[med-svn] [Git][med-team/fast5-research][master] Fix change mux test

[Nilesh Patra]

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 <hello at shayandoust.me>, Nilesh Patra <npatra974 at gmail.com>
+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
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