debian/changelog

+ngs-sdk (2.10.0-2) unstable; urgency=medium
+
+  * Drop Python2 support
+    Closes: #937139
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Remove trailing whitespace in debian/changelog
+
+ -- Andreas Tille <tille@debian.org>  Wed, 11 Sep 2019 11:10:25 +0200
+
 ngs-sdk (2.10.0-1) unstable; urgency=medium
 
   [ Olivier Sallou ]
-  * New upstream release 
+  * New upstream release
 
  -- Olivier Sallou <osallou@debian.org>  Wed, 11 Sep 2019 07:27:49 +0000
 

debian/compat

-11

debian/control

@@ -5,17 +5,16 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Vincent Danjean <vdanjean@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                d-shlibs,
-               python-markdown,
-               python-all-dev,
+               markdown,
                python3-all,
                python3-distutils,
                dh-python,
                javahelper,
                maven-repo-helper,
                default-jdk
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/ngs-sdk
 Vcs-Git: https://salsa.debian.org/med-team/ngs-sdk.git
 Homepage: https://github.com/ncbi/ngs
@@ -81,27 +80,6 @@ Description: Next Generation Sequencing language Bindings (Java bindings)
  .
  Java bindings.
 
-Package: python-ngs
-Architecture: any
-Section: python
-Depends: ${python:Depends},
-         ${misc:Depends},
-         libngs-sdk-dev (= ${binary:Version})
-Description: Next Generation Sequencing language Bindings (Python bindings)
- NGS is a new, domain-specific API for accessing reads, alignments and
- pileups produced from Next Generation Sequencing. The API itself is
- independent from any particular back-end implementation, and supports
- use of multiple back-ends simultaneously. It also provides a library for
- building new back-end "engines". The engine for accessing SRA data is
- contained within the sister repository ncbi-vdb.
- .
- The API is currently expressed in C++, Java and Python languages. The
- design makes it possible to maintain a high degree of similarity between
- the code in one language and code in another - especially between C++
- and Java.
- .
- Python bindings.
-
 Package: python3-ngs
 Architecture: any
 Section: python

debian/rules

@@ -12,11 +12,10 @@ MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 # since build-results are not ending up in the proper dir its saver to use "*" instead of "$(CPU)"
 SODIR := $(DEB_SOURCE)/$(MULTIARCH)/$(DEB_SOURCE)/$(OS)/gcc/*
 
-build2vers := $(shell pyversions -sv)
 build3vers := $(shell py3versions -sv)
 
 %:
-	dh $@ --with python2,python3,javahelper,jh_maven_repo_helper
+	dh $@ --with python3,javahelper,jh_maven_repo_helper
 
 override_dh_auto_clean:
 	if [ -e ngs-sdk/Makefile.config.$(OS).$(CPU) ] ; then \
@@ -46,7 +45,7 @@ override_dh_auto_build:
 	#cd ngs-bam && LD_LIBRARY_PATH=../$(SODIR)/rel/lib ./configure --build=$(MULTIARCH) --prefix=/usr --with-ngs-sdk-prefix=../ngs-sdk
 	#dh_auto_build --sourcedirectory=ngs-bam
 	dh_auto_build --sourcedirectory=ngs-java -- JAVAC="javac -source 1.7 -target 1.7"
-	markdown_py -f README.html README.md
+	markdown README.md > README.html
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -75,12 +74,6 @@ override_dh_install:
 		python$$i ./setup.py install --install-layout=deb --root ../debian/python3-ngs; \
 		cd .. ; \
 	done
-	dh_install -ppython-ngs
-	set -e && for i in $(build2vers); do \
-		cd ngs-python ; \
-		python$$i ./setup.py install --install-layout=deb --root ../debian/python-ngs; \
-		cd .. ; \
-	done
 	find debian -name "*.pyc" -delete
 	find debian -type d -name __pycache__ | xargs rm -rf