debian/README.source

+gclib for Debian
+================
+
+The final target which needs gclib is gffread.  This build the files
+
+  GBase.cpp
+  GArgs.cpp
+  GFaSeqGet.cpp
+  gdna.cpp
+  codons.cpp
+  gff.cpp
+  GStr.cpp
+  GFastaIndex.cpp
+  gff_utils.cpp
+
+To build proper libraries some rudimentary automake code was added as
+quilt patch.  Since the gclib source contains more C++ code that might
+be useful as well all those C++ file except the tests and the following
+source files are built and included into the library:
+
+  GBam.cpp:  This needs bam.h and sam.h while it needs to be clarified
+             from what project these header files are used
+  gdimg.cpp: This would introduce an unneeded dependency from libgd-dev
+
+
+FIXME: I tried to build mdtest but linking it against the just build
+library does not work the way I tried.  Some hint from someone who
+knows automake better than me might be helpful.
+
+
+ -- Andreas Tille <tille@debian.org>  Thu, 18 Apr 2019 12:54:42 +0200

debian/README.test

-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
-    sh run-unit-test
-
-in order to confirm its integrity.

debian/control

@@ -5,8 +5,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
-               d-shlibs,
-               libgd-dev
+               d-shlibs
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/libgclib
 Vcs-Git: https://salsa.debian.org/med-team/libgclib.git

debian/patches/autoconf.patch

@@ -4,7 +4,7 @@ Descriptions: Build proper libraries via automake
 
 --- /dev/null
 +++ b/Makefile.am
-@@ -0,0 +1,32 @@
+@@ -0,0 +1,38 @@
 +lib_LTLIBRARIES  = libgclib.la
 +
 +libgclibdir=$(includedir)
@@ -16,7 +16,6 @@ Descriptions: Build proper libraries via automake
 +                       GBase.cpp \
 +                       gcdb.cpp \
 +                       GCdbYank.cpp \
-+                       gdimg.cpp \
 +                       gdna.cpp \
 +                       GFaSeqGet.cpp \
 +                       GFastaIndex.cpp \
@@ -24,11 +23,14 @@ Descriptions: Build proper libraries via automake
 +                       gsocket.cpp \
 +                       gstopwatch.cpp \
 +                       GStr.cpp \
-+                       gtest.cpp \
 +                       GThreads.cpp
 +
-+#                       GBam.cpp # Exists but is not build by upstream Makefile
++#                       gdimg.cpp # Not build by upstream Makefile
++#				 # Would introduce unneeded dependency from libgd-dev
++#                       GBam.cpp # is not build by upstream Makefile
 +#				 # Would need bam.h / sam.h
++#                       gtest.cpp # Seems to be just a test (FIXME: create autopkgtest from it)
++
 +
 +libgclib_la_LDFLAGS = -version-info @LIB_VERSION@
 +
@@ -37,6 +39,10 @@ Descriptions: Build proper libraries via automake
 +pkgconfigdir=$(libdir)/pkgconfig
 +pkgconfig_DATA = libgclib.pc
 +
++# FIXME: Build mdtest to properly test the lib.  The code below does not work
++# mdtest_SOURCES = mdtest.cpp libgclib.a
++# mdtest_LDADD = -L. -lgclib
++# bin_PROGRAMS = mdtest
 --- /dev/null
 +++ b/libgclib.pc.in
 @@ -0,0 +1,11 @@

debian/rules

@@ -23,3 +23,6 @@ override_dh_install:
 		    debian/tmp/usr/lib/*/*.so
 	mkdir debian/$(DEB_SOURCE)-dev/usr/include/gclib
 	mv debian/$(DEB_SOURCE)-dev/usr/include/*.h* debian/$(DEB_SOURCE)-dev/usr/include/gclib
+	# delete header files of not compiled C++ source files
+	find debian/$(DEB_SOURCE)-dev -name gdimg.h -delete
+	find debian/$(DEB_SOURCE)-dev -name GBam.h -delete

debian/tests/control

-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr

debian/tests/run-unit-test

-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
-  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
-  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#