Package: python3-pandas
Version: 2.1.4+dfsg-7
Severity: wishlist
Upstream have released pandas 2.2.
(Filing this now to have a bug number - I haven't actually uploaded to
experimental yet.)
Reverse dependencies to be tested:
abinit astropy augur azure-kusto-python bmtk bqplot busco
Package: python3-pandas
Version: 2.1.4+dfsg-7
Severity: wishlist
Upstream have released pandas 2.2.
(Filing this now to have a bug number - I haven't actually uploaded to
experimental yet.)
Reverse dependencies to be tested:
abinit astropy augur azure-kusto-python bmtk bqplot busco
Source: topplot
Version: 0.2.2+repack-1
Tags: patch
Severity: serious
Justification: blocks testing migration of other packages
topplot tries to run its autopkgtest in all versions of Python (which is
good), but does not test-depend on all those versions of Python.
This previously worked
Source: topplot
Version: 0.2.2+repack-1
Tags: patch
Severity: serious
Justification: blocks testing migration of other packages
topplot tries to run its autopkgtest in all versions of Python (which is
good), but does not test-depend on all those versions of Python.
This previously worked
This bug is not *obviously* known to dask upstream, but their CI is
failing and I haven't checked why.
It happens only in Python 3.12, not 3.11:
https://ci.debian.net/packages/d/dask/unstable/amd64/45013666/
and still doesn't happen in testing, but does happen in mostly-testing
with
This bug is not *obviously* known to dask upstream, but their CI is
failing and I haven't checked why.
It happens only in Python 3.12, not 3.11:
https://ci.debian.net/packages/d/dask/unstable/amd64/45013666/
and still doesn't happen in testing, but does happen in mostly-testing
with
Control: unblock 1068104 by -1
Control: unblock 1068104 by 1068422
To avoid being blocked by this bug, the pandas version I just uploaded
temporarily disables the documentation.
This is also an option for any other affected packages that urgently
need to be uploaded. (I don't know whether
Control: unblock 1068104 by -1
Control: unblock 1068104 by 1068422
To avoid being blocked by this bug, the pandas version I just uploaded
temporarily disables the documentation.
This is also an option for any other affected packages that urgently
need to be uploaded. (I don't know whether
Rebecca N. Palmer pushed new tag debian/7.32.4-3 at Debian Med / snakemake
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Package: python3-dask
Version: 2023.12.1+dfsg-2
Severity: serious
Control: affects -1 src:pandas
Control: block 1068104 by -1
Importing dask.dataframe currently fails with the error
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a
'property' object
amd64
Package: python3-dask
Version: 2023.12.1+dfsg-2
Severity: serious
Control: affects -1 src:pandas
Control: block 1068104 by -1
Importing dask.dataframe currently fails with the error
TypeError: descriptor '__call__' for 'type' objects doesn't apply to a
'property' object
amd64
Control: tags -1 patch
Control: severity -1 serious
(probably makes nbconvert/nbsphinx unusable)
xml-html-clean is in
NEWhttps://ftp-master.debian.org/new/lxml-html-clean_0.1.0-1.html
Thanks - that and adding it to the Depends of python3-nbconvert should
fix this bug.
From codesearch,
Package: python3-nbconvert,python3-lxml
Version: 6.5.3-4,5.2.0-1
Control: affects -1 src:pandas
Control: affects -1 python3-nbsphinx
Control: block 1068104 by -1
The pandas documentation fails to build in current unstable with:
Running Sphinx v7.2.6
nbconvert not installed. Skipping notebooks.
Thanks - I plan to look at this tomorrow.
Thanks - I plan to look at this tomorrow.
Thanks - I plan to look at this tomorrow.
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what's now in Salsa should be.
(but please do *not* upload that right now, it is rather likely to have
(unrelated) issues)
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Control: reopen -1
Control: tags -1 pending
Control: tags 1066801 pending
Control: tags 1064384 pending
Sorry, that wasn't actually a fix, but what's now in Salsa should be.
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Control: reopen -1
Control: tags -1 pending
Control: tags 1066801 pending
Control: tags 1064384 pending
Sorry, that wasn't actually a fix, but what's now in Salsa should be.
Control: retitle -1 pandas: test-failing warning with new xarray
This is a warning being treated as an error, but the one in
test_to_xarray (probably due to the new version of xarray), not the
zoneinfo one. This is a FutureWarning, so it should be OK to *use* the
current pandas with the new
Control: retitle -1 pandas: test-failing warning with new xarray
This is a warning being treated as an error, but the one in
test_to_xarray (probably due to the new version of xarray), not the
zoneinfo one. This is a FutureWarning, so it should be OK to *use* the
current pandas with the new
Control: retitle -1 pandas: test-failing warning with new xarray
This is a warning being treated as an error, but the one in
test_to_xarray (probably due to the new version of xarray), not the
zoneinfo one. This is a FutureWarning, so it should be OK to *use* the
current pandas with the new
Control: forwarded -1 https://github.com/pydata/xarray/issues/7079
(actually found independently)
The above upstream report suggests that this is because netcdf-python is
no longer thread-safe.
The 3 random-autopkgtest-fail bugs (this, #1064326 and #1064370)
together seem to be more common
Control: forwarded -1 https://github.com/pydata/xarray/issues/7079
(actually found independently)
The above upstream report suggests that this is because netcdf-python is
no longer thread-safe.
The 3 random-autopkgtest-fail bugs (this, #1064326 and #1064370)
together seem to be more common
Remaining blockers for testing migration:
- python-ulmo #1044057: has a patch, please upload
- pydevd #1063274: unclear whether my patch breaks something else,
please leave alone for now
Status unclear:
- python-xarray: autopkgtest has failed 3 times, but all 3 are
(different) failures that
Remaining blockers for testing migration:
- python-ulmo #1044057: has a patch, please upload
- pydevd #1063274: unclear whether my patch breaks something else,
please leave alone for now
Status unclear:
- python-xarray: autopkgtest has failed 3 times, but all 3 are
(different) failures that
Is that a yes to>> Does just the patch (not the new upstream) also break
debugpy?or have you not tried specifically that?
(I'm looking for a quick fix for the autopkgtest fail to unblock the
pandas 2.x transition. I agree that upgrading to a new upstream is a
good idea in the long run.)
Is that a yes to>> Does just the patch (not the new upstream) also break
debugpy?or have you not tried specifically that?
(I'm looking for a quick fix for the autopkgtest fail to unblock the
pandas 2.x transition. I agree that upgrading to a new upstream is a
good idea in the long run.)
Package: python3-xarray
Version: 2023.12.0-3
The xarray autopkgtest sometimes (~20% of the time) fails with
RuntimeError: NetCDF: Not a valid ID
in tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw
Unlike the other random failures, this seems to be amd64-specific.
Exactly which
Package: python3-xarray
Version: 2023.12.0-3
The xarray autopkgtest sometimes (~20% of the time) fails with
RuntimeError: NetCDF: Not a valid ID
in tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw
Unlike the other random failures, this seems to be amd64-specific.
Exactly which
Package: python3-xarray
Version: 2023.12.0-3
xarray sometimes (~10% of the time) segfaults in
tests/test_backends.py::test_open_mfdataset_manyfiles, usually
[netcdf4-20-True-None-5] but sometimes [netcdf4-20-True-5-5].
This has happened in both Python 3.11 and 3.12, and on various
Package: python3-xarray
Version: 2023.12.0-3
xarray sometimes (~10% of the time) segfaults in
tests/test_backends.py::test_open_mfdataset_manyfiles, usually
[netcdf4-20-True-None-5] but sometimes [netcdf4-20-True-5-5].
This has happened in both Python 3.11 and 3.12, and on various
Package: python3-xarray
Version: 2023.12.0-3
The xarray autopkgtest sometimes (~10% of the time) hangs in
test_roundtrip_coordinates, and hence fails with a timeout.
Example failure log (but this is _not_ specific to pandas 2.x):
Package: python3-xarray
Version: 2023.12.0-3
The xarray autopkgtest sometimes (~10% of the time) hangs in
test_roundtrip_coordinates, and hence fails with a timeout.
Example failure log (but this is _not_ specific to pandas 2.x):
Thank you for caring about not breaking other packages, and yes, that's
a good reason to not upload that new upstream for now.
Does just the patch (not the new upstream) also break debugpy? (It
shouldn't be able to, since it only touches test code.)
Thank you for caring about not breaking other packages, and yes, that's
a good reason to not upload that new upstream for now.
Does just the patch (not the new upstream) also break debugpy? (It
shouldn't be able to, since it only touches test code.)
This has been merged but not uploaded - is there a reason it shouldn't
be, or have you just not had time?
This has been merged but not uploaded - is there a reason it shouldn't
be, or have you just not had time?
tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part
tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part
tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part
Rebecca N. Palmer pushed new tag debian/7.32.4-2 at Debian Med / snakemake
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Rebecca N. Palmer pushed new tag upstream/8.2.3 at Debian Med / snakemake
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Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake
Commits:
66a8a8a6 by Rebecca N. Palmer at 2024-01-20T10:42:57+00:00
pristine-tar data for snakemake_8.2.3.orig.tar.gz
- - - - -
2 changed files:
- + snakemake_8.2.3.orig.tar.gz.delta
- + snakemake_8.2.3
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake
Commits:
cc1b5000 by Rebecca N. Palmer at 2024-01-20T10:42:31+00:00
New upstream version 8.2.3
- - - - -
30 changed files:
- .github/workflows/docker-publish.yml
- .github/workflows/main.yml
- .github/workflows/release
Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits:
26e21c8f by Rebecca N. Palmer at 2024-02-09T19:11:31+00:00
work around patch not adding empty files
- - - - -
2 changed files:
- debian/changelog
- debian/patches/fstring.patch
Changes
Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits:
a0c4af75 by Rebecca N. Palmer at 2024-02-09T07:52:23+00:00
revert accidental interface change
- - - - -
2 changed files:
- debian/changelog
- debian/patches/fstring.patch
Changes
Control: tags -1 patch
It does sometimes happen that fixing "can't import the tests" reveals
"the tests fail". Fixed in the Salsa merge request.
Control: tags -1 patch
It does sometimes happen that fixing "can't import the tests" reveals
"the tests fail". Fixed in the Salsa merge request.
Control: tags -1 patch
See the Salsa merge request.
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Control: tags -1 patch
See the Salsa merge request.
Control: tags -1 patch
See the Salsa merge request.
Control: tag -1 pending
Hello,
Bug #1061761 in snakemake reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:
Control: tags -1 pending
This appears to be fixed in Salsa (before I reported it) - is there any
reason not to upload this now?
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Control: tags -1 pending
This appears to be fixed in Salsa (before I reported it) - is there any
reason not to upload this now?
Control: tags -1 pending
This appears to be fixed in Salsa (before I reported it) - is there any
reason not to upload this now?
Package: python3-geopandas
Version: 0.14.3-1
Severity: serious
Control: block 1043240 by -1
In pandas 2.x (now in unstable), there are a few places where geopandas
uses native-size int but the plain pandas objects used as test
references are always int64, failing the test:
Package: python3-geopandas
Version: 0.14.3-1
Severity: serious
Control: block 1043240 by -1
In pandas 2.x (now in unstable), there are a few places where geopandas
uses native-size int but the plain pandas objects used as test
references are always int64, failing the test:
Package: python3-geopandas
Version: 0.14.3-1
Severity: serious
Control: block 1043240 by -1
In pandas 2.x (now in unstable), there are a few places where geopandas
uses native-size int but the plain pandas objects used as test
references are always int64, failing the test:
Package: python3-mdanalysis
Version: 2.5.0+dfsg1-2
The autopkgtest sometimes hangs at the 85% point, causing it to time out
and fail. (This is probably a hang and not just slowness, because when
it doesn't fail, this test doesn't take anywhere near that long.)
Control: block -1 by 1063274
Thank you for uploading those fixes.
Note to self: pandas will need another upload, to remove the numba B-D
and skip those tests (because numba is not in testing), and do something
about 'ignoredtests' being slow enough to time out in i386 and arm64.
Control: block -1 by 1063274
Thank you for uploading those fixes.
Note to self: pandas will need another upload, to remove the numba B-D
and skip those tests (because numba is not in testing), and do something
about 'ignoredtests' being slow enough to time out in i386 and arm64.
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Source: pydevd
Severity: serious
Tags: patch
A pydevd test uses DataFrame.applymap(), and fails because this now
raises a FutureWarning. Replacing it with DataFrame.map() as this
message suggests would probably fix it.
Source: pydevd
Severity: serious
Tags: patch
A pydevd test uses DataFrame.applymap(), and fails because this now
raises a FutureWarning. Replacing it with DataFrame.map() as this
message suggests would probably fix it.
Package: python3-seaborn
Version: 0.13.2-1
Severity: serious
seaborn's autopkgtest failed on i386, with differences small enough that
they are plausibly rounding error (i.e. should be ignored, by using
*almost_equal instead of exact comparisons), but I haven't looked carefully.
Package: python3-seaborn
Version: 0.13.2-1
Severity: serious
seaborn's autopkgtest failed on i386, with differences small enough that
they are plausibly rounding error (i.e. should be ignored, by using
*almost_equal instead of exact comparisons), but I haven't looked carefully.
Package: python3-seaborn
Version: 0.13.2-1
Severity: serious
seaborn's autopkgtest failed on i386, with differences small enough that
they are plausibly rounding error (i.e. should be ignored, by using
*almost_equal instead of exact comparisons), but I haven't looked carefully.
--
On 03/02/2024 22:01, Andreas Tille wrote:
The point I was making in my mail was that I had trouble running the
tests in **latest** upstream version (5.2.0).
Sorry - I'd misread your previous message as you having tried 5.x, found
that it didn't work due to the missing dependency, and decided
On 03/02/2024 22:01, Andreas Tille wrote:
The point I was making in my mail was that I had trouble running the
tests in **latest** upstream version (5.2.0).
Sorry - I'd misread your previous message as you having tried 5.x, found
that it didn't work due to the missing dependency, and decided
It looks like this is at least two issues:
- Tests mix tabs and spaces, which is no longer allowed = upstream 2459
- Assumes f-strings are not tokenized, which they now are = upstream
2485/2588/2649
Fix in progress on the debian-v7 branch. (The main branch has 8.x,
which doesn't work due to
It looks like this is at least two issues:
- Tests mix tabs and spaces, which is no longer allowed = upstream 2459
- Assumes f-strings are not tokenized, which they now are = upstream
2485/2588/2649
Fix in progress on the debian-v7 branch. (The main branch has 8.x,
which doesn't work due to
Rebecca N. Palmer pushed new branch debian-v7 at Debian Med / snakemake
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Please don't skip/xfail tests - my suggestion above is an actual fix:
https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads
(In a fork because, despite its description, this is not actually a
debian-science package. The Salsa CI "fail" is because the *old*
Please don't skip/xfail tests - my suggestion above is an actual fix:
https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads
(In a fork because, despite its description, this is not actually a
debian-science package. The Salsa CI "fail" is because the *old*
My fixes are pushed to Salsa, but they're in a fork because this isn't a
debian-science package:
https://salsa.debian.org/rnpalmer-guest/influxdb-python
seaborn has now been fixed. I intend to look at python-altair later.
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My fixes are pushed to Salsa, but they're in a fork because this isn't a
debian-science package:
https://salsa.debian.org/rnpalmer-guest/influxdb-python
seaborn has now been fixed. I intend to look at python-altair later.
I intend to upload pandas 2.x to unstable soon. These packages have a
patch in their bug - please upload them (I'm a DM, I can't do that), or
if you think this patch won't work or isn't a good idea, tell me why:
dials influxdb-python python-altair python-feather-format seaborn tqdm
In
Note that this uncertainty is only around whether this is a complete fix
- even in the case where it's not, it *wouldn't* be actively worse than
doing nothing, though it would be hiding the problem.
Note that this uncertainty is only around whether this is a complete fix
- even in the case where it's not, it *wouldn't* be actively worse than
doing nothing, though it would be hiding the problem.
I intend to upload pandas 2.x to unstable soon. These packages have a
patch in their bug - please upload them (I'm a DM, I can't do that), or
if you think this patch won't work or isn't a good idea, tell me why:
dials influxdb-python python-altair python-feather-format seaborn tqdm
In
I intend to upload pandas 2.x to unstable soon. These packages have a
patch in their bug - please upload them (I'm a DM, I can't do that), or
if you think this patch won't work or isn't a good idea, tell me why:
dials influxdb-python python-altair python-feather-format seaborn tqdm
In
Some looking through the code suggests that the precision is user-set
and hence constant within a single query, and hence that this fix is OK,
but I'm not entirely certain of that.
There are ways to make pandas 2.x accept mixed time format, but I think
they're 2.x _only_ and/or slow.
Some looking through the code suggests that the precision is user-set
and hence constant within a single query, and hence that this fix is OK,
but I'm not entirely certain of that.
There are ways to make pandas 2.x accept mixed time format, but I think
they're 2.x _only_ and/or slow.
That turned out to be easier than it looked - fixing the easy one also
made the others go away. Please upload this:
https://salsa.debian.org/rnpalmer-guest/tqdm
That turned out to be easier than it looked - fixing the easy one also
made the others go away. Please upload this:
https://salsa.debian.org/rnpalmer-guest/tqdm
Control: retitle 1058160 tqdm: tests failing/hanging in Python 3.12
That works for #1053946 (pandas 2.x), but #1058160 (python 3.12) is more
than a single hanging test, and it's not immediately obvious what should
be done.
Attempted fix (caution, currently just skips the hanging test) and
Control: retitle 1058160 tqdm: tests failing/hanging in Python 3.12
That works for #1053946 (pandas 2.x), but #1058160 (python 3.12) is more
than a single hanging test, and it's not immediately obvious what should
be done.
Attempted fix (caution, currently just skips the hanging test) and
The above by itself wasn't enough, but what I have now pushed to Salsa
is. Please upload it.
The above by itself wasn't enough, but what I have now pushed to Salsa
is. Please upload it.
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That's not the only problem: some of the tests mix timestamps in
slightly different formats (with and without fractional seconds), which
is no longer allowed by default:
https://pandas.pydata.org/pandas-docs/version/2.1.4/whatsnew/v2.0.0.html#datetimes-are-now-parsed-with-a-consistent-format
On 22/01/2024 11:51, Julian Gilbey wrote:
Please could we wait until the "Python 3.12 is a supported version"
transition is completed?
How are you defining that? python3-defaults 3.11.6+ in testing? (I was
previously told 3.12-supporting pandas and numpy in testing, which has
happened. I
On 22/01/2024 11:51, Julian Gilbey wrote:
Please could we wait until the "Python 3.12 is a supported version"
transition is completed?
How are you defining that? python3-defaults 3.11.6+ in testing? (I was
previously told 3.12-supporting pandas and numpy in testing, which has
happened. I
On 22/01/2024 11:51, Julian Gilbey wrote:
Please could we wait until the "Python 3.12 is a supported version"
transition is completed?
How are you defining that? python3-defaults 3.11.6+ in testing? (I was
previously told 3.12-supporting pandas and numpy in testing, which has
happened. I
Please give back pandas_1.5.3+dfsg-11 (unstable) on i386: that looks
like a rare random failure.
(DMs can't use the self-service method.)
What, if anything, blocks the above fix from being applied now?
tqdm, influxdb-python and seaborn are the highest-popcon packages broken
by pandas 2.x.
What, if anything, blocks the above fix from being applied now?
tqdm, influxdb-python and seaborn are the highest-popcon packages broken
by pandas 2.x.
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Control: severity 1053943 1053939 1053942 1044053 1044056 serious
Control: severity 1044074 1053946 1044078 1044079 1044077 serious
Control: severity 1044071 1044067 1044068 1044055 1044060 serious
Control: severity 1044072 1044073 1044064 1053945 1044054 serious
Control: severity 1044076 1053940
Control: severity 1053943 1053939 1053942 1044053 1044056 serious
Control: severity 1044074 1053946 1044078 1044079 1044077 serious
Control: severity 1044071 1044067 1044068 1044055 1044060 serious
Control: severity 1044072 1044073 1044064 1053945 1044054 serious
Control: severity 1044076 1053940
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