[med-svn] [Git][med-team/pyranges][master] Also replace np.bool

[Andreas Tille (@tille)]

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 <tille at debian.org>  Sat, 14 Jan 2023 16:30:10 +0100
+ -- Andreas Tille <tille at debian.org>  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
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