Merge pull request #11 from jbloom22/bigdata-pcrelate2

fixed test, from_entry_expr, removed path, rebased on master

.gitignore

@@ -11,6 +11,5 @@ python/hail/docs/_build/*
 src/main/c/libsimdpp-2.0-rc2.tar.gz
 src/main/c/libsimdpp-2.0-rc2
 target
-src/main/c/lib
 src/main/resources/build-info.properties
 src/test/resources/example.v11.bgen.idx

python/hail/__init__.py

@@ -55,3 +55,5 @@
 import builtins
 __all__.extend([x for x in expr.__all__ if not hasattr(builtins, x)])
 del builtins
+
+__version__ = None  # set in hail.init()

python/hail/context.py

@@ -1,6 +1,7 @@
 from pyspark import SparkContext
 from pyspark.sql import SQLContext
 
+import hail
 from hail.genetics.reference_genome import ReferenceGenome
 from hail.typecheck import nullable, typecheck, typecheck_method, enumeration
 from hail.utils import wrap_to_list, get_env_or_default
@@ -65,6 +66,9 @@ def __init__(self, sc=None, app_name="Hail", master=None, local='local[*]',
         self._default_ref = None
         Env.hail().variant.ReferenceGenome.setDefaultReference(self._jhc, default_reference)
 
+        version = self._jhc.version()
+        hail.__version__ = version
+
         if not quiet:
             sys.stderr.write('Running on Apache Spark version {}\n'.format(self.sc.version))
             if self._jsc.uiWebUrl().isDefined():
@@ -79,20 +83,15 @@ def __init__(self, sc=None, app_name="Hail", master=None, local='local[*]',
                 '     __  __     <>__\n'
                 '    / /_/ /__  __/ /\n'
                 '   / __  / _ `/ / /\n'
-                '  /_/ /_/\_,_/_/_/   version {}\n'.format(self.version))
+                '  /_/ /_/\_,_/_/_/   version {}\n'.format(version))
 
-            if self.version.startswith('devel'):
+            if version.startswith('devel'):
                 sys.stderr.write('NOTE: This is a beta version. Interfaces may change\n'
                                  '  during the beta period. We also recommend pulling\n'
-                                 '  the latest changes weekly.')
+                                 '  the latest changes weekly.\n')
 
         install_exception_handler()
 
-
-    @property
-    def version(self):
-        return self._jhc.version()
-
     @property
     def default_reference(self):
         if not self._default_ref:

python/hail/docs/methods/impex.rst

@@ -16,6 +16,7 @@ Import / Export
     get_vcf_metadata
     import_bed
     import_bgen
+    index_bgen
     import_fam
     import_gen
     import_locus_intervals
@@ -34,6 +35,7 @@ Import / Export
 .. autofunction:: get_vcf_metadata
 .. autofunction:: import_bed
 .. autofunction:: import_bgen
+.. autofunction:: index_bgen
 .. autofunction:: import_fam
 .. autofunction:: import_gen
 .. autofunction:: import_locus_intervals

python/hail/docs/methods/index.rst

@@ -23,6 +23,7 @@ Methods
     get_vcf_metadata
     import_bed
     import_bgen
+    index_bgen
     import_fam
     import_gen
     import_locus_intervals