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 <ti...@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 <ti...@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 You're receiving this email because of your account on salsa.debian.org.
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