Bug#1053946: tqdm: FTBFS with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:tqdm Version: 4.64.1-1 Control: block 1043240 by -1 tqdm fails to build with pandas 2.1, currently in experimental. Log: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p1/+build/26770822/+files/buildlog_ubuntu-mantic-amd64.tqdm_4.64.1-1_BUILDING.txt.gz A common source

Bug#1053947: dask: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:dask Version: 2023.8.0+dfsg-2 Control: block 1043240 by -1 dask fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dask/38997774/log.gz A common source of failures is new pandas FutureWarnings in tests that

Bug#1053945: seaborn: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:seaborn Version: 0.12.2-1 Control: block 1043240 by -1 seaborn fails its tests with pandas 2.1, currently in experimental. Logs: https://ci.debian.net/data/autopkgtest/unstable/amd64/s/seaborn/38997875/log.gz https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p1/+build/267

Bug#1053944: q2-types: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:q2-types Version: 2023.7.0-1 Control: block 1043240 by -1 q2-types fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-types/38997869/log.gz A common source of failures is new pandas FutureWarnings in tes

Bug#1053943: q2-taxa: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:q2-taxa Version: 2023.7.0+dfsg-1 Control: block 1043240 by -1 q2-taxa fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-taxa/38997868/log.gz A common source of failures is new pandas FutureWarnings in t

Bug#1053942: q2-demux: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:q2-demux Version: 2023.7.0+dfsg-1 Control: block 1043240 by -1 q2-demux fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-demux/38997862/log.gz A common source of failures is new pandas FutureWarnings i

Bug#1053941: python-geopandas: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:python-geopandas Version: 0.14.0-1 Control: block 1043240 by -1 python-geopandas fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-geopandas/38997837/log.gz A common source of failures is new pand

Bug#1053940: python-cooler: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:python-cooler Version: 0.9.1-1 Control: block 1043240 by -1 python-cooler fails its autopkgtest with pandas 2.1, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-cooler/38997833/log.gz A common source of failures is new pandas FutureW

Bug#1053939: pymatgen: test failure with pandas 2.1

2023-10-14 Thread Rebecca N. Palmer
Package: src:pymatgen Version: 2023.06.23+dfsg1-2 Control: block 1043240 by -1 pymatgen fails its tests with pandas 2.1, currently in experimental. Logs: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/pymatgen/38997822/log.gz https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas

Bug#1043240: transition: pandas 1.5 -> 2.1

2023-10-14 Thread Rebecca N. Palmer
Control: retitle -1 transition: pandas 1.5 -> 2.1 pandas 2.1 is now in experimental. In addition to the above, it breaks these packages: astropy dask patsy pymatgen python-cooler python-geopandas q2-demux q2-taxa q2-types seaborn tqdm and maybe python-hypothesis. (python-pauvre and sunpy are

Bug#1053672: Apple copyright notices in test .xlsx files

2023-10-08 Thread Rebecca N. Palmer
Source: openpyxl Version: 3.0.9-2 Severity: serious licensecheck -r --copyright . on openpyxl finds these: ./openpyxl/formatting/tests/data/conditional-formatting.xlsx: UNKNOWN [Copyright: 2007 Apple Inc.] ./openpyxl/reader/tests/data/complex-styles.xlsx: UNKNOWN [Copyright: 2007 Apple Inc.]

Bug#1052454: numexpr: unnecessarily disables security check

2023-09-22 Thread Rebecca N. Palmer
Package: python3-numexpr Version: 2.8.6-2 Severity: serious Justification: block testing migration of a known security hole Tags: patch numexpr 2.8.5 introduced a security check, which was initially buggy enough to break pyfai and pandas (#1049326). Fixes for this were sent upstream, but only

Bug#1051234: tabulate: too old for pandas 2.1

2023-09-04 Thread Rebecca N. Palmer
Salsa has 0.8.10, but it's been there for some time and I don't know why it hasn't been uploaded.

Bug#1051234: tabulate: too old for pandas 2.1

2023-09-04 Thread Rebecca N. Palmer
Package: python3-tabulate Version: 0.8.9-1 Severity: wishlist Upstream pandas 2.1 will only use tabulate >= 0.8.10. Nothing obviously breaks if I override this to accept Debian's 0.8.9, but it might be better to actually update tabulate. (At least to the latest 0.8.x - I don't know whether g

Bug#1051233: openpyxl: too old for pandas 2.1

2023-09-04 Thread Rebecca N. Palmer
Package: python3-openpyxl Version: 3.0.9-2 Severity: wishlist Control: affects -1 python3-pandas Upstream pandas 2.1 will only use openpyxl >= 3.0.10. If I override this to accept Debian's 3.0.9, I get 2 test failures that plausibly might be caused by it (but I haven't actually tried it with a

Bug#1050693: sphinx: unreproducible output if the same function has two entries in the table of contents

2023-08-28 Thread Rebecca N. Palmer
Package: python3-sphinx Version: 5.3.0-7 Severity: wishlist User: reproducible-bui...@lists.alioth.debian.org Usertags: fileordering When the same function has two entries in the table of contents, that function's documentation page may be generated with the table of contents open to either of

Bug#1050619: nbclient: unreproducible output - iopub.* timestamps

2023-08-27 Thread Rebecca N. Palmer
Package: python3-nbclient Version: 0.8.0-1 Severity: wishlist Tags: patch User: reproducible-bui...@lists.alioth.debian.org Usertags: timestamps By default, nbclient includes timestamps in its output, which makes packages built with it (e.g. python-pandas-doc) unreproducible. It provides a rec

Bug#1031414: not fixed Re: libgpuarray: i386 test fail with new pocl

2023-08-21 Thread Rebecca N. Palmer
Control: severity -1 serious That wasn't a fix - log with pocl 4: https://ci.debian.net/data/autopkgtest/testing/i386/libg/libgpuarray/37023715/log.gz

Bug#1050144: emperor: FTBFS with pandas 2.0

2023-08-20 Thread Rebecca N. Palmer
Package: src:emperor Version: 1.0.3+ds-7 Control: block 1043240 by -1 emperor fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/682917876/buildlog_ubuntu-mantic-amd64.emperor_1.0.3+ds-7_BUILDING.txt.gz A common source of failures is that pandas

Bug#1045316: snakemake: clean broken

2023-08-20 Thread Rebecca N. Palmer
Control: tags -1 pending Fixed in Salsa, but please do NOT upload that version as-is (it FTBFS for an unrelated reason).

Bug#1033907: numba crashes on non-x86

2023-08-19 Thread Rebecca N. Palmer
numba also crashes on mips64el, mipsel and armhf (and s390x but that was already known; not amd64, i386 or ppc64el). However, I agree that arm64 is a good place to start trying to fix this, given how common it is. For examples, see the pandas 2.0.3+dfsg-3 / 1.5.3+dfsg-5 build logs. Given the

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
On further thought, both of those probably should be fixed in numexpr - I have pushed them to fix1049326. With those changes to numexpr, the new pandas (1.5.3+dfsg-5) should build; pytables will still also need its upstream fix.

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
stringToExpression() in this numexpr patch needs a default of True for sanitize (like the others already have), because pytables calls that directly: https://salsa.debian.org/science-team/pandas/-/jobs/4571451/raw (The other failure in there is one I plan to fix.) The two pytables tests with

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
Given that this is a security feature and we hence want it in quickly, I'd consider that patch enough to xfail/disable the remaining issues in pandas, but discussions with upstream are ongoing. (It also won't do anything about the pytables breakage, known upstream as #1044.)

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-16 Thread Rebecca N. Palmer
I pushed this fix to Salsa as the 'fix1049326' branch - it isn't enough to fix pandas by itself, but is plausibly an improvement.

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 Thread Rebecca N. Palmer
Numexpr upstream have what they think is a fix for the exception issue (though not the overflow change), but it hasn't been tested yet: https://github.com/pydata/numexpr/issues/442

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 Thread Rebecca N. Palmer
Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/54546 Control: affects -1 python3-pandas There's actually *two* bugs here: an exception in eval/query, https://github.com/pandas-dev/pandas/issues/54449, and a changed result with integer overflow, https://github.com/pandas-dev/p

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 Thread Rebecca N. Palmer
Package: python3-numexpr Version: 2.8.5-1 Severity: serious Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/54449 (actually they found it first) I only have actual logs for 2.0.x, but I suspect 1.5.x is also affected. As a short term fix, it may be possible to disable pandas' n

Bug#1043968: How to handle upstream dependencies on PyPI tzdata?

2023-08-13 Thread Rebecca N. Palmer
Note also that PyPI tzdata includes old timezone names (US/Eastern etc) that were recently moved to tzdata-legacy in Debian, and that the pandas tests/examples heavily use these names.

Bug#1044079: augur: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:augur Version: 22.1.0-1 Control: block 1043240 by -1 augur fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680698719/buildlog_ubuntu-mantic-amd64.augur_22.1.0-1_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/autopkgt

Bug#1044078: cnvkit: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:cnvkit Version: 0.9.9-2 Control: block 1043240 by -1 cnvkit fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680699189/buildlog_ubuntu-mantic-amd64.cnvkit_0.9.9-2_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/autopkg

Bug#1044077: esda: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:esda Version: 2.4.3-4 Control: block 1043240 by -1 esda fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680699664/buildlog_ubuntu-mantic-amd64.esda_2.4.3-4_BUILDING.txt.gz A common source of failures is that pandas.util.testing h

Bug#1044076: influxdb-python: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:influxdb-python Version: 5.3.1-3 Control: block 1043240 by -1 influxdb-python fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680700174/buildlog_ubuntu-mantic-amd64.influxdb-python_5.3.1-3_BUILDING.txt.gz A common source of failu

Bug#1044075: jsonpickle: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:jsonpickle Version: 3.0.0+dfsg1-1 Control: block 1043240 by -1 jsonpickle fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680700300/buildlog_ubuntu-mantic-amd64.jsonpickle_3.0.0+dfsg1-1_BUILDING.txt.gz Autopkgtest log: https://ci

Bug#1044074: python-biom-format: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-biom-format Version: 2.1.12-3build1 Control: block 1043240 by -1 python-biom-format fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701317/buildlog_ubuntu-mantic-amd64.python-biom-format_2.1.12-3build1_BUILDING.txt.gz

Bug#1044073: python-altair: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-altair Version: 4.2.0-1 Control: block 1043240 by -1 python-altair fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701318/buildlog_ubuntu-mantic-amd64.python-altair_4.2.0-1_BUILDING.txt.gz A common source of failures is

Bug#1044072: python-anndata: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-anndata Version: 0.8.0-4 Control: block 1043240 by -1 python-anndata fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701368/buildlog_ubuntu-mantic-amd64.python-anndata_0.8.0-4_BUILDING.txt.gz Autopkgtest log: https://ci

Bug#1044071: python-feather-format: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-feather-format Version: 0.3.1+dfsg1-6build1 Control: block 1043240 by -1 python-feather-format fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701469/buildlog_ubuntu-mantic-amd64.python-feather-format_0.3.1+dfsg1-6buil

Bug#1044070: python-pauvre: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-pauvre Version: 0.2.3-2 Control: block 1043240 by -1 python-pauvre fails to build with pandas 2.0, currently in experimental. https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p0/+build/26483328 (I don't know why the build log is missing.) A common source of failu

Bug#1044069: python-upsetplot: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-upsetplot Version: 0.8.0-1 Control: block 1043240 by -1 python-upsetplot fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701778/buildlog_ubuntu-mantic-amd64.python-upsetplot_0.8.0-1_BUILDING.txt.gz Autopkgtest log: http

Bug#1044068: q2templates: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2templates Version: 2022.11.1+ds-2 Control: block 1043240 by -1 q2templates fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680701792/buildlog_ubuntu-mantic-amd64.q2templates_2022.11.1+ds-2_BUILDING.txt.gz Autopkgtest log: https

Bug#1044067: sklearn-pandas: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:sklearn-pandas Version: 2.2.0-1.1 Control: block 1043240 by -1 sklearn-pandas fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680702008/buildlog_ubuntu-mantic-amd64.sklearn-pandas_2.2.0-1.1_BUILDING.txt.gz A common source of fail

Bug#1044066: python-pyani: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-pyani Version: 0.2.12-2 Control: block 1043240 by -1 python-pyani fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680702373/buildlog_ubuntu-mantic-amd64.python-pyani_0.2.12-2_BUILDING.txt.gz Autopkgtest log: https://ci.deb

Bug#1044065: python-skbio: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-skbio Version: 0.5.8-4 Control: block 1043240 by -1 python-skbio fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680702984/buildlog_ubuntu-mantic-amd64.python-skbio_0.5.8-4_BUILDING.txt.gz Autopkgtest log: https://ci.debia

Bug#1044064: pyranges: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:pyranges Version: 0.0.111+ds-4 Control: block 1043240 by -1 pyranges fails to build with pandas 2.0, currently in experimental. Build log: https://launchpadlibrarian.net/680704234/buildlog_ubuntu-mantic-amd64.pyranges_0.0.111+ds-4_BUILDING.txt.gz (This isn't just #1042046 - it fail

Bug#1044063: q2-types: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2-types Version: 2022.11.1-2 Control: block 1043240 by -1 q2-types fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-types/36575888/log.gz A common source of failures is that pandas.util.testing has be

Bug#1044061: q2-taxa: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2-taxa Version: 2022.11.1+dfsg-2 Control: block 1043240 by -1 q2-taxa fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-taxa/36575887/log.gz A common source of failures is that pandas.util.testing has

Bug#1044060: q2-quality-control: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2-quality-control Version: 2022.11.1-2 Control: block 1043240 by -1 q2-quality-control fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-quality-control/36575885/log.gz A common source of failures is

Bug#1044059: q2-demux: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2-demux Version: 2022.11.1+dfsg-2 Control: block 1043240 by -1 q2-demux fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-demux/36575881/log.gz A common source of failures is that pandas.util.testing h

Bug#1044058: q2-cutadapt: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:q2-cutadapt Version: 2022.11.1-2 Control: block 1043240 by -1 q2-cutadapt fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-cutadapt/36575880/log.gz A common source of failures is that pandas.util.tes

Bug#1044057: python-ulmo: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-ulmo Version: 0.8.8+dfsg1-1.1 Control: block 1043240 by -1 python-ulmo fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-ulmo/36575876/log.gz A common source of failures is that pandas.util

Bug#1044056: python-nanoget: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:python-nanoget Version: 1.16.1-2 Control: block 1043240 by -1 python-nanoget fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-nanoget/36575861/log.gz A common source of failures is that pandas.ut

Bug#1044055: mirtop: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:mirtop Version: 0.4.25-3 Control: block 1043240 by -1 mirtop fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/m/mirtop/36575823/log.gz A common source of failures is that pandas.util.testing has been rename

Bug#1044054: dyda: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:dyda Version: 1.41.1-1.1 Control: block 1043240 by -1 dyda fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dyda/36575804/log.gz A common source of failures is that pandas.util.testing has been renamed t

Bug#1044052: xarray-sentinel: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:xarray-sentinel Version: 0.9.5+ds-1 Control: block 1043240 by -1 xarray-sentinel fails to build with pandas 2.0, currently in experimental. Build log: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p0/+build/26483387/+files/buildlog_ubuntu-mantic-amd64.xarray-sentinel_

Bug#1044053: dials: test failure with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:dials Version: 3.12.1+dfsg3-5 Control: block 1043240 by -1 dials fails its autopkgtest with pandas 2.0, currently in experimental. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dials/36575801/log.gz A common source of failures is that pandas.util.testing has been ren

Bug#1044050: intake: FTBFS with pandas 2.0

2023-08-13 Thread Rebecca N. Palmer
Package: src:intake Version: 0.6.6-1 Control: block 1043240 by -1 intake fails to build with pandas 2.0, currently in experimental. Build log: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p0/+build/26483259/+files/buildlog_ubuntu-mantic-amd64.intake_0.6.6-1_BUILDING.txt.gz A com

Bug#1043240: transition: pandas 1.5 -> 2.0/2.1

2023-08-13 Thread Rebecca N. Palmer
dask has now been updated to a pandas 2 compatible version, allowing me to test its reverse dependencies. This found that intake and xarray-sentinel are broken by pandas 2, while python-xarray is already broken for other reasons. A common source of failures is that pandas.util.testing has bee

Bug#1043968: How to handle upstream dependencies on PyPI tzdata?

2023-08-13 Thread Rebecca N. Palmer
Package: python3-pandas Version: 2.0.3+dfsg-1 Control: notfound -1 1.5.3+dfsg-4 Control: block 1043240 by -1 python3-pip and similar Python tools usually count system python3-X as satisfying Python dependencies on X. Hence, upstream build scripts that attempt to pip install X can usually work

Bug#1043240: transition: pandas 1.5 -> 2.0

2023-08-07 Thread Rebecca N. Palmer
These packages appear to be broken *by* pandas 2.0 - I will file individual bugs when I have time: augur cnvkit dask dials dyda emperor esda influxdb-python jsonpickle macsyfinder mirtop mlpack pyranges python-altair python-anndata python-biom-format python-feather-format python-nanoget python-p

Bug#1043240: transition: pandas 1.5 -> 2.0

2023-08-07 Thread Rebecca N. Palmer
Package: python3-pandas Version: 1.5.3+dfsg-4 Severity: wishlist Control: block -1 by 1043093 pandas 2.0 is now in experimental. However (as you might expect from that version number), it breaks around 40 other packages, and it is hence likely to be some time before it moves to unstable. Ups

Bug#1043048: Please give back statsmodels on mips64el Re: (Bug#1043048: fixed in openblas 0.3.23+ds-3)

2023-08-07 Thread Rebecca N. Palmer
This does seem to have worked: the openblas build log no longer contains FATAL ERROR. Hence, please give back statsmodels on mips64el. (DMs aren't allowed to use the self-service link.)

Bug#1043093: dask: test fail with pandas 2.0

2023-08-05 Thread Rebecca N. Palmer
Package: python3-dask Version: 2022.12.1+dfsg-2 Tags: fixed-upstream pandas 2.0's test_dask fails (in Salsa CI). Upstream reports suggest that this is fixed in dask 2023.2, but I haven't checked whether upgrading dask breaks anything else. https://github.com/dask/dask/issues/10164 (I also co

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
Control: tags -1 upstream Upstream CI's mips64 qemu test has what look like the same FATAL ERRORs, in MIPS64_GENERIC but not SICORTEX, but is still listed as passing. Which suggests that they also have both parts of this bug (wrong answers on mips64el, and errors not actually failing the buil

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
The most obviously relevant change between those is that the installed BLAS changed from atlas to openblas. It looks like this wasn't a change of default, but that experimental uses libatlas and unstable uses libopenblas. (I don't know why, as the obvious dependency chain is src:statsmodels -

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
Package: libopenblas0-pthread Version: 0.3.23+ds-2 Control: affects -1 src:statsmodels Severity: serious Justification: the default BLAS should NOT silently give wrong answers (i.e. if there's no easy way to actually fix this, please switch the default on mips64el back to atlas, and consider remo

Bug#1042574: Removed package(s) from unstable

2023-08-04 Thread Rebecca N. Palmer
Control: reopen -1 Please also remove theano from experimental.

Bug#1042574: RM: theano -- RoM, broken by numpy 1.24, theano mostly abandoned upstream

2023-07-31 Thread Rebecca N. Palmer
Control: retitle -1 RM: theano -- RoM; broken, mostly abandoned On 31/07/2023 13:49, Andrius Merkys wrote: Maybe it is worth to keep src:keras for the time being, until keras 3 arrives? Similar things have happened before - src:llvm-toolchain-9 was removed well before src:beignet, making src:

Bug#1042574: RM: theano, keras, deepnano -- RoM (theano), broken by numpy 1.24, theano mostly abandoned upstream

2023-07-30 Thread Rebecca N. Palmer
Package: ftp.debian.org User: ftp.debian@packages.debian.org Usertags: remove Control: affects -1 src:theano src:deepnano src:keras Control: reopen 1026539 Control: reopen 1027215 theano has been mostly abandoned upstream since 2018. (The Aesara fork is not abandoned, but includes interface

Bug#1042043: pandas: FTBFS: failed tests

2023-07-25 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream patch This is probably caused by the new fsspec version, and is also seen in autopkgtest: https://ci.debian.net/data/autopkgtest/testing/amd64/p/pandas/36146393/log.gz Upstream fix: https://github.com/pandas-dev/pandas/commit/ce9e3d658d6efa3600a4563ca7a00e7a15b8

Bug#1041805: Acknowledgement (RM: beignet -- RoM; FTBFS with LLVM > 9, mostly replaced by intel-opencl-icd)

2023-07-23 Thread Rebecca N. Palmer
sorry, discussion on pkg-opencl-devel / debian-devel around 19 June, not actually in #974792

Bug#1041805: RM: beignet -- RoM; FTBFS with LLVM > 9, mostly replaced by intel-opencl-icd

2023-07-23 Thread Rebecca N. Palmer
Package: ftp.debian.org beignet FTBFS with LLVM > 9 (#974792), and hence cannot be built in current unstable. (The existing package probably still works, because beignet statically links LLVM to avoid #852746, but unbuildable packages are unreleasable by policy.) beignet is abandoned upstre

Bug#1041803: hyperspy: FTBFS test_image fails

2023-07-23 Thread Rebecca N. Palmer
Package: hyperspy Version: 1.7.3-1 Severity: serious hyperspy currently FTBFS with several failing tests: https://launchpadlibrarian.net/678551154/buildlog_ubuntu-mantic-amd64.hyperspy_1.7.3-1_BUILDING.txt.gz

Bug#1027215: Proposed RM: theano, keras, deepnano -- broken by numpy 1.24, theano mostly abandoned upstream

2023-07-23 Thread Rebecca N. Palmer
Control: reopen -1 1026539 theano has been mostly abandoned upstream since 2018. (The Aesara fork is not abandoned, but includes interface changes including the import name, so would break reverse dependencies not specifically altered for it.) It is currently broken (FTBFS due to multiple te

Bug#974792: Proposed RM: beignet -- RoM; FTBFS with LLVM > 9, replaced by intel-opencl-icd

2023-06-19 Thread Rebecca N. Palmer
Additional information: As a rough estimate of how much speed this would cost on older hardware, I previously measured beignet as 8-16x faster than pocl (but this will obviously depend on hardware and application). However, beignet (on hardware that can't use intel-opencl-icd) is limited to s

Bug#974792: Proposed RM: beignet -- RoM; FTBFS with LLVM > 9, replaced by intel-opencl-icd

2023-06-18 Thread Rebecca N. Palmer
beignet FTBFS with LLVM > 9 (#974792). beignet uses libllvm/libclang heavily enough that it usually has this kind of bug on a new LLVM release, but this time my attempts to fix it failed (see the Salsa CI logs). It is abandoned upstream and mostly replaced by intel-opencl-icd. (This is not a

Bug#1033589: python3-theano: module 'numpy' has no attribute 'bool'.

2023-03-27 Thread Rebecca N. Palmer
While that particular problem is easy to fix, there are other incompatibilities that aren't (see #1026539, #1027215) and I intend to let autoremoval happen.

Bug#1031414: [Pkg-opencl-devel] Bug#1031414: libgpuarray: i386 test fail with new pocl

2023-03-14 Thread Rebecca N. Palmer
On 14/03/2023 10:29, Andreas Beckmann wrote: This should have been addressed in pyopencl. Do you mean pocl or did you intend to send that to #1030298?

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

2023-03-03 Thread Rebecca N. Palmer
On 03/03/2023 06:00, Andreas Tille wrote: Ahh, so aesara is not really a "fork" but a "rename"? The original is abandoned (no new development since 2017, and now mostly unmaintained, which is probably why it has this kind of bug). Aesara is a continuation by a new upstream (possibly one that

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

2023-03-02 Thread Rebecca N. Palmer
On 02/03/2023 10:38, Andreas Tille wrote: I admit I do not see any good reason to stick to the old version if we decided before that keras/deepnano are no real blockers to even drop theano. Thus I was considering it more promising to spent my time on the latest version. 1.1.2 isn't the latest

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

2023-03-01 Thread Rebecca N. Palmer
I agree that switching to Aesara is probably the only reasonable option other than removal. (I'd given up on trying to fix 1.0, and was intending to let removal happen.) However, it's a much bigger change than is normally allowed in bookworm at this point. (1.1 includes multiple breaking cha

Bug#1031701: python3-pandas: Pandas requires version '2.0.1' or newer of 'xlrd'

2023-02-26 Thread Rebecca N. Palmer
I don't consider the lack of .xls in pandas worth a freeze exception, but consider it reasonable for others to disagree with that. As noted in the bug, there are some (possibly not-technically-valid) .xlsx files that xlrd 1 can open but openpyxl can't - _pandas_ won't be able to open those eit

Bug#1031701: python3-pandas: Pandas requires version '2.0.1' or newer of 'xlrd'

2023-02-21 Thread Rebecca N. Palmer
Control: reassign -1 python3-xlrd Control: affects -1 python3-pandas Control: retitle -1 pandas can't open xls (not xlsx) files, xlrd too old Then yes, you do need xlrd. As Debian is currently in freeze, I suggest installing it from PyPI (warning, this doesn't automatically install security up

Bug#1031706: optuna: test_create_new_trial randomly fails on s390x

2023-02-20 Thread Rebecca N. Palmer
Package: python3-optuna Severity: serious Control: affects -1 python3-pandas test_create_new_trial (both parts) sometimes fails on s390x, failing the autopkgtest. It might make sense to remove this package on s390x, if it isn't reasonable to actually fix this.

Bug#1031705: pymatgen: 7th item of test_babel randomly hangs autopkgtest

2023-02-20 Thread Rebecca N. Palmer
Package: python3-pymatgen Severity: serious Control: affects -1 python3-pandas The autopkgtest sometimes times out, and when it does, the last line is io/tests/test_babel.py and 6 'pass' dots, implying that the 7th item hung. All known instances are on amd64.

Bug#1031701: python3-pandas: Pandas requires version '2.0.1' or newer of 'xlrd'

2023-02-20 Thread Rebecca N. Palmer
Is the file you're trying to open .xlsx or .xls? Do you have python3-openpyxl installed? If .xlsx and no, try installing it. (python3-)xlrd 2.0+ can only open .xls files, not .xlsx. Hence, pandas 1.5+ read_excel() always uses (python3-)openpyxl for .xlsx files. python3-pandas already Recomm

Bug#1031414: clinfo breaks libgpuarray autopkgtest on i386: numerical deltas

2023-02-17 Thread Rebecca N. Palmer
Possibly useful here: gdb disassemble works inside pocl kernels, see #920497 for an example.

Bug#1031414: clinfo breaks libgpuarray autopkgtest on i386: numerical deltas

2023-02-16 Thread Rebecca N. Palmer
Control: reassign -1 src:pocl,src:libgpuarray Control: found -1 pocl/3.1-3 Control: found -1 libgpuarray/0.7.6-13 Control: retitle -1 libgpuarray: i386 test fail with new pocl The trigger is probably pocl, not clinfo. I don't yet know whether the bug is in pocl or libgpuarray.

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-10 Thread Rebecca N. Palmer
On 10/02/2023 06:41, Andreas Tille wrote: Am Fri, Feb 10, 2023 at 08:44:01AM +0530 schrieb Nilesh Patra: But I am not sure if this counter would be set to 2 days (from 5 days) or not -- will likely need to ask release team. As far as I observed the migration time is now 5 days (no matter wheth

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-09 Thread Rebecca N. Palmer
Upstream's reason for treating warnings as errors is just generic 'find potential problems' (https://github.com/dask/distributed/issues/6048). On 09/02/2023 21:33, Diane Trout wrote: That worked, but armel (test_steal_twice), armhf (something outright crashing) and s390x (lots) all failed. Ar

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-09 Thread Rebecca N. Palmer
On 09/02/2023 21:33, Diane Trout wrote: The place to ask is debian-release; no comment on the likely result. I'll try to ask. Looking at the old logs, I think the old "passing" test *didn't actually run* the tests (just collected them, which was enough to fail on a dask/dask.distributed mi

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-09 Thread Rebecca N. Palmer
On 09/02/2023 17:07, Diane Trout wrote: Would it make sense to drop those errors back to warnings, and do you know enough about the setup.cfg language to do it quickly? Plausibly yes but I don't actually know, and remove the 'error' line at setup.cfg:60. I went ahead and requested anoth

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-08 Thread Rebecca N. Palmer
On 09/02/2023 06:36, Diane Trout wrote: Also there's still some flaky tests as the rebuild triggered by my just committing the changelog release had a failure in "test_release_retry" I don't think I've seen that particular one before, though like several others it's a warning being treated as

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-08 Thread Rebecca N. Palmer
On 08/02/2023 22:09, Diane Trout wrote: I just got back a passed from salsa. So does anyone want to make any more changes? Or should we release this version? The *maybe* remaining issue is that test_balance_expensive_tasks[enough work to steal] seems to fail repeatedly when it fails, so if we wa

Bug#1030096: dask.distributed intermittent autopkgtest fail

2023-02-08 Thread Rebecca N. Palmer
I think I got the code to detect if IPv6 is available to work correctly so I could set the DISABLE_IPV6 environment variable that dask.distrubted supports. This probably refers to https://salsa.debian.org/python-team/packages/dask.distributed/-/blob/debian/master/debian/tests/run-tests#L11 T

Bug#1030096: Any ideas Re: #1030096 dask.distributed intermittent autopkgtest fail ?

2023-02-06 Thread Rebecca N. Palmer
On 07/02/2023 03:20, Diane Trout wrote: What's your test environment like? Salsa CI. I don't think head is hugely different from what was released in -1. The diff looks like Andreas adjusted the dask dependency version, configured a salsa CI run, and added some upstream metadata files That

Bug#1030096: Any ideas Re: #1030096 dask.distributed intermittent autopkgtest fail ?

2023-02-06 Thread Rebecca N. Palmer
I agree that xfailing the tests *may* be a reasonable solution. I'm only saying that it should be done by someone with more idea than me of whether these particular tests are important, because blindly xfailing everything that fails is effectively not having tests. If we do choose that approa

Bug#1030096: Any ideas Re: #1030096 dask.distributed intermittent autopkgtest fail ?

2023-02-06 Thread Rebecca N. Palmer
(Background: the pandas + dask transition broke dask.distributed and it was hence removed from testing; I didn't notice at the time that if we don't get it back in we lose Spyder.) On 05/02/2023 21:44, Rebecca N. Palmer wrote: I currently have this in a state where it sometimes su

Bug#1030096: #1030096 dask.distributed autopkgtest fail

2023-02-05 Thread Rebecca N. Palmer
I currently have this in a state where it sometimes succeeds and sometimes doesn't: https://salsa.debian.org/rnpalmer-guest/dask.distributed/-/tree/fix1030096 Tests I've seen to fail multiple times (and don't have a fix for): test_balance_expensive_tasks[enough work to steal] https://salsa.debia

Bug#1030096: #1030096 dask.distributed autopkgtest fail

2023-02-04 Thread Rebecca N. Palmer
That removed most of the test failures, but there seem to be a few apparently random ones left (2 runs both failed, but with different errors). On 04/02/2023 21:35, Andreas Tille wrote: Any reason to not push to master directly? I don't do that with packages that aren't mine. Also see above.

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