[med-svn] [ariba] 01/03: New upstream version 2.7.1+ds

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 94ef3c9a34507af3b17926687d4d8ea974b71a5e
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Fri Jan 27 17:47:38 2017 +0100

    New upstream version 2.7.1+ds
---
 README.md         | 2 +-
 ariba/summary.py  | 2 +-
 ariba/versions.py | 3 ++-
 setup.py          | 4 ++--
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 6d00c29..beb1ae1 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,7 @@ Once the dependencies are installed, install ARIBA using pip:
 
 ARIBA also depends on several Python packages, all of which are available
 via pip, so the above command will get those automatically if they
-are not installed. The packages are dendropy >= 4.1.0,
+are not installed. The packages are dendropy >= 4.2.0,
 pyfastaq >= 3.12.0, pysam >= 0.9.1, and pymummer >= 0.10.1.
 
 Alternatively, you can download the latest release from this github repository,
diff --git a/ariba/summary.py b/ariba/summary.py
index 5275660..de9f06f 100644
--- a/ariba/summary.py
+++ b/ariba/summary.py
@@ -334,7 +334,7 @@ class Summary:
             pdm = dendropy.PhylogeneticDistanceMatrix.from_csv(src=f, delimiter='\t')
         upgma_tree = pdm.upgma_tree()
         with open(outfile, 'w') as f:
-            print(upgma_tree.as_string("newick").replace("'", ''), end='', file=f)
+            print(upgma_tree.as_string("newick", suppress_rooting=True).replace("'", ''), end='', file=f)
 
 
     def run(self):
diff --git a/ariba/versions.py b/ariba/versions.py
index f1201e6..1d68cc1 100644
--- a/ariba/versions.py
+++ b/ariba/versions.py
@@ -5,6 +5,7 @@ from ariba import __version__ as ariba_version
 
 
 package_min_versions = {
+    'bs4': '4.1.0',
     'dendropy': '4.1.0',
     'pyfastaq': '3.12.0',
     'pysam': '0.8.1',
@@ -31,7 +32,7 @@ def get_all_versions(raise_error=True):
 
     python_packages_ok = True
 
-    for package in ['ariba', 'dendropy', 'pyfastaq', 'pymummer', 'pysam']:
+    for package in ['ariba', 'bs4', 'dendropy', 'pyfastaq', 'pymummer', 'pysam']:
         try:
             exec('import ' + package)
             version = eval(package + '.__version__')
diff --git a/setup.py b/setup.py
index 54be6c4..10c368f 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.7.0',
+    version='2.7.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},
@@ -67,7 +67,7 @@ setup(
     tests_require=['nose >= 1.3'],
     install_requires=[
         'BeautifulSoup4 >= 4.1.0',
-        'dendropy >= 4.1.0',
+        'dendropy >= 4.2.0',
         'pyfastaq >= 3.12.0',
         'pysam >= 0.9.1',
         'pymummer>=0.10.1',

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