[med-svn] [Git][med-team/python-deeptools][master] 4 commits: Cherry-pick upstream patch to fix problems with numpy 1.24 (Closes: #1027225)
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Dec 30 14:28:11 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / python-deeptools
Commits:
8582d9bb by Nilesh Patra at 2022-12-30T19:32:28+05:30
Cherry-pick upstream patch to fix problems with numpy 1.24 (Closes: #1027225)
- - - - -
6e298fab by Nilesh Patra at 2022-12-30T19:32:43+05:30
Bump Standards-Version to 4.6.2 (no changes needed)
- - - - -
f197cad6 by Nilesh Patra at 2022-12-30T14:26:35+00:00
Apply patches before running autopkgtests
- - - - -
47c53ade by Nilesh Patra at 2022-12-30T14:26:35+00:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/numpy-1.24.patch
- debian/patches/series
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-deeptools (3.5.1-3) unstable; urgency=medium
+
+ * Team Upload.
+ * Cherry-pick upstream patch to fix problems with
+ numpy 1.24 (Closes: #1027225)
+ * Bump Standards-Version to 4.6.2 (no changes needed)
+ * Apply patches before running autopkgtests
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 30 Dec 2022 19:33:06 +0530
+
python-deeptools (3.5.1-2) unstable; urgency=medium
* d/{,t/}control: depend on pytest instead of nose. (Closes: #1018477)
=====================================
debian/control
=====================================
@@ -19,7 +19,7 @@ Build-Depends: debhelper-compat (= 13),
python3-plotly (>=4.9.0),
python3-deeptoolsintervals,
python3-pytest <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-deeptools
Vcs-Git: https://salsa.debian.org/med-team/python-deeptools.git
Homepage: https://github.com/deeptools/deepTools
=====================================
debian/patches/numpy-1.24.patch
=====================================
@@ -0,0 +1,65 @@
+Description: Replace np dtypes with py builtins
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2022-12-30
+--- a/deeptools/heatmapper.py
++++ b/deeptools/heatmapper.py
+@@ -777,7 +777,7 @@
+ # split the line into bed interval and matrix values
+ region = line.split('\t')
+ chrom, start, end, name, score, strand = region[0:6]
+- matrix_row = np.ma.masked_invalid(np.fromiter(region[6:], np.float))
++ matrix_row = np.ma.masked_invalid(np.fromiter(region[6:], float))
+ matrix_rows.append(matrix_row)
+ starts = start.split(",")
+ ends = end.split(",")
+@@ -852,7 +852,7 @@
+ # join np_array values
+ # keeping nans while converting them to strings
+ if not np.ma.is_masked(score_list[idx]):
+- np.float(score_list[idx])
++ float(score_list[idx])
+ matrix_values = "\t".join(
+ np.char.mod('%f', self.matrix.matrix[idx, :]))
+ starts = ["{0}".format(x[0]) for x in region[1]]
+@@ -1345,7 +1345,7 @@
+ to_keep = []
+ score_list = np.ma.masked_invalid(np.mean(self.matrix, axis=1))
+ for idx, region in enumerate(self.regions):
+- if np.ma.is_masked(score_list[idx]) or np.float(score_list[idx]) == 0:
++ if np.ma.is_masked(score_list[idx]) or float(score_list[idx]) == 0:
+ continue
+ else:
+ to_keep.append(idx)
+--- a/deeptools/plotFingerprint.py
++++ b/deeptools/plotFingerprint.py
+@@ -240,7 +240,7 @@
+ lamb = np.mean(vec) # Average coverage
+ coverage = np.sum(vec)
+
+- chip = np.zeros(MAXLEN, dtype=np.int)
++ chip = np.zeros(MAXLEN, dtype=int)
+ for val in vec:
+ # N.B., we need to clip past the end of the array
+ if val >= MAXLEN:
+@@ -277,8 +277,8 @@
+ return np.NAN
+
+ # These will hold the coverage histograms
+- chip = np.zeros(MAXLEN, dtype=np.int)
+- input = np.zeros(MAXLEN, dtype=np.int)
++ chip = np.zeros(MAXLEN, dtype=int)
++ input = np.zeros(MAXLEN, dtype=int)
+ for row in mat:
+ # ChIP
+ val = row[idx]
+--- a/deeptools/sumCoveragePerBin.py
++++ b/deeptools/sumCoveragePerBin.py
+@@ -90,7 +90,7 @@
+ except:
+ # bigWig input, as used by plotFingerprint
+ if bamHandle.chroms(chrom):
+- _ = np.array(bamHandle.stats(chrom, regStart, regEnd, type="mean", nBins=nRegBins), dtype=np.float)
++ _ = np.array(bamHandle.stats(chrom, regStart, regEnd, type="mean", nBins=nRegBins), dtype=float)
+ _[np.isnan(_)] = 0.0
+ _ = _ * tileSize
+ coverages += _
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
tmp_inhibit_test_readFiltering.patch
python2to3_for_executables.patch
pytest.patch
+numpy-1.24.patch
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest, python3-all
+Depends: @, python3-pytest, python3-all, quilt
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,6 +1,12 @@
#!/bin/bash
set -e
+
+QUILT_PATCHES="debian/patches" quilt push -a || true
+
for py in $(py3versions -s 2> /dev/null)
do echo "Testing with $py in $(pwd):"
- pytest-3 -v deeptools
+ pytest-3 -v deeptools --ignore=.pc
done
+
+QUILT_PATCHES=debian/patches quilt pop -a || true
+rm -rf .pc/
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/e85697a653466c5551a9862e4e50121fadc89f35...47c53ade6ca08a73bf2a306ba250fb1baf7bf653
--
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/e85697a653466c5551a9862e4e50121fadc89f35...47c53ade6ca08a73bf2a306ba250fb1baf7bf653
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