[med-svn] [fast5] 01/03: Imported Upstream version 0.5.7

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository fast5.

commit 847c50fb99d93d49f95957d2d8347e328968039f
Author: Afif Elghraoui <a...@debian.org>
Date:   Sat Oct 8 04:13:36 2016 -0700

    Imported Upstream version 0.5.7
---
 .gitignore              | 1 +
 .travis.Dockerfile.in   | 3 +--
 README.org              | 2 +-
 VERSION                 | 2 +-
 python/fast5/version.py | 2 +-
 python/setup.py         | 8 ++++++--
 6 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index 113a175..cc2c46e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 /build*
 /local*
+/file.*.fast5
diff --git a/.travis.Dockerfile.in b/.travis.Dockerfile.in
index a63b01d..18e40bb 100644
--- a/.travis.Dockerfile.in
+++ b/.travis.Dockerfile.in
@@ -1,4 +1,4 @@
-FROM debian:unstable
+FROM buildpack-deps:jessie
 MAINTAINER Matei David <matei.david.at.oicr.on.ca>
 ARG DEBIAN_FRONTEND=noninteractive
 
@@ -11,7 +11,6 @@ RUN apt-get update && \
     apt-get install -y \
         build-essential \
         libhdf5-dev \
-        libboost-dev \
         libboost-python-dev \
         python2.7-minimal \
         python-setuptools \
diff --git a/README.org b/README.org
index a62c402..14a23ff 100644
--- a/README.org
+++ b/README.org
@@ -2,7 +2,7 @@
 
 ** Fast5 Library
 
-[[http://travis-ci.org/mateidavid/fast5][http://travis-ci.org/mateidavid/fast5.svg?branch=master]]
+[[http://travis-ci.org/mateidavid/fast5][http://travis-ci.org/mateidavid/fast5.svg?branch=master]]
 
[[https://tldrlegal.com/license/mit-license][http://img.shields.io/:license-mit-blue.svg]]
 
 A lightweight C++11 library to read raw signal data from Oxford Nanopore's 
Fast5 files.
 
diff --git a/VERSION b/VERSION
index b49b253..d3532a1 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.5.6
+0.5.7
diff --git a/python/fast5/version.py b/python/fast5/version.py
index 8701e4d..22e3a83 100644
--- a/python/fast5/version.py
+++ b/python/fast5/version.py
@@ -1 +1 @@
-__version__ = '0.5.6'
+__version__ = '0.5.7'
diff --git a/python/setup.py b/python/setup.py
index 77dbc70..c15cabf 100755
--- a/python/setup.py
+++ b/python/setup.py
@@ -39,9 +39,13 @@ fast5_dir = os.environ.get('FAST5_DIR', os.path.join('..', 
'src'))
 extra_compile_args = [
     '-std=c++11',
     '-Wall', '-Wextra', '-Wpedantic',
-    '-isystem', hdf5_include_dir,
-    '-isystem', boost_include_dir,
 ]
+# don't indiscriminately add /usr/include to work around bug:
+# 
https://lists.fedoraproject.org/archives/list/de...@lists.fedoraproject.org/thread/Q5SWCUUMWQ4EMS7CU2CBOZHV3WZYOOTT/
+for d in [hdf5_include_dir, boost_include_dir]:
+    if d != '/usr/include':
+        extra_compile_args += ['-isystem', d]
+
 #extra_compile_args += ['-O0', '-g3', '-ggdb', 
'-fno-eliminate-unused-debug-types', '-v']
 extra_link_args = []
 #extra_link_args += ['-v']

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