[med-svn] [Git][med-team/python-biopython][master] Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587)

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / python-biopython


Commits:
5cd5d8d2 by Dylan Aïssi at 2020-05-15T09:42:02+02:00
Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587)

- - - - -


3 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/update_tests_new_ncbi_blast.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,13 @@
 python-biopython (1.76+dfsg-2) UNRELEASED; urgency=medium
 
   * Team upload.
+
+  [ Michael R. Crusoe ]
   * debian/control: mark the -doc package as Multi-Arch: foreign
 
+  [ Dylan Aïssi ]
+  * Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587)
+
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Fri, 17 Apr 2020 10:17:15 +0200
 
 python-biopython (1.76+dfsg-1) unstable; urgency=medium


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 remove_mathml-qname.patch
 privacy_breach.patch
 exclude_docstring_tests.patch
+update_tests_new_ncbi_blast.patch


=====================================
debian/patches/update_tests_new_ncbi_blast.patch
=====================================
@@ -0,0 +1,42 @@
+From: Peter Cock <p.j.a.cock at googlemail.com>
+Origin: https://github.com/biopython/biopython/pull/2890
+Bug: https://github.com/biopython/biopython/issues/2863
+Bug-Debian: https://bugs.debian.org/959587
+Description: Test updates for NCBI BLAST DB v5
+
+--- a/Tests/test_NCBI_BLAST_tools.py
++++ b/Tests/test_NCBI_BLAST_tools.py
+@@ -210,8 +210,14 @@
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phr"))
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pin"))
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pog"))
+-        self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psd"))
+-        self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psi"))
++        self.assertTrue(
++            os.path.isfile("GenBank/NC_005816.faa.psd")
++            or os.path.isfile("GenBank/NC_005816.faa.pnd")
++        )
++        self.assertTrue(
++            os.path.isfile("GenBank/NC_005816.faa.psi")
++            or os.path.isfile("GenBank/NC_005816.faa.pni")
++        )
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psq"))
+ 
+     def test_fasta_db_nucl(self):
+@@ -245,8 +251,14 @@
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhr"))
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nin"))
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nog"))
+-        self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd"))
+-        self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsi"))
++        self.assertTrue(
++            os.path.isfile("GenBank/NC_005816.fna.nsd")
++            or os.path.isfile("GenBank/NC_005816.fna.nnd")
++        )
++        self.assertTrue(
++            os.path.isfile("GenBank/NC_005816.fna.nsi")
++            or os.path.isfile("GenBank/NC_005816.fna.nni")
++        )
+         self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsq"))
+ 
+     # makeblastdb makes files in the same dir as the input, clean these up



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/5cd5d8d28352dc1e9206bd2e9b891eb2bc590fd6

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/5cd5d8d28352dc1e9206bd2e9b891eb2bc590fd6
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