Michael R. Crusoe pushed to branch master at Debian Med / cnvkit
Commits:
0c7b10bf by Michael R. Crusoe at 2018-06-19T14:54:00-07:00
python3-future
- - - - -
98a7e5e7 by Michael R. Crusoe at 2018-06-19T14:58:19-07:00
fix override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
- - - - -
85927dc4 by Michael R. Crusoe at 2018-06-19T15:02:49-07:00
switch to /usr/share/dpkg/pkg-info.mk
- - - - -
07946303 by Michael R. Crusoe at 2018-06-19T15:13:02-07:00
release
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/python3compat.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+cnvkit (0.9.3-2) unstable; urgency=medium
+
+ * Add missing build-dep on python3-future. (Closes: #901877)
+ * debian/rules: fix override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
+
+ -- Michael R. Crusoe <michael.cru...@gmail.com> Tue, 19 Jun 2018 15:05:43
-0700
+
cnvkit (0.9.3-1) unstable; urgency=medium
* New upstream version.
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -17,6 +17,7 @@ Build-Depends: debhelper (>= 11~),
python3-scipy,
python3-matplotlib,
python3-pyvcf,
+ python3-future,
r-cran-pscbs
# python-subprocess32 # required only for python2
Standards-Version: 4.1.4
=====================================
debian/patches/python3compat.patch
=====================================
--- a/debian/patches/python3compat.patch
+++ b/debian/patches/python3compat.patch
@@ -1,3 +1,4 @@
+Description: enable building with Python3
Index: cnvkit/test/Makefile
===================================================================
--- cnvkit.orig/test/Makefile
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -3,14 +3,7 @@
export LC_ALL=C.UTF-8
export PYBUILD_NAME=cnvkit
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e
's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print
$$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}'
debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
+include /usr/share/dpkg/pkg-info.mk
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -42,14 +35,14 @@ override_dh_auto_install:
help2man --no-info --version-option=version \
--name="a command-line toolkit for copy number analysis." \
./cnvkit > debian/cnvkit.1
- PYTHONPATH=$$PYTHONPATH:. debian/genmanpages.py ${VERSION}
+ PYTHONPATH=$$PYTHONPATH:. debian/genmanpages.py ${DEB_VERSION_UPSTREAM}
# no longer distributed
#cd scripts && PYTHONPATH=../ help2man --no-info \
- # --version-string=${VERSION} --help-option='-h' \
+ # --version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
# ./cnvkit-refFlat2bed --name='Generate a BED file of the genes
or exons in the reference genome given in UCSC refFlat.txt format.' \
# > ../debian/cnvkit-refFlat2bed.1;
cd scripts && PYTHONPATH=../ help2man --no-info \
- --version-string=${VERSION} --help-option='-h' \
+ --version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
./cnvkit-reference2targets --name='Extract target and
antitarget BED files from a CNVkit reference file.' \
> ../debian/cnvkit-reference2targets.1;
cd scripts && for script in *; do \
@@ -59,7 +52,9 @@ override_dh_auto_install:
#mv genome2access.py scripts/ # no longer distributed
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd test && ${MAKE}
+endif
override_dh_auto_clean:
cd test && ${MAKE} clean || /bin/true
View it on GitLab:
https://salsa.debian.org/med-team/cnvkit/compare/1e7b5cf12678d5057a477f789c7ca4eb0a1263cc...079463032f42e52d77e5942a1ac91170a775dd1e
--
View it on GitLab:
https://salsa.debian.org/med-team/cnvkit/compare/1e7b5cf12678d5057a477f789c7ca4eb0a1263cc...079463032f42e52d77e5942a1ac91170a775dd1e
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