[med-svn] [Git][med-team/last-align][master] 3 commits: Remove fix-959866.patch: Fixed internally in simde
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Aug 9 13:13:56 BST 2021
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
90c3a174 by Nilesh Patra at 2021-08-09T17:19:09+05:30
Remove fix-959866.patch: Fixed internally in simde
- - - - -
60b445b9 by Nilesh Patra at 2021-08-09T17:24:57+05:30
Drop 2to3.patch, fix shebang
- - - - -
ad501126 by Nilesh Patra at 2021-08-09T17:33:48+05:30
Interim changelog entry
- - - - -
5 changed files:
- debian/changelog
- − debian/patches/2to3.patch
- − debian/patches/fix-959866.patch
- + debian/patches/fix-shebang.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -2,15 +2,20 @@ last-align (1254-1) UNRELEASED; urgency=medium
* d/watch: Fix fetch URL - last-align has moved to gitlab
* New upstream version 1254
- * d/p/2to3.patch: scripts has moved to bin, change
* d/p/helpMakefiles.patch: Refresh helpmakefile.patch
* d/p/simde: Attempt adapting simde to new upstream
+ * Drop Patches:
+ - Drop d/p/fix-959866.patch: Since the problem has been internally
+ fixed in simde
+ - Drop d/p/2to3.patch: The new upstream is now compatible with both
+ python2 and python3, hence these changes are un-needed.
+ Added d/p/fix-shebang.patch to fix shebang in python script, as
+ a replacement.
* d/rules:
- Attempt adapting to new upstream version
- Add rest manpages
- Install all lastdb5 based binaries
- Install new fasta+fastq scripts
- * Add shebang for fasta-nr
* d/debian/last-align.doc-base.last-align-manual:
The manual page has moved to last-cookbook.rst
* d/tests/last-test: Add additional tests
@@ -20,7 +25,7 @@ last-align (1254-1) UNRELEASED; urgency=medium
* d/salsa-ci.yml: Disable blhc and reprotest
* d/lintian-overrides: Add lintian override for maf-cut manpage
- -- Nilesh Patra <nilesh at debian.org> Fri, 06 Aug 2021 14:51:19 +0530
+ -- Nilesh Patra <nilesh at debian.org> Mon, 09 Aug 2021 17:25:05 +0530
last-align (1179-1) unstable; urgency=medium
=====================================
debian/patches/2to3.patch deleted
=====================================
@@ -1,187 +0,0 @@
-Description: Use 2to3 to port to Python3
-Bug-Debian: https://bugs.debian.org/943148
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 22 Nov 2019 11:23:44 +0100
-
---- a/bin/last-dotplot
-+++ b/bin/last-dotplot
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/python3
- # Author: Martin C. Frith 2008
- # SPDX-License-Identifier: GPL-3.0-or-later
-
-@@ -264,12 +264,12 @@
- yield oldBeg, maxEnd
-
- def mergedRangesPerSeq(coverDict):
-- for k, v in coverDict.items():
-+ for k, v in list(coverDict.items()):
- v.sort()
- yield k, list(mergedRanges(v))
-
- def coveredLength(mergedCoverDict):
-- return sum(sum(e - b for b, e in v) for v in mergedCoverDict.values())
-+ return sum(sum(e - b for b, e in v) for v in list(mergedCoverDict.values()))
-
- def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):
- maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")
-@@ -310,7 +310,7 @@
- def natural_sort_key(my_string):
- '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
- parts = re.split(r'(\d+)', my_string)
-- parts[1::2] = map(int, parts[1::2])
-+ parts[1::2] = list(map(int, parts[1::2]))
- return parts
-
- def nameKey(oneSeqRanges):
-@@ -581,7 +581,7 @@
- def expandedSeqDict(seqDict):
- '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
- newDict = seqDict.copy()
-- for name, x in seqDict.items():
-+ for name, x in list(seqDict.items()):
- if "." in name:
- base = name.split(".")[-1]
- if base in newDict: # an ambiguous case was found:
-@@ -621,7 +621,7 @@
- yield layer, color, seqName, beg, end, itemName
-
- def commaSeparatedInts(text):
-- return map(int, text.rstrip(",").split(","))
-+ return list(map(int, text.rstrip(",").split(",")))
-
- def readGenePred(opts, fileName, rangeDict):
- for line in myOpen(fileName):
---- a/bin/last-map-probs
-+++ b/bin/last-map-probs
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
-
- # Copyright 2010, 2011, 2012, 2014 Martin C. Frith
-
---- a/bin/last-postmask
-+++ b/bin/last-postmask
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
-
- # Copyright 2014 Martin C. Frith
-
-@@ -37,7 +37,7 @@
-
- def fastScoreMatrix(rowHeads, colHeads, matrix, deleteCost, insertCost):
- matrixLen = 128
-- defaultScore = min(map(min, matrix))
-+ defaultScore = min(list(map(min, matrix)))
- fastMatrix = [[defaultScore for i in range(matrixLen)]
- for j in range(matrixLen)]
- for i, x in enumerate(rowHeads):
-@@ -111,7 +111,7 @@
- if i.startswith("B="): bIns = int(i[2:])
- if i.startswith("e="): minScore = int(i[2:])
- if i.startswith("S="): strandParam = int(i[2:])
-- if nf > 2 and max(map(len, fields)) == 1:
-+ if nf > 2 and max(list(map(len, fields))) == 1:
- colHeads = fields[1:]
- elif nf == len(colHeads) + 2 and len(fields[1]) == 1:
- rowHeads.append(fields[1])
---- a/bin/last-train
-+++ b/bin/last-train
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
- # Copyright 2015 Martin C. Frith
- # SPDX-License-Identifier: GPL-3.0-or-later
-
-@@ -265,7 +265,7 @@
- writeMatrixBody(outFile, prefix, alphabet, matrix, "%6s")
-
- def matProbsFromCounts(counts, opts):
-- r = range(len(counts))
-+ r = list(range(len(counts)))
- if opts.revsym: # add complement (reverse strand) substitutions
- counts = [[counts[i][j] + counts[-1-i][-1-j] for j in r] for i in r]
- if opts.matsym: # symmetrize the substitution matrix
---- a/bin/maf-convert
-+++ b/bin/maf-convert
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
- # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
- # SPDX-License-Identifier: GPL-3.0-or-later
- # Seems to work with Python 2.x, x>=6
---- a/bin/maf-cut
-+++ b/bin/maf-cut
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/python3
- # Author: Martin C. Frith 2018
-
- from __future__ import print_function
-@@ -71,12 +71,12 @@
-
- def mafFieldWidths(mafRecords):
- sRecords = (i for i in mafRecords if i[0] == "s")
-- sColumns = zip(*sRecords)
-+ sColumns = list(zip(*sRecords))
- for i in sColumns:
-- yield max(map(len, i))
-+ yield max(list(map(len, i)))
-
- def printMafLine(fieldWidths, fields):
-- formatParams = itertools.chain.from_iterable(zip(fieldWidths, fields))
-+ formatParams = itertools.chain.from_iterable(list(zip(fieldWidths, fields)))
- print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))
-
- def cutOneMaf(cutRange, mafLines):
---- a/bin/maf-join
-+++ b/bin/maf-join
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
-
- # Copyright 2009, 2010, 2011 Martin C. Frith
-
-@@ -229,7 +229,7 @@
- while True:
- maf = theInput.peek()
- if maf.after(referenceMaf): break
-- maf = theInput.next()
-+ maf = next(theInput)
- if not maf.before(referenceMaf): yield maf
- except StopIteration: pass
-
---- a/bin/maf-swap
-+++ b/bin/maf-swap
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
- # Author: Martin C. Frith
- # SPDX-License-Identifier: GPL-3.0-or-later
-
-@@ -71,12 +71,12 @@
-
- def sLineFieldWidths(mafLines):
- sLines = (i for i in mafLines if i[0] == "s")
-- sColumns = zip(*sLines)
-+ sColumns = list(zip(*sLines))
- for i in sColumns:
-- yield max(map(len, i))
-+ yield max(list(map(len, i)))
-
- def joinedMafS(fieldWidths, words):
-- formatParams = itertools.chain.from_iterable(zip(fieldWidths, words))
-+ formatParams = itertools.chain.from_iterable(list(zip(fieldWidths, words)))
- return "%*s %-*s %*s %*s %*s %*s %*s\n" % tuple(formatParams)
-
- def joinedMafLine(words, fieldWidths):
---- a/bin/fasta-nr
-+++ b/bin/fasta-nr
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#!/usr/bin/python3
- # Author: Martin C. Frith 2021
-
- # xxx This is inefficient: ok for smallish data
=====================================
debian/patches/fix-959866.patch deleted
=====================================
@@ -1,25 +0,0 @@
-Description: Fix FTBFS #959866
-On ppc64el, altivec.h redefines bool, pixel and vector which can collide with
-c++ types.
-This altivec.h inclusion is done with the introduction of simde.
-As altivec.h explains, it's possible to undefine those for C++ compatibility in
-src/GappedXdropAligner.hh which let it define the variables that other files
-will use while not impacting simde.
-Author: Frédéric Bonnard <frediz at debian.org>
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/src/GappedXdropAligner.hh
-+++ b/src/GappedXdropAligner.hh
-@@ -51,6 +51,12 @@
- #include "mcf_simd.hh"
- #include "ScoreMatrixRow.hh"
-
-+#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)
-+# undef vector
-+# undef pixel
-+# undef bool
-+#endif
-+
- #include <iosfwd>
- #include <stddef.h> // size_t
- #include <vector>
=====================================
debian/patches/fix-shebang.patch
=====================================
@@ -0,0 +1,75 @@
+Description: Fix shebang to the right location in python scripts
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-08-09
+--- a/bin/fasta-nr
++++ b/bin/fasta-nr
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Author: Martin C. Frith 2021
+
+ # xxx This is inefficient: ok for smallish data
+--- a/bin/last-dotplot
++++ b/bin/last-dotplot
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Author: Martin C. Frith 2008
+ # SPDX-License-Identifier: GPL-3.0-or-later
+
+--- a/bin/last-map-probs
++++ b/bin/last-map-probs
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+
+ # Copyright 2010, 2011, 2012, 2014 Martin C. Frith
+
+--- a/bin/last-postmask
++++ b/bin/last-postmask
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+
+ # Copyright 2014 Martin C. Frith
+
+--- a/bin/last-train
++++ b/bin/last-train
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Copyright 2015 Martin C. Frith
+ # SPDX-License-Identifier: GPL-3.0-or-later
+
+--- a/bin/maf-convert
++++ b/bin/maf-convert
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
+ # SPDX-License-Identifier: GPL-3.0-or-later
+ # Seems to work with Python 2.x, x>=6
+--- a/bin/maf-cut
++++ b/bin/maf-cut
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Author: Martin C. Frith 2018
+
+ from __future__ import print_function
+--- a/bin/maf-join
++++ b/bin/maf-join
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+
+ # Copyright 2009, 2010, 2011 Martin C. Frith
+
+--- a/bin/maf-swap
++++ b/bin/maf-swap
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ # Author: Martin C. Frith
+ # SPDX-License-Identifier: GPL-3.0-or-later
+
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
-2to3.patch
helpMakefiles.patch
simde
-fix-959866.patch
+fix-shebang.patch
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/0d74a463004f4aa99339a2e096976025fefa341b...ad50112696d3c33953d390de717219dda0fc6525
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/0d74a463004f4aa99339a2e096976025fefa341b...ad50112696d3c33953d390de717219dda0fc6525
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