debian/README.source

@@ -3,7 +3,3 @@ khmer with changes they made. See third-party/seqan/ChangeLog for details. The
 most important change is a bugfix which was acknowledged by the SeqAn developers
 but will not be fixed until the version 2.0 release of SeqAn:
 https://github.com/seqan/seqan/issues/720
-
-Skip packaging khmer v2.1.2 until cython version 0.26.1 in in Debian or
-https://github.com/cython/cython/commit/18bba8ff0261206db9243c2b1721633cb798af54
-is patched in

debian/changelog

+khmer (2.1.2+dfsg-5) unstable; urgency=medium
+
+  * Fix liboxli-dev autopkgtest.
+  * debian/khmer.metainfo.xml: Use a component ID in reverse domain-name
+    format.
+  * shrink khmer-common and silence many lintian warnings by symlinking to the
+    relevant files in python3-guzzle-sphinx-theme
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 08 Jan 2019 06:16:30 -0800
+
 khmer (2.1.2+dfsg-4) unstable; urgency=medium
 
   * Team upload.

debian/clean

 fakehome/
 debian/*.1
 .pybuild/
+.pytest_cache/
 khmer.egg-info/
 khmer/_oxli/*.cp*
 khmer/_khmer.cpython*

debian/control

@@ -21,8 +21,7 @@ Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                libbz2-dev,
                asciidoctor,
-               libjs-jquery,
-               libjs-twitter-bootstrap
+	       rdfind
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/khmer
 Vcs-Git: https://salsa.debian.org/med-team/khmer.git
@@ -33,7 +32,8 @@ Architecture: all
 Multi-Arch: foreign
 Depends: file,
          ${misc:Depends},
-         ${sphinxdoc:Depends}
+         ${sphinxdoc:Depends},
+	 python3-guzzle-sphinx-theme
 Description: common files for the khmer project tools
  khmer is a library and suite of command line tools for working with DNA
  sequence. It is primarily aimed at short-read sequencing data such as

debian/khmer-common.lintian-overrides

-khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt

debian/khmer.lintian-overrides

-# These files are unchanged files from upstream tarball.  There is no problem for a reproducible build
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz
-
 # The test data are provided in different compression methods intentionally to test different compression methods
 # Since they are small anyway there is no reason to work around this
 khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2

debian/khmer.metainfo.xml

 <?xml version="1.0" encoding="UTF-8"?>
 <component>
-  <id>oxli</id>
+  <id>io.readthedocs.khmer</id>
   <metadata_license>MIT</metadata_license>
   <name>khmer</name>
   <summary>in-memory DNA sequence kmer counting, filtering &amp; graph traversal</summary>

debian/patches/fix_liboxli_test

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix liboxli sanity check test
+--- khmer.orig/src/oxli/test-compile.cc
++++ khmer/src/oxli/test-compile.cc
+@@ -39,10 +39,10 @@
+ // This file is used to test compilation with liboxli.a/liboxli.so, after
+ // installation
+ 
+-#include <oxli/hashtable.hh>
++#include <oxli/hashgraph.hh>
+ 
+ int main()
+ {
+-    oxli::Countgraph test(1,1);
++    oxli::Countgraph test(1,{1});
+     return 0;
+ }

debian/patches/series

@@ -10,3 +10,4 @@ cpython-bug-empty-exceptions
 amend-skip
 setup.py-py3
 python3
+fix_liboxli_test

debian/rules

@@ -28,7 +28,8 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PYBUILD_SYSTEM=custom \
 	    PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \
 	    cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \
-	    -m 'not known_failing and not jenkins and not huge'" dh_auto_test
+	    -m 'not known_failing and not jenkins and not huge and not noroot'\
+	    -q" dh_auto_test
 endif
 
 override_dh_auto_clean:
@@ -42,5 +43,10 @@ override_dh_install:
 	find debian/khmer -name .gitignore -delete
 
 override_dh_sphinxdoc:
-	dh_sphinxdoc -X jquery.js
-
+	dh_sphinxdoc
+	rdfind -makesymlinks true -followsymlinks true\
+		/usr/lib/python3/dist-packages/guzzle_sphinx_theme \
+		$(shell find debian/khmer-common | grep -i -v citation)
+	rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt
+	cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \
+		ln -s ../../CITATION citations.rst.txt

debian/tests/run-unit-test

@@ -2,8 +2,8 @@
 
 pkg=khmer
 if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+	ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
 fi
-cd $ADTTMP
+cd "$ADTTMP"
 PATH=/usr/lib/khmer/bin/:$PATH python3 -m pytest --pyarg khmer \
-	-m 'not known_failing and not huge'
+	-m 'not known_failing and not huge and not noroot' -q

debian/tests/test-liboxli-dev

@@ -2,17 +2,20 @@
 
 pkg=khmer
 if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
 fi
-cd $ADTTMP
+cd "$ADTTMP"
 
-c++ -o test-prog-static -static -std=c++11 `pkg-config oxli --static --cflags` -I/usr/include/oxli/smhasher \
-  /usr/share/doc/khmer-common/test-compile.cc `pkg-config oxli --static --libs`
+c++ -o test-prog-static -static -std=c++11 \
+	$(pkg-config oxli --static --cflags) -I/usr/include/oxli/smhasher \
+	/usr/share/doc/khmer-common/test-compile.cc \
+	$(pkg-config oxli --static --libs)
 
 ./test-prog-static
 
-c++ -o test-prog-dynamic -std=c++11 `pkg-config oxli --cflags` -I/usr/include/oxli/smhasher \
-	/usr/share/doc/khmer-common/test-compile.cc `pkg-config oxli --libs`
+c++ -o test-prog-dynamic -std=c++11 $(pkg-config oxli --cflags) \
+	-I/usr/include/oxli/smhasher \
+	/usr/share/doc/khmer-common/test-compile.cc $(pkg-config oxli --libs)
 
 ./test-prog-dynamic