From 04b720c17145a2c41a867d16216990ecbbd28cbe Mon Sep 17 00:00:00 2001
From: sagitter <sagitter@fedoraproject.org>
Date: Jun 21 2018 18:30:01 +0000
Subject: New patch for fixing Nexus/AlignIO tests (python-3.7.0 issue)


---

diff --git a/python-biopython-bug1693.patch b/python-biopython-bug1693.patch
deleted file mode 100644
index 9f158ea..0000000
--- a/python-biopython-bug1693.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-index 18b0a9f9c7..6faf95e569 100644
---- a/Bio/Nexus/Nexus.py
-+++ b/Bio/Nexus/Nexus.py
-@@ -444,6 +444,8 @@ def _kill_comments_and_break_lines(text):
- 
-     NOTE: this function is very slow for large files, and obsolete when using C extension cnexus
-     """
-+    if not text:
-+        return ""
-     contents = iter(text)
-     newtext = []
-     newline = []
diff --git a/python-biopython-bug1695.patch b/python-biopython-bug1695.patch
new file mode 100644
index 0000000..a356131
--- /dev/null
+++ b/python-biopython-bug1695.patch
@@ -0,0 +1,108 @@
+From 1d4c4a16c49d95d3c52e77c1e62c687ec64b284d Mon Sep 17 00:00:00 2001
+From: peterjc <p.j.a.cock@googlemail.com>
+Date: Thu, 21 Jun 2018 14:29:31 +0100
+Subject: [PATCH 1/3] Avoid leaking StopIteration in Bio/bgzf.py
+
+Still using this as an internal end-of-file, thus
+end-of-iteration signal, which is perhaps not ideal.
+
+See https://www.python.org/dev/peps/pep-0479/
+---
+ Bio/bgzf.py | 15 +++++++++++----
+ 1 file changed, 11 insertions(+), 4 deletions(-)
+
+diff --git a/Bio/bgzf.py b/Bio/bgzf.py
+index efa6262afa..e539ec4905 100755
+--- a/Bio/bgzf.py
++++ b/Bio/bgzf.py
+@@ -391,18 +391,25 @@ def BgzfBlocks(handle):
+     data_start = 0
+     while True:
+         start_offset = handle.tell()
+-        # This may raise StopIteration which is perfect here
+-        block_length, data = _load_bgzf_block(handle)
++        try:
++            block_length, data = _load_bgzf_block(handle)
++        except StopIteration:
++            break
+         data_len = len(data)
+         yield start_offset, block_length, data_start, data_len
+         data_start += data_len
+ 
+ 
+ def _load_bgzf_block(handle, text_mode=False):
+-    """Load the next BGZF block of compressed data (PRIVATE)."""
++    """Load the next BGZF block of compressed data (PRIVATE).
++
++    Returns a tuple (block size and data), or at end of file
++    will raise StopIteration.
++    """
+     magic = handle.read(4)
+     if not magic:
+-        # End of file
++        # End of file - should we signal this differently now?
++        # See https://www.python.org/dev/peps/pep-0479/
+         raise StopIteration
+     if magic != _bgzf_magic:
+         raise ValueError(r"A BGZF (e.g. a BAM file) block should start with "
+
+From 0694c396ef7988e3c032d27e86fb131257812687 Mon Sep 17 00:00:00 2001
+From: peterjc <p.j.a.cock@googlemail.com>
+Date: Thu, 21 Jun 2018 16:12:14 +0100
+Subject: [PATCH 2/3] Return None in generator functions, not StopIteration
+
+See https://www.python.org/dev/peps/pep-0479/
+---
+ Bio/TogoWS/__init__.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Bio/TogoWS/__init__.py b/Bio/TogoWS/__init__.py
+index 4018244bcf..3cf5309c8a 100644
+--- a/Bio/TogoWS/__init__.py
++++ b/Bio/TogoWS/__init__.py
+@@ -199,7 +199,7 @@ def search_iter(db, query, limit=None, batch=100):
+     """
+     count = search_count(db, query)
+     if not count:
+-        raise StopIteration
++        return
+     # NOTE - We leave it to TogoWS to enforce any upper bound on each
+     # batch, they currently return an HTTP 400 Bad Request if above 100.
+     remain = count
+
+From 86eb2275448da22aa6976c6c7c46f9779af95cf1 Mon Sep 17 00:00:00 2001
+From: peterjc <p.j.a.cock@googlemail.com>
+Date: Thu, 21 Jun 2018 16:22:51 +0100
+Subject: [PATCH 3/3] Fix Nexus StopIteration error under Python 3.7.0rc1
+
+Reported as Biopython GitHub issue #1693 via Fedora
+packaging work for Python 3.7.
+
+The StopIteration from the Nexus comment parsing could
+propogate up to AlignIO and cause a failure there too.
+See:
+
+https://github.com/biopython/biopython/issues/1693
+
+This is in some way triggered by the changes for PEP479,
+where inappropriate StopIteration exceptions get turned
+into RuntimeError exceptions instead, see:
+
+https://www.python.org/dev/peps/pep-0479/
+---
+ Bio/Nexus/Nexus.py | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/Bio/Nexus/Nexus.py b/Bio/Nexus/Nexus.py
+index 18b0a9f9c7..6faf95e569 100644
+--- a/Bio/Nexus/Nexus.py
++++ b/Bio/Nexus/Nexus.py
+@@ -444,6 +444,8 @@ def _kill_comments_and_break_lines(text):
+ 
+     NOTE: this function is very slow for large files, and obsolete when using C extension cnexus
+     """
++    if not text:
++        return ""
+     contents = iter(text)
+     newtext = []
+     newline = []
diff --git a/python-biopython.spec b/python-biopython.spec
index 14a1eb6..fbeaec6 100644
--- a/python-biopython.spec
+++ b/python-biopython.spec
@@ -31,7 +31,8 @@ Summary:          Python tools for computational molecular biology
 Source0:          https://github.com/biopython/biopython/archive/biopython-171.tar.gz#/biopython-biopython-171.tar.gz
 
 # https://github.com/biopython/biopython/issues/1693
-Patch0:           python-biopython-bug1693.patch
+# # https://github.com/biopython/biopython/issues/1695
+Patch0:           python-biopython-bug1695.patch
 
 # Starting from biopython-1.69, BioPython is released under the
 # "Biopython License Agreement"; it looks like a MIT variant