Merge pull request #394 from akmorrow13/maint_spark2_2.11-0.0.1

Maint spark2 2.11 0.0.1

mango-assembly/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
@@ -70,7 +70,7 @@
                 </relocation>
               </relocations>
               <transformers>
-                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
               </transformers>
             </configuration>
           </execution>

mango-cli/pom.xml

@@ -1,12 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
 
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <artifactId>mango-cli</artifactId>

mango-core/pom.xml

@@ -1,12 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
 
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <artifactId>mango-core</artifactId>

mango-distribution/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

mango-python/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

mango-python/setup.py

@@ -19,6 +19,12 @@
 from setuptools import find_packages, setup
 from version import version as mango_version
 from pip.req import parse_requirements
+import os
+
+# Utility function to read the README file.
+# Used for the long_description.
+def read(fname):
+    return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
 # parse_requirements() returns generator of pip.req.InstallRequirement objects
 install_reqs = parse_requirements('requirements.txt', session='hack')
@@ -36,4 +42,5 @@
     dependency_links=[
         'https://test.pypi.org/simple/bdgenomics-adam/'
     ],
+    long_description=read('README.md'),
     packages=find_packages(exclude=['*.test.*']))

mango-python/version.py

@@ -17,7 +17,7 @@
 #
 from __future__ import print_function
 
-version = '0.0.1a2'
+version = '0.0.2a0'
 
 if __name__ == '__main__':
     print(version)

mango-viz/bdgenomics/mango/pileup/_version.py

@@ -16,5 +16,5 @@
 # limitations under the License.
 #
 
-version_info = (0, 0, '1a1')
+version_info = (0, 0, '2a0')
 __version__ = '.'.join(map(str, version_info))

mango-viz/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.mango</groupId>
     <artifactId>mango-parent</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

mango-viz/setup.py

@@ -40,7 +40,13 @@
 log.info('setup.py entered')
 log.info('$PATH=%s' % os.environ['PATH'])
 
-LONG_DESCRIPTION = 'bdgenomics.mango.pileup'
+# Utility function to read the README file.
+# Used for the long_description.
+def read(fname):
+    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+
+
+LONG_DESCRIPTION = read("README.md")
 
 def js_prerelease(command, strict=False):
     """decorator for building minified js/css prior to another command"""

pom.xml

@@ -1,18 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
   <parent>
     <groupId>org.sonatype.oss</groupId>
     <artifactId>oss-parent</artifactId>
     <version>7</version>
-    <relativePath/>
+    <relativePath />
   </parent>
 
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.bdgenomics.mango</groupId>
   <artifactId>mango-parent</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
+  <version>0.0.2-SNAPSHOT</version>
   <packaging>pom</packaging>
   <name>mango</name>