Bug#1026539: theano FTBFS

2023-01-03 Thread Rebecca N. Palmer
Please do *not* upload theano 1.12 to unstable - it's the Aesara version, which may seriously break backward compatibility. I haven't had time to properly look at this bug yet.

Bug#1026539: theano FTBFS

2023-01-03 Thread Rebecca N. Palmer
Please do *not* upload theano 1.12 to unstable - it's the Aesara version, which may seriously break backward compatibility. I haven't had time to properly look at this bug yet.

Bug#1026539: theano FTBFS

2023-01-03 Thread Rebecca N. Palmer
Please do *not* upload theano 1.12 to unstable - it's the Aesara version, which may seriously break backward compatibility. I haven't had time to properly look at this bug yet. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1024906: apparently fixed Re: dask autopkgtest fail with python 3.11

2022-12-03 Thread Rebecca N. Palmer
This combination stopped failing on 2022-11-22/23 (without a dask upload, suggesting it was fixed somewhere other than dask itself). Hence, I suggest closing this bug.

Bug#1024906: apparently fixed Re: dask autopkgtest fail with python 3.11

2022-12-03 Thread Rebecca N. Palmer
This combination stopped failing on 2022-11-22/23 (without a dask upload, suggesting it was fixed somewhere other than dask itself). Hence, I suggest closing this bug.

Bug#1025393: dask: autopkgtest fail with pandas 1.5

2022-12-03 Thread Rebecca N. Palmer
Package: python3-dask Version: 2022.02.0+dfsg-2 Tags: fixed-upstream Control: block 1022571 by -1 With pandas 1.5 (currently in experimental), the dask autopkgtest fails: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dask/28842796/log.gz This appears to be fixed upstream, but I

Bug#1017573: python3-ulmo: autopkgtest fail with pandas 1.4

2022-11-30 Thread Rebecca N. Palmer
Control: reopen -1 On 13/11/2022 15:02, Rebecca N. Palmer wrote: It looks like this has been fixed somewhere other than the ulmo package (I don't know where), as the autopkgtest now passes with pandas 1.4/1.5. No it doesn't - it's being run with pandas 1.3 because pandas 1.5 declares

Bug#1017573: python3-ulmo: autopkgtest fail with pandas 1.4

2022-11-30 Thread Rebecca N. Palmer
Control: reopen -1 On 13/11/2022 15:02, Rebecca N. Palmer wrote: It looks like this has been fixed somewhere other than the ulmo package (I don't know where), as the autopkgtest now passes with pandas 1.4/1.5. No it doesn't - it's being run with pandas 1.3 because pandas 1.5 declares

Bug#1000922: llvmlite: uninstallable due to llvm-11 removal

2022-11-27 Thread Rebecca N. Palmer
Control: severity -1 grave Control: merge -1 1024795 Control: retitle -1 llvmlite: uninstallable due to llvm-11 removal It looks like closing and reopening this removed its "blocks" relationship to 1000941 (the llvm-11 removal request). Hence, llvm-11 has now been removed, making llvmlite

Bug#1000922: llvmlite: uninstallable due to llvm-11 removal

2022-11-27 Thread Rebecca N. Palmer
Control: severity -1 grave Control: merge -1 1024795 Control: retitle -1 llvmlite: uninstallable due to llvm-11 removal It looks like closing and reopening this removed its "blocks" relationship to 1000941 (the llvm-11 removal request). Hence, llvm-11 has now been removed, making llvmlite

Bug#1022571: pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Control: severity -1 wishlist Control: retitle -1 transition: pandas 1.3/1.4 -> 1.5 Control: tags -1 fixed-in-experimental pandas 1.5.1 is now in experimental. It appears to break emperor, q2templates and statsmodels. (Compared to 1.4; also python-skbio (#1017574) compared to 1.3.)

Bug#1022571: pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Control: severity -1 wishlist Control: retitle -1 transition: pandas 1.3/1.4 -> 1.5 Control: tags -1 fixed-in-experimental pandas 1.5.1 is now in experimental. It appears to break emperor, q2templates and statsmodels. (Compared to 1.4; also python-skbio (#1017574) compared to 1.3.)

Bug#1017574: python3-skbio: FTBFS/autopkgtest fail with pandas 1.4/1.5

2022-11-25 Thread Rebecca N. Palmer
Control: block 1022571 by -1 This still fails with pandas 1.5. Build log: https://launchpadlibrarian.net/633830773/buildlog_ubuntu-lunar-amd64.python-skbio_0.5.6-6build2_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-skbio/28542505/log.gz

Bug#1024821: q2templates: FTBFS/autopkgtest fail with pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Package: q2templates Version: 2022.8.0+ds-1 Control: block 1022571 by -1 Tests fail with pandas 1.5 (currently in experimental). Build log: https://launchpadlibrarian.net/633830688/buildlog_ubuntu-lunar-amd64.q2templates_2022.8.0+ds-1_BUILDING.txt.gz Autopkgtest log:

Bug#1024820: emperor: FTBFS/autopkgtest fail with pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Package: python3-emperor Version: 1.0.3+ds-4 Control: block 1022571 by -1 Tests fail with pandas 1.5 (currently in experimental). Build log: https://launchpadlibrarian.net/633828020/buildlog_ubuntu-lunar-amd64.emperor_1.0.3+ds-4_BUILDING.txt.gz Autopkgtest log:

Bug#1020060: statsmodels sometimes FTBFS

2022-11-13 Thread Rebecca N. Palmer
It also doesn't fail on the buildds. (The failed binNMU of statsmodels for Python 3.11 is instead the expected result of trying to build statsmodels on a Python version without pandas - pandas failed due to #1023965.) Is there anything special about the mass-rebuild environment that might

Bug#1020060: statsmodels sometimes FTBFS

2022-11-13 Thread Rebecca N. Palmer
It also doesn't fail on the buildds. (The failed binNMU of statsmodels for Python 3.11 is instead the expected result of trying to build statsmodels on a Python version without pandas - pandas failed due to #1023965.) Is there anything special about the mass-rebuild environment that might

Bug#1020060: statsmodels sometimes FTBFS

2022-11-13 Thread Rebecca N. Palmer
It also doesn't fail on the buildds. (The failed binNMU of statsmodels for Python 3.11 is instead the expected result of trying to build statsmodels on a Python version without pandas - pandas failed due to #1023965.) Is there anything special about the mass-rebuild environment that might

Bug#1023965: pandas FTBFS with Python 3.11 as supported version

2022-11-13 Thread Rebecca N. Palmer
Control: block 1021984 by -1 Control: tags -1 fixed-upstream fixed-in-experimental There's more than just those 2[0]. Some are tests that expect an error and check the message (not just the type), and fail because the message has been reworded - these should be trivial to fix. The 2 in

Bug#1023965: pandas FTBFS with Python 3.11 as supported version

2022-11-13 Thread Rebecca N. Palmer
Control: block 1021984 by -1 Control: tags -1 fixed-upstream fixed-in-experimental There's more than just those 2[0]. Some are tests that expect an error and check the message (not just the type), and fail because the message has been reworded - these should be trivial to fix. The 2 in

Bug#1023965: pandas FTBFS with Python 3.11 as supported version

2022-11-13 Thread Rebecca N. Palmer
Control: block 1021984 by -1 Control: tags -1 fixed-upstream fixed-in-experimental There's more than just those 2[0]. Some are tests that expect an error and check the message (not just the type), and fail because the message has been reworded - these should be trivial to fix. The 2 in

Bug#1023986: parso: too old to parse Python 3.11

2022-11-13 Thread Rebecca N. Palmer
Package: python3-parso Version: 0.8.1-1 Tags: fixed-upstream Control: block 1023965 1021984 by -1 Attempting to use parso on Python 3.11 gives an error that this is not supported. (e.g. some pandas tests do this -

Bug#1020060: statsmodels: FTBFS: make[1]: *** [debian/rules:105: override_dh_auto_test] Error 1

2022-09-19 Thread Rebecca N. Palmer
This is the same test as #1014278 / upstream 8341, but now on amd64. From the upstream discussion, it may be a numerically unstable test. It doesn't fail everywhere: a test build on Salsa CI passed, as did the last debci runs. (reproducible-builds FTBFS on the second build, on amd64/sid

Bug#1020060: statsmodels: FTBFS: make[1]: *** [debian/rules:105: override_dh_auto_test] Error 1

2022-09-19 Thread Rebecca N. Palmer
This is the same test as #1014278 / upstream 8341, but now on amd64. From the upstream discussion, it may be a numerically unstable test. It doesn't fail everywhere: a test build on Salsa CI passed, as did the last debci runs. (reproducible-builds FTBFS on the second build, on amd64/sid

Bug#1020060: statsmodels: FTBFS: make[1]: *** [debian/rules:105: override_dh_auto_test] Error 1

2022-09-19 Thread Rebecca N. Palmer
This is the same test as #1014278 / upstream 8341, but now on amd64. From the upstream discussion, it may be a numerically unstable test. It doesn't fail everywhere: a test build on Salsa CI passed, as did the last debci runs. (reproducible-builds FTBFS on the second build, on amd64/sid

[med-svn] [Git][med-team/snakemake][master] retry CI (after pushing other branches)

2022-03-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 8868dd08 by Rebecca N. Palmer at 2022-03-31T21:16:57+01:00 retry CI (after pushing other branches) - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/snakemake] Pushed new tag upstream/7.3.3

2022-03-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag upstream/7.3.3 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/upstream/7.3.3 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][pristine-tar] pristine-tar data for snakemake_7.3.3.orig.tar.gz

2022-03-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: c0852f2c by Rebecca N. Palmer at 2022-03-29T21:00:04+01:00 pristine-tar data for snakemake_7.3.3.orig.tar.gz - - - - - 2 changed files: - + snakemake_7.3.3.orig.tar.gz.delta - + snakemake_7.3.3

[med-svn] [Git][med-team/snakemake][upstream] New upstream version 7.3.3

2022-03-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake Commits: b1bb3d3f by Rebecca N. Palmer at 2022-03-29T20:59:38+01:00 New upstream version 7.3.3 - - - - - 30 changed files: - .github/workflows/main.yml - .gitpod.yml - .readthedocs.yml - CHANGELOG.md - LICENSE.md

[med-svn] [Git][med-team/snakemake][master] 2 commits: skip a test that now needs python3-retry, add missing test-depends

2022-03-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 6be4ab3c by Rebecca N. Palmer at 2022-03-30T07:41:06+01:00 skip a test that now needs python3-retry, add missing test-depends - - - - - 8f6abdbf by Rebecca N. Palmer at 2022-03-30T07:42:41+01:00 Update Lintian

[med-svn] [Git][med-team/snakemake][master] fix test skips

2022-03-29 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 978041ef by Rebecca N. Palmer at 2022-03-29T23:06:40+01:00 fix test skips - - - - - 3 changed files: - debian/changelog - debian/rules - debian/tests/run-unit-test Changes

[med-svn] [Git][med-team/snakemake][master] 6 commits: New upstream version 7.3.3

2022-03-29 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: b1bb3d3f by Rebecca N. Palmer at 2022-03-29T20:59:38+01:00 New upstream version 7.3.3 - - - - - b2e06151 by Rebecca N. Palmer at 2022-03-29T21:00:04+01:00 Update upstream source from tag upstream/7.3.3 Update

[med-svn] [Git][med-team/snakemake] Pushed new tag debian/6.15.5-1

2022-03-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag debian/6.15.5-1 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/6.15.5-1 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake] Pushed new tag upstream/6.15.5

2022-03-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag upstream/6.15.5 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/upstream/6.15.5 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][pristine-tar] pristine-tar data for snakemake_6.15.5.orig.tar.gz

2022-03-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: 55fcf68f by Rebecca N. Palmer at 2022-02-20T13:30:09+00:00 pristine-tar data for snakemake_6.15.5.orig.tar.gz - - - - - 2 changed files: - + snakemake_6.15.5.orig.tar.gz.delta - + snakemake_6.15.5

[med-svn] [Git][med-team/snakemake][master] 2 commits: Tests: skip peppy tests (not in Debian).

2022-02-20 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: da1a9e8d by Rebecca N. Palmer at 2022-02-20T14:41:54+00:00 Tests: skip peppy tests (not in Debian). - - - - - 1d9c1c81 by Rebecca N. Palmer at 2022-02-20T14:53:22+00:00 Tests: use Python 3 subprocesses

[med-svn] [Git][med-team/snakemake][master] Remove drmaa Recommends, as that package is broken (see #951704).

2022-02-20 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 3e2242a4 by Rebecca N. Palmer at 2022-02-20T13:58:27+00:00 Remove drmaa Recommends, as that package is broken (see #951704). - - - - - 3 changed files: - debian/README.source - debian/changelog - debian/control

Re: Is snakemake using drmaa?

2022-02-20 Thread Rebecca N. Palmer
I didn't mean that these other non-packaged options were direct alternatives to drmaa, only that snakemake already doesn't have all its features available in Debian without installing external packages, and that I don't consider losing one more to be a serious bug. If anyone _wants_ to work

Re: Is snakemake using drmaa?

2022-02-19 Thread Rebecca N. Palmer
The documentation says: https://github.com/snakemake/snakemake/blob/main/docs/tutorial/additional_features.rst#cluster-execution https://github.com/snakemake/snakemake/blob/main/docs/executing/cluster.rst I don't know how up to date this is, but the code to use drmaa is still there. snakemake

Re: pandas 1.3.5+dfsg-2 autopkgtest failures

2022-02-05 Thread Rebecca N. Palmer
pandas has now migrated (on both Debian and Ubuntu). I have uploaded versions of statsmodels and snakemake that should (almost always) avoid these test failures, and reported the partd failure as #1005045.

[med-svn] [Git][med-team/snakemake][pristine-tar] 2 commits: pristine-tar data for snakemake_6.15.1.orig.tar.gz

2022-02-05 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: f4fe5afd by Rebecca N. Palmer at 2022-02-01T21:13:29+00:00 pristine-tar data for snakemake_6.15.1.orig.tar.gz - - - - - 3bb6c55c by Rebecca N. Palmer at 2022-02-05T21:21:16+00:00 Merge branch pristine-tar

[med-svn] [Git][med-team/snakemake][upstream] 2 commits: New upstream version 6.15.1

2022-02-05 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake Commits: cb7ce873 by Rebecca N. Palmer at 2022-02-01T21:13:08+00:00 New upstream version 6.15.1 - - - - - bebee42a by Rebecca N. Palmer at 2022-02-05T21:21:48+00:00 Merge branch upstream of salsa.debian.org:med-team

[med-svn] [Git][med-team/snakemake] Pushed new tag debian/6.15.1-2

2022-02-05 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag debian/6.15.1-2 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/6.15.1-2 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][master] Timeout and retry an intermittently hanging autopkgtest.

2022-02-04 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 5b3400fa by Rebecca N. Palmer at 2022-02-04T22:36:43+00:00 Timeout and retry an intermittently hanging autopkgtest. - - - - - 3 changed files: - debian/changelog - debian/rules - debian/tests/run-unit-test

pandas 1.3.5+dfsg-2 autopkgtest failures

2022-02-03 Thread Rebecca N. Palmer
In Debian (only change from -1 should be disabling some tests, i.e. real pandas-related failures are unlikely): mdtraj/amd64: upstream tests pass but a warning is printed to stderr, which autopkgtest counts as a fail partd/ppc64el: save/load of a plain string fails snakemake/i386: hang in

RFS: splitting the snakemake package into main and -doc

2022-02-02 Thread Rebecca N. Palmer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Please upload snakemake 6.15.1-1 to unstable (Salsa HEAD = commit ID 8bf4db496feed2fa84f23018acba0033e321ef69). This splits the binary package into snakemake and snakemake-doc, which I can't do myself because DMs can't upload NEW packages.

[med-svn] [Git][med-team/snakemake][master] Try again to fix sphinx locale (see #998059)

2022-02-01 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 8bf4db49 by Rebecca N. Palmer at 2022-02-02T07:36:30+00:00 Try again to fix sphinx locale (see #998059) - - - - - 2 changed files: - debian/changelog - debian/rules Changes

[med-svn] [Git][med-team/snakemake][master] salsa-ci: properly enable diffoscope

2022-02-01 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: f113de42 by Rebecca N. Palmer at 2022-02-01T22:24:58+00:00 salsa-ci: properly enable diffoscope - - - - - 2 changed files: - debian/changelog - debian/salsa-ci.yml Changes

[med-svn] [Git][med-team/snakemake][master] Tests: skip another new conda-using test.

2022-02-01 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 2d75b16c by Rebecca N. Palmer at 2022-02-01T21:53:58+00:00 Tests: skip another new conda-using test. - - - - - 3 changed files: - debian/changelog - debian/rules - debian/tests/run-unit-test Changes

[med-svn] [Git][med-team/snakemake][master] 4 commits: salsa-ci: disable atomic reprotest (always meant to be a one-off

2022-02-01 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 5467e2a2 by Rebecca N. Palmer at 2022-02-01T21:12:19+00:00 salsa-ci: disable atomic reprotest (always meant to be a one-off given how resource-heavy it might be) but keep diffoscope - - - - - cb7ce873 by Rebecca N

[med-svn] [Git][med-team/snakemake][master] 2 commits: Tests: skip an FTP-using test.

2022-02-01 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 50113c1d by Rebecca N. Palmer at 2022-02-01T20:25:46+00:00 Tests: skip an FTP-using test. - - - - - 4e527e8b by Rebecca N. Palmer at 2022-02-01T20:27:39+00:00 salsa-ci: run additional reproducibility tests

[med-svn] [Git][med-team/snakemake] Pushed new tag upstream/6.14.0

2022-01-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag upstream/6.14.0 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/upstream/6.14.0 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][upstream] New upstream version 6.14.0

2022-01-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake Commits: 1ee51741 by Rebecca N. Palmer at 2022-01-26T21:13:21+00:00 New upstream version 6.14.0 - - - - - 30 changed files: - CHANGELOG.md - docs/getting_started/installation.rst - docs/project_info/more_resources.rst

[med-svn] [Git][med-team/snakemake][pristine-tar] pristine-tar data for snakemake_6.14.0.orig.tar.gz

2022-01-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: 160bfcfa by Rebecca N. Palmer at 2022-01-26T21:13:41+00:00 pristine-tar data for snakemake_6.14.0.orig.tar.gz - - - - - 2 changed files: - + snakemake_6.14.0.orig.tar.gz.delta - + snakemake_6.14.0

[med-svn] [Git][med-team/snakemake][master] 8 commits: New upstream version 6.14.0

2022-01-31 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 1ee51741 by Rebecca N. Palmer at 2022-01-26T21:13:21+00:00 New upstream version 6.14.0 - - - - - 6dcfe9a3 by Rebecca N. Palmer at 2022-01-26T21:13:41+00:00 Update upstream source from tag upstream/6.14.0 Update

Solved Re: How to turn off Salsa CI for a package?

2022-01-29 Thread Rebecca N. Palmer
The issue turned out to be that the pandas repository's settings were pointed to a CI settings file outside the repository, so it wasn't even looking at my debian/salsa-ci.yml. As suggested by Eriberto's link, this setting is found at (starting from the repository's page in Salsa, logged in)

How to turn off Salsa CI for a package?

2022-01-27 Thread Rebecca N. Palmer
The default (I'm not sure if this is a global or per-team default) Salsa CI pipeline tries to build and test packages on every commit. For pandas, this always hits the 1 hour timeout, and hence "fails" uselessly (wasting both the server's resources, and my attention when a failure alert

[med-svn] [Git][med-team/snakemake] Pushed new tag debian/6.12.3-1

2022-01-11 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag debian/6.12.3-1 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/6.12.3-1 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][master] finalize for upload to unstable

2022-01-11 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: b21b17a1 by Rebecca N. Palmer at 2022-01-11T21:23:02+00:00 finalize for upload to unstable - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/snakemake] Pushed new tag upstream/6.12.3

2022-01-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed new tag upstream/6.12.3 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/upstream/6.12.3 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/snakemake][upstream] New upstream version 6.12.3

2022-01-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake Commits: 48c2b38f by Rebecca N. Palmer at 2022-01-08T19:36:27+00:00 New upstream version 6.12.3 - - - - - 30 changed files: - .github/workflows/conventional-prs.yml - .github/workflows/main.yml - CHANGELOG.md - docs

[med-svn] [Git][med-team/snakemake][pristine-tar] pristine-tar data for snakemake_6.12.3.orig.tar.gz

2022-01-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: 4ed119e2 by Rebecca N. Palmer at 2022-01-08T19:36:46+00:00 pristine-tar data for snakemake_6.12.3.orig.tar.gz - - - - - 2 changed files: - + snakemake_6.12.3.orig.tar.gz.delta - + snakemake_6.12.3

[med-svn] [Git][med-team/snakemake][master] 6 commits: New upstream version 6.10.0+dfsg1

2022-01-08 Thread Rebecca N. Palmer (@rnpalmer-guest)
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake Commits: 89e5483e by Nilesh Patra at 2021-11-10T01:03:44+05:30 New upstream version 6.10.0+dfsg1 - - - - - f5e50c2a by Rebecca N. Palmer at 2022-01-08T19:34:09+00:00 Remove unnecessary repack. - - - - - 48c2b38f by Rebecca N

Re: Bug#1001516: python-statsmodels-doc (and maybe others?): Broken search capability due to incompatible change in new sphinx 4.3

2021-12-11 Thread Rebecca N. Palmer
The statsmodels in unstable (though not testing) is already built against sphinx 4.3, but this sounds like it might affect other packages. Is that likely, and if so, what should we do about it?

Re: Bug#999415: transition: pandas 1.1 -> 1.3 - to unstable now or not?

2021-11-28 Thread Rebecca N. Palmer
After build-testing about half of the reverse dependencies, failures that look new-pandas-related are cfgrib #1000726, joypy #1000727, python-skbio #1000752, and maybe hyperspy (not filed yet). python-skbio and hyperspy already FTBFS for unrelated reasons (but fail more tests with new

Re: Bug#999415: transition: pandas 1.1 -> 1.3 - to unstable now or not?

2021-11-28 Thread Rebecca N. Palmer
After build-testing about half of the reverse dependencies, failures that look new-pandas-related are cfgrib #1000726, joypy #1000727, python-skbio #1000752, and maybe hyperspy (not filed yet). python-skbio and hyperspy already FTBFS for unrelated reasons (but fail more tests with new

Re: Bug#999415: transition: pandas 1.1 -> 1.3

2021-11-21 Thread Rebecca N. Palmer
Control: block 996584 by -1 On 21/11/2021 06:30, Graham Inggs wrote: It might be easier to upgrade to 1.2.4 first, then 1,3,x later. Probably not, given that we're now trying to add Python 3.10 support (#996584), and pandas upstream's work on that is recent (maybe still unfinished):

Re: transition: pandas 1.1 -> 1.3

2021-11-11 Thread Rebecca N. Palmer
I was already planning to try a build+autopkgtest of the reverse dependencies, and probably an upload to experimental (it's also common for pandas to fail a few tests on non-amd64), at some point, but not just yet. (The last time I did this was #969650.) Thanks for the tools suggestions. I

transition: pandas 1.1 -> 1.3

2021-11-10 Thread Rebecca N. Palmer
Source: pandas Version: 1.1.5+dfsg-2 Severity: wishlist On 10/11/2021 17:14, Andreas Tille wrote: pandas is lagging behind upstream by several versions. I guess we should try to get in sync with upstream a bit more. Yes, but please don't upload this yet: it's common for a pandas upgrade to

Bug#992673: libgpuarray *gemv, *ger test fails

2021-10-26 Thread Rebecca N. Palmer
Control: tags -1 pending (fixed in Salsa, as far as I consider it my bug) It looks like both of these originate further down the stack, not in libgpuarray: The *ger error code is an OpenCL compile failure from inside clblast, so likely either pocl or clblast. The *gemv problem appears to

Bug#992673: libgpuarray *gemv, *ger test fails

2021-10-26 Thread Rebecca N. Palmer
Control: tags -1 pending (fixed in Salsa, as far as I consider it my bug) It looks like both of these originate further down the stack, not in libgpuarray: The *ger error code is an OpenCL compile failure from inside clblast, so likely either pocl or clblast. The *gemv problem appears to

Bug#992673: libgpuarray *gemv, *ger test fails

2021-10-26 Thread Rebecca N. Palmer
Control: tags -1 pending (fixed in Salsa, as far as I consider it my bug) It looks like both of these originate further down the stack, not in libgpuarray: The *ger error code is an OpenCL compile failure from inside clblast, so likely either pocl or clblast. The *gemv problem appears to

Bug#997908: pocl: Assertion `td->printf_buffer != NULL' failed on armel/armhf

2021-10-26 Thread Rebecca N. Palmer
Source: pocl Version: 1.8-1 (Filing this as something to refer to when I disable those tests; it may or may not actually be worth fixing.) Since some time in August, all the packages that use pocl for their autopkgtests have been failing on armel/armhf (but not arm64) with either Assertion

Bug#997382: theano FTBFS - sphinx 4.2?

2021-10-24 Thread Rebecca N. Palmer
Control: tags -1 patch This looks similar to #997026, and the same fix appears to work. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#997382: theano FTBFS - sphinx 4.2?

2021-10-24 Thread Rebecca N. Palmer
Control: tags -1 patch This looks similar to #997026, and the same fix appears to work.

Bug#997382: theano FTBFS - sphinx 4.2?

2021-10-24 Thread Rebecca N. Palmer
Control: tags -1 patch This looks similar to #997026, and the same fix appears to work.

Bug#997081: statsmodels FTBFS - tests fail

2021-10-24 Thread Rebecca N. Palmer
Reproduced here; not obviously known upstream. Autopkgtest says it started between 2021-08-30 and 2021-09-14 in unstable, between 2021-10-10 and 2021-10-18 in testing. It might be easiest to upgrade to 0.13.0 (if it fixes this - I haven't checked yet), given that we should do that anyway at

Bug#997081: statsmodels FTBFS - tests fail

2021-10-24 Thread Rebecca N. Palmer
Reproduced here; not obviously known upstream. Autopkgtest says it started between 2021-08-30 and 2021-09-14 in unstable, between 2021-10-10 and 2021-10-18 in testing. It might be easiest to upgrade to 0.13.0 (if it fixes this - I haven't checked yet), given that we should do that anyway at

Bug#997081: statsmodels FTBFS - tests fail

2021-10-24 Thread Rebecca N. Palmer
Reproduced here; not obviously known upstream. Autopkgtest says it started between 2021-08-30 and 2021-09-14 in unstable, between 2021-10-10 and 2021-10-18 in testing. It might be easiest to upgrade to 0.13.0 (if it fixes this - I haven't checked yet), given that we should do that anyway at

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-18 Thread Rebecca N. Palmer
On 18/10/2021 08:15, Nilesh Patra wrote: On Mon, Oct 18, 2021 at 01:32:30AM +0200, Steffen Möller wrote: Is anyone continuing the update of snakemake now? @Rebecca, could you look into it now that pulp is done? Currently, there is just a very few failing tests -- I guess most are due to some

Bug#963041: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Rebecca N. Palmer
On 15/10/2021 14:46, Andreas Tille wrote: Hi Rebecca and whoever might care. As usual snakemake is troublesome to upgrade. I have injected the latest version into Git but there are lots of failed tests. It would be great if someone could care about this. Kind regards Andreas. I

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Rebecca N. Palmer
On 15/10/2021 14:46, Andreas Tille wrote: Hi Rebecca and whoever might care. As usual snakemake is troublesome to upgrade. I have injected the latest version into Git but there are lots of failed tests. It would be great if someone could care about this. Kind regards Andreas. I

Bug#995415: unblock: theano/1.0.5+dfsg-3 - not really a regression

2021-09-30 Thread Rebecca N. Palmer
Package: release.debian.org User: release.debian@packages.debian.org Usertags: unblock Severity: normal theano 1.0.5+dfsg-3 is currently held in unstable for an autopkgtest "regression" on armhf. The test in question (smoketestgpu) is currently skipped in plain testing because it depends

Bug#995415: unblock: theano/1.0.5+dfsg-3 - not really a regression

2021-09-30 Thread Rebecca N. Palmer
Package: release.debian.org User: release.debian@packages.debian.org Usertags: unblock Severity: normal theano 1.0.5+dfsg-3 is currently held in unstable for an autopkgtest "regression" on armhf. The test in question (smoketestgpu) is currently skipped in plain testing because it depends

Bug#974792: beignet FTBFS with llvm-toolchain-11

2021-09-30 Thread Rebecca N. Palmer
I'm not aware of a fix for this, and beignet is abandoned upstream and mostly useful for old hardware (on newer hardware it is replaced by intel-opencl-icd). However, I may look at it more later (and at least try llvm-toolchain-12, though I'd expect that to be worse if anything). Hence, I'm

Bug#974789: beignet FTBFS with llvm-toolchain-11

2021-09-30 Thread Rebecca N. Palmer
I'm not aware of a fix for this, and beignet is abandoned upstream and mostly useful for old hardware (on newer hardware it is replaced by intel-opencl-icd). However, I may look at it more later (and at least try llvm-toolchain-12, though I'd expect that to be worse if anything). Hence, I'm

Bug#994833: [Pkg-opencl-devel] Bug#994833: OpenCL programs abort when intel-opencl-icd is installed

2021-09-22 Thread Rebecca N. Palmer
On 22/09/2021 07:32, Andreas Beckmann wrote: We will proably still run into problems if different ICDs built against different LLVM versions are going to be loaded at the same time (e.g. pocl/llvm9 and intel/llvm1x) because the different llvm versions seem to stomp on each others internal

Bug#994833: [Pkg-opencl-devel] Bug#994833: OpenCL programs abort when intel-opencl-icd is installed

2021-09-22 Thread Rebecca N. Palmer
On 22/09/2021 07:32, Andreas Beckmann wrote: We will proably still run into problems if different ICDs built against different LLVM versions are going to be loaded at the same time (e.g. pocl/llvm9 and intel/llvm1x) because the different llvm versions seem to stomp on each others internal

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
There's also this test failure on arm64 (which is at least a crash not a wrong answer), again with clblast not clblas. It probably isn't a new problem either: the tests were previously run with clblas only. (The "regression" on ppc64el is that the test has never been installable there and

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
There's also this test failure on arm64 (which is at least a crash not a wrong answer), again with clblast not clblas. It probably isn't a new problem either: the tests were previously run with clblas only. (The "regression" on ppc64el is that the test has never been installable there and

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
There's also this test failure on arm64 (which is at least a crash not a wrong answer), again with clblast not clblas. It probably isn't a new problem either: the tests were previously run with clblas only. (The "regression" on ppc64el is that the test has never been installable there and

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
Control: retitle -1 libgpuarray: *gemv broken on libclblast For now I have disabled *gemv when used with libclblast, to make this bug an explicit error rather than a silently wrong answer. These functions are still available with clblas, but that has enough other issues

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
Control: retitle -1 libgpuarray: *gemv broken on libclblast For now I have disabled *gemv when used with libclblast, to make this bug an explicit error rather than a silently wrong answer. These functions are still available with clblas, but that has enough other issues

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
Control: retitle -1 libgpuarray: *gemv broken on libclblast For now I have disabled *gemv when used with libclblast, to make this bug an explicit error rather than a silently wrong answer. These functions are still available with clblas, but that has enough other issues

Bug#993107: theano: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-29 Thread Rebecca N. Palmer
Control: tags -1 pending This is the same underlying problem as #992673, but for this one it looks like switching to clblast is enough to pass the tests we actually run. (Which isn't all of them because the GPU part of theano has never fully worked under OpenCL, but we already warn the user

Bug#993107: theano: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-29 Thread Rebecca N. Palmer
Control: tags -1 pending This is the same underlying problem as #992673, but for this one it looks like switching to clblast is enough to pass the tests we actually run. (Which isn't all of them because the GPU part of theano has never fully worked under OpenCL, but we already warn the user

Bug#993107: theano: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-29 Thread Rebecca N. Palmer
Control: tags -1 pending This is the same underlying problem as #992673, but for this one it looks like switching to clblast is enough to pass the tests we actually run. (Which isn't all of them because the GPU part of theano has never fully worked under OpenCL, but we already warn the user

Bug#992673: libgpuarray: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-22 Thread Rebecca N. Palmer
clblas has been replaced by clblast, so I tried switching to that, but doing so makes a varying number of cases of test_gemv fail, e.g. == FAIL: pygpu.tests.test_blas.test_gemv((128, 50), 'float32', 'c', True, False, 2, True,

Bug#992673: libgpuarray: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-22 Thread Rebecca N. Palmer
clblas has been replaced by clblast, so I tried switching to that, but doing so makes a varying number of cases of test_gemv fail, e.g. == FAIL: pygpu.tests.test_blas.test_gemv((128, 50), 'float32', 'c', True, False, 2, True,

Bug#992673: libgpuarray: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-22 Thread Rebecca N. Palmer
clblas has been replaced by clblast, so I tried switching to that, but doing so makes a varying number of cases of test_gemv fail, e.g. == FAIL: pygpu.tests.test_blas.test_gemv((128, 50), 'float32', 'c', True, False, 2, True,

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