diff -Nru transtermhp-2.09/debian/changelog transtermhp-2.09/debian/changelog --- transtermhp-2.09/debian/changelog 2020-03-22 16:01:07.000000000 +0000 +++ transtermhp-2.09/debian/changelog 2020-08-20 12:26:55.000000000 +0000 @@ -1,8 +1,26 @@ -transtermhp (2.09-4build1) focal; urgency=medium +transtermhp (2.09-5) unstable; urgency=medium - * No-change rebuild for libgcc-s1 package name change. + * Team Upload. + [ Steffen Moeller ] + * d/u/metadata: yamllint + * Update metadata with ref to conda - -- Matthias Klose Sun, 22 Mar 2020 17:01:07 +0100 + [ Nilesh Patra ] + * Add python3 support + * Add autopkgtests + * Install relevant examples + * Add patch description + * Fix with cme + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- + update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Use secure URI in Homepage field. + * Set field Upstream-Contact in debian/copyright. + * Remove obsolete field Contact from debian/upstream/metadata (already present + in machine-readable debian/copyright). + + -- Nilesh Patra Thu, 20 Aug 2020 17:56:55 +0530 transtermhp (2.09-4) unstable; urgency=medium diff -Nru transtermhp-2.09/debian/compat transtermhp-2.09/debian/compat --- transtermhp-2.09/debian/compat 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru transtermhp-2.09/debian/control transtermhp-2.09/debian/control --- transtermhp-2.09/debian/control 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/control 2020-08-20 12:26:55.000000000 +0000 @@ -5,11 +5,12 @@ Fabian Klötzl Section: science Priority: optional -Build-Depends: debhelper (>= 11) -Standards-Version: 4.1.4 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/transtermhp Vcs-Git: https://salsa.debian.org/med-team/transtermhp.git -Homepage: http://transterm.cbcb.umd.edu/ +Homepage: https://transterm.cbcb.umd.edu/ +Rules-Requires-Root: no Package: transtermhp Architecture: any diff -Nru transtermhp-2.09/debian/copyright transtermhp-2.09/debian/copyright --- transtermhp-2.09/debian/copyright 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/copyright 2020-08-20 12:26:55.000000000 +0000 @@ -1,9 +1,10 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: transterm_hp -Source: http://transterm.cbcb.umd.edu/index.php +Source: https://transterm.cbcb.umd.edu/index.php Files-Excluded: 2ndscore transterm +Upstream-Contact: Carl Kingsford Files: * Copyright: Carl Kingsford carlk@umiacs.umd.edu @@ -33,7 +34,7 @@ GNU General Public License for more details. . You should have received a copy of the GNU General Public License - along with this program. If not, see + along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". diff -Nru transtermhp-2.09/debian/patches/2to3.patch transtermhp-2.09/debian/patches/2to3.patch --- transtermhp-2.09/debian/patches/2to3.patch 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/patches/2to3.patch 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,115 @@ +Author: Nilesh Patra +Description: Remove python-2 relevant code, use python3 support. +Last Changed: August 20, 2020 +--- a/make_expterm.py ++++ b/make_expterm.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + + import sys + +@@ -73,11 +73,11 @@ + j = int((tail - min_tail[at])/dy) + + if i == 0 or j == 0: +- print >> sys.stderr, at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy ++ print(at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy, file=sys.stderr) + + if not (0 <= i < num_bins and 0 <= j < num_bins): +- print >> sys.stderr, "WARNING: out of range values:", i, j, at, hp, tail +- print >> sys.stderr, "Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at] ++ print("WARNING: out of range values:", i, j, at, hp, tail, file=sys.stderr) ++ print("Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at], file=sys.stderr) + continue + + D[at][i][j] += 1 +@@ -90,12 +90,12 @@ + def warn_if_out_of_range(value, rng, title): + if value <= rng[0] or value >= rng[1]: + if title not in warned: +- print >> sys.stderr, "@" * 60 +- print >> sys.stderr, """WARNING: random %s generated with energy lower than supplied range. ++ print("@" * 60, file=sys.stderr) ++ print("""WARNING: random %s generated with energy lower than supplied range. + Such examples are ignored. I suggest you re-run calibrate.sh after changing +- the lowerbound in the range variable therein.""" % (title) +- print >> sys.stderr, "Range = ", rng, "Seen = ", value +- print >> sys.stderr, "@" * 60 ++ the lowerbound in the range variable therein.""" % (title), file=sys.stderr) ++ print("Range = ", rng, "Seen = ", value, file=sys.stderr) ++ print("@" * 60, file=sys.stderr) + warned[title] = True + return True + return False +@@ -105,8 +105,8 @@ + """Write out the matrix (transposed)""" + for j in range(len(A)): + for i in range(len(A)): +- print A[i][j], +- print ++ print(A[i][j], end=' ') ++ print() + + + def main(): +@@ -118,14 +118,14 @@ + #tail_range = (float(sys.argv[6]), float(sys.argv[7])) + + # print the header +- print seqlen, num_bins # hp_range[0], hp_range[1], tail_range[0], tail_range[1] ++ print(seqlen, num_bins) # hp_range[0], hp_range[1], tail_range[0], tail_range[1] + + set_ranges_from_file(infile, num_bins) + D = hist2d_from_file(infile, num_bins) #, hp_range, tail_range) + + # for every at value, compute and print the matrix + for at in sorted(D): +- print at, min_hp[at], max_hp[at], min_tail[at], max_tail[at] ++ print(at, min_hp[at], max_hp[at], min_tail[at], max_tail[at]) + print_matrix(D[at]) + + if __name__ == '__main__': main() +--- a/random_fasta.py ++++ b/random_fasta.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + + # generate a FASTA file with length random characters + import random, sys +@@ -11,7 +11,7 @@ + + def random_fasta(fasta, length, at): + fasta = open(fasta, 'w') +- print >> fasta, ">random uniform length=", length ++ print(">random uniform length=", length, file=fasta) + + for i in range(1,length+1): + fasta.write(random_base(at)) +@@ -26,7 +26,7 @@ + i += random.randint(5, 500) + j = i + random.randint(200, 2000) + if(j < length): +- print >> coords, "UNK", i, j, "random" ++ print("UNK", i, j, "random", file=coords) + i = j + coords.close() + +--- a/calibrate.sh ++++ b/calibrate.sh +@@ -52,11 +52,11 @@ + MAKE_EXPTERM=`findprog make_expterm.py` + + #============================== +-# Ensure python is avialable ++# Ensure python3 is avialable + #============================== + +-if [ ! -x "`which python`" ] ; then +- echo "`basename $0`: python must be installed to run calibration scripts" > /dev/stderr ++if [ ! -x "`which python3`" ] ; then ++ echo "`basename $0`: python3 must be installed to run calibration scripts" > /dev/stderr + exit 3 + fi + diff -Nru transtermhp-2.09/debian/patches/series transtermhp-2.09/debian/patches/series --- transtermhp-2.09/debian/patches/series 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/patches/series 2020-08-20 12:26:55.000000000 +0000 @@ -1,3 +1,4 @@ hardening.patch 0002-read_seq-return-NULL-instead-of-false.patch 0003-Don-t-overwrite-CXXFLAGS.patch +2to3.patch diff -Nru transtermhp-2.09/debian/salsa-ci.yml transtermhp-2.09/debian/salsa-ci.yml --- transtermhp-2.09/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/salsa-ci.yml 2020-08-20 12:26:55.000000000 +0000 @@ -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 diff -Nru transtermhp-2.09/debian/tests/control transtermhp-2.09/debian/tests/control --- transtermhp-2.09/debian/tests/control 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/tests/control 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @, python3 +Restrictions: allow-stderr + diff -Nru transtermhp-2.09/debian/tests/data/infile.fasta transtermhp-2.09/debian/tests/data/infile.fasta --- transtermhp-2.09/debian/tests/data/infile.fasta 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/tests/data/infile.fasta 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,38 @@ +>9258 +GGCGGUCGGAGGGACUCACCCUCUGACCUCUCCA +>9361 +UGGCCACCACCUGGAAUUCAGAAUGGGGCGCCCAGAACGCACCAGGGCCUGGGGUUGGGAUUCCCGAGUGGGAGCCCUUGGGGCGCUGGGAAUGCGGAGGCCGGGGCUGCUUUGGCUCCUGUCAGAGCCCUUCGGCCAUCCCUGACCUAGAACCUGACGUGAGUGGACCCCAGACCUCCCGCUCUCCAGGUGUUUCCAGACUGUUCCCUGAGAGCGGAGCCCAGCCCCUGCCCCUCCCCACAGGACGCACUCCCUAUUUAUGUUUGCACUAGAGGUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUGACCAAUUAACUUAUUUAUUCGGGAGGUUGGGGUGUCCCAGGGGACCCAGCGUAGGGACAGCCUUGGCUCUGGCGUGUUUUCUGUGAAAACGGAGCCGAGCCGUGGGCUGCUCCCCCUUGGCCUCCUGGCCUCCGUGCCUCCCUUCGCUUAUGUUUUGAAGAAAUAUUUAUCUGAUCAAGUUGUCUGAAUAAUGCUGAUUUGGUGACAGGCUGUCGCUACAUCGCUGAACCUCUGCUCCCCAGGGGAGUUUUGUCUGUAACCGCCCUACUGGUCAGUGGCGAGAAAUAAAAUGUGCUUAGAAAAG +>9365 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+GGGGGAUGCAUGCAGAUCAUUCACCACCCAGCCCAUCGCCCUCCCUGUCCUGCCAUUCCCAUUGGGCCUCCUCGUCCCCGAAAGGAAGGGGGACGAGCCGGGUCUCUAAGUCAUCACCCCGAACAACAACACUUAGAACUUGAGAUGCAAGGAUGUGUGACUCAGACCAGACCGGGGGCACUGACCACCGCAGCCUGGAAUCCAAACUGGGGCUUGCAGAACCCACUGGGUCUCCAGAUGCAAAUGGGGACACCUGAAAUGUGGAGGUCUCCUUGAGCCUCCGGCUCACUUCCGAAGAUCUGAGGAGUCCUCACCCAGAACUUGGCAUGACCUCCGACCUCCCUUGCACCGAAAGUUUCUAGACCCUCCCCUAAGAGAUGAAGCCCCCCGCCACGUGGCACUAGUCAGCCCUCUAUUUAUGUUUGCACUGAGAAUUAUUUAUUAUUUAUUAUUUAUAUAUUUAUUUAUUUCCUGGUGAAUGUAUUUAUUCAGGAGGUCGGGGAACCUGGGGGAUCCAGUGUUGGGGGUUGCCUGAGCUCAGACAUGUUUUCUAUGAAAAUGGAGCUGGAAUGUAGGCUGCUCCCACCCCGCUUCCUGGCCUCCUUACCUCCCUGUGCUUGUGGAUUUAUCGAUCGAGUUGUCUGGAUAAUGCUGAUUUGGCGACAGACUGUUGCUAUCUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUGCCUGUAAUCGUCCUACUGGUCAGUGGCGAAAAAUAAAGUUUGCUUAGAAAAG +>9544 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+GGCGACUGGCGUGUUCAUCCGUUCUCUACCCAGCCCCUGUCCCCGACUCUGACCCCCAUUACUCUGACCCCUUUAUCGUCUACUCCUCAGAGCCCCCAAUCUGUGUCCUUCUAACUUAGAAAGGGAAUUGUGGCUCUGGGUCCAACUCCGGGCUCAGAAUUUCCAACAACUACGAUGCUCAGAAACACACGAGACGCUGAAGUAGUGGCCUGGAUUGCGGGCUGCUCAUGAGCCGCCACCGGCAAGGAUUCCAAUGGGCUUUCGGAACUCACUGGAUCCCGGAAUGUCGAUGCCUGAGUGGAUCGGGGGAGUGGAGGGGGGAGUGGAUCAGGCUGCCUCUGGCUCACAAGGCUGCUGAAGAUGUCUCAGGCCUCCCUUCCUUCCUUCCUUCCCUCCCUCAGAGCUUCCCAGACUGUUCCCUGAGGCACAGCGCCCAGCCUUCCUUACGGAACCCCCUCUAUUUAUAAUUGCACCUGUGACUAUUUAUUUAUUAUUUAUUAUUUAUUUAUUUGCUUAUGAAUGUAUUUAUUUGGAAGGCCGGGGCGUCCUGGAGGACCCAGCGUUGGGAAGCUGUCUUCAGGCCAACAUGUUUUCUGUGAAAACGGAGCUAAACUACCAGCUAUCCCCAUCUGGUCCCCCACCCCUGCCUCGUUGCCUCCCCCCUUUUCUUUUGCUUAUGUUUAAAACAAGAUAUUUAUCUAACCCAGUUGUCUUAAUAAUGCUGAUUUGGUGACCAGGCUGUCGCUACAUCACUGAACCUCUGCUCCCCACGGGAGCCGUGACUGUAAUCGCCCUACGGGUCAUUGAGAGAAAUAAAGUUCGCUUGGAAAAG +>10141 +UAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUACUGAUGAUUGUAUUUAUUUGGAAGGUUAGAGUGUCCAGGGCCCAUCAGAGGAACAGUCCGGGGUCAGACAUGUUUUCUGUGAAAACAGAAUGAAAUGCAGACUGUUCCCACCUGGCCUCUCGGCCUCUGAACCUUCUUUUGCUUUUUAAAAAACAUACUAUUUAUCUAAUCCAGUAUCUUAAUAAUCUGAUUUGGUGACCAACUGUCGCUGCAUCGCUGAAACUCUGCUCCCCAGGGGAGUUGUCUGUAAUCGUCCUACUGGUCAGUGGCGAGAAAUAAAGACUGCUUAGAAAAG +>13616 +GAGAAAAGGGAAGUAAUACCCCCAACCUCCAUACUCUUCUUCACUCCCUACUUAACUUUUAUCGGUCUUCUUCCUUGUCCCUAGAAGGGUCCUUUUCUGGAUCAGGAAAAUGGUUCCGCAGUCUGGGAAUUAGAGUUUAGAACAAUCUAGAAUAUGAUAAAGGACAUUGAGAAACCAAGGAUCAGAAGAAUGAGAAUAGCUGUAUAAAUUGGCUGCAUAUCGAGGACCAUGGAAAUAUGGGAUCCAGAGUAACAUAAAAAUCUAUUAAGAAAUCCGUGUGCUGAAACAAAUUUAGAACCUAGAUAAAAACUGCAACCUGGAGACCAAGGGUACAGUUCCUAACACACAGAACAAGGACUAGCCCUAAAAGCCUGACCUGAGGGAAAGGAUCCUCUUUACUCUAGACCCUCUUUACUCUUUACCACUCUCUGAGAUAUAUCUGAUUUAGACCCAAUGUUGAAAUCUAGUUCUUUCCUGUUCUAUUUAUUGUGAUGCAGGAGCCAUGCCUUUUGCUUUCCCCCUCCCCCGAAGCGGCUUCUGUUAUUUAUGAUUGGAUAAUAUGGUUAUUUAUUUAUUUAUUAUUUAUUUAUUUAUUCUUAAGUGUAUUUAUUGAGAAGGUUAUCAUUCAUGGGGGGACACAGAUGUUGAGGUUUCCCCCAGCUCAGGAGUAUUUUCUAUGAAAAUGGAGCUGAAGCAAGGGGUGCUUCUAUCCUGGCCCCUUGAUCACCCUCCCACCUGCCUAUUUUUAAAAAUUAUCUGAUUUUAUUACAUUGUUGAUUUAGUGGCUAUGCGUCGCUGUAUCUCUGAACCUGUGCUCCCCAGGGGAGUCGUGUCUGUAAGCGCCCUAUUUGUCAGUGGUGAGAAAUAAACUUUGCUUUGAAAAG +>28377 +GGAAAUCCCCUCUUACCUGGUCCCAUUACUUUCCUUUUUUGUGCCCACUCCCCAAAUGCUGCCUCGUCGGGUCAAAACUGUAAACUG +>42254 +CCUGAGAACGUGGCCGCCUUCCCCGCGGGGGCUCGCUCCAUCUAUUUAUGUUUGCACUUGUGAUUAUUUAUUAUUUAUUUAUUAUUUAUUUAUUUGCCAGUGGAUAUAUUUAUUCAGGAGGUCGGGGAGACCCUACAUCGAAGCUGGCCUGGCUCGGACAUGUUUUCUGUGAAAACCGAGGUUGUUCCCAGCCAGUCUCUUGGUCUCCAGGCCUCCUUUGCAAGUGGUUUUAUUUAUCCGAUCAAAUUGUCUACGUUAAUGCUGAUUUGGUGACUAACUGUCGCUGCAUCGCUGAACCUCUGCUCCCCAGGGGAGUUGUGUCUGUAAUCGCCCUACUGGUCAGUGGCGAGAAAUAAAGUGUGCUUAGAAAAG diff -Nru transtermhp-2.09/debian/tests/README transtermhp-2.09/debian/tests/README --- transtermhp-2.09/debian/tests/README 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/tests/README 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,5 @@ +Tests for transtermhp +==================== + +The data for tests has been referenced from: + http://crispr.otago.ac.nz/newTTDB/ diff -Nru transtermhp-2.09/debian/tests/run-unit-test transtermhp-2.09/debian/tests/run-unit-test --- transtermhp-2.09/debian/tests/run-unit-test 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/tests/run-unit-test 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +pkg=transtermhp + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * +export PATH=.:$PATH +ls +echo 'Test 1' +./calibrate.sh expterm.dat +echo 'PASS' + +echo 'Test 2' +./mfold_rna.sh 2ndscore infile.fasta > test2.out +echo 'PASS' + diff -Nru transtermhp-2.09/debian/transtermhp.examples transtermhp-2.09/debian/transtermhp.examples --- transtermhp-2.09/debian/transtermhp.examples 1970-01-01 00:00:00.000000000 +0000 +++ transtermhp-2.09/debian/transtermhp.examples 2020-08-20 12:26:55.000000000 +0000 @@ -0,0 +1,6 @@ +debian/tests/data/* +expterm.dat +mfold_rna.sh +calibrate.sh +make_expterm.py +random_fasta.py diff -Nru transtermhp-2.09/debian/transtermhp.install transtermhp-2.09/debian/transtermhp.install --- transtermhp-2.09/debian/transtermhp.install 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/transtermhp.install 2020-08-20 12:26:55.000000000 +0000 @@ -1,7 +1,3 @@ transterm usr/bin 2ndscore usr/bin expterm.dat usr/share/transtermhp/ -calibrate.sh usr/share/doc/transtermhp/examples -mfold_rna.sh usr/share/doc/transtermhp/examples -make_expterm.py usr/share/doc/transtermhp/examples -random_fasta.py usr/share/doc/transtermhp/examples diff -Nru transtermhp-2.09/debian/upstream/metadata transtermhp-2.09/debian/upstream/metadata --- transtermhp-2.09/debian/upstream/metadata 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/upstream/metadata 2020-08-20 12:26:55.000000000 +0000 @@ -1,7 +1,7 @@ -Contact: Carl Kingsford Name: TransTermHP Reference: - Author: Carleton L Kingsford and Kunmi Ayanbule and Steven L Salzberg + Author: > + Carleton L Kingsford and Kunmi Ayanbule and Steven L Salzberg Title: > Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake @@ -10,14 +10,16 @@ Volume: 8 Number: 2 Pages: R22 - URL: http://genomebiology.com/2007/8/2/R22/abstract + URL: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-2-r22 DOI: 10.1186/gb-2007-8-2-r22 PMID: 17313685 - eprint: http://genomebiology.com/content/pdf/gb-2007-8-2-r22.pdf + eprint: https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-2-r22 Registry: - Name: OMICtools Entry: OMICS_06165 - Name: SciCrunch Entry: SCR_008244 - Name: bio.tools - Entry: NA \ No newline at end of file + Entry: NA + - Name: conda:bioconda + Entry: transtermhp diff -Nru transtermhp-2.09/debian/watch transtermhp-2.09/debian/watch --- transtermhp-2.09/debian/watch 2018-06-01 18:43:35.000000000 +0000 +++ transtermhp-2.09/debian/watch 2020-08-20 12:26:55.000000000 +0000 @@ -1,4 +1,4 @@ version=3 opts=dversionmangle=s/[~\+]dfsg// \ - http://transterm.cbcb.umd.edu/transterm_hp_v(.*)\.zip + https://transterm.cbcb.umd.edu/transterm_hp_v(.*)\.zip