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 fails more tests with pandas 2 than with
pandas 1.5.)

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.

Hi again,

Am Sat, Feb 17, 2024 at 07:31:48PM +0100 schrieb s3v:

thanks a lot for all your fixes you provided for Debian Med packages.
There are a few remaining issues, which I would love to ask you step by
step.  I found a patch for pyranges[1] which solves all issues but one:

My attempt to fix this by

+--- a/tests/helpers.py
++++ b/tests/helpers.py
+@@ -57,6 +57,7 @@ def assert_df_equal(df1, df2):
+     print(df2.index)
+     print("index equal", df1.index == df2.index)
+
++    df1["Cluster"] = df1["Cluster"].astype(np.int64)
+     pd.testing.assert_frame_equal(df1, df2)
+
+     pd.options.mode.chained_assignment = "warn"

totally failed and introduced a new series of failures basically saying
pandas/_libs/hashtable_class_helper.pxi:7088: KeyError

Any suggestion how to fix that issue?

Kind regards
     Andreas.



[1] https://salsa.debian.org/med-team/pyranges/-/blob/master/debian/patches/pandas2.0.patch?ref_type=heads

We believe that the bug you reported is fixed in the latest version of
pyranges, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1044064@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emollier@debian.org> (supplier of updated pyranges package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Fri, 23 Feb 2024 15:39:01 +0100
Source: pyranges
Architecture: source
Version: 0.0.111+ds-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1044064
Changes:
 pyranges (0.0.111+ds-7) unstable; urgency=medium
 .
   [ Andreas Tille ]
   * Fix for Pandas 2.0
     Closes: #1044064
 .
   [ Étienne Mollier ]
   * fix-test_unary.patch: new.
     This patch fixes a remaining test failure affecting dtype conversion.
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