[med-svn] [khmer] 01/02: fix patch

[Michael Crusoe]

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misterc-guest pushed a commit to branch experimental-2.1
in repository khmer.

commit 2388f23c46a9c9535d345741d9ed0e8f7670ed3d
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Mon Feb 20 05:36:17 2017 -0800

    fix patch
---
 debian/patches/amend-skip | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/debian/patches/amend-skip b/debian/patches/amend-skip
index 8264ee7..25a34ec 100644
--- a/debian/patches/amend-skip
+++ b/debian/patches/amend-skip
@@ -20,16 +20,23 @@ Subject: Fix fatal pytest.skip usage
      return [os.path.normpath(s) for s in glob.glob(path)]
 --- khmer.orig/tests/khmer_tst_utils.py
 +++ khmer/tests/khmer_tst_utils.py
-@@ -186,9 +186,9 @@
+@@ -186,7 +186,7 @@
              status = _runscript(scriptname, sandbox=sandbox)
          except SystemExit as err:
              status = err.code
 -        except:  # pylint: disable=bare-except
--            traceback.print_exc(file=sys.stderr)
--            status = -1
-+        #except:  # pylint: disable=bare-except
-+        #    traceback.print_exc(file=sys.stderr)
-+        #    status = -1
++        except (OSError, ValueError, TypeError):
+             traceback.print_exc(file=sys.stderr)
+             status = -1
      finally:
-         sys.argv = oldargs
-         out, err = sys.stdout.getvalue(), sys.stderr.getvalue()
+--- khmer.orig/scripts/extract-paired-reads.py
++++ khmer/scripts/extract-paired-reads.py
+@@ -168,7 +168,7 @@
+     paired_fp.close()
+ 
+     if n_pe == 0:
+-        raise Exception("no paired reads!? check file formats...")
++        raise TypeError("no paired reads!? check file formats...")
+ 
+     print('DONE; read %d sequences,'
+           ' %d pairs and %d singletons' %

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