[med-svn] [Git][med-team/pyranges][master] [skip ci] Fix for Pandas 2.0 - not finished thus do not waste computing cycles on Salsa CI

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / pyranges


Commits:
89839d44 by Andreas Tille at 2024-02-18T07:04:42+01:00
[skip ci] Fix for Pandas 2.0 - not finished thus do not waste computing cycles on Salsa CI

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/pandas2.0.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+pyranges (0.0.111+ds-7) UNRELEASED; urgency=medium
+
+  * Team upload
+  * Fix for Pandas 2.0
+    Closes: #1044064
+
+ -- Andreas Tille <tille at debian.org>  Sun, 18 Feb 2024 07:02:12 +0100
+
 pyranges (0.0.111+ds-6) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/pandas2.0.patch
=====================================
@@ -0,0 +1,36 @@
+Description: Fix for Pandas 2.0
+Bug-Debian: https://bugs.debian.org/1044064
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 18 Feb 2024 07:02:12 +0100
+
+--- a/tests/test_binary.py
++++ b/tests/test_binary.py
+@@ -346,7 +346,7 @@ def test_nearest(gr, gr2, nearest_how, o
+     bedtools_df.Distance = bedtools_df.Distance.abs()
+ 
+     bedtools_df = bedtools_df[bedtools_df.Chromosome2 != "."]
+-    bedtools_df = bedtools_df.drop("Chromosome2", 1)
++    bedtools_df = bedtools_df.drop("Chromosome2", axis=1)
+ 
+     result = gr.nearest(
+         gr2, strandedness=strandedness, overlap=overlap, how=nearest_how)
+@@ -541,7 +541,7 @@ def test_k_nearest(gr, gr2, nearest_how,
+     bedtools_df.Distance = bedtools_df.Distance.abs()
+ 
+     bedtools_df = bedtools_df[bedtools_df.Chromosome2 != "."]
+-    bedtools_df = bedtools_df.drop("Chromosome2", 1)
++    bedtools_df = bedtools_df.drop("Chromosome2", axis=1)
+ 
+     # cannot test with k > 1 because bedtools algo has different syntax
+     # cannot test keep_duplicates "all" or None/False properly, as the semantics is different for bedtools
+--- a/pyranges/pyranges.py
++++ b/pyranges/pyranges.py
+@@ -2500,7 +2500,7 @@ class PyRanges():
+ 
+         result = pr.PyRanges(new_result)
+ 
+-        if not result.__IX__.is_monotonic:
++        if not result.__IX__.is_monotonic_increasing:
+             result = result.sort("__IX__")
+ 
+         result = result.drop(like="__IX__|__k__")


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ reorder.patch
 numpy_1.24.patch
 healthcheck-all.patch
 no_install_depends_cython.patch
+pandas2.0.patch



View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/commit/89839d44daba7558fe356bf9480193a36b465ca6

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/commit/89839d44daba7558fe356bf9480193a36b465ca6
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