This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository pbgenomicconsensus.
commit 5d23226d65dba45bba1d800bf82a38ca4e94ae02 Author: Afif Elghraoui <[email protected]> Date: Sat Jan 21 15:36:15 2017 -0800 Adapt test suite for missing pbtestdata --- debian/control | 2 +- debian/patches/missing-testdata.patch | 49 +++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + debian/tests/control | 2 -- 4 files changed, 51 insertions(+), 3 deletions(-) diff --git a/debian/control b/debian/control index 4b36a4d..7b5afde 100644 --- a/debian/control +++ b/debian/control @@ -17,7 +17,7 @@ Build-Depends: python-h5py (>= 2.0.1), python-numpy (>= 1.6.0), # Test-Depends: - pbtestdata, +# pbtestdata, (#832311) python-nose, python-cram, Standards-Version: 3.9.8 diff --git a/debian/patches/missing-testdata.patch b/debian/patches/missing-testdata.patch new file mode 100644 index 0000000..f7dbf3e --- /dev/null +++ b/debian/patches/missing-testdata.patch @@ -0,0 +1,49 @@ +Description: Disable test require missing package pbtestdata + pbtestdata is not yet available in Debian (due to now resolved issue + of missing explicit license terms), so we cannot run this test. +Author: Afif Elghraoui <[email protected]> +Forwarded: not-needed +Last-Update: 2016-01-21 +--- pbgenomicconsensus.orig/tests/unit/test_tool_contract.py ++++ pbgenomicconsensus/tests/unit/test_tool_contract.py +@@ -5,7 +5,11 @@ + from pbcore.io import openDataSet, ContigSet + import pbcommand.testkit + +-import pbtestdata ++try: ++ import pbtestdata ++ have_pbtestdata = True ++except ImportError: ++ have_pbtestdata = False + + DATA_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "data") + assert os.path.isdir(DATA_DIR) +@@ -73,16 +77,17 @@ + } + + +-class TestSummarizeConsensus(pbcommand.testkit.PbTestApp): +- DRIVER_BASE = "summarizeConsensus" +- DRIVER_EMIT = DRIVER_BASE + " --emit-tool-contract " +- DRIVER_RESOLVE = DRIVER_BASE + " --resolved-tool-contract " +- REQUIRES_PBCORE = True +- INPUT_FILES = [ +- pbtestdata.get_file("alignment-summary-gff"), +- pbtestdata.get_file("variants-gff") +- ] +- TASK_OPTIONS = {} ++#@unittest.skipIf(not have_pbtestdata, "pbtestdata is not installed") ++#class TestSummarizeConsensus(pbcommand.testkit.PbTestApp): ++# DRIVER_BASE = "summarizeConsensus" ++# DRIVER_EMIT = DRIVER_BASE + " --emit-tool-contract " ++# DRIVER_RESOLVE = DRIVER_BASE + " --resolved-tool-contract " ++# REQUIRES_PBCORE = True ++# INPUT_FILES = [ ++# pbtestdata.get_file("alignment-summary-gff"), ++# pbtestdata.get_file("variants-gff") ++# ] ++# TASK_OPTIONS = {} + + + if __name__ == "__main__": diff --git a/debian/patches/series b/debian/patches/series index 7db6f24..00448f4 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ spelling.patch verbose-testing.patch no-poa-convenience-script.patch +missing-testdata.patch diff --git a/debian/tests/control b/debian/tests/control index 3d92c7a..813cd3c 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -4,7 +4,6 @@ Depends: python-nose, python-cram, make, - pbtestdata, Restrictions: allow-stderr Test-Command: make extra-tests @@ -12,4 +11,3 @@ Depends: @, python-cram, make, - pbtestdata, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
