Nilesh Patra pushed to branch master at Debian Med / qcumber
Commits: 6574efe6 by Nilesh Patra at 2020-09-18T20:46:47+05:30 Add config.txt from past version since debconf seems to rely on a basic config heavily - - - - - 5eb435b8 by Nilesh Patra at 2020-09-18T20:47:12+05:30 qcumber.py in now Qcumber-2 - - - - - 42928461 by Nilesh Patra at 2020-09-18T20:47:21+05:30 Generate adapters.fa as per build.sh - - - - - f43cd71b by Nilesh Patra at 2020-09-18T20:47:36+05:30 Fix line break; - - - - - 259491b8 by Nilesh Patra at 2020-09-18T20:57:22+05:30 Fix lintian - - - - - 8f9dfafc by Nilesh Patra at 2020-09-18T21:01:45+05:30 Update upstream/metadata - - - - - e3ef8384 by Nilesh Patra at 2020-09-18T21:02:15+05:30 Rename tags - - - - - 38331fd5 by Nilesh Patra at 2020-09-18T21:07:47+05:30 Add python3 shebang wherever necessary - - - - - 5b384d1a by Nilesh Patra at 2020-09-18T22:27:34+05:30 Fix lintian tags - - - - - 89915f65 by Nilesh Patra at 2020-09-18T22:28:01+05:30 compat: 13 - - - - - c30fa3e7 by Nilesh Patra at 2020-09-18T22:28:09+05:30 Update changelog - - - - - 12 changed files: - debian/bin/qcumber - debian/changelog - + debian/config.txt - debian/control - debian/copyright - debian/install - debian/lintian-overrides - + debian/patches/add-python-shebang.patch - debian/patches/series - debian/rules - + debian/source/lintian-overrides - debian/upstream/metadata Changes: ===================================== debian/bin/qcumber ===================================== @@ -2,4 +2,4 @@ # Wrapper needed to let QCumber properly find its configuration file # in the same dir as the Python3 code resides -python3 /usr/share/qcumber/QCumber.py "$@" +python3 /usr/share/qcumber/QCumber-2 "$@" ===================================== debian/changelog ===================================== @@ -1,5 +1,6 @@ qcumber (2.3.0-1) UNRELEASED; urgency=medium + * Team Upload. [ Andreas Tille ] * New usptream version * Remove ancient X-Python-Version field @@ -24,10 +25,19 @@ qcumber (2.3.0-1) UNRELEASED; urgency=medium * Fix html file to use system libs * Bump standards version to 4.5.0 * Fix watch + * Add config.txt from past version since + debconf seems to rely on a basic config heavily + * qcumber.py in now Qcumber-2 + * Generate adapters.fa as per build.sh + * Fix line break; + * Fix lintian + * Update upstream/metadata + * Rename tags + * Add python3 shebang wherever necessary TODO: Upstream should tag latest version -> see https://gitlab.com/RKIBioinformaticsPipelines/QCumber/-/issues/27 - -- Nilesh Patra <[email protected]> Mon, 17 Feb 2020 19:13:32 +0530 + -- Nilesh Patra <[email protected]> Fri, 18 Sep 2020 21:08:05 +0530 qcumber (1.0.14+dfsg-1) unstable; urgency=medium ===================================== debian/config.txt ===================================== @@ -0,0 +1,3 @@ +[DEFAULT] +kraken_db = +adapter = /usr/share/trimmomatic ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, ===================================== debian/copyright ===================================== @@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: QCumber Upstream-Contact: Vivi Lieu <[email protected]> Source: https://gitlab.com/RKIBioinformaticsPipelines/QCumber/tags + Files: * Copyright: 2016-2017 Vivi Lieu <[email protected]> License: LGPL-3+ ===================================== debian/install ===================================== @@ -1,9 +1,10 @@ *.py usr/share/qcumber config/adapters.fa etc/qcumber -config/config.txt etc/qcumber +debian/config.txt etc/qcumber config/parameter.txt etc/qcumber *.tex usr/share/qcumber Rscripts usr/share/qcumber *.html usr/share/qcumber debian/bin usr +QCumber-2 usr/share/qcumber modules usr/share/qcumber ===================================== debian/lintian-overrides ===================================== @@ -1,6 +1,2 @@ # Empty File qcumber: executable-not-elf-or-script usr/share/qcumber/modules/__init__.py -# Cannot modify manapage -- created via help2man -qcumber: manpage-has-errors-from-man usr/share/man/man1/qcumber.1.gz 9: warning [p 1, 1.8i]: cannot adjust line -# Both binaries share the same manpage -qcumber: binary-without-manpage usr/bin/QCumber-2 ===================================== debian/patches/add-python-shebang.patch ===================================== @@ -0,0 +1,33 @@ +Author: Nilesh Patra <[email protected]> +Description: Add python3 shebang where necessary +Last-Changed: September 18, 2020 +Forwarded: Not-Needed +--- a/input_utils.py ++++ b/input_utils.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/python3 + # -*- coding: utf-8 -*- + '''utils module for snakemake pipeline + +--- a/modules/json_output.py ++++ b/modules/json_output.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/python3 + import json + import re + import sys +--- a/modules/utils.py ++++ b/modules/utils.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/python3 + import fileinput + import matplotlib.pyplot as plt + import numpy +--- a/test/test_qcumber2.py ++++ b/test/test_qcumber2.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python3 ++#!/usr/bin/python3 + # -*- coding: utf-8 -*- + from contextlib import contextmanager, ExitStack + import argparse ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ check_fasta.patch make_executable.patch fix_html_file_licenses.patch +add-python-shebang.patch ===================================== debian/rules ===================================== @@ -3,7 +3,13 @@ # DH_VERBOSE := 1 %: - dh $@ --with python3 --buildsystem=pybuild + dh $@ --with python3 # --buildsystem=pybuild + +override_dh_install: + adapter_path=/usr/share/trimmomatic + cat /usr/share/trimmomatic/* > config/adapters.fa + sed -i.bak "s#ADAPTER_PATH = \"\"#ADAPTER_PATH = \"${adapter_path}\"#g" QCumber-2 + dh_install override_dh_compress: dh_compress --exclude=.pdf ===================================== debian/source/lintian-overrides ===================================== @@ -0,0 +1,5 @@ +# False Positives +qcumber source: source-is-missing .pc* +qcumber source: source-contains-prebuilt-javascript-object .pc* +qcumber source: very-long-line-length-in-source-file .pc* +qcumber source: embedded-script-includes-copyright-statement .pc* ===================================== debian/upstream/metadata ===================================== @@ -7,3 +7,10 @@ Registry: Entry: qcumber - Name: SciCrunch Entry: NA +--- +Archive: GitHub +Bug-Database: https://gitlab.com/RKIBioinformaticsPipelines/QCumber/issues +Bug-Submit: https://gitlab.com/RKIBioinformaticsPipelines/QCumber/issues/new +Changelog: https://gitlab.com/RKIBioinformaticsPipelines/QCumber/tags +Repository: https://gitlab.com/RKIBioinformaticsPipelines/QCumber.git +Repository-Browse: https://gitlab.com/RKIBioinformaticsPipelines/QCumber View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/17519e967ed98c5ee18b30ace2d529a423bb9156...c30fa3e7a169b2c6f203eae2258cf618ce1ca720 -- View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/17519e967ed98c5ee18b30ace2d529a423bb9156...c30fa3e7a169b2c6f203eae2258cf618ce1ca720 You're receiving this email because of your account on salsa.debian.org.
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