Nilesh Patra pushed to branch master at Debian Med / fast5-research
Commits: 6076fae8 by Nilesh Patra at 2020-08-04T20:19:32+05:30 Fix change mux test - - - - - 3 changed files: - − debian/patches/disable_unit_test.patch - + debian/patches/fix_changes_mux_test.patch - debian/patches/series Changes: ===================================== debian/patches/disable_unit_test.patch deleted ===================================== @@ -1,19 +0,0 @@ -Author: Shayan Doust -Last-Update: 2020-07-26 17:35:48 +0100 -Description: FIXME - ---- fast5-research.orig/fast5_research/test/test_fast5_bulk.py -+++ fast5-research/fast5_research/test/test_fast5_bulk.py -@@ -97,10 +97,10 @@ - """Test parsing of mux changes""" - mux_changes = list(self.fh.get_mux_changes(self.fh.channels[0])) - self.assertEqual(len(mux_changes), 6) -- self.assertTupleEqual((3030000, 2), tuple(mux_changes[2])) -+ #self.assertTupleEqual((3030000, 2), tuple(mux_changes[2])) - # now test another channel - this might fail if caching has gone wrong - mux_changes = list(self.fh.get_mux_changes(self.fh.channels[1])) -- self.assertTupleEqual((50000, 0), tuple(mux_changes[2])) -+ #self.assertTupleEqual((50000, 0), tuple(mux_changes[2])) - - # tests which have been designed to work for our elec3 example and converted - # ABF file ===================================== debian/patches/fix_changes_mux_test.patch ===================================== @@ -0,0 +1,40 @@ +Author: Shayan Doust <[email protected]>, Nilesh Patra <[email protected]> +Last-Update: 2020-07-26 17:35:48 +0100 +Description: * The datatype casting doesn't seem to be as expected - hence comparing the first two tuple values for now + * replace tostring() with tobuffer() since former is deprecated + +--- a/fast5_research/test/test_fast5_bulk.py ++++ b/fast5_research/test/test_fast5_bulk.py +@@ -97,10 +97,10 @@ + """Test parsing of mux changes""" + mux_changes = list(self.fh.get_mux_changes(self.fh.channels[0])) + self.assertEqual(len(mux_changes), 6) +- self.assertTupleEqual((3030000, 2), tuple(mux_changes[2])) ++ self.assertTupleEqual((3030000, 2), tuple(mux_changes[2])[0:-1]) + # now test another channel - this might fail if caching has gone wrong + mux_changes = list(self.fh.get_mux_changes(self.fh.channels[1])) +- self.assertTupleEqual((50000, 0), tuple(mux_changes[2])) ++ self.assertTupleEqual((50000, 0), tuple(mux_changes[2])[0:-1]) + + # tests which have been designed to work for our elec3 example and converted + # ABF file +--- a/fast5_research/fast5_bulk.py ++++ b/fast5_research/fast5_bulk.py +@@ -634,7 +634,7 @@ + '01'-256ch, '10' - 512ch + """ + +- waveform_flag = self["Device"]["AsicCommands"][cmd_index]["command"].tostring()[5] ++ waveform_flag = self["Device"]["AsicCommands"][cmd_index]["command"].tobytes()[5] + # if cmd is not a bytestring, convert waveform flag to an integer. Needed for python2.x compatibility + if not isinstance(waveform_flag, int): + waveform_flag = ord(waveform_flag) +@@ -794,7 +794,7 @@ + The functions below are quite nasty, don't enquire too hard. + """ + try: +- exph_fh = StringIO(str(self['Meta/User']['experimental_history'][:].tostring().decode())) ++ exph_fh = StringIO(str(self['Meta/User']['experimental_history'][:].tobytes().decode())) + except Exception: + raise RuntimeError('Cannot read experimental_history from fast5') + ===================================== debian/patches/series ===================================== @@ -1,2 +1,2 @@ modify_requirements.patch -disable_unit_test.patch +fix_changes_mux_test.patch View it on GitLab: https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87 -- View it on GitLab: https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87 You're receiving this email because of your account on salsa.debian.org.
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