[med-svn] [Git][med-team/arden][master] 8 commits: d/changelog: new autopkgtests closes bugs.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Oct 20 21:52:34 BST 2024
Étienne Mollier pushed to branch master at Debian Med / arden
Commits:
a2186db0 by Étienne Mollier at 2024-10-20T22:10:15+02:00
d/changelog: new autopkgtests closes bugs.
- - - - -
304b3cd3 by Étienne Mollier at 2024-10-20T22:33:59+02:00
htseq-type.patch: new: fix one bug caught by autopkgtests.
- - - - -
ad49f976 by Étienne Mollier at 2024-10-20T22:38:04+02:00
division-by-zero.patch: new: fix said error.
- - - - -
623114c5 by Étienne Mollier at 2024-10-20T22:44:53+02:00
key-error.patch: new: fix type mismatch causing a KeyError.
This has been caught by the newly introduced autopkgtest.
- - - - -
be6341c0 by Étienne Mollier at 2024-10-20T22:49:03+02:00
syntax-warning.patch: new: fix multiple syntax warnings.
Closes: #1085326
- - - - -
08b7bb85 by Étienne Mollier at 2024-10-20T22:49:53+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
9ee9c581 by Étienne Mollier at 2024-10-20T22:50:20+02:00
d/control: add myself to uploaders.
- - - - -
99b5870f by Étienne Mollier at 2024-10-20T22:52:14+02:00
Ready for upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/division-by-zero.patch
- + debian/patches/htseq-type.patch
- + debian/patches/key-error.patch
- debian/patches/series
- + debian/patches/syntax-warning.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-arden (1.0-6) UNRELEASED; urgency=medium
+arden (1.0-6) unstable; urgency=medium
+ [ Andreas Tille ]
* Packaging update
* Standards-Version: 4.6.2 (routine-update)
* debhelper-compat 13 (routine-update)
@@ -8,9 +9,18 @@ arden (1.0-6) UNRELEASED; urgency=medium
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Archive.
* lintian-overrides (see lintian bug #1017966)
- * Add autopkgtest
-
- -- Andreas Tille <tille at debian.org> Sat, 21 Jan 2023 07:29:38 +0100
+ * Add autopkgtest (Closes: #1035113, #1036488)
+
+ [ Étienne Mollier ]
+ * htseq-type.patch: new: fix one bug caught by autopkgtests.
+ * division-by-zero.patch: new: fix said error.
+ * key-error.patch: new: fix type mismatch causing a KeyError.
+ This has been caught by the newly introduced autopkgtest.
+ * syntax-warning.patch: new: fix multiple syntax warnings. (Closes: #1085326)
+ * d/control: declare compliance to standards version 4.7.0.
+ * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 20 Oct 2024 22:51:33 +0200
arden (1.0-5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,12 +1,13 @@
Source: arden
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/arden
Vcs-Git: https://salsa.debian.org/med-team/arden.git
Homepage: http://sourceforge.net/projects/arden/
=====================================
debian/patches/division-by-zero.patch
=====================================
@@ -0,0 +1,20 @@
+Description: fix a division by zero error caught by the autopkgtest.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-10-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- arden.orig/core/ReadAndWrite.py
++++ arden/core/ReadAndWrite.py
+@@ -184,5 +184,8 @@
+ else:
+ not_hamming+=1
+ print(("#hamming distance REF-ART\t"+ str(hamming)))
+- print(("avg. distance:\t" + str(len(original)/float(hamming))))
+- print("###########################\r\n")
+\ No newline at end of file
++ if hamming == 0:
++ print("avg. distance:\tnan")
++ else:
++ print(("avg. distance:\t" + str(len(original)/float(hamming))))
++ print("###########################\r\n")
=====================================
debian/patches/htseq-type.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix failure to use HTSeq.Sequence.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-10-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- arden.orig/arden-create
++++ arden/arden-create
+@@ -221,7 +221,7 @@
+ #3. Step: Mutate DNA /AA
+ print("\tMutate DNA...")
+ # generate artifical genome sequence
+- AR = HTSeq.Sequence(IM.mutate_random(Reference.seq,AminoA,distance,pdic,rev,ArtHead,random,outputpath),ArtHead)
++ AR = HTSeq.Sequence(IM.mutate_random(Reference.seq,AminoA,distance,pdic,rev,ArtHead,random,outputpath).encode(),ArtHead)
+ # write AR to output fasta
+ RAW.writefile(AR,outputpath+"/"+ArtHead+".fasta")
+
=====================================
debian/patches/key-error.patch
=====================================
@@ -0,0 +1,19 @@
+Description: make sure seq is an actual str().
+ This is yet another instance of bug caught by autopkgtest.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-10-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- arden.orig/core/ReadAndWrite.py
++++ arden/core/ReadAndWrite.py
+@@ -85,7 +85,8 @@
+ @param shallwrite: Decides if percentages values are written to the output.
+ """
+ Nndic={"A":0,"C":0,"G":0,"T":0,"N":0}
+-
++
++ seq = seq.decode()
+ for i in range(0,len(seq)):
+ Nndic[seq[i]]+=1
+ s=len(seq)
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,6 @@
spelling.patch
2to3_new.patch
+htseq-type.patch
+division-by-zero.patch
+key-error.patch
+syntax-warning.patch
=====================================
debian/patches/syntax-warning.patch
=====================================
@@ -0,0 +1,67 @@
+Description: fix multiple SyntaxWarnings upon package installation.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1085326
+Forwarded: no
+Last-Update: 2024-10-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- arden.orig/core/AnalyseMapping.py
++++ arden/core/AnalyseMapping.py
+@@ -166,7 +166,7 @@
+
+ # mismatches are calculated as cigar XM - MDtag occurrences of numbers
+ # which indicate mismatches
+- mism = sum([i.size for i in cigar if i.type=="M"]) - getsum(re.findall("(\d+)", alngt.optional_field("MD")))
++ mism = sum([i.size for i in cigar if i.type=="M"]) - getsum(re.findall(r"(\d+)", alngt.optional_field("MD")))
+
+
+ nm = alngt.optional_field("NM")
+@@ -249,15 +249,15 @@
+ @rtype: gaps,mismatches
+ @return: Parsed gaps and mismatches
+ """
+- deletions = getsum(re.findall("(\d+)D", cigar))
+- insertions = getsum(re.findall("(\d+)I", cigar))
++ deletions = getsum(re.findall(r"(\d+)D", cigar))
++ insertions = getsum(re.findall(r"(\d+)I", cigar))
+ gaps = int(insertions + deletions)
+
+ # mismatches are:
+ # ALL Matches from CIGAR - RealMatches from MDTag
+ #
+
+- mismatch = getsum(re.findall("(\d+)M", cigar)) - getsum(re.findall("(\d+)", mdtag))
++ mismatch = getsum(re.findall(r"(\d+)M", cigar)) - getsum(re.findall(r"(\d+)", mdtag))
+
+
+ #print ("%s\t%s\t%s\t%s\t%s\t%s" %(mdtag,cigar,deletions,insertions,mismatch,gaps))
+@@ -648,7 +648,7 @@
+
+ # gives the number of XX back
+ # valid tags: X0,XM (number of missmatches
+- m = re.search(tag + ":i:(\d+)", line)
++ m = re.search(tag + r":i:(\d+)", line)
+ besthits = m.group(1)
+
+ return(besthits)
+@@ -714,7 +714,7 @@
+ # S - does not extend...
+ # P - does not extend...
+ # H - does not extend...
+- match = re.findall("(\d+)[MDN]", cigar)
++ match = re.findall(r"(\d+)[MDN]", cigar)
+ sumOfMatches = 0
+ for item in match:
+ sumOfMatches += int(item)
+@@ -914,9 +914,9 @@
+ qualstr = columns[10].strip()
+ tags = " ".join(columns[11:])
+
+- mdtag = re.search("MD:Z:([^\s]+)", tags).group(1)
++ mdtag = re.search(r"MD:Z:([^\s]+)", tags).group(1)
+ try:
+- mdtag = re.search("MD:Z:([^\s]+)", tags).group(1)
++ mdtag = re.search(r"MD:Z:([^\s]+)", tags).group(1)
+ gaps, mism = getMisGap(mdtag, cigar)
+ except:
+ gaps = 0
View it on GitLab: https://salsa.debian.org/med-team/arden/-/compare/effd41349ce48a5d833a363fe00b75b7e8e225ad...99b5870f140230f49011a4f9536b792c7de8a200
--
View it on GitLab: https://salsa.debian.org/med-team/arden/-/compare/effd41349ce48a5d833a363fe00b75b7e8e225ad...99b5870f140230f49011a4f9536b792c7de8a200
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