[med-svn] [python-pbh5tools] 02/08: Run cram tests at build time now that cram is packaged in Debian

[Afif Elghraoui]

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

afif-guest pushed a commit to branch master
in repository python-pbh5tools.

commit ec17c33bd80d6d3644d756ac56ed6833e6311e4f
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Nov 15 00:08:25 2015 -0800

    Run cram tests at build time now that cram is packaged in Debian
    
    The cram tests are still not run for autopkgtest because there
    is a failure due to autopkgtest #798066.
---
 debian/TODO                          |  8 --------
 debian/control                       |  1 +
 debian/patches/pbcore-change.patch   | 18 ++++++++++++++++++
 debian/patches/series                |  3 ++-
 debian/patches/verbose-testing.patch | 23 +++++++++++++++++++++++
 debian/rules                         |  6 +-----
 6 files changed, 45 insertions(+), 14 deletions(-)

diff --git a/debian/TODO b/debian/TODO
deleted file mode 100644
index 9b5e9c4..0000000
--- a/debian/TODO
+++ /dev/null
@@ -1,8 +0,0 @@
-* Package python-cram.
-   cram is required to run some of the tests.
-   cram's source is at <https://bitbucket.org/brodie/cram>.
-   It's also listed in the python package index.
-* Add python-cram as build-dependency and remove override_dh_auto_test.
-* Deal with architecture-dependent portions of the python module.
-   There's a C shared library that is compiled as part of the setup.py
-   build.
diff --git a/debian/control b/debian/control
index 9f573a4..8bd9b30 100644
--- a/debian/control
+++ b/debian/control
@@ -10,6 +10,7 @@ Build-Depends: debhelper (>= 9),
 	       python-pbcore,
 	       python-sphinx,
                python-nose,
+	       python-cram,
                pandoc
 Standards-Version: 3.9.6
 Homepage: https://github.com/PacificBiosciences/pbh5tools
diff --git a/debian/patches/pbcore-change.patch b/debian/patches/pbcore-change.patch
new file mode 100644
index 0000000..94a18ce
--- /dev/null
+++ b/debian/patches/pbcore-change.patch
@@ -0,0 +1,18 @@
+Description: Fix pbcore import statement
+Origin: upstream
+Applied-Upstream: 14493e6bd48ba442a07301e8069d79caa02efbb9
+Last-Update: 2014-12-24
+--- python-pbh5tools.orig/tests/test_cmph5lib_CmpH5Merge.py
++++ python-pbh5tools/tests/test_cmph5lib_CmpH5Merge.py
+@@ -3,9 +3,9 @@
+ import logging
+ import unittest
+ import shutil
+-
+-from pbcore.io.CmpH5IO import CmpH5Reader
+ import sys
++
++from pbcore.io import CmpH5Reader
+ from pbh5tools.CmpH5Select import cmpH5Select
+ from pbh5tools.CmpH5Merge import cmpH5Merge
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 5c2cfbf..bece2a1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 default-doc-theme
-enable-nosetests
+pbcore-change.patch
+verbose-testing.patch
diff --git a/debian/patches/verbose-testing.patch b/debian/patches/verbose-testing.patch
new file mode 100644
index 0000000..9e187f2
--- /dev/null
+++ b/debian/patches/verbose-testing.patch
@@ -0,0 +1,23 @@
+Description: Make tests verbose when called from upstream build system
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-11-14
+--- python-pbh5tools.orig/Makefile
++++ python-pbh5tools/Makefile
+@@ -17,13 +17,13 @@
+ 	python setup.py develop
+ 
+ test: examples
+-	find tests -name "*.py" | xargs nosetests
+-	find tests/cram -name "*.t" | xargs cram 
++	find tests -name "*.py" | xargs nosetests -v
++	find tests/cram -name "*.t" | xargs cram -v
+ doc:
+ 	sphinx-apidoc -T -f -o doc src/ && cd doc && make html
+ 
+ examples:
+-	cram doc/examples.t
++	cram -v doc/examples.t
+ 	sed 's/^  /    /' doc/examples.t > doc/examples.md
+ 
+ example-rendered: examples
diff --git a/debian/rules b/debian/rules
index 7a76793..83854d0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -24,13 +24,9 @@ override_dh_install:
 	mv $(BINDIR)/bash5tools.py $(BINDIR)/bash5tools
 	mv $(BINDIR)/cmph5tools.py $(BINDIR)/cmph5tools
 
-# cram is not in Debian, but required to run some of the tests.
-# This override skips building the tests to allow full package build in
-# the meantime.
-# cram's source is at https://bitbucket.org/brodie/cram
 override_dh_auto_test:
 	PYBUILD_SYSTEM=custom \
-	PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
+	PYBUILD_TEST_ARGS="PATH=$(CURDIR)/build/scripts-2.7:$$PATH $(MAKE) test" \
 	  dh_auto_test
 
 override_dh_auto_clean:

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbh5tools.git