From: Afif Elghraoui <afif@debian.org>
Date: Mon, 20 Jun 2016 01:06:57 +0000 (-0700)
Subject: Drop obsolete patches
X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~222
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=9e083015995158ce58a533407e9a3b5a3449c036;p=python-pysam.git

Drop obsolete patches
---

diff --git a/debian/TODO b/debian/TODO
deleted file mode 100644
index 83ce291..0000000
--- a/debian/TODO
+++ /dev/null
@@ -1,4 +0,0 @@
-* Fix tests requiring network access
-   All tests should be passing now.
-   The ones that fail are failing because of network access issues.
-   Once this is fixed, the exit status of dh_auto_test should not be ignored.
diff --git a/debian/patches/compile-test.patch b/debian/patches/compile-test.patch
deleted file mode 100644
index d8f1ffc..0000000
--- a/debian/patches/compile-test.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: Fix compile-test
-Author: Afif Elghraoui <afif@debian.org>
-Forwarded: no
-Last-Update: 2016-03-09
---- python-pysam.orig/tests/compile_test.py
-+++ python-pysam/tests/compile_test.py
-@@ -15,7 +15,7 @@
- 
- 
- import pyximport
--pyximport.install(build_in_temp=False)
-+pyximport.install(build_in_temp=True)
- import _compile_test
- 
- import unittest
diff --git a/debian/patches/disable-tests-requiring-network.patch b/debian/patches/disable-tests-requiring-network.patch
deleted file mode 100644
index bc7872d..0000000
--- a/debian/patches/disable-tests-requiring-network.patch
+++ /dev/null
@@ -1,89 +0,0 @@
-Description: Disable tests requiring network access
-Author: Afif Elghraoui <afif@ghraoui.name>
-Forwarded: no
-Last-Update: 2015-11-13
---- python-pysam.orig/tests/tabix_test.py
-+++ python-pysam/tests/tabix_test.py
-@@ -1124,11 +1124,12 @@
-     local = os.path.join(DATADIR, "example.gtf.gz")
- 
-     def setUp(self):
--        self.remote_file = pysam.TabixFile(self.url, "r")
-+        if checkURL(self.url):
-+            self.remote_file = pysam.TabixFile(self.url, "r")
-         self.local_file = pysam.TabixFile(self.local, "r")
- 
-     def testFetchAll(self):
--        if not checkURL(self.url):
-+        if checkURL(self.url) == False:
-             return
- 
-         remote_result = list(self.remote_file.fetch())
-@@ -1139,14 +1140,15 @@
-             self.assertEqual(x, y)
- 
-     def testHeader(self):
--        self.assertEqual(list(self.local_file.header), [])
--        self.assertRaises(AttributeError,
--                          getattr,
--                          self.remote_file,
--                          "header")
-+        if checkURL(self.url):
-+            self.assertEqual(list(self.local_file.header), [])
-+            self.assertRaises(AttributeError,
-+                              getattr,
-+                              self.remote_file,
-+                              "header")
- 
-     def tearDown(self):
--        self.remote_file.close()
-+#        self.remote_file.close()
-         self.local_file.close()
- 
- 
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -2466,12 +2466,16 @@
-             filepath_index=os.path.join(DATADIR, 'ex1.cram.crai'))
- 
-     def testRemoteExplicitIndexBAM(self):
--        samfile = pysam.AlignmentFile(
--            "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam",
--            "rb",
--            filepath_index=os.path.join(DATADIR, 'ex1.bam.bai'))
-+        url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam"
-+        if checkURL(url):
-+            samfile = pysam.AlignmentFile(
-+                url,
-+                "rb",
-+                filepath_index=os.path.join(DATADIR, 'ex1.bam.bai'))
- 
--        samfile.fetch("chr1")
-+            samfile.fetch("chr1")
-+        else:
-+            pass
- 
- 
- class TestVerbosity(unittest.TestCase):
---- python-pysam.orig/tests/faidx_test.py
-+++ python-pysam/tests/faidx_test.py
-@@ -173,12 +173,13 @@
- 
- 
-     def testFTPView(self):
--        if not checkURL(self.url):
--            return
--        f = pysam.Fastafile(self.url)
--        self.assertEqual(
--            len(f.fetch("chr1", 0, 1000)),
--            1000)
-+        if checkURL(self.url):
-+            f = pysam.Fastafile(self.url)
-+            self.assertEqual(
-+                len(f.fetch("chr1", 0, 1000)),
-+                1000)
-+        else:
-+            return True
- 
- 
- if __name__ == "__main__":
diff --git a/debian/patches/series b/debian/patches/series
index 917fbdc..2f83d47 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
 external-htslib.patch
-disable-tests-requiring-network.patch
 rpath.patch
-compile-test.patch