Dear maintainer, > I've prepared an NMU for datalad-container (versioned as 1.1.6-0.1) and > uploaded it to DELAYED/14. Please feel free to tell me if I should > cancel it. > cu > Adrian -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#1010941: python-argcomplete salvaging and possible team (re)join
Hi Marco, Marc and the Team,
I have just uploaded to --delayed 5 a workaround fix for #1010941
(FTBFS). The diff is attached
I have a clone at https://salsa.debian.org/yoh/python-argcomplete
with Marc's NMU imported, and my NMU changes on top. So could be a good
starting point to update packaging to a new release ;)
would also be nice to add tags (may be original from Marco?) for prior
upstream/debian releases.
Cheers,
On Wed, 27 Apr 2022, Marc Dequènes (duck) wrote:
> Quack,
> python-argcomplete has not been actively maintained and I did a NMU last
> year that got unacknowledged. I intend to salvage it. I think it would make
> sense to maintain it under the team's umbrella, which leads me to…
> I was part of the "Python Modules Team" between 2006 and 2009 but since then
> did not maintain Python packages except for some sponsoring (mainly
> postfix-mta-sts-resolver and dico related packages but not team-maintained
> although wikitrans was in the Python Modules Team as the Maintainer field
> attest). I'd be glad to rejoin if you would allow me. I don't know if I
> would have time to work on other team packages but occasionally I should be
> able to give a hand.
> I have read and agree to the policy on:
> https://salsa.debian.org/python-team/tools/python-modules/blob/master/policy.rst
> I am not familiar with gbp-pq but I looked at the doc and it seems quite
> interesting. The rest of the workflow is is almost identical to what I'm
> used to and should not be a problem.
> Regards.
> \_o<
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW: http://www.linkedin.com/in/yarik
diff -Nru python-argcomplete-1.12.3/debian/changelog python-argcomplete-1.12.3/debian/changelog
--- python-argcomplete-1.12.3/debian/changelog 2021-09-28 10:29:56.0 -0400
+++ python-argcomplete-1.12.3/debian/changelog 2022-05-13 13:07:30.0 -0400
@@ -1,3 +1,12 @@
+python-argcomplete (1.12.3-0.2) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * debian/rules
+- provide workaround for tests to not fail (Closes: #1010941).
+ Upstream issue: https://github.com/kislyuk/argcomplete/issues/337
+
+ -- Yaroslav Halchenko Fri, 13 May 2022 13:07:30 -0400
+
python-argcomplete (1.12.3-0.1) unstable; urgency=medium
* Non-maintainer upload.
diff -Nru python-argcomplete-1.12.3/debian/rules python-argcomplete-1.12.3/debian/rules
--- python-argcomplete-1.12.3/debian/rules 2021-09-28 10:29:56.0 -0400
+++ python-argcomplete-1.12.3/debian/rules 2022-05-13 13:07:30.0 -0400
@@ -26,6 +26,17 @@
cp debian/$$i.1 debian/python3-argcomplete/usr/share/man/man1/$${i}3.1; \
done
+# Workaround
+# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1010941
+# https://github.com/kislyuk/argcomplete/issues/337#issuecomment-771835184
+override_dh_auto_test:
+ echo "set enable-bracketed-paste off" > .inputrc
+ INPUTRC=$(CURDIR)/.inputrc dh_auto_test
+
+override_dh_auto_clean:
+ rm -f .inputrc
+ dh_auto_clean
+
generate_manpages:
VERSION=$$(./setup.py -V) ; \
for file in \
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Description: PGP signature
Bug#1010941: FTBFS due to tests 56 tests failing
Package: python3-argcomplete Version: 1.12.3-0.1 Severity: serious Tags: ftbfs Justification: fails to build from source Wanted to build a backport but failed to have it built even in current sid. A complete log is at http://www.onerussian.com/tmp/python-argcomplete_1.12.3-0.1_amd64.build and here is a typical (they are all of the same kind - not matching desired empty string) fail: == FAIL: test_wordbreak_chars (test.test.TestBashGlobal) -- Traceback (most recent call last): File "/build/python-argcomplete-1.12.3/test/test.py", line 1215, in setUp self.assertEqual(output, '') AssertionError: '\x1b[?2004l\r\x1b[?2004h' != '' - ^[[?2004l^M- ^[[?2004h -- System Information: Debian Release: bookworm/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable-security'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.16.0-6-amd64 (SMP w/12 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-argcomplete depends on: ii python3 3.9.8-1 python3-argcomplete recommends no packages. python3-argcomplete suggests no packages. -- debconf-show failed
Bug#1010897: ITP: python3-versioningit -- PEP 518 driven setuptools plugin for auto-versioning using git/hg
Package: wnpp Severity: wishlist Owner: Yaroslav Halchenko X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: python3-versioningit Version : 1.1.1 Upstream Author : John T. Wodder II * URL : https://github.com/jwodder/versioningit * License : MIT Programming Lang: Python Description : PEP 518 driven setuptools plugin for auto-versioning using git/hg versioningit is yet another setuptools plugin for automatically determining your package's version based on your version control repository's tags. Unlike others, it allows easy customization of the version format and even lets you easily override the separate functions used for version extraction and calculation. Features: - Installed & configured through PEP 518's pyproject.toml - Supports Git, modern Git archives, and Mercurial - Formatting of the final version uses format template strings, with fields for basic VCS information and separate template strings for distanced vs. dirty vs. distanced-and-dirty repository states - Can optionally write the final version to a file for loading at runtime - Provides custom setuptools commands for inserting the final version into a source file at build time - The individual methods for VCS querying, tag-to-version calculation, version bumping, version formatting, and writing the version to a file can all be customized using either functions defined alongside one's project code or via publicly-distributed entry points - Can alternatively be used as a library for use in setup.py or the like, in case you don't want to or can't configure it via pyproject.toml - The only thing it does is calculate your version and optionally write it to a file; there's no overriding of your sdist contents based on what's in your Git repository, especially not without a way to turn it off, because that would just be rude.
Bug#1010168: RFP: python3-pytest-fail-slow -- pytest plugin for making tests fail that take too long to run
Package: wnpp Severity: wishlist X-Debbugs-Cc: debian-pyt...@lists.debian.org * Package name: python3-pytest-fail-slow Version : 0.1.0 Upstream Author : John Thorvald Wodder II * URL : https://github.com/jwodder/pytest-fail-slow/ * License : MIT/X Programming Lang: Python Description : pytest plugin for making tests fail that take too long to run pytest-fail-slow is a pytest plugin for making tests fail that take too long to run. It adds a --fail-slow DURATION command-line option to pytest that causes any & all otherwise-passing tests that run for longer than the given duration to be marked as failures, and it adds a @pytest.mark.fail_slow(DURATION) marker for making an individual test fail if it runs for longer than the given duration. If --fail-slow is given and a test has the @fail_slow() marker, the duration given by the marker takes precedence for that test. It will likely be necessary for testing the next (0.17) release of DataLad package.
Bug#1009985: RFP: memray -- memory profiler for Python
Package: wnpp Severity: wishlist X-Debbugs-Cc: debian-pyt...@lists.debian.org * Package name: memray Version : 1.0.3 Upstream Author : Bloomberg LP * URL : https://github.com/bloomberg/memray * License : Apache 2.0 Programming Lang: Python Description : memory profiler for Python Memray is a memory profiler for Python. It can track memory allocations in Python code, in native extension modules, and in the Python interpreter itself. It can generate several different types of reports to help you analyze the captured memory usage data. While commonly used as a CLI tool, it can also be used as a library to perform more fine-grained profiling tasks. It was open-sourced only recently, LICENSE with Apache 2.0 was added only 12 days ago.
Bug#1006909: impressive: Fails to find any pages in the presentation
On Tue, 15 Mar 2022, Martin Fiedler wrote:
> Hi Gunnar,
> > Hmmm... But please do take note that I _did_ have mupdf-tools
> > installed when Impressive failed to analyze the PDF
> > document.
> Did you though? Impressive detected "Poppler/Xpdf" as the renderer,
> which is an indicator of the absence of mupdf-tools. If you can confirm
> that "mutool -v" works on your system (in the sense of: prints a version
> number instead of a "command not found" message), I'd have some homework
> to do though ;)
Dear Gunnar,
Could you please confirm that mupdf-tools were installed and
functioning? I know that sounds implausible given that it is a hard
dependency but having no pdftk{,-java} installed I was able to use
impressive just fine.
or Martin -- did you do some homework and figured smth out which is now
released?
Cheers,
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW: http://www.linkedin.com/in/yarik
Bug#1006909: impressive: Fails to find any pages in the presentation
Thank you Gunnar. Dear Martin, Please refresh my mind -- is pdftk a strict requirement now for impressive or should still be optional, whenever mupdf-tools (>= 1.5) | poppler-utils would be the tools to require? Gunnar reports that without pdftk he had no luck seeing a presentation. Cheers, On Mon, 07 Mar 2022, Gunnar Wolf wrote: > Package: impressive > Version: 0.13.0~beta2-2 > Severity: important > Tags: patch > Whenever I try to open a PDF presentation with impressive, I get the > following error message: > Welcome to Impressive version 0.13.0-beta2 (SVN r298) > pygame 1.9.6 > Hello from the pygame community. https://www.pygame.org/contribute.html > Detected screen size: 1920x1080 pixels > PDF renderer: Xpdf/Poppler > pdftkParse() FAILED > WARNING: The input file `/tmp/testfile.pdf' could not be analyzed. > The presentation doesn't have any pages, quitting. > Do note that I am running this on ARM64, and using Wayland. > And... Oh! This seems to be due to a missing dependency! I was > checking through the list of versions of depends/recommends/suggests > (am not running reportbug from the affected system), and turns out > that installing pdftk (or rather, pdftk-java, as pdftk is now just a > transitional package) fixes the issue. Just for completeness sake, the > PDF renderer is still marked to be Xpdf/Poppler, but now it reports > "OpenGL renderer: FD630" and... works! :-D > -- System Information: > Debian Release: bookworm/sid > APT prefers unstable > APT policy: (500, 'unstable') > Architecture: arm64 > Kernel: Linux 5.16.0-3-amd64 (SMP w/8 CPU threads; PREEMPT) > Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), > LANGUAGE=en_US:en > Shell: /bin/sh linked to /usr/bin/dash > Init: systemd (via /run/systemd/system) > LSM: AppArmor: enabled > Versions of packages impressive depends on: > ii poppler-utils 20.09.0-3.1 > ii python3 3.9.8-1 > ii python3-pil 9.0.1-1 > pn python3-pygame 1.9.6+dfsg-5 > Versions of packages impressive recommends: > ii ffmpeg 7:4.3.1-3+b2 > ii mplayer2:1.4+ds1-1+b1 > ii perl 5.34.0-3 > ii xdg-utils 1.1.3-4.1 > Versions of packages impressive suggests: > ii ghostscript 9.55.0~dfsg-3 > pn latex-beamer > pn pdftk > diff --git a/debian/control b/debian/control > index 12a1a9d..981c495 100644 > --- a/debian/control > +++ b/debian/control > @@ -28,13 +28,13 @@ Depends: python3, > python3-pygame, > python3-pil, > mupdf-tools (>= 1.5) | poppler-utils, > + pdftk-java, > Recommends: mplayer, > ffmpeg, > perl, > xdg-utils > Suggests: ghostscript, >latex-beamer, > - pdftk, > Conflicts: keyjnote (<< 0.10.2r-0) > Provides: keyjnote > Replaces: keyjnote (<< 0.10.2r-0) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#995171: need newer release
> I can't see this in master branch. > > I have started to update packaging for 3.9.4+ds1 but got stuck on > > updating the 2nd patch which seems "too involved" for a go-ignorant me. > > Any help would be welcomed. I have pushed update of source tree etc > To what branch? oh, I didn't spot that `gbp push` doesn't push not yet tagged work? pushed now: (git)lena:~exppsy/singularity-container[master] $> gbp push gbp:info: Pushing upstream/3.9.4+ds1 to origin gbp:info: Pushing refs/heads/upstream to origin:refs/heads/upstream gbp:info: Pushing refs/heads/pristine-tar to origin:refs/heads/pristine-tar $> git push Enumerating objects: 3237, done. Counting objects: 100% (3209/3209), done. Delta compression using up to 12 threads Compressing objects: 100% (2143/2143), done. Writing objects: 100% (2572/2572), 3.14 MiB | 1.64 MiB/s, done. Total 2572 (delta 622), reused 1954 (delta 300), pack-reused 0 remote: Resolving deltas: 100% (622/622), completed with 237 local objects. To salsa.debian.org:hpc-team/singularity-container.git aa00514f8..fb5dcc7b6 master -> master * [new tag] debian/2.6.1-2+nd2 -> debian/2.6.1-2+nd2 * [new tag] upstream/3.2.1+ds -> upstream/3.2.1+ds > Kind regards > Andreas. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#995171: need newer release
On Mon, 24 Jan 2022, Andreas Tille wrote:
> $ apt showsrc singularity-container | grep Uploaders
> Uploaders: Dave Love , Mehdi Dogguy ,
> Yaroslav Halchenko , Afif Elghraoui ,
> Dmitry Smirnov , Benda Xu
> shows you as Uploader of singularity-container. Is there any reason you
> file this bug report instead of simply uploading a new version of this
> package?
because it is maintained by the Debian HPC Team
and I either did not have time or "foo" to update the packaging.
And that is what I typically do even when working "by myself" - to
record relevant issues against corresponding project/package in that
project/package issue tracker.
> When doing so I'd recommend the following patch:
> diff --git a/debian/watch b/debian/watch
> index 140951c..e4f994d 100644
> --- a/debian/watch
> +++ b/debian/watch
> @@ -6,4 +6,4 @@ repacksuffix=+ds1,\
> repack,compression=xz,\
> dversionmangle=s{[+~](dfsg|ds)\d*}{},\
> " https://github.com/sylabs/singularity/releases \
> - (?:.*/)?singularity-(\d[\d\.]*)\.tar\.gz
> + (?:.*/)?singularity-ce-(\d[\d\.]*)\.tar\.gz
cool -- applied
> I admit I've never used singularity before but this might change in the
> near future.
I hope so -- singularity is current bread for containerized
computing in scientific context.
> Thus I'm wondering why we have 4 open bugs with CVE
> numbers and are lagging several versions behind upstream. May be there
> is a good reason to stick to the outdated security problematic version
> which I simply do not understand?
shortage of time/ppl?
I have started to update packaging for 3.9.4+ds1 but got stuck on
updating the 2nd patch which seems "too involved" for a go-ignorant me.
Any help would be welcomed. I have pushed update of source tree etc
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW: http://www.linkedin.com/in/yarik
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Bug#1003290: ITP: mricrogl -- magnetic resonance image conversion, viewing and analysis
Package: wnpp Severity: wishlist Owner: Yaroslav Halchenko X-Debbugs-Cc: debian-de...@lists.debian.org, Debian Med Packaging Team * Package name: mricrogl Version : 1.2.20211006 Upstream Author : Chris Rorden * URL : https://github.com/rordenlab/MRIcroGL * License : BSD-2-clause Programming Lang: Pascal Description : magnetic resonance image conversion, viewing and analysis This is a GUI-based visualization and analysis tool for medical imaging. . This package provides the MRIcroGL executable. Packaging will be largely based on mricron packaging originally done by NeuroDebian team, and now maintained by the glorious Debian Med.
Bug#937209: openopt: Python2 removal in sid/bullseye
> openopt seems dead upstream and has been dropped from testing for almost > two years, let's remove it? sounds good to me -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#995171: need newer release
Package: singularity-container Version: 3.5.2+ds1-1 Severity: normal Current upstream release is 3.8.3 https://github.com/sylabs/singularity/releases/tag/v3.8.3 I expect it having addressed a number (if not all) CVE issues we have opened in debian against the package. For thta reason marking this issue at least as normal, instead of wishlist. -- System Information: Debian Release: 11.0 APT prefers unstable APT policy: (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'oldstable-updates'), (100, 'stable'), (100, 'oldstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.10.0-7-amd64 (SMP w/12 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages singularity-container depends on: ii ca-certificates 20210119 ii containernetworking-plugins 0.9.0-1+b3 ii libc62.31-12 ii libseccomp2 2.5.1-1 ii squashfs-tools 1:4.4-2 Versions of packages singularity-container recommends: ii e2fsprogs 1.46.2-1 singularity-container suggests no packages. -- Configuration Files: /etc/singularity/singularity.conf changed [not included] -- debconf-show failed
Bug#993970: RFP: python3-pathvalidate -- Python library to sanitize/validate a string such as filenames/file-paths/etc
Package: wnpp Severity: wishlist X-Debbugs-Cc: python-modules-t...@lists.alioth.debian.org * Package name: python3-pathvalidate Version : 2.4.1 Upstream Author : https://github.com/thombashi * URL : https://github.com/thombashi/pathvalidate * License : MIT/X Programming Lang: Python Description : Python library to sanitize/validate a string such as filenames/file-paths/etc Features - Sanitize/Validate a string as a: file name, file path - file name/path argument validator/sanitizer for argparse and click - Multi platform support: - sanitize/validate file names/paths for a specific platform (Linux/Windows/macOS/Posix) or universal (platform independent) - Multibyte character support I ended up on this module by googling for ways to verify if any given filename/path is "legit". In DataLad project we relied on side effect of pathlib.Path().exists() to blow up for filenames not supported by OS. Since Python 3.9 it no longer has that side-effect so we have switched to rely on the side-effect of .resolve() which still does blow up, but who knows if it would be in the future.
Bug#988420: Please provide newer upstream (2.8.1 ATM)
Package: python3-zarr Version: 2.6.1+ds-1 Severity: wishlist Otherwise I get (git)lena:~/proj/misc/ome-zarr-py[master]git $> ome_zarr info http://dandiarchive.s3.amazonaws.com/largeuploads/blobs/150slab.zarr/ ERROR:ome_zarr.cli:not a zarr: None whenever using ome-zarr (not in debian yet) and the problem goes away with upgrade of python3-zarr to 2.8.1 thank you in advance! -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.9.0-4-amd64 (SMP w/12 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-zarr depends on: ii libjs-sphinxdoc 3.3.1-1 ii python3 3.9.0-4 ii python3-asciitree0.3.3-2 ii python3-fasteners0.14.1-2 ii python3-numcodecs0.7.3+ds-1 ii python3-numpy1:1.19.5-1 ii sphinx-rtd-theme-common 0.5.0+dfsg-1 python3-zarr recommends no packages. Versions of packages python3-zarr suggests: ii jupyter-notebook 6.1.5-1 ii python3-h5py 2.10.0-9 -- debconf-show failed
Bug#895055: ITP: python-sounddevice -- Python module to play and record sound
retitle -1 RFP: python3-sounddevice -- Python module to play and record sounds thanks thanks On Tue, 09 Mar 2021, Paul Menzel wrote: > I also found an application requiring this Python library. > The current version is 0.4.1 and probably the name now should be > python3-sounddevice. Thanks for chiming in FWIW, unlikely I would find time to package it, so retitling to RFP -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#983883: newer (patch) upstream release (0.8.7) is available
On Thu, 04 Mar 2021, Emmanuel Arias wrote: >Hi Yaroslav, >Thanks for the report. >After a quick diff between tags, I can show that isn't a new >patch version. >If I'm not wrong there're some new implementations. So, if you're ok I It isfine with me -- I am still exploring it for my usecase and bugs are to be fixed up anyways, so no rush on my end to get that particular version into debian -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#983883: newer (patch) upstream release (0.8.7) is available
Package: python3-fsspec Version: 0.8.4-1 Severity: wishlist Since patch release, I expect that it is largely if not only bugfixes, so may be still could get into bullseye? unfortunately the only changelog I found https://github.com/intake/filesystem_spec/blob/master/docs/source/changelog.rst is not entirely complete and suggests that it did gain new features since 0.8.4 -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.9.0-4-amd64 (SMP w/12 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-fsspec depends on: ii python3 3.9.0-4 python3-fsspec recommends no packages. Versions of packages python3-fsspec suggests: pn python-fsspec-doc -- debconf-show failed
Bug#982050: There are fresh upstream releases (8.9.11 ATM) which address security and other issues
There are updated packages floating around... BCCing someone who might facilitate pinging etc. I bet if changes pushed somewhere, should be easy to get updated package finalized etc On Fri, 19 Feb 2021, Diane Trout wrote: > I had been wondering if the htcondor package is effectively orphaned. > There hasn't been any activity in quite some time. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#980967: closed by Debian FTP Masters (reply to Yaroslav Halchenko ) (Bug#980967: fixed in bats 1.2.1-2)
On Mon, 15 Feb 2021, Paul Gevers wrote: > Hi Yaroslav, > On 15-02-2021 05:51, Debian Bug Tracking System wrote: > > bats (1.2.1-2) unstable; urgency=medium > > . > >* debian/patches > > - adopted patch from https://github.com/bats-core/bats-core/pull/387 to > >resolve "bats-exec-test: command not found" (Closes: #980967) > This seems to be not enough. The test now fails with: yeah, earlier this morning I was told that the failing test was not a red herring... ;) I have uploaded -3 few hours back which should have address this : > /usr/lib/bats-core/preprocessing.bash: line 16: bats-preprocess: command > not found -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#978257: pynwb is marked for autoremoval from testing
failed to arrive with working minimal patch against that elderly 1.2.1 FWIW built current snapshot which seems to be ok. but I am reluctant to upload that one since it has breaking (we have no rev-depends though in debian ATM) changes. On Sun, 14 Feb 2021, Andreas Tille wrote: > Hi Yaroslav, > could you please have a look. I'm occupied by many other things and will not > care for this one. > Kind regards -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#982120: heudiconv still depends on python
Thanks, on it. also needs a patch now for datalad 0.14 deprecation On Sat, 06 Feb 2021, Adrian Bunk wrote: > Package: heudiconv > Version: 0.9.0-1 > Severity: serious > This looks like a forgotten conversion: > https://sources.debian.org/src/heudiconv/0.9.0-1/debian/control/#L28 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#982119: dcmstack: autopkgtest failure
Thanks! Test building and will upload if all good with $> git show commit e9f88704d2fd8bf5f0053904222e66dcc69db621 (HEAD -> debian, tag: debian/0.8-2) Author: Yaroslav Halchenko Date: Sat Feb 6 12:29:39 2021 -0500 Replace nosetests-3 with python3 -m nose for autopkgtest invocation (Closes: #982119) diff --git a/debian/changelog b/debian/changelog index a5b654f..ff77288 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +dcmstack (0.8-2) unstable; urgency=medium + + * Replace nosetests-3 with python3 -m nose for autopkgtest invocation +(Closes: #982119) + + -- Yaroslav Halchenko Sat, 06 Feb 2021 12:29:32 -0500 + dcmstack (0.8-1) unstable; urgency=medium * Fresh upstream release diff --git a/debian/tests/control b/debian/tests/control index 4a50d35..47277d7 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,2 +1,2 @@ -Test-Command: nosetests-3 . +Test-Command: python3 -m nose . Depends: @, @builddeps@ On Sat, 06 Feb 2021, Adrian Bunk wrote: > Source: dcmstack > Version: 0.8-1 > Severity: serious > https://ci.debian.net/data/autopkgtest/testing/amd64/d/dcmstack/10273343/log.gz > ... > autopkgtest [00:00:03]: test command1: nosetests-3 . > autopkgtest [00:00:03]: test command1: [--- > bash: line 1: nosetests-3: command not found > autopkgtest [00:00:04]: test command1: ---] > autopkgtest [00:00:04]: test command1: - - - - - - - - - - results - - - - - > - - - - - > command1 FAIL non-zero exit status 127 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#982050: There are fresh upstream releases (8.9.11 ATM) which address security and other issues
Package: htcondor Version: 8.6.8~dfsg.1-2 Severity: normal 8.6.8~dfsg.1-1 was uploaded over 3 years ago. Since then multiple upstream releases were made, possibly (didn't check) addressing CVE of Bugs with severity grave 1) #963777 condor: CVE-2019-18823 and possibly Bugs with severity serious 2) #925657 condor: ftbfs with GCC-9 3) #966726 condor: Unversioned Python removal in sid/bullseye In our case we also encountered "buffer overflow detected" upon running condor_q -json and it is unlikely worth filing a new issue without checking first if a upstream work of the past 3 years has likely addressed it. So it would be great to see a newer version of condor be shipped in Debian. Cheers, -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.9.0-4-amd64 (SMP w/12 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages htcondor depends on: ii adduser 3.118 ii debconf [debconf-2.0] 1.5.74 ii libc6 2.31-5 pn libcgroup1 pn libclassad8 ii libcom-err2 1.45.6-1 ii libcurl4 7.72.0-1 ii libdate-manip-perl6.83-1 ii libexpat1 2.2.10-1 ii libgcc-s1 [libgcc1] 10.2.1-1 pn libglobus-callout0 pn libglobus-common0 pn libglobus-ftp-client2 pn libglobus-gass-transfer2 pn libglobus-gram-client3 pn libglobus-gram-protocol3 pn libglobus-gsi-callback0 pn libglobus-gsi-cert-utils0 pn libglobus-gsi-credential1 pn libglobus-gsi-openssl-error0 pn libglobus-gsi-proxy-core0 pn libglobus-gsi-proxy-ssl1 pn libglobus-gsi-sysconfig1 pn libglobus-gss-assist3 pn libglobus-gssapi-error2 pn libglobus-gssapi-gsi4 pn libglobus-io3 pn libglobus-openssl-module0 pn libglobus-rsl2 pn libglobus-xio0 ii libgomp1 10.2.1-1 ii libgssapi-krb5-2 1.18.3-4 ii libk5crypto3 1.18.3-4 ii libkrb5-3 1.18.3-4 ii libkrb5support0 1.18.3-4 ii libldap-2.4-2 2.4.56+dfsg-1 ii libltdl7 2.4.6-14 ii libpcre3 2:8.39-13 ii libssl1.1 1.1.1h-1 ii libstdc++610.2.1-1 ii libuuid1 2.36.1-2 ii libvirt0 6.9.0-1+b2 ii libx11-6 2:1.7.0-2 ii libxext6 2:1.3.3-1+b2 ii libxss1 1:1.2.3-1 ii lsb-base 11.1.0 ii perl 5.32.0-6 pn python ii zlib1g1:1.2.11.dfsg-2 Versions of packages htcondor recommends: pn dmtcp pn ecryptfs-utils Versions of packages htcondor suggests: pn coop-computing-tools ii docker.io 20.10.0+dfsg2-1 ii singularity-container 3.5.2+ds1-1 pn slurm-client
Bug#980779: incompatible with python 3.9 - syntax error
Package: python3-uritemplate
Version: 0.6-4
Severity: important
Got following exception with python3.9 (now default for python3) while trying
to run the tests for our code where we react to deprecation warnings etc
...
venvs/dev3/lib/python3.9/site-packages/pyout/__init__.py:10: in
from pyout.elements import schema
venvs/dev3/lib/python3.9/site-packages/pyout/elements.py:5: in
import jsonschema
/usr/lib/python3/dist-packages/jsonschema/__init__.py:14: in
from jsonschema._format import (
/usr/lib/python3/dist-packages/jsonschema/_format.py:411: in
import uritemplate.exceptions
E File "/usr/lib/python3/dist-packages/uritemplate/__init__.py",
line 36
E TEMPLATE = re.compile("{([^\}]+)}")
E ^
E SyntaxError: invalid escape sequence \}
This package needs to react to two existing already reported where active
new maintainer upstream probably already addressed this issue:
1) #945530 python-uritemplate: upstream have changed hands
2) #974040 python3-uritemplate: New upstream version is available (new
upstream maintainer)
at least looking at
https://github.com/python-hyper/uritemplate/blob/master/uritemplate/template.py#L22
template_re = re.compile('{([^}]+)}')
it seems tobe kosher
-- System Information:
Debian Release: bullseye/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'unstable-debug'), (100, 'stable-updates'), (100, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.9.0-4-amd64 (SMP w/12 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-uritemplate depends on:
ii python3 3.9.0-4
python3-uritemplate recommends no packages.
python3-uritemplate suggests no packages.
-- debconf-show failed
Bug#975166: connectome-workbench: FTBFS: qwt_painter_command.h:85:22: error: field ‘clipPath’ has incomplete type ‘QPainterPath
Great, thanks for the info and the buzz -- missed this, will try now and upload if all good. Cheers, On Wed, 13 Jan 2021, s3v wrote: > Dear Maintainer, > I tried to build your package in a sid chroot environment > and I confirm that patch fixes this issue. > Kind Regards -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#979469: missing dependency on (surprise!) golang-docker-credential-helpers, renders basic "pull" non-functional
Package: python3-docker
Version: 4.1.0-1.2
Severity: important
"minimal" example:
$> python3 -c 'import docker as d; c = d.from_env();
c.images.pull("debian:latest")'
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python3/dist-packages/docker/models/images.py", line
444, in pull
pull_log = self.client.api.pull(
File "/usr/lib/python3/dist-packages/docker/api/image.py", line 396,
in pull
header = auth.get_config_header(self, registry)
File "/usr/lib/python3/dist-packages/docker/auth.py", line 47, in
get_config_header
authcfg = resolve_authconfig(
File "/usr/lib/python3/dist-packages/docker/auth.py", line 324, in
resolve_authconfig
return authconfig.resolve_authconfig(registry)
File "/usr/lib/python3/dist-packages/docker/auth.py", line 235, in
resolve_authconfig
cfg = self._resolve_authconfig_credstore(registry, store_name)
File "/usr/lib/python3/dist-packages/docker/auth.py", line 262, in
_resolve_authconfig_credstore
store = self._get_store_instance(credstore_name)
File "/usr/lib/python3/dist-packages/docker/auth.py", line 286, in
_get_store_instance
self._stores[name] = credentials.Store(
File "/usr/lib/python3/dist-packages/docker/credentials/store.py",
line 23, in __init__
raise errors.InitializationError(
docker.credentials.errors.InitializationError:
docker-credential-secretservice not installed or not available in PATH
while image is "legit" and available:
$> docker pull debian:latest
latest: Pulling from library/debian
Digest:
sha256:22d4552b9f96fd0ea943cb846d58b069d4df297673636055a3d984b3ccac6a28
Status: Downloaded newer image for debian:latest
docker.io/library/debian:latest
initially discovered while trying docker-compose up, e.g.:
$> git clone https://github.com/datalad/datalad-registry && cd
datalad-registry && docker-compose up
Cloning into 'datalad-registry'...
remote: Enumerating objects: 368, done.
remote: Counting objects: 100% (368/368), done.
remote: Compressing objects: 100% (170/170), done.
remote: Total 368 (delta 223), reused 322 (delta 177), pack-reused 0
Receiving objects: 100% (368/368), 54.58 KiB | 1.76 MiB/s, done.
Resolving deltas: 100% (223/223), done.
COPYING Dockerfile README.md datalad_registry/
docker-compose.broker.yml docker-compose.yml docs/ flask* pyproject.toml
setup.cfg setup.py up*
Pulling broker (rabbitmq:3-alpine)...
Traceback (most recent call last):
File "/usr/bin/docker-compose", line 11, in
load_entry_point('docker-compose==1.25.0', 'console_scripts',
'docker-compose')()
trim
File "/usr/lib/python3/dist-packages/docker/auth.py", line 286, in
_get_store_instance
self._stores[name] = credentials.Store(
File "/usr/lib/python3/dist-packages/docker/credentials/store.py",
line 23, in __init__
raise errors.InitializationError(
docker.credentials.errors.InitializationError:
docker-credential-secretservice not installed or not available in PATH
after I found that docker-credential-secretservice within
golang-docker-credential-helpers and apt-get installed that package, pull
seems to work:
$> python3 -c 'import docker as d; c = d.from_env();
print(c.images.pull("debian:latest"))'
-- System Information:
Debian Release: bullseye/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'unstable-debug'), (100, 'stable-updates'), (100, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.9.0-4-amd64 (SMP w/12 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-docker depends on:
ii python33.9.0-4
ii python3-distutils 3.8.6-1
ii python3-requests 2.24.0+dfsg-1
ii python3-six1.15.0-2
ii python3-websocket 0.57.0-1
python3-docker recommends no packages.
python3-docker suggests no packages.
-- debconf-show failed
Bug#932197: Bug#937144: Request to join the Neurodebian group
On Thu, 30 Apr 2020, Moritz Mühlenhoff wrote: > > Thanks for the hint. While this could possibly speet up the upload of > > nipype I for myself are fine with waiting for the new Build-Depends. > > Anybody who wants to speed up things is kindly invited to add this patch > > and upload. > What's the status here? python-etelemetry is now in the archive and testing. FWIW: I just uploaded rdflib 5.0.0 (recent nipype needs that version if any) and pushed initial changes to nipype's packaging git for 1.6.0 . Will try to find more time over weekend to finalize packaging update (if no other new depends etc) -- needed for heudiconv package (currently present nipype version incorrectly handles some DWIs, FYI for those who care ;)). -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#959138: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')
FWIW those were reported "upstream" https://github.com/nipy/nipy/issues/466 unfortunately I had no time to look at them (again :-/) On Tue, 08 Dec 2020, Andreas Tille wrote: > 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: -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#976325: [ans...@debian.org: Bug#976325: src:libgdf: invalid maintainer address]
On Thu, 03 Dec 2020, Rafael Laboissière wrote: > Dear Yaroslav and Michael, > Are you aware of the problem related in Bug#976325, regarding the email > address t...@neuro.debian.net? thanks Rafael. I think that elderly mail server didn't re-emerge from the dead upon recent power outage. I will tend to it within few days or we figure out some alternative solution to bring that email address back in service Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#972166: Rising severities
Feel welcome to NMU without delay. Sorry for being slow etc. Thank you! On Sun, 25 Oct 2020, Lisandro Damián Nicanor Pérez Meyer wrote: > severity 972163 serious > severity 972166 serious > block 972176 by 972163 > block 972176 by 972166 > thanks > Hi! We are close to begin the Qt transition that will remove > qt5-default, so I'm raising the severities. If everything goes well > I'll be NMUing your package today with an upload to delayed/5. Of > course feel free to ping me if needed. > Thanks, Lisandro. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#972537: please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3
Source: hdf5
Version: 1.12.0+repack-1~exp2
Severity: wishlist
Overall patch below worked for me now now hdf5 tools work with ros3 driver,
e.g.
$> h5ls -r --vfd=ros3
https://dandiarchive.s3.amazonaws.com/girder-assetstore/6a/2f/6a2fe9e83746474790c504b9c8abb3ae
/Group
/acquisition Group
/acquisition/lick_times Group
..
diff --git a/debian/control.in b/debian/control.in
index e5d14995..17f67763 100644
--- a/debian/control.in
+++ b/debian/control.in
@@ -13,6 +13,8 @@ Build-Depends: debhelper (>= 10~),
chrpath,
libaec-dev,
default-jdk-headless (>= 2:1.7) [!hppa !hurd-i386],
+ libcurl4-openssl-dev,
+ libssl-dev,
javahelper [!hppa !hurd-i386]
Build-Depends-Indep: doxygen,
php-cli
diff --git a/debian/rules b/debian/rules
index 42962deb..ec072691 100755
--- a/debian/rules
+++ b/debian/rules
@@ -103,7 +103,7 @@ CONFIGURE_FLAGS = --prefix=/usr --host=$(DEB_HOST_GNU_TYPE)
\
--enable-shared --enable-build-mode=$(USE_PROD) \
--disable-sharedlib-rpath --with-zlib
--with-default-api-version=v18 \
--with-szlib \
- --enable-fortran --enable-fortran2003
+ --enable-fortran --enable-fortran2003 --enable-ros3-vfd
FLAVOR_FLAGS = --includedir=\$${prefix}/include/hdf5/$(1) \
--with-flavor=$(1) \
-- System Information:
Debian Release: bullseye/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'unstable-debug'), (100, 'stable-updates'), (100, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Bug#970895: duecredit: new upstream release available
On Fri, 25 Sep 2020, Yaroslav Halchenko wrote: > I see that in april of this year I looked into updating the package, it > needed rnc2rng. I have packaged it. And it is in Debian now: > python3-rnc2rng FTR, uploaded rnc2rng 2.6.4 and now waiting for it to appear since citeproc 0.5.1 needs >= 2.6.3~. I am planing to upload citeproc as soon as that appears. I tested that the build seems to build ok. pushed all current changes to git for citeproc (CCing team) After citeproc is uploaded, will tend to duecredit Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#970895: duecredit: new upstream release available
On Fri, 25 Sep 2020, Drew Parsons wrote: > Source: duecredit > Severity: normal > I'm getting problems running tests for mdanalysis with some broken > citations generated by duecredit, > see https://github.com/MDAnalysis/mdanalysis/issues/2954 yikes, thanks for letting me know followed up - I think it is more of citeproc issue although I might have indeed worked around at duecredit level, forgot by now > Upstream suggests the latest version of duecredit might help the > problem. > Could you upload duecredit 0.8.0 ? I was ready to upload 0.8.0 as soon as I released it, but the problem was that it needs citeproc >= 0.4, and we have only 0.3.0-6 . https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923560 to have that happen, but the package is under Debian QA maintainership... I see that in april of this year I looked into updating the package, it needed rnc2rng. I have packaged it. And it is in Debian now: python3-rnc2rng so there should be no reason to delay upload of that one. Most likely I need to adopt citeproc from the QA group... doing all that now, if you don't hear back with closing this issue, feel free to ping me again. PS life is hard, also ran into super fresh https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=970912 while trying to update my cowbuild envs -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#970815: provide .desktop file so fstl could be added as an application to open files in Files GUI
Package: fstl Version: 0.9.3-1+b1 Severity: wishlist Subject Thanks! ;) -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages fstl depends on: ii libc62.30-4 ii libgcc-s1 [libgcc1] 10-20200418-1 ii libgcc1 1:10-20200418-1 ii libgl1 1.3.0-7 ii libgl1-mesa-dri 20.1.5-1 ii libqt5core5a 5.14.2+dfsg-4 ii libqt5gui5 5.14.2+dfsg-4 ii libqt5opengl55.14.2+dfsg-4 ii libqt5widgets5 5.14.2+dfsg-4 ii libstdc++6 10-20200418-1 fstl recommends no packages. fstl suggests no packages. -- debconf-show failed
Bug#969908: a number of more recent releases (with MANY bug fixes) are available
Source: git-annex Version: 8.20200330-1 Severity: normal There were a number of releases since then: 8.20200330 8.20200501 8.20200522 8.20200617 8.20200720 8.20200720.1 8.20200810 many of those brought up fixes to many aspects of git-annex. ATM in datalad we ran into an issue with custom special remotes which seems to be fixed in current master and most likely in the most recent release. An update to debian package would be appreciated! Cheers, -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
Bug#969034: Please drop last sentence from description
Control: tags -1 pending pushed http://github.com/datalad/datalad/commit/d42acef188ef7dbba90e7c4acbd0a07433f428cc On Wed, 26 Aug 2020, David Prévot wrote: > Package: datalad > Severity: minor > Hi, > Thanks for packaging this tool I just discovered via DebConf20. > The description ends with >Install without > Recommends if you need only core functionality. > but the datalad package doesn’t have any recommends. Please drop this > (now?) useless sentence. > Regards -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#968290: please update to 3.37.90 upstream (SIXEL support added)
Package: gnome-terminal Version: 3.36.2-1 Severity: wishlist There are some really cool apps which make use of SIXEL. Some terminals (e.g. xterm) already have support for it. gnome-terminal only (very recently! apparently) recently added support for it in 3.37.90. $> git show 3.37.90 | head -n 20 tag 3.37.90 Tagger: Christian Persch Date: Sat Aug 8 22:02:09 2020 +0200 Version 3.37.90 Git-EVTag-v0-SHA512: d61e6d9e149a2ffa59f6ad9f2efeb93d2a7606697227d41ac678a13ce707c18018dae21b09a41afa6c63669f783fbdfe7735fac9e081f7faf6b2998efa723cef commit 0acb0d1d8da957ab43d73cb51d3142fc99c28ca7 Author: Christian Persch Date: Sat Aug 8 21:57:15 2020 +0200 profile: Add pref to enable SIXEL When VTE was built with SIXEL support, show a checkbox in the compatibility prefs to enable it. https://gitlab.gnome.org/GNOME/vte/-/issues/253 It would be really cool if stock (could go to experimental I guess if some concerns over stability etc) gnome-terminal in Debian gained sixel support as well. thank you very much in advance! -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages gnome-terminal depends on: ii dbus-user-session [default-dbus-session-bus] 1.12.16-2 ii dbus-x11 [dbus-session-bus] 1.12.16-2 ii dconf-gsettings-backend [gsettings-backend] 0.36.0-1 ii gnome-terminal-data 3.36.1.1-3 ii gsettings-desktop-schemas 3.36.0-1 ii libatk1.0-0 2.36.0-2 ii libc6 2.30-4 ii libdconf1 0.36.0-1 ii libglib2.0-0 2.64.2-1 ii libgtk-3-03.24.20-1 ii libpango-1.0-01.44.7-4 ii libuuid1 2.34-0.1 ii libvte-2.91-0 0.60.3-1 ii libx11-6 2:1.6.9-2 Versions of packages gnome-terminal recommends: ii gvfs 1.44.1-1 ii nautilus-extension-gnome-terminal 3.36.2-1 ii yelp 3.34.0-1 gnome-terminal suggests no packages. -- debconf-show failed
Bug#937090: mrtrix: Python2 removal in sid/bullseye
Sorry about delay. Yes, mrtrix3 is Afaik the way to go. Please file RM On July 26, 2020 7:20:03 AM EDT, "Moritz Mühlenhoff" wrote: >On Fri, Jul 10, 2020 at 01:07:27PM +0200, Andreas Tille wrote: >> Hi Moritz, >> >> On Tue, Jun 30, 2020 at 08:14:15PM +0200, Moritz Mühlenhoff wrote: >> > >> > Given that there's a separate mrtrix3 source package which is >ported to >> > Python 3, should src:mrtrix simply be removed now? >> >> I wished Michael or Yaroslav would answer this question. I'm just >> helping to maintain this package and do not have the slightest >interest >> in it - may be the interest to see it go to have less work ... > >Michael, Yaroslow, what do you think? > >Cheers, >Moritz
Bug#964650: pydicom: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.8 returned exit code 13
On Fri, 17 Jul 2020, Andreas Tille wrote: > Control: tags -1 help > Hi, > the new upstream version I've just pushed to git solves the issue thanks! > that is reported here, but I'm running into a different issue: >TypeError: data type 'uint15' not understood I do not understand it either, in the sense that I have never seen such a beast in real life. > Any help is welcome google lead me to https://bugzilla.redhat.com/show_bug.cgi?id=1838435_source=feedburner_medium=feed_campaign=Feed%3A+rawhide-new-7days+%28Bugzilla+Bugs%29 which points to https://github.com/pydicom/pydicom/issues/1119 which says to be fixed by https://github.com/pydicom/pydicom/pull/1114 which is not really related ... will look into it later... > Andreas. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 WWW: http://www.linkedin.com/in/yarik
Bug#963548: 83.0.4103.116-1 too risky
FWIW, I see that ffmpeg is the one providing libswscale5 .
Two days ago when I upgraded it to 4.3-2 obs-studio started to crash on
the following image:
http://www.onerussian.com/tmp/panic_room_crash_libswscale5.jpg
full url to traceback there
http://www.onerussian.com/tmp/obs-segfault1.txt
I now downgraded ffmpeg to the 4.2.2-3 from snapshots
lena# cat /etc/apt/sources.list.d/ffmpeg-snapshot.list
# 4.2.2-3 to see if help with chromium
deb [trusted=yes]
https://snapshot.debian.org/archive/debian/20200611T024431Z/ sid main contrib
non-free
apt-get install
{ffmpeg,libavcodec58,libavdevice58,libavfilter7,libavformat58,libavresample4,libavutil56,libpostproc55,libswresample3,libswscale5}=7:4.2.2-3
but chromium 83.0.4103.116-2 still crashed. Downgrading chromium as well
now to see if helps
On Fri, 26 Jun 2020, 積丹尼 Dan Jacobson wrote:
> Yup, downgrading chromium-common from 83.0.4103.116-1 to 81.0.4044.92-1,
> and installing ffmpeg 4.2
> (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963080)
> brings back some sanity.
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW: http://www.linkedin.com/in/yarik
Bug#938605: svgtune: Python2 removal in sid/bullseye - reopen 938605
Old python ones are listed only as alternative dependencies to easy backports for ancient systems. https://packages.debian.org/sid/svgtune I don't think this package holds any python removal On June 20, 2020 12:49:59 AM EDT, Sandro Tosi wrote: >Control: reopen -1 > >This bug was closed, but the package has still some dependencies >towards >Python2 packages, in details: > >(binary:svgtune)Depends->python >(binary:svgtune)Depends->python-lxml > >Re-opening, so that they can be taken care of. -- Yaroslav O. Halchenko (mobile version) Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, NH, USA
Bug#937485: pymvpa2: Python2 removal in sid/bullseye
As the upstream and Debian maintainer for it, I am ok with it. It could be easily made to build for python 3 but tests would show that it is not entirely kosher. I better reupload it when it i an sure it is functioning correctly again On June 13, 2020 1:16:58 PM EDT, "Moritz Mühlenhoff" wrote: >On Mon, Feb 03, 2020 at 08:36:43AM +1100, Stuart Prescott wrote: >> Dear maintainers, >> >> In the last update on pymvpa2, it sounded like upstream would soon >have sorted >> Python 3 compatibility and the FTBFS bugs for the package would soon >be fixed. >> However, there has been no upstream activity in the referenced PR >> https://github.com/PyMVPA/PyMVPA/pull/525 for many months. >> >> What are the prospects for a fixed package in the buster release >cycle? Given >> that it will have to go through NEW to gain the Python 3 module >package in any >> case, are we at the stage where it should just be removed from >Debian, perhaps >> to be reintroduced later when upstream work is completed? >> >> (There's a cost to keeping buggy packages in Debian in that they >occupy >> people's time when dealing with transitions or bug squashing. Even >finding the >> packaging Vcs to see if there has been yet-to-be uploaded progress on >these >> bugs is excessively difficult right now) > >Indeed, let's remove it from unstable for now? > >Cheers, >Moritz
Bug#954444: fresh release availability would be appreciated
Package: neomutt Version: 20191207+dfsg.1-1.1 Followup-For: Bug #95 Just discovered neomutt for myself, thought to try, but it pukes on my muttrc configuration. Before investigating and complaining want to make sure to try most recent release. Thank you in advance! -- Package-specific info: NeoMutt 20191207
Bug#961896: nuitka: Please make another source-only upload to allow testing migration
Thanks for the buzz! I really need to change my helper for uploads process to make sure they are source only ones by default. I will wait for the upstream Kay who is also the maintainer :-) - a new release might be not too far away. On May 30, 2020 9:38:57 PM EDT, Boyuan Yang wrote: >Source: nuitka >Severity: important >Version: 0.6.8.3+ds-1 >Tags: sid bullseye >X-Debbugs-CC: kay.ha...@gmail.com y...@debian.org > > >Hi Yaroslav and Kay, > >It looks like all previous uploads for package nuitka in Debian are not >source-only uploads. As a result, this package has been missing in >Debian Testing for quite some time. > >I see that all uploads are sponsored by Yaroslav. Please make sure to >make source-only uploads in the future to avoid issues like this one. >For more information about source-only upload, see >https://wiki.debian.org/SourceOnlyUpload . -- Yaroslav O. Halchenko (mobile version) Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, NH, USA
Bug#961721: please update to more recent upstream release (1.27.2)
Package: recoll Version: 1.26.7-1 Severity: wishlist seems no rush, majority of fixes seems to be windows related: https://www.lesbonscomptes.com/recoll/pages/release-1.27.html -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages recoll depends on: ii recollcmd 1.26.7-1+b1 ii recollgui 1.26.7-1+b1 recoll recommends no packages. recoll suggests no packages. -- debconf-show failed
Bug#910108: RFP: git-bug -- Distributed bug tracker embedded in Git
I would have loved to see this one in debian as well! May be someone from Debian Go Team could have paved the way On Tue, 02 Oct 2018, Antoine Beaupre wrote: > Package: wnpp > Severity: wishlist > * Package name: git-bug > Version : 0.3.0 > Upstream Author : Michael Muré > * URL : https://github.com/MichaelMure/git-bug > * License : GPL-3+ > Programming Lang: Golang > Description : Distributed bug tracker embedded in Git > git-bug is a distributed bug tracker embedded in git. It uses git's > internal storage so no files are added in your project. > As you would do with commits and branches, you can push your bugs to > the same git remote you are already using to collaborate with other > people. > == > I've been maintaining bugs-everywhere (BE) in Debian for a while now, > which accomplishes a similar goal, but with bugs stored in branches > (or in files? i forgot). In any case, BE is unmaintained now and this > looks like a promising alternative, particularly with future two-way > integration with upstream bugtrackers (e.g. GitHub import for now). > It probably has (too many) golang dependencies that need to be bundled > and all that usual stuff. > Golang team maintenance, most likely. Documented here to share it with > the Debian community and make sure there's no work duplicated. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#961051: the 3.0 release is finally out!
Source: mrtrix3 Version: 3.0~rc3+git135-g2b8e7d0c2-5 Severity: wishlist https://www.mrtrix.org/2020/04/23/mrtrix-3-0-0-has-arrived/ Thank you Team in advance! -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
Bug#927076: Prelim Packaging
On Mon, 20 Jan 2020, Barak A. Pearlmutter wrote: > I have a tentative packaging in the debian branch of > github.com/barak/xournalpp and unless there are any objections or > issues arising, plan to upload it in due course. Please please please proceed ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#945739: symeig - RM?
the last changelog msg I see is
symeig (1.5-2) unstable; urgency=low
* Deprecating symeig as a separate package -- functionality was
included in
scipy (>=0.7.0), please use scipy.linalg.eigh instead.
* Transitional packages became architecture 'all' instead of 'any'
* Boosted policy to 3.8.3:
- -dbg got correct "section: debug" and "priority: extra"
-- Yaroslav Halchenko Mon, 16 Nov 2009
08:55:44 -0500
so indeed it is time for it to RiP ;) please RM
On Wed, 13 May 2020, Scott Talbert wrote:
> Hi,
> It seems that symeig has no (longer?) reverse depends and it seems to be
> abandoned upstream. Is the best solution just to remove it?
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
Bug#960464: RFP: datajoint -- a framework for scientific workflow management based on relational principles
Package: wnpp Severity: wishlist * Package name: datajoint-python Version : 0.12.5 Upstream Author : DataJoint team * URL : https://github.com/datajoint/datajoint-python * License : LGPL-2 Programming Lang: Python Description : a framework for scientific workflow management based on relational principles DataJoint for Python is a framework for scientific workflow management based on relational principles. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, computing, and querying data.
Bug#959940: hdmf FTBFS with h5py 2.10.0
Package: python3-h5py
Version: 2.10.0-7
Followup-For: Bug #959940
Please see https://github.com/hdmf-dev/hdmf/issues/343#issuecomment-625972582
for possibly more info:
@tillea @yarikoptic the debian port contains this code in
h5py_2.10.0-7.debian/debian/wrapper_module/h5py/__init__.py
from sys import modules as sys_modules
# [snip]
# make generic h5py module behaviour the same as specific builds
# by importing public and weak internal symbols (single _underscore)
api = [ k for k in _h5py.__dict__.keys() if not k.startswith('__') and
not k.endswith('__') ]
this_module=sys_modules[__name__]
for key in api:
# "imports" symbols (makes them accessible)
setattr(this_module,key,getattr(_h5py,key))
# rename symbols as properties of toplevel h5py module
sys_modules['h5py.{}'.format(key)] = getattr(_h5py,key)
Since remove_deprecated_highlevel_module_2f41c78.patch is not
applied, the api list includes 'highlevel' so then
sys.modules['h5py.highlevel'] is set to h5py.highlevel. This is
problematic
because sys.modules is traversed in the context manager for
unittest.TestCase.assertWarns and getattr is called on it, but
h5py.highlevel
is intentionally lazily imported by h5py, I think, because it is
deprecated. So
one solution might be to apply the patch. Another might be to add and
not k ==
'highlevel' to the line that sets api above.
In the above "patch" is the remove_deprecated_highlevel_module_2f41c78.patch
patch
which was disabled in
commit ed17e72dc2fa47f590b78632401512546d3d3e1e
Author: Drew Parsons
Date: Sun Apr 5 18:31:33 2020 +0800
disable upstream patches and update drop_deprecation_tests.patch
aid HDF5 transition by giving bitshuffle more time to update
(see Bug#955456)
changes to drop_deprecation_tests.patch needed to pass h5py
tests
diff --git a/debian/patches/series b/debian/patches/series
index 6753f8e..9f3468d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,8 +7,8 @@ fix_2.10_docs.patch
hdf5_pkgconfig.patch
build_flavour.patch
stop_circular_dep.patch
-drop_deprecated_dtype_6a77b91.patch
-remove_deprecated_highlevel_module_2f41c78.patch
-file_default_read_5e71c49.patch
+#drop_deprecated_dtype_6a77b91.patch
+#remove_deprecated_highlevel_module_2f41c78.patch
+#file_default_read_5e71c49.patch
drop_deprecation_tests.patch
tests_as_local_build.patch
Cheers,
-- System Information:
Debian Release: bullseye/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'unstable-debug'), (100, 'stable-updates'), (100, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.6.0-1-amd64 (SMP w/12 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-h5py depends on:
ii python3-h5py-serial 2.10.0-7
python3-h5py recommends no packages.
Versions of packages python3-h5py suggests:
pn python-h5py-doc
-- no debconf information
Bug#959911: python3.7: No module named '_cffi_backend'
Package: python3-cryptography Version: 2.8-4 Severity: important I am not sure if it is more pertinent to python3-cffi or one of its packages. I am still using python3.7 which is AFAIK still supported on sid. But with it, it fails to import (using it via keyrings module): $> docker run -it --rm debian:sid root@c911d74fa6cb:/# apt-get update -qqq; apt-get install -y python3.7 python3-cryptography >/dev/null debconf: delaying package configuration, since apt-utils is not installed root@c911d74fa6cb:/# python3.7 -c 'import cryptography.hazmat.primitives.constant_time' Traceback (most recent call last): File "", line 1, in File "/usr/lib/python3/dist-packages/cryptography/hazmat/primitives/constant_time.py", line 11, in from cryptography.hazmat.bindings._constant_time import lib ModuleNotFoundError: No module named '_cffi_backend' root@c911d74fa6cb:/# ls -l /usr/lib/python3/dist-packages/cryptography/hazmat/bindings/ total 824 -rw-r--r-- 1 root root246 Oct 17 2019 __init__.py drwxr-xr-x 2 root root 4096 May 6 20:49 __pycache__ -rw-r--r-- 1 root root 14512 Apr 4 22:53 _constant_time.abi3.so -rw-r--r-- 1 root root 795160 Apr 4 22:53 _openssl.abi3.so -rw-r--r-- 1 root root 14488 Apr 4 22:53 _padding.abi3.so drwxr-xr-x 3 root root 4096 May 6 20:48 openssl it imports fine with python3.8 in sid. I wonder if that is the .abi3 which is not compatible with python 3.7? -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.5.0-rc5-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-cryptography depends on: ii libc62.30-4 ii libssl1.11.1.1g-1 ii python3 3.8.2-3 ii python3-cffi-backend [python3-cffi-backend-api-min] 1.14.0-2 pn python3-cffi-backend-api-max ii python3-six 1.14.0-3 python3-cryptography recommends no packages. Versions of packages python3-cryptography suggests: pn python-cryptography-doc pn python3-cryptography-vectors -- no debconf information
Bug#959725: RM: svgtune -- RoQA; Inactive Upstream; Unmaintained; Affected by Python2 Removal
Please hold off on removal... I will update the package for python3 On Mon, 04 May 2020, Boyuan Yang wrote: > Package: ftp.debian.org > Severity: normal > User: ftp.debian@packages.debian.org > Usertags: remove > X-Debbugs-CC: deb...@onerussian.com y...@debian.org > Dear FTP Masters, > As discussed in https://bugs.debian.org/956652 , please remove svgtune > from the Debian archive. > This package is python2-only and has not seen upstream activity as > well as Debian packaging activity in the last 5 years. The current > package maintainer did not reply to the package removal request at > https://bugs.debian.org/956652 . -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#959575: neurodebian: FTBFS: (process:15028): WARNING **: 05:07:11.653: Unable to create profile directory (Permission denied) (13)
On Sun, 03 May 2020, Lucas Nussbaum wrote: > > [ ! -d build/icons ] && mkdir -p build/icons > > inkscape artwork/icon.svg -w 32 -h 32 \ > > -e build/icons/neurodebian.png > > ** (process:15028): WARNING **: 05:07:11.653: Unable to create profile > > directory (Permission denied) (13) > > Unable to init server: Could not connect: Connection refused > > Unknown option -e > > make[1]: *** [debian/rules:28: override_dh_auto_build] Error 1 FTR, reason is that inkscape switched from -e to -o. Upload fixing that is being prepared -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#937431: pyepl: Python2 removal in sid/bullseye
> > yes, AFAIK it is dead. Let's RM. you ? me ? ;) > Please go ahead :-) FTR #959213 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#959213: RM: pyepl -- ROM; dead upstream, not guaranteed python3 compatibility
Package: ftp.debian.org Severity: normal all said in the subject line. Upstream CCed just in case ;-)
Bug#932197: Bug#937144: Request to join the Neurodebian group
On Thu, 30 Apr 2020, Moritz Mühlenhoff wrote: > On Wed, Feb 26, 2020 at 04:15:03PM +0100, Andreas Tille wrote: > > On Wed, Feb 26, 2020 at 08:37:30AM -0500, Yaroslav Halchenko wrote: > > > thank you Andreas!!! > > > re etelemetry: I made it optional for previous version of the > > > package: > > > $> quilt series > > > deb-no-demand-on-etelemetry > > > $> git describe > > > debian/0.6.0-1 > > Thanks for the hint. While this could possibly speet up the upload of > > nipype I for myself are fine with waiting for the new Build-Depends. > > Anybody who wants to speed up things is kindly invited to add this patch > > and upload. > What's the status here? python-etelemetry is now in the archive and testing. my problem with any version of nipype ended up stalling tests with python3.8. See e.g. https://github.com/nipy/nipype/pull/3154 for interactions with upstream and now a dedicated issue https://github.com/nipy/nipype/issues/3209 I guess what we could do is to upload currently present in debian version with python 3.8 testing disabled and hope for the best ;) I will exercise (update packaging and see if builds/test otherwise ok with 3.7 etc) that now Then we wait for python3-rdflib 5.0 being uploaded (just submitted a wishlist bug report to have it updated), and upload fresh snapshot (or release if by then done) of nipype. any suggestions to the plan? ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#959205: fresh (13 days old) 5.0.0 release is out, will be needed for nipype
Package: python3-rdflib Version: 4.2.2-5 Severity: wishlist https://github.com/RDFLib/rdflib/releases and nipype introduced 5.0.0 as minimal dependency: https://github.com/nipy/nipype/pull/3154/files#diff-652049a763b24d096b8211ef8d633748R113 it would be great if 5.0.0 was uploaded to Debian -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug'), (100, 'stable-updates'), (100, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.5.0-rc5-amd64 (SMP w/12 CPU cores) Kernel taint flags: TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-rdflib depends on: ii python33.8.2-3 ii python3-isodate0.6.0-2 ii python3-pyparsing 2.4.6-2 Versions of packages python3-rdflib recommends: ii python3-html5lib 1.0.1-3 ii python3-sparqlwrapper 1.8.5-1 Versions of packages python3-rdflib suggests: pn python-rdflib-doc -- no debconf information
Bug#937431: pyepl: Python2 removal in sid/bullseye
On Thu, 30 Apr 2020, Moritz Mühlenhoff wrote: > On Fri, Aug 30, 2019 at 07:33:35AM +, Matthias Klose wrote: > > Package: src:pyepl > > Version: 1.1.0+git12-g365f8e3-3 > > Severity: normal > > Tags: sid bullseye > > User: debian-pyt...@lists.debian.org > > Usertags: py2removal > > Python2 becomes end-of-live upstream, and Debian aims to remove > > Python2 from the distribution, as discussed in > > https://lists.debian.org/debian-python/2019/07/msg00080.html > > Your package either build-depends, depends on Python2, or uses Python2 > > in the autopkg tests. Please stop using Python2, and fix this issue > > by one of the following actions. > pyepl is dead upstream, let's remove it? yes, AFAIK it is dead. Let's RM. you ? me ? ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#936857: libfreenect: diff for version 1:0.5.3-2
Thanks for the alert, FWIW, done now: (git)lena:~exppsy/libfreenect[debian]git $> gbp push salsa gbp:info: Pushing debian/1%0.5.3-1 to salsa gbp:info: Pushing upstream/0.5.3 to salsa gbp:info: Pushing refs/heads/debian to salsa:refs/heads/debian gbp:info: Pushing refs/heads/dfsg to salsa:refs/heads/dfsg On Thu, 09 Apr 2020, Sandro Tosi wrote: > FTR, i sent my changes this way instead on git because HEAD doesnt > contain the 1:0.5.3-1 upload > -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#936857: libfreenect: diff for version 1:0.5.3-2
On Thu, 09 Apr 2020, Sandro Tosi wrote: > Control: tags 936857 + patch > Dear maintainer, > I've prepared an upload for libfreenect (versioned as 1:0.5.3-2). The diff > is attached to this message. Thank you Sandro! -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#942936: datalad-container: diff for NMU version 1.0.0-1.1
d'oh -- missed that one, thank you Sando, I will apply the patch and upload as -2. Cheers, On Sun, 29 Mar 2020, Sandro Tosi wrote: > Control: tags 942936 + patch > Dear maintainer, > I've prepared an NMU for datalad-container (versioned as 1.0.0-1.1). The diff > is attached to this message. > Regards. > diff -Nru datalad-container-1.0.0/debian/changelog > datalad-container-1.0.0/debian/changelog > --- datalad-container-1.0.0/debian/changelog 2020-02-24 10:31:21.0 > -0500 > +++ datalad-container-1.0.0/debian/changelog 2020-03-29 11:57:39.0 > -0400 > @@ -1,3 +1,10 @@ > +datalad-container (1.0.0-1.1) unstable; urgency=medium > + > + * Non-maintainer upload. > + * Use python3-requests; Closes: #942936 > + > + -- Sandro Tosi Sun, 29 Mar 2020 11:57:39 -0400 > + > datalad-container (1.0.0-1) unstable; urgency=medium >* Fresh upstream release > diff -Nru datalad-container-1.0.0/debian/control > datalad-container-1.0.0/debian/control > --- datalad-container-1.0.0/debian/control2020-02-24 10:31:21.0 > -0500 > +++ datalad-container-1.0.0/debian/control2020-03-29 11:54:49.0 > -0400 > @@ -6,7 +6,7 @@ > debhelper (>= 10), > dh-python, > datalad (>= 0.12~), > - python-requests (>= 1.2), > + python3-requests (>= 1.2), > python3-setuptools, > python3-all, > python3-nose, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#954579: datalad-container: FTBFS: build-dependency not installable: datalad (>= 0.11.5~)
On Sun, 22 Mar 2020, Lucas Nussbaum wrote: > Source: datalad-container > Version: 0.5.0-1 Thank you for the report. 1.0.0-1 was built but forgotten to be uploaded at the end of Feb. Now it would need to wait until datalad 0.12.4 is uploaded first which would resolve incompatibilities with recent git annex and git releases. Hopefully later today/tomorrow Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#942615: no-changes source-only NMU
On Fri, 06 Mar 2020, Paul Gevers wrote: > Control: tags -1 pending > Dear maintainer, > I have uploaded a no-changes source only version to DELAYED/15. Please > tell me if I should delay or cancel the upload. oh, I have missed that https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=942615 and that it was awaiting THANKS!! Please feel welcome to reupload without delay -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#951982: fixed upstream
FWIW, this issue should be fully addressed in recent releases. in Debian we have 4.30.0-1, upstream release is v4.43.0, and this issue was fixed in https://github.com/tqdm/tqdm/commit/0fcf9ed4c191fa224afd5581ac1a47b2cf80bc54#diff-79a0b30dff238cd3aa6b9f8e665a57a0 pandas: support v1.0.0 (so even for the version of pandas in experimental) which is $> git describe --contains 0fcf9ed4c191fa224afd5581ac1a47b2cf80bc54 v4.42.1^2~3 so, updating to the most recent release should resolve this issue and prevent avalanche of removes from testing. -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#932197: Bug#937144: Request to join the Neurodebian group
thank you Andreas!!! re etelemetry: I made it optional for previous version of the package: $> quilt series deb-no-demand-on-etelemetry $> git describe debian/0.6.0-1 On Tue, 25 Feb 2020, Andreas Tille wrote: > Hi, > here is some update I'm also forwarding to NeuroDebian Team list to have > some public record of the current status. > On Thu, Feb 20, 2020 at 01:36:35AM +1100, Stuart Prescott wrote: > > I also looked at nipype (but its source is very odd and I can't build what > > is > > in the repo; I think that was .gitattributes related but end up fixing it) > I have updated nipype in the Git repository I moved to Debian Med team[1] > The latest upstream version needs a new dependency python3-etelemetry > which I packaged and uploaded to new (see #952558) > I've also tried to build heudiconv in Git[2]. It builds so far but tests > accessing remote locations to download data need to be disabled. That's > where I'm stoping for now. > Kind regards >Andreas. > [1] https://salsa.debian.org/med-team/nipype > [2] https://salsa.debian.org/med-team/heudiconv -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#869237: I would have loved to see it in debian as well
oh, apparently it survived in ubuntu land: https://launchpad.net/ubuntu/+source/oprofile/1.3.0-0ubuntu9 On Mon, 24 Feb 2020, Yaroslav Halchenko wrote: > Just +1 on having this package in Debian ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Bug#869237: I would have loved to see it in debian as well
Just +1 on having this package in Debian ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik signature.asc Description: PGP signature
Bug#937249: closed by Abhijith PA (Bug#937249: fixed in patool 1.12-4)
On Thu, 06 Feb 2020, Yaroslav Halchenko wrote: > On Wed, 15 Jan 2020, Abhijith PA wrote: > > Hi Adrian, > > On 15/01/20 5:47 pm, Adrian Bunk wrote: > > > On Tue, Dec 17, 2019 at 03:21:07PM +, Debian Bug Tracking System > > > wrote: > > >> ... > > >> Architecture: source all > > >> Version: 1.12-4 > > >> ... > > > Please make a source-only upload to allow testing migration. > > Currently I don't have any change to make a new source only upload. But > > I am working on one of its lintian warning[1]. Once it is solved, I will > > make a source only upload. > should it be uploaded with a new revision just for the sake of source > only upload? I have sinned the same way and probably do the same for > datalad the issue needs to be resolved, so I have made source only upload of 1.12-4.1 into 3 days delayed. Let me know if I should delay longer or reupload without delay. The only change was changelog (attached) Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik From 91ef4904d036de9c81b41098adf5cc5894516496 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 12 Feb 2020 23:56:19 -0500 Subject: [PATCH] changelog for 1.12-4.1 -- source only upload --- debian/changelog | 7 +++ 1 file changed, 7 insertions(+) diff --git a/debian/changelog b/debian/changelog index a519270..dc566f2 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +patool (1.12-4.1) unstable; urgency=medium + + * Non-maintainer upload. + * source-only upload to allow migration to bullseye + + -- Yaroslav Halchenko Wed, 12 Feb 2020 23:55:28 -0500 + patool (1.12-4) unstable; urgency=medium [ Ondřej Nový ] -- 2.24.0 signature.asc Description: PGP signature
