[med-svn] [Git][med-team/qcumber][master] 11 commits: Add config.txt from past version since debconf seems to rely on a basic config heavily
Nilesh Patra
gitlab at salsa.debian.org
Fri Sep 18 17:58:25 BST 2020
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 <npatra974 at gmail.com> Mon, 17 Feb 2020 19:13:32 +0530
+ -- Nilesh Patra <npatra974 at gmail.com> 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 <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,
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 <LieuV at rki.de>
Source: https://gitlab.com/RKIBioinformaticsPipelines/QCumber/tags
+
Files: *
Copyright: 2016-2017 Vivi Lieu <LieuV at rki.de>
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 <npatra974 at gmail.com>
+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
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