Merge pull request #271 from sanger-pathogens/v2.14.1_bug_fix_branch

Backed out MANIFEST.in change, bumped release number to v2.14.1 and added fix for issue 263

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Change Log
 
+[v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.0...v2.14.1)
+
+**Fixed bugs:**
+
+- Ariba fails to install from PyPI due to missing .h files in distribution. Related to MANIFEST.in change in [\#269](https://github.com/sanger-pathogens/ariba/pull/269)
+- Fix for Issue [\#263](https://github.com/sanger-pathogens/ariba/issues/263)
+
 [v2.14.0](https://github.com/sanger-pathogens/ariba/tree/v2.14.0) (2019-06-06)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.5...v2.14.0)
 

Dockerfile

@@ -34,7 +34,7 @@ RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.14.0 \
+  && git checkout v2.14.1 \
   && python3 setup.py test \
   && python3 setup.py install
 

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include third_party *.h

ariba/clusters.py

@@ -168,7 +168,7 @@ def __init__(self,
         if self.verbose:
             print('Temporary directory:', self.tmp_dir)
 
-        for i in [x for x in dir(signal) if x.startswith("SIG") and x not in {'SIGCHLD', 'SIGCLD', 'SIGPIPE'}]:
+        for i in [x for x in dir(signal) if x.startswith("SIG") and x not in {'SIGCHLD', 'SIGCLD', 'SIGPIPE', 'SIGTSTP', 'SIGCONT'}]:
             try:
                 signum = getattr(signal, i)
                 signal.signal(signum, self._receive_signal)

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.0',
+    version='2.14.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},