Bug#1053944: q2-types: test failure with pandas 2.1 (Was: Bug#1044068: q2templates: FTBFS with pandas 2.0)
Control: tags -1 help
Hi again,
thanks again for your great help. I admit I need some help for q2-types as
well. While log in the bug report vanished you will easily find things like
TypeError: read_csv() got an unexpected keyword argument 'squeeze'
when trying to build the package.
I've found an issue at pandas upstream[1] which inspired me to the patch
--- a/q2_types/sample_data/tests/test_transformer.py
+++ b/q2_types/sample_data/tests/test_transformer.py
@@ -28,8 +28,8 @@ class TestTransformers(TestPluginBase):
obs = transformer(exp)
# Squeeze equals true to return series instead of dataframe
-obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0,
- squeeze=True)
+obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0)
+obs.squeeze("columns")
assert_series_equal(exp, obs)
which is obviously wrong since it leads to
# Squeeze equals true to return series instead of dataframe
obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0)
obs.squeeze("columns")
> assert_series_equal(exp, obs)
Probably a better solution can be found at stackoverflow[2] to use
DataFrame.squeeze('columns') but I'm simply lacking an example how to use
this.
Finally this is not the only error and I would appreciate any helping hint
(patch?) to get the package ported to recent pandas.
Kind regards
Andreas.
[1] https://github.com/pandas-dev/pandas/issues/43242
[2]
https://stackoverflow.com/questions/76684141/why-am-i-getting-an-error-when-using-squeeze-keyword-in-read-csv
Am Fri, Feb 16, 2024 at 10:48:59AM +0100 schrieb s3v:
> ...
> Kind Regards
--
http://fam-tille.de
Bug#1044068: q2templates: FTBFS with pandas 2.0
Hi, thanks a lot for all your help! I've just uploaded q2templates. If you have more hints to pandas2 related bugs these are very welcome. Kind regards Andreas. Am Fri, Feb 16, 2024 at 02:29:15PM +0100 schrieb s3v: > Hi, > > sorry for writing again but, after removing override for auto_test in > d/rules and s/python3/python3-all in d/control for Build-Depends, > tests fail with Python 3.12: > > dh_auto_clean > I: pybuild base:305: python3.12 setup.py clean > /build/q2templates-2023.9.0+ds/versioneer.py:422: SyntaxWarning: invalid > escape sequence '\s' > LONG_VERSION_PY['git'] = ''' > Traceback (most recent call last): > File "/build/q2templates-2023.9.0+ds/setup.py", line 14, in > version=versioneer.get_version(), > > File "/build/q2templates-2023.9.0+ds/versioneer.py", line 1481, in > get_version > return get_versions()["version"] > ^^ > File "/build/q2templates-2023.9.0+ds/versioneer.py", line 1413, in > get_versions > cfg = get_config_from_root(root) > ^^ > File "/build/q2templates-2023.9.0+ds/versioneer.py", line 343, in > get_config_from_root > parser = configparser.SafeConfigParser() > ^ > AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. > Did you mean: 'RawConfigParser'? > E: pybuild pybuild:391: clean: plugin distutils failed with: exit code=1: > python3.12 setup.py clean > > Kind Regards > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#1044068: q2templates: FTBFS with pandas 2.0
Hi, sorry for writing again but, after removing override for auto_test in d/rules and s/python3/python3-all in d/control for Build-Depends, tests fail with Python 3.12: dh_auto_clean I: pybuild base:305: python3.12 setup.py clean /build/q2templates-2023.9.0+ds/versioneer.py:422: SyntaxWarning: invalid escape sequence '\s' LONG_VERSION_PY['git'] = ''' Traceback (most recent call last): File "/build/q2templates-2023.9.0+ds/setup.py", line 14, in version=versioneer.get_version(), File "/build/q2templates-2023.9.0+ds/versioneer.py", line 1481, in get_version return get_versions()["version"] ^^ File "/build/q2templates-2023.9.0+ds/versioneer.py", line 1413, in get_versions cfg = get_config_from_root(root) ^^ File "/build/q2templates-2023.9.0+ds/versioneer.py", line 343, in get_config_from_root parser = configparser.SafeConfigParser() ^ AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'? E: pybuild pybuild:391: clean: plugin distutils failed with: exit code=1: python3.12 setup.py clean Kind Regards
Bug#1044068: q2templates: FTBFS with pandas 2.0
Dear Maintainer,
According to [1][2]|
Support for negative integer for :attr:`pd.options.display.max_colwidth`
is deprecated in favor of using ``None`` (:issue:`31532`)|
I guess this line:
with pd.option_context('display.max_colwidth', -1):
should be changed in:
with pd.option_context('display.max_colwidth', None):
in [3].
I've not tested #1053942[4] disappears after this bug is fixed.
Kind Regards
[1] https://github.com/pandas-dev/pandas/pull/31569
[2]
https://sources.debian.org/src/pandas/2.1.4%2Bdfsg-4/doc/source/whatsnew/v1.0.1.rst/#L46
[3]
https://sources.debian.org/src/q2templates/2023.9.0%2Bds-1/q2templates/util.py/#L46
[4] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1053942
Bug#1044068: q2templates: FTBFS with pandas 2.0
Hi Rebecca, I've checked several Debian Med packages for your assumption that replacing pandas.util.testing might help but non of the candidates I've checked was caused by this. I'm rather seeing quite strange errors like in the case of q2templates here in Salsa CI https://salsa.debian.org/med-team/q2templates/-/jobs/5247852 Do you have any hint how to fix this? Kind regards Andreas. -- http://fam-tille.de
Bug#1044068: q2templates: FTBFS with pandas 2.0
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://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2templates/36575889/log.gz A common source of failures is that pandas.util.testing has been renamed to pandas.testing. Both names were available in all 1.x versions (and hence in Debian stable and oldstable), so Debian packages that were using this can immediately switch unconditionally.
