Andreas Tille pushed to branch master at Debian Med / pyranges
Commits: 5f31038b by Andreas Tille at 2023-01-14T18:02:18+01:00 Also replace np.bool - - - - - 2 changed files: - debian/changelog - debian/patches/numpy_1.24.patch Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -pyranges (0.0.111+ds-4) UNRELEASED; urgency=medium +pyranges (0.0.111+ds-4) unstable; urgency=medium * Team upload. * Adapt to numpy 1.24 @@ -6,7 +6,7 @@ pyranges (0.0.111+ds-4) UNRELEASED; urgency=medium * Standards-Version: 4.6.2 (routine-update) * No tab in license text (routine-update) - -- Andreas Tille <[email protected]> Sat, 14 Jan 2023 16:30:10 +0100 + -- Andreas Tille <[email protected]> Sat, 14 Jan 2023 16:32:08 +0100 pyranges (0.0.111+ds-3) unstable; urgency=medium ===================================== debian/patches/numpy_1.24.patch ===================================== @@ -14,3 +14,43 @@ Last-Update: Sat, 14 Jan 2023 16:30:10 +0100 sep="\t") result = gr.coverage(gr2, strandedness=strandedness) +--- a/pyranges/pyranges.py ++++ b/pyranges/pyranges.py +@@ -1705,7 +1705,7 @@ class PyRanges(): + For printing, the PyRanges was sorted on Chromosome and Strand. + """ + +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[:n] = True + return self[subsetter] + +@@ -3571,7 +3571,7 @@ class PyRanges(): + ValueError: Cannot take a larger sample than population when 'replace=False' + """ + sample = np.random.choice(len(self), size=n, replace=False) +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[sample] = True + return self[subsetter] + +@@ -4533,7 +4533,7 @@ class PyRanges(): + For printing, the PyRanges was sorted on Chromosome and Strand. + """ + +- subsetter = np.zeros(len(self), dtype=np.bool) ++ subsetter = np.zeros(len(self), dtype=bool) + subsetter[(len(self) - n):] = True + return self[subsetter] + +--- a/tests/hypothesis_helper.py ++++ b/tests/hypothesis_helper.py +@@ -269,7 +269,7 @@ def genomicfeature(draw): + dataset = getattr(pr.data, dataset_name)() + dataset = dataset[dataset.Feature.isin(["gene", "transcript", "exon"])] + +- # subsetter = draw(arrays(np.bool, shape=len(dataset))) ++ # subsetter = draw(arrays(bool, shape=len(dataset))) + gene_ids = list(dataset.gene_id.drop_duplicates()) + genes = draw( + st.lists(st.sampled_from(gene_ids), unique="True", min_size=1)) View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/commit/5f31038b23defd2a58d0901fcab3a29f1e3f5d32 -- View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/commit/5f31038b23defd2a58d0901fcab3a29f1e3f5d32 You're receiving this email because of your account on salsa.debian.org.
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