Michael R. Crusoe pushed to branch master at Debian Med / seqan2

Commits:
8dee2cd3 by Michael R. Crusoe at 2018-02-19T02:15:23-08:00
Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.

- - - - -


8 changed files:

- debian/changelog
- debian/clean
- debian/control
- + debian/libseqan2-dev.docs
- − debian/libseqan2-dev.install
- debian/rules
- debian/tests/control
- debian/tests/run-tests


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+seqan2 (2.4.0+dfsg-8) unstable; urgency=medium
+
+  * Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.
+  * Use seperate build directory for the -dev package so we can run cmake with
+    -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+
+ -- Michael R. Crusoe <michael.cru...@gmail.com>  Mon, 19 Feb 2018 02:15:18 
-0800
+
 seqan2 (2.4.0+dfsg-7) unstable; urgency=medium
 
   * Split override_dh_install into -arch and -indep


=====================================
debian/clean
=====================================
--- a/debian/clean
+++ b/debian/clean
@@ -1,2 +1,3 @@
 fakehome/
 debian/files
+build/


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -6,9 +6,9 @@ Uploaders: Andreas Tille <ti...@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
-               python
-Build-Depends-Arch: cmake,
-                    zlib1g-dev,
+               python,
+               cmake
+Build-Depends-Arch: zlib1g-dev,
                     libbz2-dev,
                     libbam-dev,
                     libboost-dev,


=====================================
debian/libseqan2-dev.docs
=====================================
--- /dev/null
+++ b/debian/libseqan2-dev.docs
@@ -0,0 +1 @@
+README.rst


=====================================
debian/libseqan2-dev.install deleted
=====================================
--- a/debian/libseqan2-dev.install
+++ /dev/null
@@ -1,3 +0,0 @@
-include/seqan                  usr/include
-util/cmake/seqan-config.cmake  usr/share/cmake/seqan
-seqan-2.pc                     usr/share/pkgconfig


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -44,11 +44,13 @@ pkgdev=libseqan2-dev
 
 override_dh_auto_configure-arch:
        export DEB_BUILD_ARCH=${DEB_BUILD_ARCH} ; \
-       dh_auto_configure -- \
+       dh_auto_configure --arch -- \
                -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \
                -DSEQAN_DISABLE_VERSION_CHECK=YES
 
-override_dh_auto_configure-indep: ;
+override_dh_auto_configure-indep:
+       dh_auto_configure --indep -B build -- \
+               -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1
 
 override_dh_auto_build-arch:
        dh_auto_build --arch ${MAX_PARALLEL}
@@ -58,16 +60,13 @@ override_dh_auto_build-arch:
        # Seems there is no sphinx module bibtex - thus deactivating creation 
of html manual
        # cd manual && make html
 
-override_dh_auto_build-indep:
-       sed -e "s=@CMAKE_INSTALL_PREFIX@=/usr=g" \
-           -e "s/@SEQAN_VERSION_STRING@/$(DEB_VERSION_UPSTREAM_REVISION)/g" \
-           -e "s/@CMAKE_PROJECT_NAME@/seqan/g" \
-           -e "s=@CMAKE_INSTALL_FULL_INCLUDEDIR@=/usr/include=g" \
-           util/pkgconfig/seqan.pc.in > seqan-2.pc
+override_dh_auto_install-indep:
+       dh_auto_install --indep -B build --destdir=$(CURDIR)/debian/$(pkgdev)/
+       rm -Rf $(CURDIR)/debian/$(pkgdev)/usr/share/doc/seqan
 
 override_dh_install-indep:
        dh_install --indep
-       # Delete additional LICENSE files
+       # Delete additional LICENSE and compiled Python files
        if [ -d $(CURDIR)/debian/$(pkgdev) ] ; then \
            find $(CURDIR)/debian/$(pkgdev) -type f -name LICENSE -delete ; \
            find $(CURDIR)/debian/$(pkgdev) -type f -name "*.pyc" -delete ; \
@@ -90,36 +89,26 @@ override_dh_auto_clean:
            mv $${header} `echo $$header | sed 's?orig/??'` ; \
          done ; \
        fi
-       rm -rf orig seqan-2.pc
+       rm -rf orig
 
 override_dh_installman-arch:
-       dh_link -a
+       dh_link --arch
        if [ -d $(CURDIR)/debian/$(pkgapps)/usr/bin ] ; then \
                find $(CURDIR)/debian/$(pkgapps)/usr/bin -type l -xtype l 
-delete ; \
        fi
        $(CURDIR)/debian/generate_manpages
-       #for bin in `ls $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin` ; do \
-       #    if [ -x $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/`basename 
$${bin}` ] ; then \
-       #        ln -s ../lib/seqan/bin/`basename $${bin}` 
$(CURDIR)/debian/$(pkgapps)/usr/bin/`basename $${bin}` ; \
-       #    fi ; \
-       #    if echo $${bin} | grep -q '\.sh$$' ; then \
-       #        ln -s ../lib/seqan/bin/$${bin} 
$(CURDIR)/debian/$(pkgapps)/usr/bin/`basename $${bin} .sh` ; \
-       #    fi ; \
-       #done
-       # we generate only those manpages where binaries are linked to /usr/bin
-       dh_installman -a
+       dh_installman --arch
 
 override_dh_link-arch:
-       dh_link
+       dh_link --arch
        # Some binaries (eg. splazer) are not built in 32-bit architectures so
        # remove their (broken) symlinks.
        if [ -d $(CURDIR)/debian/$(pkgapps)/usr/bin ] ; then \
            find $(CURDIR)/debian/$(pkgapps)/usr/bin -type l -xtype l -delete ; 
\
        fi
 
-override_dh_fixperms-indep:
-       dh_fixperms
+override_dh_fixperms-arch:
+       dh_fixperms --arch
        for bin in `ls $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/*.sh` ; do 
\
            chmod +x $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/`basename 
$${bin}` ; \
        done
-       find $(CURDIR)/debian/$(pkgdev)/usr/share/cmake -type f -exec chmod -x 
{} \;


=====================================
debian/tests/control
=====================================
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1,3 +1,3 @@
 Tests: run-tests
-Depends: seqan-apps
+Depends: @, @builddeps@, zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev
 Restrictions: allow-stderr


=====================================
debian/tests/run-tests
=====================================
--- a/debian/tests/run-tests
+++ b/debian/tests/run-tests
@@ -1,8 +1,12 @@
-#!/bin/sh -e
+#!/bin/sh -ex
 
 mkdir build
 cd build
-cmake ../
+cmake ../ -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None \
+       -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \
+       -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON \
+       -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \
+       -DSEQAN_DISABLE_VERSION_CHECK=YES
 rmdir bin
 ln -s /usr/lib/seqan/bin bin
 ctest --tests-regex 'app_.*' --parallel $(nproc)



View it on GitLab: 
https://salsa.debian.org/med-team/seqan2/commit/8dee2cd37cabfc9a419cb3466761c4572622600e

---
View it on GitLab: 
https://salsa.debian.org/med-team/seqan2/commit/8dee2cd37cabfc9a419cb3466761c4572622600e
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