[med-svn] [Git][med-team/macs][master] 9 commits: README.test needs to be in debian/ dir, spelling changes, add README.test +…

Andreas Tille gitlab at salsa.debian.org
Mon Feb 19 08:32:46 UTC 2018 

Andreas Tille pushed to branch master at Debian Med / macs


Commits:
f4b9f1ed by Andreas Tille at 2018-02-19T08:35:24+01:00
README.test needs to be in debian/ dir, spelling changes, add README.test + run-unit-test to package doc dir

- - - - -
bddd3cf3 by Andreas Tille at 2018-02-19T08:56:33+01:00
Example data were compressed in the packaging process and thus need to be uncompressed

- - - - -
2a8f764f by Andreas Tille at 2018-02-19T09:01:05+01:00
d/rules: Do not parse d/changelog

- - - - -
783a8c88 by Andreas Tille at 2018-02-19T09:02:05+01:00
Remove Tim Booth and H. Soon Gweon from Uploaders

- - - - -
bc3d2390 by Andreas Tille at 2018-02-19T09:02:22+01:00
Standards-Version: 4.1.3

- - - - -
37d04ce7 by Andreas Tille at 2018-02-19T09:02:50+01:00
hardening=+all

- - - - -
99791913 by Andreas Tille at 2018-02-19T09:03:11+01:00
debhelper 11

- - - - -
b9684156 by Andreas Tille at 2018-02-19T09:22:28+01:00
There is no dir examples/ neither are there and "*.tree" files - do not attempt to install non-existing files which breaks higher debhelper compat level

- - - - -
7c3b8d96 by Andreas Tille at 2018-02-19T09:23:42+01:00
There is no such package macs-example-data declared in debian/control thus this file is superflous

- - - - -


9 changed files:

- README.test → debian/README.test
- debian/changelog
- debian/compat
- debian/control
- debian/docs
- − debian/macs-example-data.install
- debian/macs.examples
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
README.test → debian/README.test
=====================================
--- a/README.test
+++ b/debian/README.test
@@ -1,4 +1,4 @@
-otes on how this package can be tested.
+Notes on how this package can be tested.
 
 
 This package can be tested by executing
@@ -7,6 +7,6 @@ This package can be tested by executing
 
 in order to confirm its integrity.
 
-Notes : the sample data are recovered from; https://github.com/arq5x/  They are both ‘.BED’ 
+Note: The sample data are recovered from https://github.com/arq5x/  They are both ‘.BED’ 
 file extensions. However the macs package install instructions is
 using the ‘BAM’ extension format. If anyone has any recommendation on where to find sample data in this format it will be much appreciated :)


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,11 @@ macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
   * debian/upstream/metadata:
      - UTF-8 notation of names rather than TeX syntax
      - added eprint
+  * d/rules: Do not parse d/changelog
+  * Remove Tim Booth and H. Soon Gweon from Uploaders
+  * Standards-Version: 4.1.3
+  * hardening=+all
+  * debhelper 11
 
  -- Andreas Tille <tille at debian.org>  Wed, 10 Aug 2016 08:15:22 +0200
 


=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,17 @@
 Source: macs
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
-           Tim Booth <tbooth at ceh.ac.uk>,
-           H. Soon Gweon <hyugwe at ceh.ac.uk>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all-dev,
                python-numpy,
                python-setuptools,
                help2man,
                cython
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/macs.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/macs.git
 Homepage: http://github.com/taoliu/MACS/


=====================================
debian/docs
=====================================
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,3 @@
 README.rst
+debian/README.test
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/macs-example-data.install deleted
=====================================
--- a/debian/macs-example-data.install
+++ /dev/null
@@ -1,4 +0,0 @@
-debian/examples/aluY.chr1.bed	usr/share/doc/macs/examples
-debian/examples/gerp.chr1.bed	usr/share/doc/macs/examples
-debian/README.test		usr/share/doc/macs
-debian/tests/run-unit-test	usr/share/doc/macs


=====================================
debian/macs.examples
=====================================
--- a/debian/macs.examples
+++ b/debian/macs.examples
@@ -1,3 +1 @@
-examples/*
 debian/examples/*
-release/common/*.tree


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,9 +1,10 @@
 #!/usr/bin/make -f
 
 export PYBUILD_NAME=MACS2
-export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
-DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+include /usr/share/dpkg/default.mk
+
 subcommands=callpeak bdgpeakcall bdgbroadcall bdgcmp bdgopt cmbreps bdgdiff \
 	      filterdup predictd pileup randsample refinepeak
 tagline=\- Model\-based Analysis for ChIP\-Sequencing
@@ -26,7 +27,7 @@ override_dh_auto_build:
 		> debian/macs2_$${subcommand}-man-include; done
 	for subcommand in ${subcommands}; do \
 		PYTHONPATH=./.pybuild/pythonX.Y_2.7/build/ help2man \
-		--no-discard-stderr --no-info --version-string="$(VERSION)" \
+		--no-discard-stderr --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
 		--include debian/macs2_$${subcommand}-man-include \
 		"python bin/macs2 $${subcommand}" > \
 		debian/macs2_$${subcommand}.1; done


=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -13,6 +13,7 @@ fi
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
+gunzip *.gz
 
 macs2 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
 macs2 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1



View it on GitLab: https://salsa.debian.org/med-team/macs/compare/2cc4ef8c16c90241faae96bb59042278d910b357...7c3b8d967668f7e8542b498ccb4619be930efb5b

---
View it on GitLab: https://salsa.debian.org/med-team/macs/compare/2cc4ef8c16c90241faae96bb59042278d910b357...7c3b8d967668f7e8542b498ccb4619be930efb5b
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