[med-svn] [Git][med-team/arden][master] 11 commits: routine-update: Packaging update
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Jan 21 10:47:03 GMT 2023
Andreas Tille pushed to branch master at Debian Med / arden
Commits:
4a858355 by Andreas Tille at 2023-01-21T07:29:39+01:00
routine-update: Packaging update
- - - - -
a425b7d5 by Andreas Tille at 2023-01-21T07:29:39+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
ef76075c by Andreas Tille at 2023-01-21T07:29:39+01:00
routine-update: debhelper-compat 13
- - - - -
16e77476 by Andreas Tille at 2023-01-21T07:29:43+01:00
routine-update: rename debian/NEWS.Debian debian/NEWS
- - - - -
39b995b9 by Andreas Tille at 2023-01-21T07:29:43+01:00
routine-update: Add salsa-ci file
- - - - -
6a9b7e24 by Andreas Tille at 2023-01-21T07:29:43+01:00
routine-update: Rules-Requires-Root: no
- - - - -
4de556c7 by Andreas Tille at 2023-01-21T07:29:53+01:00
Set upstream metadata fields: Archive.
Changes-By: lintian-brush
- - - - -
89a062a1 by Andreas Tille at 2023-01-21T07:31:30+01:00
NEWS was renamed
- - - - -
c1102418 by Andreas Tille at 2023-01-21T08:54:46+01:00
lintian-overrides (see lintian bug #1017966)
- - - - -
ef44c976 by Andreas Tille at 2023-01-21T10:03:42+01:00
Add autopkgtest
- - - - -
effd4134 by Andreas Tille at 2023-01-21T11:46:44+01:00
Start fixing 2to3 transition where issues become obvious in connection with autopkgtest
- - - - -
13 changed files:
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- debian/control
- debian/docs
- + debian/examples
- debian/patches/2to3_new.patch
- + debian/salsa-ci.yml
- + debian/source/lintian-overrides
- + debian/tests/control
- + debian/tests/data/README
- + debian/tests/data/sample.fasta
- + debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+arden (1.0-6) UNRELEASED; urgency=medium
+
+ * Packaging update
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * rename debian/NEWS.Debian debian/NEWS (routine-update)
+ * Add salsa-ci file (routine-update)
+ * 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
+
arden (1.0-5) unstable; urgency=medium
[ Jelmer Vernooij ]
=====================================
debian/control
=====================================
@@ -3,13 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all
-Standards-Version: 4.4.0
+Standards-Version: 4.6.2
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/
+Rules-Requires-Root: no
Package: arden
Architecture: all
=====================================
debian/docs
=====================================
@@ -1 +1 @@
-debian/NEWS.Debian
+debian/NEWS
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*.fasta
=====================================
debian/patches/2to3_new.patch
=====================================
@@ -478,20 +478,35 @@ Last-Update: Fri, 13 Sep 2019 09:51:05 +0200
isvalid = INI.isvalidtriplet(item,Codon)
''' Hamming distance 1, AA is not equal to the given AA,forbid mutation to stopcodon '''
if (isvalid == True and AA !=INI.genetic_code[item] and INI.genetic_code[item]!="*"):
-@@ -280,9 +280,9 @@ def mutate_random(DNA,AminoAcid,distance
-
- # stats (INI.savepickle(pdic,header+"_pdic_e"))
- print("\r\n########Some stats:########")
-- print("DNA length:\t" + str(len(DNA)))
-- print("max substitutions:\t" + str(len(DNA)/distance))
-- print("#Balanced Mutations:\t" + str(succ_counter))
-+ print(("DNA length:\t" + str(len(DNA))))
-+ print(("max substitutions:\t" + str(len(DNA)/distance)))
-+ print(("#Balanced Mutations:\t" + str(succ_counter)))
+@@ -140,7 +140,7 @@ def mutate_random(DNA,AminoAcid,distance
+ # generate start positions for mutation (the samplespace)
+ samplespace = []
+- for i in range (2,len(AminoAcid),distance/3):
++ for i in range (2,len(AminoAcid),int(distance/3)):
+ samplespace.append(i)
- return ("".join(dna_list))
-\ No newline at end of file
+
+@@ -149,7 +149,8 @@ def mutate_random(DNA,AminoAcid,distance
+ r.shuffle(samplespace)
+ else:
+ pass
+-
++
++ DNA = str(DNA, 'utf-8')
+ dna_list = list(DNA)
+ AminoAcid_list = list(AminoAcid)
+
+@@ -162,6 +163,9 @@ def mutate_random(DNA,AminoAcid,distance
+ succ_counter = 0
+ fail_counter = 0
+ skip = 0
++ new_AA_triplet = ''
++ new_triplet = ''
++ position = 0
+
+ ''' Main loop over the AminoAcid'''
+ for i in samplespace:
--- a/core/PlotData.py
+++ b/core/PlotData.py
@@ -29,7 +29,7 @@ import pylab as p
@@ -532,6 +547,15 @@ Last-Update: Fri, 13 Sep 2019 09:51:05 +0200
import random
''' INIT DICTIONARIES '''
+@@ -109,7 +109,7 @@ def trans_seq(DNA):
+ prot = ""
+ rest=""
+
+- DNA = "".join(DNA)
++ DNA = str(DNA, 'utf-8')
+ for i in range(0,len(DNA),3):
+ # Codon exceeds length
+ if(i+3 > len(DNA)):
@@ -145,7 +145,7 @@ def savepickle(dictionary,outputname):
"""
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# See lintian bug #1017966
+arden source: source-is-missing
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/README
=====================================
@@ -0,0 +1,2 @@
+sample.fasta was copiead from lagan package
+
=====================================
debian/tests/data/sample.fasta
=====================================
@@ -0,0 +1,25 @@
+>sample1
+GGCATGTCCAGAAAATCCAAGTGCCTCTTCCTCTTGATCTTCTCCAACGATGTCCAGA
+AAATCCAAGTGCCTCATTCCTCTTGATCTTCTCCAGGCATGTCCAGAAAATCCAAGTG
+CCTCTTCCTCTCTGATCTTCTCCTCGGTTGGTCCAGAAAATCCAAGTGCCTCTTCCTC
+TTGATCTTCTCCAGAAATGTCCAGAAAATCCAAGTAGCCTCTTCCTCTTGATCGGCTC
+CAGAAATGTCCAGAAAAATCCAAGTGCCTCTTCCTCTTGATCGGCTCCATAAATGTCC
+AGAAAATCCAACGTGCCTCTTCCTCTTGATCGGCTCCAGAAATGTCCAGAAATATCCA
+AGTGCCTCTTCCTCTTGATCGGCTCCTTA
+>sample2
+CGATCCCAAATCCAAGTGCCTCAGAGTCTACTTGATCTTCAATTCAGATCCCAAATCC
+AAGTGCCTCAGAGTCTACTTGAATCTTCTATCGGGTCCCAAATCCAAGTGCCTCAGAG
+TCTACTTGATCTTCTCTCTCGATCCCATATCCAAGTGCCTCCTAGAGTCTACTTGATC
+TTCTCGATAACCAAAATCCAAGTGCCTCAGAGTCTACTTCACTCTTCTCGACTAACCC
+AAATCCAAGTGCCTCAGATGAGTCTACTTCCTCTTCTCATAACTCAAATCCAAGTGCC
+TCAGAGTCTAACTTCCTCTTCTCGAATAACCCAAATCCAAGTGCCTCAGAGTGTCTAC
+TTCCTCTTCTCG
+>sample3
+TACCCAAATCCAAGTGCCTCAGCGTCTAATAAAACAAGTCTTGATCTTCAACTCCTCC
+CAAATCCAAGTGCAACCTCAGCCGCTAATAAAAAGTCTTGATCTTCTCGCGTCCGGCA
+AATCCAAGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGGAGTCCCAAATCCA
+AGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGAGGAACAACAAATCCAAGTG
+CCTCAAGCGCTAATAAAAAGTCCCGATCTTCTCGTGACAATACAAATCCAAGTGCCTC
+AGCGCTAATAAAAAGTCCCGATCTTCTCCCGTGTAAACAAATCCAAGTGCCTCAGCGC
+TAATAAAAAGTCCCGATCTTCTCTGGTAACACAACAAATCCAAGTCACGCCTCAGATA
+CGCTAATAAAAAGTCCCGATCTTCTC
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,16 @@
+#!/bin/bash
+set -e
+
+pkg=arden
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+arden-create results/ sample.fasta -d 18
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Archive: SourceForge
Reference:
- Author: Sven H. Giese and Franziska Zickmann and Bernhard Y. Renard
Title: >
View it on GitLab: https://salsa.debian.org/med-team/arden/-/compare/af98067a7861ed997a6b371b45db564c18394f90...effd41349ce48a5d833a363fe00b75b7e8e225ad
--
View it on GitLab: https://salsa.debian.org/med-team/arden/-/compare/af98067a7861ed997a6b371b45db564c18394f90...effd41349ce48a5d833a363fe00b75b7e8e225ad
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