[med-svn] [jellyfish] 05/06: Add autopkgtest

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository jellyfish.

commit cf20f9581a2054bfd83d36eb26441877919051df
Author: Andreas Tille <tille at debian.org>
Date:   Wed Oct 8 22:25:20 2014 +0200

    Add autopkgtest
---
 debian/README.test              |  9 +++++++++
 debian/changelog                |  1 +
 debian/control                  |  7 ++++---
 debian/jellyfish-examples.links |  1 +
 debian/jellyfish.docs           |  3 ++-
 debian/tests/control            |  3 +++
 debian/tests/run-unit-test      | 35 +++++++++++++++++++++++++++++++++++
 7 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..678be3f
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you need to install the package
+jellyfish-examples and than you can run
+
+   sh run-unit-test
+
+in this directory.
\ No newline at end of file
diff --git a/debian/changelog b/debian/changelog
index 4f688a4..d75dcfc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -14,6 +14,7 @@ jellyfish (2.1.4-1) UNRELEASED; urgency=medium
     failed - add lintian override to use internal one
   * Split libjellyfish and libjellyfish-dev packages up from single
     package, add jellyfish-examples package containing test suite
+  * Add autopkgtest
 
  -- Andreas Tille <tille at debian.org>  Sat, 04 Oct 2014 19:06:43 +0200
 
diff --git a/debian/control b/debian/control
index 42cd984..aa79d13 100644
--- a/debian/control
+++ b/debian/control
@@ -21,7 +21,7 @@ Package: jellyfish
 Architecture: any-amd64
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libjellyfish-2.0-2 (= ${source:Version})
+         libjellyfish-2.0-2 (= ${binary:Version})
 Description: count k-mers in DNA sequences
  JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
  DNA. A k-mer is a substring of length k, and counting the occurrences
@@ -65,7 +65,7 @@ Architecture: any-amd64
 Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libjellyfish-2.0-2 (= ${source:Version})
+         libjellyfish-2.0-2 (= ${binary:Version})
 Description: count k-mers in DNA sequences (development files of jellyfish)
  JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
  DNA. A k-mer is a substring of length k, and counting the occurrences
@@ -86,7 +86,8 @@ Description: count k-mers in DNA sequences (development files of jellyfish)
 
 Package: jellyfish-examples
 Architecture: any-amd64
-Depends: ${shlibs:Depends},
+Depends: jellyfish,
+         ${shlibs:Depends},
          ${misc:Depends}
 Description: count k-mers in DNA sequences (examples for testing)
  JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
diff --git a/debian/jellyfish-examples.links b/debian/jellyfish-examples.links
new file mode 100644
index 0000000..3c8edc3
--- /dev/null
+++ b/debian/jellyfish-examples.links
@@ -0,0 +1 @@
+usr/bin/jellyfish	usr/lib/jellyfish/bin/jellyfish
diff --git a/debian/jellyfish.docs b/debian/jellyfish.docs
index 64b0214..9dfe4a1 100644
--- a/debian/jellyfish.docs
+++ b/debian/jellyfish.docs
@@ -1,2 +1,3 @@
-README
 doc/jellyfish.pdf
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..25377fc
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..547cf14
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,35 @@
+#!/bin/sh -e
+
+pkg=jellyfish
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+mkdir tests
+cp -a /usr/share/doc/jellyfish-examples/examples/* tests
+sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" tests/compat.sh
+tests/generate_sequence.sh
+sh tests/parallel_hashing.sh
+sh tests/merge.sh
+sh tests/bloom_filter.sh
+echo "If you have a *really* powerful machine you can run this *really* big test by prepending"
+echo "  'BIG=1' "
+echo "before the following line"
+sh tests/big.sh
+sh tests/subset_hashing.sh
+##############################################################################################
+# It seems the following failures in the following test are planed ...
+#
+# $ jellyfish count -t 2 -g multi_file_fail_cmds -G 2 -C -m 15 -s 2M -o multi_file_fail.jf
+# Command 'false' exited with error status 1
+# Some generator commands failed
+# $ jellyfish count -t 2 -C -m 15 -s 2M -o multi_file_fail.jf non_existent_sequence.fa
+# terminate called after throwing an instance of 'std::runtime_error'
+#   what():  Can't open file 'non_existent_sequence.fa'
+# Aborted
+#
+sh tests/multi_file.sh
+#############################################################################################
+sh tests/bloom_counter.sh
+sh tests/large_key.sh
+/usr/lib/jellyfish/bin/test_all

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